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Sample records for analysis reveal damage

  1. Systems Analysis of the Dynamic Inflammatory Response to Tissue Damage Reveals Spatiotemporal Properties of the Wound Attractant Gradient.

    PubMed

    Weavers, Helen; Liepe, Juliane; Sim, Aaron; Wood, Will; Martin, Paul; Stumpf, Michael P H

    2016-08-08

    In the acute inflammatory phase following tissue damage, cells of the innate immune system are rapidly recruited to sites of injury by pro-inflammatory mediators released at the wound site. Although advances in live imaging allow us to directly visualize this process in vivo, the precise identity and properties of the primary immune damage attractants remain unclear, as it is currently impossible to directly observe and accurately measure these signals in tissues. Here, we demonstrate that detailed information about the attractant signals can be extracted directly from the in vivo behavior of the responding immune cells. By applying inference-based computational approaches to analyze the in vivo dynamics of the Drosophila inflammatory response, we gain new detailed insight into the spatiotemporal properties of the attractant gradient. In particular, we show that the wound attractant is released by wound margin cells, rather than by the wounded tissue per se, and that it diffuses away from this source at rates far slower than those of previously implicated signals such as H2O2 and ATP, ruling out these fast mediators as the primary chemoattractant. We then predict, and experimentally test, how competing attractant signals might interact in space and time to regulate multi-step cell navigation in the complex environment of a healing wound, revealing a period of receptor desensitization after initial exposure to the damage attractant. Extending our analysis to model much larger wounds, we uncover a dynamic behavioral change in the responding immune cells in vivo that is prognostic of whether a wound will subsequently heal or not. VIDEO ABSTRACT.

  2. A systematic analysis of factors localized to damaged chromatin reveals PARP-dependent recruitment of transcription factors

    PubMed Central

    Izhar, Lior; Adamson, Britt; Ciccia, Alberto; Lewis, Jedd; Pontano-Vaites, Laura; Leng, Yumei; Liang, Anthony C.; Westbrook, Thomas F.; Harper, J. Wade; Elledge, Stephen J.

    2015-01-01

    Localization to sites of DNA damage is a hallmark of DNA damage response (DDR) proteins. To identify new DDR factors, we screened epitope-tagged proteins for localization to sites of chromatin damaged by UV laser microirradiation and found >120 proteins that localize to damaged chromatin. These include the BAF tumor suppressor complex and the ALS candidate protein TAF15. TAF15 contains multiple domains that bind damaged chromatin in a PARP-dependent manner, suggesting a possible role as glue that tethers multiple PAR chains together. Many positives were transcription factors and >70% of randomly tested transcription factors localized to sites of DNA damage and approximately 90% were PARP-dependent for localization. Mutational analyses showed that localization to damaged chromatin is DNA-binding domain-dependent. By examining Hoechst staining patterns at damage sites, we see evidence of chromatin decompaction that is PARP-dependent. We propose that PARP-regulated chromatin remodeling at sites of damage allows transient accessibility of DNA-binding proteins. PMID:26004182

  3. In situ analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine oxidation reveals sequence- and agent-specific damage spectra.

    PubMed

    Lim, Kok Seong; Cui, Liang; Taghizadeh, Koli; Wishnok, John S; Chan, Wan; DeMott, Michael S; Babu, I Ramesh; Tannenbaum, Steven R; Dedon, Peter C

    2012-10-31

    Guanine is a major target for oxidation in DNA, with 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) as a major product. 8-oxodG is itself significantly more susceptible to oxidation than guanine, with the resulting damage consisting of more than 10 different products. This complexity has hampered efforts to understand the determinants of biologically relevant DNA oxidation chemistry. To address this problem, we have developed a high mass accuracy mass spectrometric method to quantify oxidation products arising site specifically in DNA. We applied this method to quantify the role of sequence context in defining the spectrum of damage products arising from oxidation of 8-oxodG by two oxidants: nitrosoperoxycarbonate (ONOOCO(2)(-)), a macrophage-derived chemical mediator of inflammation, and the classical one-electron oxidant, riboflavin-mediated photooxidation. The results reveal the predominance of dehydroguanidinohydantoin (DGh) in 8-oxodG oxidation by both oxidants. While the relative quantities of 8-oxodG oxidation products arising from ONOOCO(2)(-) did not vary as a function of sequence context, products of riboflavin-mediated photooxidation of 8-oxodG were highly sequence dependent. Several of the 8-oxodG oxidation products underwent hydrolytic conversion to new products with half-lives of 2-7 h. The results have implications for understanding the chemistry of DNA oxidation and the biological response to the damage, with DNA damage recognition and repair systems faced with a complex and dynamic set of damage targets.

  4. Rapid Approaches Towards DNA Damage Analysis

    PubMed Central

    Crews, N.; Paidipalli, Manasa

    2013-01-01

    The severe effects of DNA damage on human health have led to a tremendous amount of research being focused. Owing to the importance of damage detection, different approaches for the detection and quantification of the damaged DNA will be presented. In this work, we have modeled DNA damage using well-known mutagens: UV radiation to create photoproducts and restriction enzyme digestion to create double strand breaks. We will show that quantitative PCR (qPCR), a widely known measure of detecting the presence of the target DNA can be used to quantify photoproducts/intramolecular DNA damage. Our results indicate that a comparison of the initial concentration available in the undamaged and the damaged samples can be used to reveal the effect of damaged DNA in its amplification. By analyzing multiple regions using this technique, their relative susceptibility to damage can be measured. We also show that high-resolution melting analysis (HRMA), a measure of the bond energy between two DNA strands, can be used to quantify double strand breaks. The strand breaks resulted in a change in the overall distribution of the bond energy thus causing variations in the melting profile. HRMA has also been examined to compare DNA damage resulting from UV-A, UV-B and UV-C irradiation. The evaluation techniques demonstrated can potentially be extended to various types of DNA damage.

  5. Microarray Analysis of Murine Retinal Light Damage Reveals Changes in Iron Regulatory, Complement, and Antioxidant Genes in the Neurosensory Retina and Isolated RPE

    PubMed Central

    Hadziahmetovic, Majda; Kumar, Usha; Song, Ying; Grieco, Steven; Song, Delu; Li, Yafeng; Tobias, John W.; Dunaief, Joshua L.

    2012-01-01

    Purpose. The purpose of this study was to investigate light damage–induced transcript changes within neurosensory retina (NSR) and isolated retinal pigment epithelium (RPE). Similar studies have been conducted previously, but were usually limited to the NSR and only a portion of the transcriptome. Herein most of the transcriptome, not just in the NSR but also in isolated RPE, was queried. Methods. Mice were exposed to 10,000 lux cool white fluorescent light for 18 hours and euthanized 4 hours after photic injury. NSR and isolated RPE were collected, and RNA was isolated. DNA microarray hybridization was conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Microarray analysis was performed using probe intensity data derived from the Mouse Gene 1.0 ST Array. For the genes of interest, confirmation of gene expression was done using quantitative real-time PCR. Immunofluorescence assessed protein levels and localization. Results. Numerous iron regulatory genes were significantly changed in the light-exposed NSR and RPE. Several of these gene expression changes favored an iron-overloaded state. For example, the transferrin receptor was upregulated in both light-exposed NSR and RPE. Consistent with this, there was stronger transferrin receptor immunoreactivity in the light-exposed retinas. Significant changes in gene expression following light damage were also observed in oxidative stress and complement system genes. Conclusions. The concept of a photooxidative stress–induced vicious cycle of increased iron uptake leading to further oxidative stress was introduced. PMID:22736611

  6. Meta-analysis of 49 549 individuals imputed with the 1000 Genomes Project reveals an exonic damaging variant in ANGPTL4 determining fasting TG levels

    PubMed Central

    van Leeuwen, Elisabeth M; Sabo, Aniko; Bis, Joshua C; Huffman, Jennifer E; Manichaikul, Ani; Smith, Albert V; Feitosa, Mary F; Demissie, Serkalem; Joshi, Peter K; Duan, Qing; Marten, Jonathan; van Klinken, Jan B; Surakka, Ida; Nolte, Ilja M; Zhang, Weihua; Mbarek, Hamdi; Li-Gao, Ruifang; Trompet, Stella; Verweij, Niek; Evangelou, Evangelos; Lyytikäinen, Leo-Pekka; Tayo, Bamidele O; Deelen, Joris; van der Most, Peter J; van der Laan, Sander W; Arking, Dan E; Morrison, Alanna; Dehghan, Abbas; Franco, Oscar H; Hofman, Albert; Rivadeneira, Fernando; Sijbrands, Eric J; Uitterlinden, Andre G; Mychaleckyj, Josyf C; Campbell, Archie; Hocking, Lynne J; Padmanabhan, Sandosh; Brody, Jennifer A; Rice, Kenneth M; White, Charles C; Harris, Tamara; Isaacs, Aaron; Campbell, Harry; Lange, Leslie A; Rudan, Igor; Kolcic, Ivana; Navarro, Pau; Zemunik, Tatijana; Salomaa, Veikko; Kooner, Angad S; Kooner, Jaspal S; Lehne, Benjamin; Scott, William R; Tan, Sian-Tsung; de Geus, Eco J; Milaneschi, Yuri; Penninx, Brenda W J H; Willemsen, Gonneke; de Mutsert, Renée; Ford, Ian; Gansevoort, Ron T; Segura-Lepe, Marcelo P; Raitakari, Olli T; Viikari, Jorma S; Nikus, Kjell; Forrester, Terrence; McKenzie, Colin A; de Craen, Anton J M; de Ruijter, Hester M; Pasterkamp, Gerard; Snieder, Harold; Oldehinkel, Albertine J; Slagboom, P Eline; Cooper, Richard S; Kähönen, Mika; Lehtimäki, Terho; Elliott, Paul; van der Harst, Pim; Jukema, J Wouter; Mook-Kanamori, Dennis O; Boomsma, Dorret I; Chambers, John C; Swertz, Morris; Ripatti, Samuli; Willems van Dijk, Ko; Vitart, Veronique; Polasek, Ozren; Hayward, Caroline; Wilson, James G; Wilson, James F; Gudnason, Vilmundur; Rich, Stephen S; Psaty, Bruce M; Borecki, Ingrid B; Boerwinkle, Eric; Rotter, Jerome I; Cupples, L Adrienne; van Duijn, Cornelia M

    2016-01-01

    Background So far, more than 170 loci have been associated with circulating lipid levels through genome-wide association studies (GWAS). These associations are largely driven by common variants, their function is often not known, and many are likely to be markers for the causal variants. In this study we aimed to identify more new rare and low-frequency functional variants associated with circulating lipid levels. Methods We used the 1000 Genomes Project as a reference panel for the imputations of GWAS data from ∼60 000 individuals in the discovery stage and ∼90 000 samples in the replication stage. Results Our study resulted in the identification of five new associations with circulating lipid levels at four loci. All four loci are within genes that can be linked biologically to lipid metabolism. One of the variants, rs116843064, is a damaging missense variant within the ANGPTL4 gene. Conclusions This study illustrates that GWAS with high-scale imputation may still help us unravel the biological mechanism behind circulating lipid levels. PMID:27036123

  7. Different precursor populations revealed by microscopic studies of bulk damage in KDP and DKDP crystals

    SciTech Connect

    DeMange, P; Negres, R A; Radousky, H B; Demos, S G

    2005-10-31

    We present experimental results aiming to reveal the relationship between damage initiating defect populations in KDP and DKDP crystals under irradiation at different wavelengths. Our results indicate that there is more than one type of defects leading to damage initiation, each defect acting as damage initiators over a different wavelength range. Results showing disparities in the morphology of damage sites from exposure at different wavelengths provides additional evidence for the presence of multiple types of defects responsible for damage initiation.

  8. Gear Damage Detection Using Oil Debris Analysis

    NASA Technical Reports Server (NTRS)

    Dempsey, Paula J.

    2001-01-01

    The purpose of this paper was to verify, when using an oil debris sensor, that accumulated mass predicts gear pitting damage and to identify a method to set threshold limits for damaged gears. Oil debris data was collected from 8 experiments with no damage and 8 with pitting damage in the NASA Glenn Spur Gear Fatigue Rig. Oil debris feature analysis was performed on this data. Video images of damage progression were also collected from 6 of the experiments with pitting damage. During each test, data from an oil debris sensor was monitored and recorded for the occurrence of pitting damage. The data measured from the oil debris sensor during experiments with damage and with no damage was used to identify membership functions to build a simple fuzzy logic model. Using fuzzy logic techniques and the oil debris data, threshold limits were defined that discriminate between stages of pitting wear. Results indicate accumulated mass combined with fuzzy logic analysis techniques is a good predictor of pitting damage on spur gears.

  9. Flood damage claims reveal insights about surface runoff in Switzerland

    NASA Astrophysics Data System (ADS)

    Bernet, D. B.; Prasuhn, V.; Weingartner, R.

    2015-12-01

    A few case studies in Switzerland exemplify that not only overtopping water bodies frequently cause damages to buildings. Reportedly, a large share of the total loss due to flooding in Switzerland goes back to surface runoff that is formed and is propagating outside of regular watercourses. Nevertheless, little is known about when, where and why such surface runoff occurs. The described process encompasses surface runoff formation, followed by unchannelised overland flow until a water body is reached. It is understood as a type of flash flood, has short response times and occurs diffusely in the landscape. Thus, the process is difficult to observe and study directly. A promising source indicating surface runoff indirectly are houseowners' damage claims recorded by Swiss Public Insurance Companies for Buildings (PICB). In most of Switzerland, PICB hold a monopoly position and insure (almost) every building. Consequently, PICB generally register all damages to buildings caused by an insured natural hazard (including surface runoff) within the respective zones. We have gathered gapless flood related claim records of most of all Swiss PICB covering more than the last two decades on average. Based on a subset, we have developed a methodology to differentiate claims related to surface runoff from other causes. This allows us to assess the number of claims as well as total loss related to surface runoff and compare these to the numbers of overtopping watercourses. Furthermore, with the good data coverage, we are able to analyze surface runoff related claims in space and time, from which we can infer spatial and temporal characteristics of surface runoff. Although the delivered data of PICB are heterogeneous and, consequently, time-consuming to harmonize, our first results show that exploiting these damage claim records is feasible and worthwhile to learn more about surface runoff in Switzerland.

  10. Femtosecond near-infrared laser microirradiation reveals a crucial role for PARP signaling on factor assemblies at DNA damage sites

    PubMed Central

    Saquilabon Cruz, Gladys Mae; Kong, Xiangduo; Silva, Bárbara Alcaraz; Khatibzadeh, Nima; Thai, Ryan; Berns, Michael W.; Yokomori, Kyoko

    2016-01-01

    Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affect the amounts and types of damage and the DDR. We compared different irradiation conditions using a femtosecond near-infrared laser and found distinct damage site recruitment thresholds for 53BP1 and TRF2 correlating with the dose-dependent increase of strand breaks and damage complexity. Low input-power microirradiation that induces relatively simple strand breaks led to robust recruitment of 53BP1 but not TRF2. In contrast, increased strand breaks with complex damage including crosslinking and base damage generated by high input-power microirradiation resulted in TRF2 recruitment to damage sites with no 53BP1 clustering. We found that poly(ADP-ribose) polymerase (PARP) activation distinguishes between the two damage states and that PARP activation is essential for rapid TRF2 recruitment while suppressing 53BP1 accumulation at damage sites. Thus, our results reveal that careful titration of laser irradiation conditions allows induction of varying amounts and complexities of DNA damage that are gauged by differential PARP activation regulating protein assembly at the damage site. PMID:26424850

  11. Nano-cathodoluminescence reveals the effect of electron damage on the optical properties of nitride optoelectronics and the damage threshold

    NASA Astrophysics Data System (ADS)

    Griffiths, James T.; Zhang, Siyuan; Lhuillier, Jeremy; Zhu, Dandan; Fu, Wai Yuen; Howkins, Ashley; Boyd, Ian; Stowe, David; Wallis, David J.; Humphreys, Colin J.; Oliver, Rachel A.

    2016-10-01

    Nano-cathodoluminescence (Nano-CL) reveals optical emission from individual InGaN quantum wells for applications in optoelectronic devices. We show the luminescent intensity decays over time with exposure to the electron beam for energies between 80 and 200 keV. Measurements of the CL intensity over time show an exponential decline in intensity, which we propose is due to the formation of nitrogen Frenkel defects. The measured CL damage decreases with reductions in the electron accelerating voltage and we suggest that the electron induced structural damage may be suppressed below the proposed damage threshold. The electron beam induced damage leads to a non-radiative region that extends over the measured minority carrier diffusion length. Nano-CL may thus serve as a powerful technique to study III-nitride optoelectronics.

  12. Damage analysis in Al thin films fatigued at ultrahigh frequencies

    NASA Astrophysics Data System (ADS)

    Eberl, Christoph; Spolenak, Ralph; Kraft, Oliver; Kubat, Franz; Ruile, Werner; Arzt, Eduard

    2006-06-01

    A quantitative damage analysis provides insight into the damage mechanisms and lifetimes of aluminum thin films fatigued at ultrahigh frequencies. Surface acoustic wave test devices were used to test continuous and patterned Al thin films up to more than 1014 cycles. The analysis revealed increasing extrusion and void formation concentrated at grain boundaries. This finding and the observed grain growth indicate a high material flux at the grain boundaries induced by the cyclic load. A correlation between device degradation and defect density is established which is explained by a theoretical model. For stress amplitudes as low as 14 MPa lifetime measurements showed no fatigue limit for 420 nm Al thin films.

  13. Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks.

    PubMed

    Zhou, Chunshui; Elia, Andrew E H; Naylor, Maria L; Dephoure, Noah; Ballif, Bryan A; Goel, Gautam; Xu, Qikai; Ng, Aylwin; Chou, Danny M; Xavier, Ramnik J; Gygi, Steven P; Elledge, Stephen J

    2016-06-28

    The DNA damage response (DDR) is regulated by a protein kinase signaling cascade that orchestrates DNA repair and other processes. Identifying the substrate effectors of these kinases is critical for understanding the underlying physiology and mechanism of the response. We have used quantitative mass spectrometry to profile DDR-dependent phosphorylation in budding yeast and genetically explored the dependency of these phosphorylation events on the DDR kinases MEC1, RAD53, CHK1, and DUN1. Based on these screens, a database containing many novel DDR-regulated phosphorylation events has been established. Phosphorylation of many of these proteins has been validated by quantitative peptide phospho-immunoprecipitation and examined for functional relevance to the DDR through large-scale analysis of sensitivity to DNA damage in yeast deletion strains. We reveal a link between DDR signaling and the metabolic pathways of inositol phosphate and phosphatidyl inositol synthesis, which are required for resistance to DNA damage. We also uncover links between the DDR and TOR signaling as well as translation regulation. Taken together, these data shed new light on the organization of DDR signaling in budding yeast.

  14. Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks

    PubMed Central

    Zhou, Chunshui; Elia, Andrew E. H.; Naylor, Maria L.; Ballif, Bryan A.; Goel, Gautam; Xu, Qikai; Ng, Aylwin; Chou, Danny M.; Xavier, Ramnik J.; Gygi, Steven P.; Elledge, Stephen J.

    2016-01-01

    The DNA damage response (DDR) is regulated by a protein kinase signaling cascade that orchestrates DNA repair and other processes. Identifying the substrate effectors of these kinases is critical for understanding the underlying physiology and mechanism of the response. We have used quantitative mass spectrometry to profile DDR-dependent phosphorylation in budding yeast and genetically explored the dependency of these phosphorylation events on the DDR kinases MEC1, RAD53, CHK1, and DUN1. Based on these screens, a database containing many novel DDR-regulated phosphorylation events has been established. Phosphorylation of many of these proteins has been validated by quantitative peptide phospho-immunoprecipitation and examined for functional relevance to the DDR through large-scale analysis of sensitivity to DNA damage in yeast deletion strains. We reveal a link between DDR signaling and the metabolic pathways of inositol phosphate and phosphatidyl inositol synthesis, which are required for resistance to DNA damage. We also uncover links between the DDR and TOR signaling as well as translation regulation. Taken together, these data shed new light on the organization of DDR signaling in budding yeast. PMID:27298372

  15. Equivalent damage validation by variable cluster analysis

    NASA Astrophysics Data System (ADS)

    Drago, Carlo; Ferlito, Rachele; Zucconi, Maria

    2016-06-01

    The main aim of this work is to perform a clustering analysis on the damage relieved in the old center of L'Aquila after the earthquake occurred on April 6, 2009 and to validate an Indicator of Equivalent Damage ED that summarizes the information reported on the AeDES card regarding the level of damage and their extension on the surface of the buildings. In particular we used a sample of 13442 masonry buildings located in an area characterized by a Macroseismic Intensity equal to 8 [1]. The aim is to ensure the coherence between the clusters and its hierarchy identified in the data of damage detected and in the data of the ED elaborated.

  16. Analysis of Boling's laser-damage morphology

    SciTech Connect

    Sparks, M.S.

    1980-08-15

    Boling observed that his total-internal-reflection laser-damage sites in glass closely resembled the scattering cross section for small (ka << 1), perfectly conducting sphere and suggested that a very small plasma formed and grew to a larger size, still with ka << 1 satisfied. Even with ka = 1, for which the cross section is different from that observed, the scattered field still is too small to explain the damage in terms of constructive interference between the incident- and scattered fields. Furthermore, the characteristic shape of the scattering cross section that matches the damage patterns is for circular polarization or unpolarized light, in contrast to the experimental plane polarizations. Extending the ideas to include effects of the scattered field outside the glass, such as plasma formation, and to include the correct field (with interesting polarization, including longitudinal circuler polarization at certain distances from the surface) incident on the sphere may explain the experiments. Additional experiments and analysis would be useful to determine if the extended model is valid and to investigate related materials improvement, nondestructive testing, and the relation between laser damage, plasma initiation, and failure under stress, all initiated at small isolated spots.

  17. Dark progression reveals slow timescales for radiation damage between T = 180 and 240 K

    PubMed Central

    Warkentin, Matthew; Badeau, Ryan; Hopkins, Jesse; Thorne, Robert E.

    2011-01-01

    Can radiation damage to protein crystals be ‘outrun’ by collecting a structural data set before damage is manifested? Recent experiments using ultra-intense pulses from a free-electron laser show that the answer is yes. Here, evidence is presented that significant reductions in global damage at temperatures above 200 K may be possible using conventional X-ray sources and current or soon-to-be available detectors. Specifically, ‘dark progression’ (an increase in damage with time after the X-rays have been turned off) was observed at temperatures between 180 and 240 K and on timescales from 200 to 1200 s. This allowed estimation of the temperature-dependent timescale for damage. The rate of dark progression is consistent with an Arrhenius law with an activation energy of 14 kJ mol−1. This is comparable to the activation energy for the solvent-coupled diffusive damage processes responsible for the rapid increase in radiation sensitivity as crystals are warmed above the glass transition near 200 K. Analysis suggests that at T = 300 K data-collection times of the order of 1 s (and longer at lower temperatures) may allow significant reductions in global radiation damage, facilitating structure solution on crystals with liquid solvent. No dark progression was observed below T = 180 K, indicating that no important damage process is slowed through this timescale window in this temperature range. PMID:21904032

  18. Cross-Sectional Nakagami Images in Passive Stretches Reveal Damage of Injured Muscles

    PubMed Central

    Lin, Shih-Ping; Lin, Yi-Hsun; Fan, Shih-Chen; Huang, Bu-Miin; Lin, Wei-Yin; Wang, Shyh-Hau; Shung, K. Kirk; Su, Fong-Chin; Wu, Chia-Ching

    2016-01-01

    Muscle strain is still awanting a noninvasive quantitatively diagnosis tool. High frequency ultrasound (HFU) improves image resolution for monitoring changes of tissue structures, but the biomechanical factors may influence ultrasonography during injury detection. We aim to illustrate the ultrasonic parameters to present the histological damage of overstretched muscle with the consideration of biomechanical factors. Gastrocnemius muscles from mice were assembled and ex vivo passive stretching was performed before or after injury. After injury, the muscle significantly decreased mechanical strength. Ultrasonic images were obtained by HFU at different deformations to scan in cross and longitudinal orientations of muscle. The ultrasonography was quantified by echogenicity and Nakagami parameters (NP) for structural evaluation and correlated with histological results. The injured muscle at its original length exhibited decreased echogenicity and NP from HFU images. Cross-sectional ultrasonography revealed a loss of correlation between NP and passive muscle stretching that suggested a special scatterer pattern in the cross section of injured muscle. The independence of NP during passive stretching of injured muscle was confirmed by histological findings in ruptured collagen fibers, decreased muscle density, and increased intermuscular fiber space. Thus, HFU analysis of NP in cross section represents muscle injury that may benefit the clinical diagnosis. PMID:27034946

  19. Cross-Sectional Nakagami Images in Passive Stretches Reveal Damage of Injured Muscles.

    PubMed

    Lin, Shih-Ping; Lin, Yi-Hsun; Fan, Shih-Chen; Huang, Bu-Miin; Lin, Wei-Yin; Wang, Shyh-Hau; Shung, K Kirk; Su, Fong-Chin; Wu, Chia-Ching

    2016-01-01

    Muscle strain is still awanting a noninvasive quantitatively diagnosis tool. High frequency ultrasound (HFU) improves image resolution for monitoring changes of tissue structures, but the biomechanical factors may influence ultrasonography during injury detection. We aim to illustrate the ultrasonic parameters to present the histological damage of overstretched muscle with the consideration of biomechanical factors. Gastrocnemius muscles from mice were assembled and ex vivo passive stretching was performed before or after injury. After injury, the muscle significantly decreased mechanical strength. Ultrasonic images were obtained by HFU at different deformations to scan in cross and longitudinal orientations of muscle. The ultrasonography was quantified by echogenicity and Nakagami parameters (NP) for structural evaluation and correlated with histological results. The injured muscle at its original length exhibited decreased echogenicity and NP from HFU images. Cross-sectional ultrasonography revealed a loss of correlation between NP and passive muscle stretching that suggested a special scatterer pattern in the cross section of injured muscle. The independence of NP during passive stretching of injured muscle was confirmed by histological findings in ruptured collagen fibers, decreased muscle density, and increased intermuscular fiber space. Thus, HFU analysis of NP in cross section represents muscle injury that may benefit the clinical diagnosis.

  20. Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses

    PubMed Central

    Narendrula-Kotha, Ramya; Nkongolo, Kabwe K.

    2017-01-01

    Aims To assess the effects of dolomitic limestone applications on soil microbial communities’ dynamics and bacterial and fungal biomass, relative abundance, and diversity in metal reclaimed regions. Methods and Results The study was conducted in reclaimed mining sites and metal uncontaminated areas. The limestone applications were performed over 35 years ago. Total microbial biomass was determined by Phospholipid fatty acids. Bacterial and fungal relative abundance and diversity were assessed using 454 pyrosequencing. There was a significant increase of total microbial biomass in limed sites (342 ng/g) compared to unlimed areas (149 ng/g). Chao1 estimates followed the same trend. But the total number of OTUs (Operational Taxonomic Units) in limed (463 OTUs) and unlimed (473 OTUs) soil samples for bacteria were similar. For fungi, OTUs were 96 and 81 for limed and unlimed soil samples, respectively. Likewise, Simpson and Shannon diversity indices revealed no significant differences between limed and unlimed sites. Bacterial and fungal groups specific to either limed or unlimed sites were identified. Five major bacterial phyla including Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, and Proteobacteria were found. The latter was the most prevalent phylum in all the samples with a relative abundance of 50%. Bradyrhizobiaceae family with 12 genera including the nitrogen fixing Bradirhizobium genus was more abundant in limed sites compared to unlimed areas. For fungi, Ascomycota was the most predominant phylum in unlimed soils (46%) while Basidiomycota phylum represented 86% of all fungi in the limed areas. Conclusion Detailed analysis of the data revealed that although soil liming increases significantly the amount of microbial biomass, the level of species diversity remain statistically unchanged even though the microbial compositions of the damaged and restored sites are different. Significance and Impact of the study Soil liming still have a significant

  1. Accurate 3d Scanning of Damaged Ancient Greek Inscriptions for Revealing Weathered Letters

    NASA Astrophysics Data System (ADS)

    Papadaki, A. I.; Agrafiotis, P.; Georgopoulos, A.; Prignitz, S.

    2015-02-01

    In this paper two non-invasive non-destructive alternative techniques to the traditional and invasive technique of squeezes are presented alongside with specialized developed processing methods, aiming to help the epigraphists to reveal and analyse weathered letters in ancient Greek inscriptions carved in masonry or marble. The resulting 3D model would serve as a detailed basis for the epigraphists to try to decipher the inscription. The data were collected by using a Structured Light scanner. The creation of the final accurate three dimensional model is a complicated procedure requiring large computation cost and human effort. It includes the collection of geometric data in limited space and time, the creation of the surface, the noise filtering and the merging of individual surfaces. The use of structured light scanners is time consuming and requires costly hardware and software. Therefore an alternative methodology for collecting 3D data of the inscriptions was also implemented for reasons of comparison. Hence, image sequences from varying distances were collected using a calibrated DSLR camera aiming to reconstruct the 3D scene through SfM techniques in order to evaluate the efficiency and the level of precision and detail of the obtained reconstructed inscriptions. Problems in the acquisition processes as well as difficulties in the alignment step and mesh optimization are also encountered. A meta-processing framework is proposed and analysed. Finally, the results of processing and analysis and the different 3D models are critically inspected and then evaluated by a specialist in terms of accuracy, quality and detail of the model and the capability of revealing damaged and "hidden" letters.

  2. Statistical Analysis of Japanese Structural Damage Data

    DTIC Science & Technology

    1977-01-01

    Calculated Peak Overpressure Data ......... .. 36 Figure 4. Frequency Functions for Assumed Damage Laws ............ .. 38 Figure 5. Conversions to Value of...Buildings .... .......... .. 92 Figure 20. Effect of Damage Law on Confidence Regions ............ .. 97 * Figure 21. Comparison of Confidence Limits on...Value of ad (Cumulative Log Normal Damage Law ) ...... ............ .. 99 * Figure 22. Comparison of Confidence Limits on Value of ad (Cumulative Log

  3. Characterization of Multiple Light Damage Paradigms Reveals Regional Differences in Photoreceptor Loss

    PubMed Central

    Thomas, Jennifer L.; Nelson, Craig M.; Luo, Xixia; Hyde, David R.; Thummel, Ryan

    2012-01-01

    Zebrafish provide an attractive model to study the retinal response to photoreceptor apoptosis due to its remarkable ability to spontaneously regenerate retinal neurons following damage. There are currently two widely used light-induced retinal degeneration models to damage photoreceptors in the adult zebrafish. One model uses constant bright light, whereas the other uses a short exposure to extremely intense ultraviolet light. Although both models are currently used, it is unclear whether they differ in regard to the extent of photoreceptor damage or the subsequent regeneration response. Here we report a thorough analysis of the photoreceptor damage and subsequent proliferation response elicited by each individual treatment, as well as by the concomitant use of both treatments. We show a differential loss of rod and cone photoreceptors with each treatment. Additionally, we show that the extent of proliferation observed in the retina directly correlates with the severity of photoreceptor loss. We also demonstrate that both the ventral and posterior regions of the retina are partially protected from light damage. Finally, we show that combining a short ultraviolet exposure followed by a constant bright light treatment largely eliminates the neuroprotected regions, resulting in widespread loss of rod and cone photoreceptors and a robust regenerative response throughout the retina. PMID:22425727

  4. Mutational strand asymmetries in cancer genomes reveal mechanisms of DNA damage and repair

    PubMed Central

    Haradhvala, Nicholas J.; Polak, Paz; Stojanov, Petar; Covington, Kyle R.; Shinbrot, Eve; Hess, Julian; Rheinbay, Esther; Kim, Jaegil; Maruvka, Yosef; Braunstein, Lior Z.; Kamburov, Atanas; Hanawalt, Philip C.; Wheeler, David A.; Koren, Amnon; Lawrence, Michael S.; Getz, Gad

    2016-01-01

    Mutational processes constantly shape the somatic genome, leading to immunity, aging, and other diseases. When cancer is the outcome, we are afforded a glimpse into these processes by the clonal expansion of the malignant cell. Here, we characterize a less explored layer of the mutational landscape of cancer: mutational asymmetries between the two DNA strands. Analyzing whole genome sequences of 590 tumors from 14 different cancer types, we reveal widespread asymmetries across mutagenic processes, with transcriptional (“T-class”) asymmetry dominating UV-, smoking-, and liver-cancer-associated mutations, and replicative (“R-class”) asymmetry dominating POLE-, APOBEC-, and MSI-associated mutations. We report a striking phenomenon of Transcription-Coupled Damage (TCD) on the non-transcribed DNA strand, and provide evidence that APOBEC mutagenesis occurs on the lagging-strand template during DNA replication. As more genomes are sequenced, studying and classifying their asymmetries will illuminate the underlying biological mechanisms of DNA damage and repair. PMID:26806129

  5. Structural Damage Prediction and Analysis for Hypervelocity Impacts: Handbook

    NASA Technical Reports Server (NTRS)

    Elfer, N. C.

    1996-01-01

    This handbook reviews the analysis of structural damage on spacecraft due to hypervelocity impacts by meteoroid and space debris. These impacts can potentially cause structural damage to a Space Station module wall. This damage ranges from craters, bulges, minor penetrations, and spall to critical damage associated with a large hole, or even rupture. The analysis of damage depends on a variety of assumptions and the area of most concern is at a velocity beyond well controlled laboratory capability. In the analysis of critical damage, one of the key questions is how much momentum can actually be transfered to the pressure vessel wall. When penetration occurs without maximum bulging at high velocity and obliquities (if less momentum is deposited in the rear wall), then large tears and rupture may be avoided. In analysis of rupture effects of cylindrical geometry, biaxial loading, bending of the crack, a central hole strain rate and R-curve effects are discussed.

  6. Thermographic analysis of surface damage in teeth

    NASA Astrophysics Data System (ADS)

    Conde-Contreras, M.; Bante-Guerra, J.; Hernandez-Garcia, E.; Hernandez, A. M.; Trujillo, S.; Quintana, P.; Alvarado-Gil, J. J.

    2008-02-01

    The analysis of the surface of teeth is an important field of research and technological development due to the importance of dental pieces in health and aesthetics. The presence of cracks as well as the etching effects on teeth surface, due to different chemical agents, affects not only the appearance of teeth but its integrity. In this work, laser thermography analysis of dental pieces with damage in the form of cracks is presented. The technique consists in the illumination of the surface at the center of the sample, using a 300 mW pulsed solid state laser beam focused with a gradium lens, and monitoring the spatial and temporal distribution of the temperature field. The heating of the sample is monitored using a focal plane array infrared camera, sensitive in the spectral range 7.5-13 μm with a noise equivalent temperature difference of 0.12°C. The data acquisition was performed by the PC firewire port using a PCI-8254R card and a home-made program in Labview 8.0 was used for data acquisition. The images were processed in a home-made linux program to obtain the experimental table values. Our results are compared with position and frequency scans obtained by infrared photothermal radiometry. It is shown that the crack in the tooth appears as an increase in the photothermal signal. In contrast, the thermographic image shows a more detailed structure in which close to the crack the temperature increases, but at the crack the signal falls.

  7. Fatigue damage analysis under variable amplitude cycling

    NASA Technical Reports Server (NTRS)

    Leis, B. N.; Forte, T. P.

    1983-01-01

    This paper explores the suitability of a recently proposed mean stress parameter and introduces a nonlinear damage accumulation procedure. Data covering a range of positive and negative stress ratios from +0.6 to -2.66, for several aluminum alloys and steels, are assembled and shown to be well correlated by a simple damage parameter. A nonlinear damage accumulation postulate is advanced to replace the usual linear procedure. Results of critical experiments performed to assess the suitability of the postulate are introduced and shown to support a non-linear criterion. The implications of this work related to variable amplitude life prediction are discussed.

  8. Comparative Analysis of Interaction of Human and Yeast DNA Damage Recognition Complexes with Damaged DNA in Nucleotide Excision Repair*

    PubMed Central

    Krasikova, Yuliya S.; Rechkunova, Nadejda I.; Maltseva, Ekaterina A.; Pestryakov, Pavel E.; Petruseva, Irina O.; Sugasawa, Kaoru; Chen, Xuejing; Min, Jung-Hyun; Lavrik, Olga I.

    2013-01-01

    The human XPC-RAD23B complex and its yeast ortholog, Rad4-Rad23, are the primary initiators of global genome nucleotide excision repair. The interaction of these proteins with damaged DNA was analyzed using model DNA duplexes containing a single fluorescein-substituted dUMP analog as a lesion. An electrophoretic mobility shift assay revealed similarity between human and yeast proteins in DNA binding. Quantitative analyses of XPC/Rad4 binding to the model DNA structures were performed by fluorescent depolarization measurements. XPC-RAD23B and Rad4-Rad23 proteins demonstrate approximately equal binding affinity to the damaged DNA duplex (KD ∼ (0.5 ± 0.1) and (0.6 ± 0.3) nm, respectively). Using photoreactive DNA containing 5-iodo-dUMP in defined positions, XPC/Rad4 location on damaged DNA was shown. Under conditions of equimolar binding to DNA both proteins exhibited the highest level of cross-links to 5I-dUMP located exactly opposite the damaged nucleotide. The positioning of the XPC and Rad4 proteins on damaged DNA by photocross-linking footprinting is consistent with x-ray analysis of the Rad4-DNA crystal complex. The identity of the XPC and Rad4 location illustrates the common principles of structure organization of DNA damage-scanning proteins from different Eukarya organisms. PMID:23443653

  9. Revealing Student Teacher's Thinking through Dilemma Analysis

    ERIC Educational Resources Information Center

    Talanquer, Vicente; Tomanek, Debra; Novodvorsky, Ingrid

    2007-01-01

    We explore the potential of dilemma analysis as an assessment tool to reveal student teachers' thinking and concerns about their practice. For this purpose we analyze the dilemma analyses completed by 22 student teachers enrolled in our science teacher preparation program over a period of four semesters. Student teachers' dilemmas fall into two…

  10. A method of damage mechanics analysis for solder material

    SciTech Connect

    Fang, H.E.; Chow, C.L.; Yang, Fan

    1997-06-01

    This paper presents as a method of damage mechanics analysis for solder joint material stressed to extensive plastic deformation. The material chosen for the current work is the 60Sn-40Pb eutectic alloy due to its wide use. The analysis is based on the thermodynamic theory of irreversible processes. With the introduction of a set of internal state variables, known as damage variables, and a damage effect tensor, a damage dissipative potential function is proposed to enable the formulation of the constitutive equations of elasticity and plasticity coupled with damage. The equations of damage evolution are also derived to monitor damage initiation and growth. Before a damage analysis can be performed with a finite element analysis, the mechanical properties of the chosen solder joint material and its damage variables must first be determined. A method of experimental analysis was developed and used to successfully measure the highly strain sensitive 60Sn-40Pb solder material. The measured properties are presented and various characteristics of the solder material are examined and discussed. 7 refs., 8 figs.

  11. Nonlinear damage analysis: Postulate and evaluation

    NASA Technical Reports Server (NTRS)

    Leis, B. N.; Forte, T. P.

    1983-01-01

    The objective of this program is to assess the viability of a damage postulate which asserts that the fatigue resistance curve of a metal is history dependent due to inelastic action. The study focusses on OFE copper because this simple model material accentuates the inelastic action central to the damage postulate. Data relevant to damage evolution and crack initiation are developed via a study of surface topography. The effects of surface layer residual stresses are explored via comparative testing as were the effects in initial prestraining. The results of the study very clearly show the deformation history dependence of the fatigue resistance of OFE copper. Furthermore the concept of deformation history dependence is shown to qualitatively explain the fatigue resistance of all histories considered. Likewise quantitative predictions for block cycle histories are found to accurately track the observed results. In this respect the assertion that damage per cycle for a given level of the damage parameter is deformation history dependent appears to be physically justified.

  12. Analysis of optics damage growth at the National Ignition Facility

    NASA Astrophysics Data System (ADS)

    Liao, Z. M.; Nostrand, M.; Whitman, P.; Bude, J.

    2015-11-01

    Optics damage growth modeling and analysis at the National Ignition Facility (NIF) has been performed on fused silica. We will show the results of single shot growth comparisons, damage site lifetime comparisons as well as growth metrics for each individual NIF beamline. These results help validate the consistency of the damage growth models and allow us to have confidence in our strategic planning in regards to projected optic usage.

  13. The dig task: a simple scent discrimination reveals deficits following frontal brain damage.

    PubMed

    Martens, Kris M; Vonder Haar, Cole; Hutsell, Blake A; Hoane, Michael R

    2013-01-04

    Cognitive impairment is the most frequent cause of disability in humans following brain damage, yet the behavioral tasks used to assess cognition in rodent models of brain injury is lacking. Borrowing from the operant literature our laboratory utilized a basic scent discrimination paradigm in order to assess deficits in frontally-injured rats. Previously we have briefly described the Dig task and demonstrated that rats with frontal brain damage show severe deficits across multiple tests within the task. Here we present a more detailed protocol for this task. Rats are placed into a chamber and allowed to discriminate between two scented sands, one of which contains a reinforcer. The trial ends after the rat either correctly discriminates (defined as digging in the correct scented sand), incorrectly discriminates, or 30 sec elapses. Rats that correctly discriminate are allowed to recover and consume the reinforcer. Rats that discriminate incorrectly are immediately removed from the chamber. This can continue through a variety of reversals and novel scents. The primary analysis is the accuracy for each scent pairing (cumulative proportion correct for each scent). The general findings from the Dig task suggest that it is a simple experimental preparation that can assess deficits in rats with bilateral frontal cortical damage compared to rats with unilateral parietal damage. The Dig task can also be easily incorporated into an existing cognitive test battery. The use of more tasks such as this one can lead to more accurate testing of frontal function following injury, which may lead to therapeutic options for treatment. All animal use was conducted in accordance with protocols approved by the Institutional Animal Care and Use Committee.

  14. Progressive Damage Analysis of Bonded Composite Joints

    NASA Technical Reports Server (NTRS)

    Leone, Frank A., Jr.; Girolamo, Donato; Davila, Carlos G.

    2012-01-01

    The present work is related to the development and application of progressive damage modeling techniques to bonded joint technology. The joint designs studied in this work include a conventional composite splice joint and a NASA-patented durable redundant joint. Both designs involve honeycomb sandwich structures with carbon/epoxy facesheets joined using adhesively bonded doublers.Progressive damage modeling allows for the prediction of the initiation and evolution of damage within a structure. For structures that include multiple material systems, such as the joint designs under consideration, the number of potential failure mechanisms that must be accounted for drastically increases the complexity of the analyses. Potential failure mechanisms include fiber fracture, intraply matrix cracking, delamination, core crushing, adhesive failure, and their interactions. The bonded joints were modeled using highly parametric, explicitly solved finite element models, with damage modeling implemented via custom user-written subroutines. Each ply was discretely meshed using three-dimensional solid elements. Layers of cohesive elements were included between each ply to account for the possibility of delaminations and were used to model the adhesive layers forming the joint. Good correlation with experimental results was achieved both in terms of load-displacement history and the predicted failure mechanism(s).

  15. Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling

    PubMed Central

    Li, Renfeng; Pinto, Sneha M.; Shaw, Patrick G.; Huang, Tai-Chung; Wan, Jun; Qian, Jiang; Gowda, Harsha; Wu, Xinyan; Lv, Dong-Wen; Zhang, Kun; Manda, Srikanth S.; Pandey, Akhilesh; Hayward, S. Diane

    2015-01-01

    Epstein-Barr virus (EBV) is etiologically linked to infectious mononucleosis and several human cancers. EBV encodes a conserved protein kinase BGLF4 that plays a key role in the viral life cycle. To provide new insight into the host proteins regulated by BGLF4, we utilized stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics to compare site-specific phosphorylation in BGLF4-expressing Akata B cells. Our analysis revealed BGLF4-mediated hyperphosphorylation of 3,046 unique sites corresponding to 1,328 proteins. Frequency analysis of these phosphosites revealed a proline-rich motif signature downstream of BGLF4, indicating a broader substrate recognition for BGLF4 than its cellular ortholog cyclin-dependent kinase 1 (CDK1). Further, motif analysis of the hyperphosphorylated sites revealed enrichment in ATM, ATR and Aurora kinase substrates while functional analyses revealed significant enrichment of pathways related to the DNA damage response (DDR), mitosis and cell cycle. Phosphorylation of proteins associated with the mitotic spindle assembly checkpoint (SAC) indicated checkpoint activation, an event that inactivates the anaphase promoting complex/cyclosome, APC/C. Furthermore, we demonstrated that BGLF4 binds to and directly phosphorylates the key cellular proteins PP1, MPS1 and CDC20 that lie upstream of SAC activation and APC/C inhibition. Consistent with APC/C inactivation, we found that BGLF4 stabilizes the expression of many known APC/C substrates. We also noted hyperphosphorylation of 22 proteins associated the nuclear pore complex, which may contribute to nuclear pore disassembly and SAC activation. A drug that inhibits mitotic checkpoint activation also suppressed the accumulation of extracellular EBV virus. Taken together, our data reveal that, in addition to the DDR, manipulation of mitotic kinase signaling and SAC activation are mechanisms associated with lytic EBV replication. All MS data have been deposited in

  16. Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants

    PubMed Central

    Sánchez, Arancha; Roguev, Assen; Krogan, Nevan J.; Russell, Paul

    2015-01-01

    Brc1, which was first identified as a high-copy, allele-specific suppressor of a mutation impairing the Smc5-Smc6 holocomplex in Schizosaccharomyces pombe, protects genome integrity during normal DNA replication and when cells are exposed to toxic compounds that stall or collapse replication forks. The C-terminal tandem BRCT (BRCA1 C-terminus) domain of fission yeast Brc1 docks with phosphorylated histone H2A (γH2A)-marked chromatin formed by ATR/Rad3 checkpoint kinase at arrested and damaged replication forks; however, how Brc1 functions in relation to other genome protection modules remains unclear. Here, an epistatic mini-array profile reveals critical requirements for Brc1 in mutants that are defective in multiple DNA damage response pathways, including checkpoint signaling by Rad3-Rad26/ATR-ATRIP kinase, DNA repair by Smc5-Smc6 holocomplex, replication fork stabilization by Mrc1/claspin and Swi1-Swi3/Timeless-Tipin, and control of ubiquitin-regulated proteolysis by the COP9 signalosome (CSN). Exogenous genotoxins enhance these negative genetic interactions. Rad52 and RPA foci are increased in CSN-defective cells, and loss of γH2A increases genotoxin sensitivity, indicating a critical role for the γH2A-Brc1 module in stabilizing replication forks in CSN-defective cells. A negative genetic interaction with the Nse6 subunit of Smc5-Smc6 holocomplex indicates that the DNA repair functions of Brc1 and Smc5-Smc6 holocomplex are at least partially independent. Rtt107, the Brc1 homolog in Saccharomyces cerevisiae, has a very different pattern of genetic interactions, indicating evolutionary divergence of functions and DNA damage responses. PMID:25795664

  17. Controlled DNA double-strand break induction in mice reveals post-damage transcriptome stability.

    PubMed

    Kim, Jeongkyu; Sturgill, David; Tran, Andy D; Sinclair, David A; Oberdoerffer, Philipp

    2016-04-20

    DNA double-strand breaks (DSBs) and their repair can cause extensive epigenetic changes. As a result, DSBs have been proposed to promote transcriptional and, ultimately, physiological dysfunction via both cell-intrinsic and cell-non-autonomous pathways. Studying the consequences of DSBs in higher organisms has, however, been hindered by a scarcity of tools for controlled DSB induction. Here, we describe a mouse model that allows for both tissue-specific and temporally controlled DSB formation at ∼140 defined genomic loci. Using this model, we show that DSBs promote a DNA damage signaling-dependent decrease in gene expression in primary cells specifically at break-bearing genes, which is reversed upon DSB repair. Importantly, we demonstrate that restoration of gene expression can occur independently of cell cycle progression, underlining its relevance for normal tissue maintenance. Consistent with this, we observe no evidence for persistent transcriptional repression in response to a multi-day course of continuous DSB formation and repair in mouse lymphocytes in vivo Together, our findings reveal an unexpected capacity of primary cells to maintain transcriptome integrity in response to DSBs, pointing to a limited role for DNA damage as a mediator of cell-autonomous epigenetic dysfunction.

  18. Damage functions for climate-related hazards: unification and uncertainty analysis

    NASA Astrophysics Data System (ADS)

    Prahl, Boris F.; Rybski, Diego; Boettle, Markus; Kropp, Jürgen P.

    2016-05-01

    Most climate change impacts manifest in the form of natural hazards. Damage assessment typically relies on damage functions that translate the magnitude of extreme events to a quantifiable damage. In practice, the availability of damage functions is limited due to a lack of data sources and a lack of understanding of damage processes. The study of the characteristics of damage functions for different hazards could strengthen the theoretical foundation of damage functions and support their development and validation. Accordingly, we investigate analogies of damage functions for coastal flooding and for wind storms and identify a unified approach. This approach has general applicability for granular portfolios and may also be applied, for example, to heat-related mortality. Moreover, the unification enables the transfer of methodology between hazards and a consistent treatment of uncertainty. This is demonstrated by a sensitivity analysis on the basis of two simple case studies (for coastal flood and storm damage). The analysis reveals the relevance of the various uncertainty sources at varying hazard magnitude and on both the microscale and the macroscale level. Main findings are the dominance of uncertainty from the hazard magnitude and the persistent behaviour of intrinsic uncertainties on both scale levels. Our results shed light on the general role of uncertainties and provide useful insight for the application of the unified approach.

  19. Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks

    PubMed Central

    Willis, Nicholas A.; Zhou, Chunshui; Elia, Andrew E. H.; Murray, Johanne M.; Carr, Antony M.; Elledge, Stephen J.; Rhind, Nicholas

    2016-01-01

    The cellular response to DNA damage during S-phase regulates a complicated network of processes, including cell-cycle progression, gene expression, DNA replication kinetics, and DNA repair. In fission yeast, this S-phase DNA damage response (DDR) is coordinated by two protein kinases: Rad3, the ortholog of mammalian ATR, and Cds1, the ortholog of mammalian Chk2. Although several critical downstream targets of Rad3 and Cds1 have been identified, most of their presumed targets are unknown, including the targets responsible for regulating replication kinetics and coordinating replication and repair. To characterize targets of the S-phase DDR, we identified proteins phosphorylated in response to methyl methanesulfonate (MMS)-induced S-phase DNA damage in wild-type, rad3∆, and cds1∆ cells by proteome-wide mass spectrometry. We found a broad range of S-phase–specific DDR targets involved in gene expression, stress response, regulation of mitosis and cytokinesis, and DNA replication and repair. These targets are highly enriched for proteins required for viability in response to MMS, indicating their biological significance. Furthermore, the regulation of these proteins is similar in fission and budding yeast, across 300 My of evolution, demonstrating a deep conservation of S-phase DDR targets and suggesting that these targets may be critical for maintaining genome stability in response to S-phase DNA damage across eukaryotes. PMID:27298342

  20. Revealing Student Teachers' Thinking through Dilemma Analysis

    NASA Astrophysics Data System (ADS)

    Talanquer, Vicente; Tomanek, Debra; Novodvorsky, Ingrid

    2007-06-01

    We explore the potential of dilemma analysis as an assessment tool to reveal student teachers’ thinking and concerns about their practice. For this purpose we analyze the dilemma analyses completed by 22 student teachers enrolled in our science teacher preparation program over a period of four semesters. Student teachers’ dilemmas fall into two main groups: dilemmas about student performance and dilemmas associated with instructional decisions. These dilemmas reveal a variety of concerns that student teachers have about their work. In particular, concerns about lack of student motivation and its consequences on performance and instruction play a central role in student teachers’ thinking. The recognition of common patterns of thought in our student teacher thinking has made us reflect on and re-evaluate important components of the curriculum in our science teacher preparation program.

  1. Photoinduced Oxidative DNA Damage Revealed by an Agarose Gel Nicking Assay: A Biophysical Chemistry Laboratory Experiment

    NASA Astrophysics Data System (ADS)

    Shafirovich, Vladimir; Singh, Carolyn; Geacintov, Nicholas E.

    2003-11-01

    Oxidative damage of DNA molecules associated with electron-transfer reactions is an important phenomenon in living cells, which can lead to mutations and contribute to carcinogenesis and the aging processes. This article describes the design of several simple experiments to explore DNA damage initiated by photoinduced electron-transfer reactions sensitized by the acridine derivative, proflavine (PF). A supercoiled DNA agarose gel nicking assay is employed as a sensitive probe of DNA strand cleavage. A low-cost experimental and computer-interfaced imaging apparatus is described allowing for the digital recording and analysis of the gel electrophoresis results. The first experiment describes the formation of direct strand breaks in double-stranded DNA induced by photoexcitation of the intercalated PF molecules. The second experiment demonstrates that the addition of the well-known electron acceptor, methylviologen, gives rise to a significant enhancement of the photochemical DNA strand cleavage effect. This occurs by an electron transfer step to methylviologen that renders the inital photoinduced charge separation between photoexcited PF and DNA irreversible. The third experiment demonstrates that the action spectrum of the DNA photocleavage matches the absorption spectrum of DNA-bound, intercalated PF molecules, which differs from that of free PF molecules. This result demonstrates that the photoinduced DNA strand cleavage is initiated by intercalated rather than free PF molecules.

  2. Adhesive Characterization and Progressive Damage Analysis of Bonded Composite Joints

    NASA Technical Reports Server (NTRS)

    Girolamo, Donato; Davila, Carlos G.; Leone, Frank A.; Lin, Shih-Yung

    2014-01-01

    The results of an experimental/numerical campaign aimed to develop progressive damage analysis (PDA) tools for predicting the strength of a composite bonded joint under tensile loads are presented. The PDA is based on continuum damage mechanics (CDM) to account for intralaminar damage, and cohesive laws to account for interlaminar and adhesive damage. The adhesive response is characterized using standard fracture specimens and digital image correlation (DIC). The displacement fields measured by DIC are used to calculate the J-integrals, from which the associated cohesive laws of the structural adhesive can be derived. A finite element model of a sandwich conventional splice joint (CSJ) under tensile loads was developed. The simulations indicate that the model is capable of predicting the interactions of damage modes that lead to the failure of the joint.

  3. Damage Detection and Analysis in CFRPs Using Acoustic Emission Technique

    NASA Astrophysics Data System (ADS)

    Whitlow, Travis Laron

    Real time monitoring of damage is an important aspect of life management of critical structures. Acoustic emission (AE) techniques allow for measurement and assessment of damage in real time. Acoustic emission parameters such as signal amplitude and duration were monitored during the loading sequences. Criteria that can indicate the onset of critical damage to the structure were developed. Tracking the damage as it happens gives a better analysis of the failure evolution that will allow for a more accurate determination of structural life. The main challenge is distinguishing between legitimate damage signals and "false positives" which are unrelated to damage growth. Such false positives can be related to electrical noise, friction, or mechanical vibrations. This research focuses on monitoring signals of damage growth in carbon fiber reinforced polymers (CFRPs) and separating the relevant signals from the false ones. In this Dissertation, acoustic emission signals from CFRP specimens were experimentally recorded and analyzed. The objectives of this work are: (1) perform static and fatigue loading of CFRP composite specimens and measure the associated AE signals, (2) accurately determine the AE parameters (energy, frequency, duration, etc.) of signals generated during failure of such specimens, (3) use fiber optic sensors to monitor the strain distribution of the damage zone and relate these changes in strain measurements to AE data.

  4. Real-Time Tracking of Parental Histones Reveals Their Contribution to Chromatin Integrity Following DNA Damage.

    PubMed

    Adam, Salomé; Dabin, Juliette; Chevallier, Odile; Leroy, Olivier; Baldeyron, Céline; Corpet, Armelle; Lomonte, Patrick; Renaud, Olivier; Almouzni, Geneviève; Polo, Sophie E

    2016-10-06

    Chromatin integrity is critical for cell function and identity but is challenged by DNA damage. To understand how chromatin architecture and the information that it conveys are preserved or altered following genotoxic stress, we established a system for real-time tracking of parental histones, which characterize the pre-damage chromatin state. Focusing on histone H3 dynamics after local UVC irradiation in human cells, we demonstrate that parental histones rapidly redistribute around damaged regions by a dual mechanism combining chromatin opening and histone mobilization on chromatin. Importantly, parental histones almost entirely recover and mix with new histones in repairing chromatin. Our data further define a close coordination of parental histone dynamics with DNA repair progression through the damage sensor DDB2 (DNA damage-binding protein 2). We speculate that this mechanism may contribute to maintaining a memory of the original chromatin landscape and may help preserve epigenome stability in response to DNA damage.

  5. Analysis of nonlinear deformations and damage in CFRP textile laminates

    NASA Astrophysics Data System (ADS)

    Ullah, H.; Harland, A. R.; Lucas, T.; Price, D.; Silberschmidt, V. V.

    2011-07-01

    Carbon fibre-reinforced polymer (CFRP) textile composites are widely used in aerospace, automotive and construction components and structures thanks to their relatively low production costs, higher delamination and impact strength. They can also be used in various products in sports industry. These products are usually exposed to different in-service conditions such as large bending deformation and multiple impacts. Composite materials usually demonstrate multiple modes of damage and fracture due to their heterogeneity and microstructure, in contrast to more traditional homogeneous structural materials like metals and alloys. Damage evolution affects both their in-service properties and performance that can deteriorate with time. These damage modes need adequate means of analysis and investigation, the major approaches being experimental characterisation, numerical simulations and microtomography analysis. This research deals with a deformation behaviour and damage in composite laminates linked to their quasi-static bending. Experimental tests are carried out to characterise the behaviour of woven CFRP material under large-deflection bending. Two-dimensional finite element (FE) models are implemented in the commercial code Abaqus/Explicit to study the deformation behaviour and damage in woven CFRP laminates. Multiple layers of bilinear cohesive-zone elements are employed to model the onset and progression of inter-ply delamination process. X-ray Micro-Computed Tomography (MicroCT) analysis is carried out to investigate internal damage mechanisms such as cracking and delaminations. The obtained results of simulations are in agreement with experimental data and MicroCT scans.

  6. Application Of Shakedown Analysis To Cyclic Creep Damage Limits

    SciTech Connect

    Carter, Peter; Jetter, Robert I; Sham, Sam

    2012-01-01

    Shakedown analysis may be used to provide a conservative estimate of local rupture and hence cyclic creep damage for use in a creep-fatigue assessment. The shakedown analysis is based on an elastic-perfectly plastic material with a temperature-dependent pseudo yield stress defined to guarantee that a shakedown solution exists which does not exceed rupture stress and temperature for a defined life. The ratio of design life to the estimated maximum cyclic life is the shakedown creep damage. The methodology does not require stress classification and is also applicable to cycles over the full range of temperature above and below the creep regime. Full cyclic creep and damage analysis is the alternative when shakedown analysis appears to be excessively conservative.

  7. Damage functions for climate-related hazards: unification and uncertainty analysis

    NASA Astrophysics Data System (ADS)

    Prahl, B. F.; Rybski, D.; Boettle, M.; Kropp, J. P.

    2015-11-01

    Most climate change impacts manifest in the form of natural hazards. For example, sea-level rise and changes in storm climatology are expected to increase the frequency and magnitude of flooding events. In practice there is a need for comprehensive damage assessment at an intermediate level of complexity. Answering this need, we reveal the common grounds of macroscale damage functions employed in storm damage, coastal-flood damage, and heat mortality assessment. The universal approach offers both bottom-up and top-down damage evaluation, employing either an explicit or an implicit portfolio description. Putting emphasis on the treatment of data uncertainties, we perform a sensitivity analysis across different scales. We find that the behaviour of intrinsic uncertainties on the microscale level (i.e. single item) does still persist on the macroscale level (i.e. portfolio). Furthermore, the analysis of uncertainties can reveal their specific relevance, allowing for simplification of the modelling chain. Our results shed light on the role of uncertainties and provide useful insight for the application of a unified damage function.

  8. Spiral Bevel Gear Damage Detection Using Decision Fusion Analysis

    NASA Technical Reports Server (NTRS)

    Dempsey, Paula J.; Handschuh, Robert F.; Afjeh, Abdollah A.

    2002-01-01

    A diagnostic tool for detecting damage to spiral bevel gears was developed. Two different monitoring technologies, oil debris analysis and vibration, were integrated using data fusion into a health monitoring system for detecting surface fatigue pitting damage on gears. This integrated system showed improved detection and decision-making capabilities as compared to using individual monitoring technologies. This diagnostic tool was evaluated by collecting vibration and oil debris data from fatigue tests performed in the NASA Glenn Spiral Bevel Gear Fatigue Rigs. Data was collected during experiments performed in this test rig when pitting damage occurred. Results show that combining the vibration and oil debris measurement technologies improves the detection of pitting damage on spiral bevel gears.

  9. Sensitivity Analysis for Dynamic Failure and Damage in Metallic Structures

    DTIC Science & Technology

    2005-03-01

    respect to the nominal alloy composition at the center of weld surface (Point 6 of Figure 7) -21 - U CO 2000 - * cE axc -2000 o" "....". . -401.11𔃺 1󈧄...Final Report Sensitivity Analysis for Dynamic Failure and Damage in Metallic Structures Office of Naval Research 800 North Quincy Street Arlington...3/31/05 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Sensitivity Analysis for Dynamic Failure and Damage in Metallic Structures Sb. GRANT NUMBER N000

  10. Thermomechanical analysis of a damaged thermal protection system

    NASA Astrophysics Data System (ADS)

    Ng, Wei Heok

    Research on the effects of damage on the thermomechanical performance and structural integrity of thermal protection systems (TPS) has been limited. The objective of this research is to address this need by conducting experiments and finite element (FE) analysis on damaged TPS. The TPS selected for study is the High-Temperature Reusable Insulation (HRSI) tiles that are used extensively on NASA's Space Shuttle Orbiter. The TPS considered, which consists of a LI-900 tile, the strain isolator pad and the underlying structure, is subjected to the thermal loading and re-entry static pressure of the Access to Space reference vehicle. The damage to the TPS emulates hypervelocity-impact-type damage, which is approximated in the current research by a cylindrical hole ending with a spherical cap. Preliminary FE analysis using several simplifying assumptions, was conducted to determine the accuracy of using an approximate axisymmetric model compared to a complete three-dimensional model for both heat transfer and thermal stress analyses. Temperature results from the two models were found to be reasonable close; however, thermal stress results displayed significant differences. The sensitivity of the FE results to the various simplifying assumptions was also examined and it was concluded that for reliable results, the simplifying assumptions were not acceptable. Subsequently, an exact three-dimensional model was developed and validated by comparison with experimental data. Re-entry static pressures and temperatures were simulated using a high-temperature experimental facility that consists of a quartz radiant heater and a vacuum chamber with appropriate instrumentation. This facility was developed during the course of this dissertation. Temperatures on the top and bottom surfaces of the TPS specimen as well as strains in the underlying structure were recorded for FE model validation. The validated FE model was then combined with improved thermal loads based on the interactions

  11. Nonlinear damage detection in composite structures using bispectral analysis

    NASA Astrophysics Data System (ADS)

    Ciampa, Francesco; Pickering, Simon; Scarselli, Gennaro; Meo, Michele

    2014-03-01

    Literature offers a quantitative number of diagnostic methods that can continuously provide detailed information of the material defects and damages in aerospace and civil engineering applications. Indeed, low velocity impact damages can considerably degrade the integrity of structural components and, if not detected, they can result in catastrophic failure conditions. This paper presents a nonlinear Structural Health Monitoring (SHM) method, based on ultrasonic guided waves (GW), for the detection of the nonlinear signature in a damaged composite structure. The proposed technique, based on a bispectral analysis of ultrasonic input waveforms, allows for the evaluation of the nonlinear response due to the presence of cracks and delaminations. Indeed, such a methodology was used to characterize the nonlinear behaviour of the structure, by exploiting the frequency mixing of the original waveform acquired from a sparse array of sensors. The robustness of bispectral analysis was experimentally demonstrated on a damaged carbon fibre reinforce plastic (CFRP) composite panel, and the nonlinear source was retrieved with a high level of accuracy. Unlike other linear and nonlinear ultrasonic methods for damage detection, this methodology does not require any baseline with the undamaged structure for the evaluation of the nonlinear source, nor a priori knowledge of the mechanical properties of the specimen. Moreover, bispectral analysis can be considered as a nonlinear elastic wave spectroscopy (NEWS) technique for materials showing either classical or non-classical nonlinear behaviour.

  12. Analysis of damaging hydrogeological events in a Mediterranean region (Calabria)

    NASA Astrophysics Data System (ADS)

    Aceto, Luigi; Caloiero, Tommaso; Pasqua, A. A.; Petrucci, Olga

    2016-10-01

    Damaging Hydrogeological Events (DHEs) are periods of severe weather conditions affecting wide areas for several days, and causing mainly damaging landslides and floods. In order to characterise the DHEs, we analysed the historical series of the events that affected a Mediterranean region (Calabria, southern Italy) throughout 92 years of observation. Depending on their magnitude, we classified the events as: major catastrophic, catastrophic, extraordinary and ordinary. In winter events, damaged areas and damage were greater than those resulting from the other seasons. Nevertheless, the majority of the events took place in autumn, when, in addition to landslides, a relevant percentage of flash floods and floods also occurred. Results also show that the frequency of major catastrophic and catastrophic events has decreased since 1971, and that, in recent decades, Calabria has suffered from damaging effects even though rain did not reached extreme characteristics. In fact, the duration of triggering rain, the maximum daily rain of the events and the out coming frequency of the high return period of rain show a decreasing pattern throughout the study period. As to what concerns the damaging phenomena, landslides were identified as the most frequent in every season and in every type of events, the eastern side of the region was the most frequently and heavily damaged. According to literature, the trend of number of victims per event is also decreasing. The proposed analysis can be applied to different study areas in order to assess the relative magnitude of DHEs and their evolution throughout the years. The classification criterion can be useful to compare different events for either scientific or insurance purposes, and to identify the typical rainfall-damage scenario of a study area.

  13. DETECTION OF DNA DAMAGE USING MELTING ANALYSIS TECHNIQUES

    EPA Science Inventory

    A rapid and simple fluorescence screening assay for UV radiation-, chemical-, and enzyme-induced DNA damage is reported. This assay is based on a melting/annealing analysis technique and has been used with both calf thymus DNA and plasmid DNA (puc 19 plasmid from E. coli). DN...

  14. Structural Damage Prediction and Analysis for Hypervelocity Impact: Consulting

    NASA Technical Reports Server (NTRS)

    1995-01-01

    A portion of the contract NAS8-38856, 'Structural Damage Prediction and Analysis for Hypervelocity Impacts,' from NASA Marshall Space Flight Center (MSFC), included consulting which was to be documented in the final report. This attachment to the final report contains memos produced as part of that consulting.

  15. Analysis of free radical damage within single cells using flow cytometry

    SciTech Connect

    Vaughan, A.T.; Allan, I.M.; Gordon, D.J.; Grdina, D.J.; Milner, A.M. )

    1991-01-01

    The data presented here illustrates the additional information that can be gained on single cell biological effects by using a method of damage estimation based on single cells. The experiments involving primarily free radical damage carried out using H{sub 2}O2 and the radioprotectors cysteamine and WR 1065, both revealed data that could not have been obtained from a macroscopic study of free radical-DNA chemistry and analysis of reaction products. This serves to emphasise the difficulty in extrapolating both free radical based and other chemical reactions to effects seen in living systems.

  16. Aspergillus fumigatus spore proteomics and genetics reveal that VeA represses DefA-mediated DNA damage response.

    PubMed

    Shin, Kwang-Soo; Park, Hee-Soo; Kim, Young; Heo, In-Beom; Kim, Young Hwan; Yu, Jae-Hyuk

    2016-10-04

    Aspergillus fumigatus reproduces and infects host by forming a high number of small asexual spores (conidia). The velvet proteins are global transcriptional regulators governing the complex process of conidiogenesis in this fungus. Here, to further understand the velvet-mediated regulation, we carried out comparative proteomic analyses of conidia of wild type (WT) and three velvet mutants (ΔveA, ΔvelB and ΔvosA). Cluster analysis of 184 protein spots showing at least 1.5-fold differential accumulation between WT and mutants reveal the clustering of WT- ΔveA and ΔvelB-ΔvosA. Among 43 proteins identified by Nano-LC-ESI-MS/MS, 23 including several heat shock proteins showed more than two-fold reduction in both the ∆velB and ∆vosA conidia. On the contrary, three proteins exhibited more than five-fold increase in ∆veA only, including the putative RNA polymerase II degradation factor DefA. The deletion of defA resulted in a reduced number of conidia and restricted colony growth. In addition, the defA deletion mutant conidia showed hypersensitivity against the DNA damaging agents NQO and MMS, while the ΔveA mutant conidia were more resistant against to NQO. Taken together, we propose that VeA controls protein level of DefA in conidia, which are dormant and equipped with multiple layers of protection against environmental cues.

  17. The Effects of Revealed Information on Catastrophe Loss Projection Models' Characterization of Risk: Damage Vulnerability Evidence from Florida.

    PubMed

    Karl, J Bradley; Medders, Lorilee A; Maroney, Patrick F

    2016-06-01

    We examine whether the risk characterization estimated by catastrophic loss projection models is sensitive to the revelation of new information regarding risk type. We use commercial loss projection models from two widely employed modeling firms to estimate the expected hurricane losses of Florida Atlantic University's building stock, both including and excluding secondary information regarding hurricane mitigation features that influence damage vulnerability. We then compare the results of the models without and with this revealed information and find that the revelation of additional, secondary information influences modeled losses for the windstorm-exposed university building stock, primarily evidenced by meaningful percent differences in the loss exceedance output indicated after secondary modifiers are incorporated in the analysis. Secondary risk characteristics for the data set studied appear to have substantially greater impact on probable maximum loss estimates than on average annual loss estimates. While it may be intuitively expected for catastrophe models to indicate that secondary risk characteristics hold value for reducing modeled losses, the finding that the primary value of secondary risk characteristics is in reduction of losses in the "tail" (low probability, high severity) events is less intuitive, and therefore especially interesting. Further, we address the benefit-cost tradeoffs that commercial entities must consider when deciding whether to undergo the data collection necessary to include secondary information in modeling. Although we assert the long-term benefit-cost tradeoff is positive for virtually every entity, we acknowledge short-term disincentives to such an effort.

  18. Analysis of tank damage during the 1994 Northridge earthquake

    SciTech Connect

    Haroun, M.A.; Bhatia, H.

    1995-12-31

    The damage sustained by cylindrical liquid storage tanks during the 1994 Northridge earthquake is summarized. It included elephant foot buckling, anchor failure and roof-shell connection separation. A few of the important lessons learned, in particular, as related to the accuracy of code computations in predicting the actual behavior of these structures are outlined. A detailed case study is presented to illustrate the application of current seismic design standards to a damaged unanchored tank and to demonstrate the use of a state-of-the-art finite element analysis in assessing the seismic safety of the same tank.

  19. Sample EP Flow Analysis of Severely Damaged Networks

    SciTech Connect

    Werley, Kenneth Alan; McCown, Andrew William

    2016-10-12

    These are slides for a presentation at the working group meeting of the WESC SREMP Software Product Integration Team on sample EP flow analysis of severely damaged networks. The following topics are covered: ERCOT EP Transmission Model; Zoomed in to Houston and Overlaying StreetAtlas; EMPACT Solve/Dispatch/Shedding Options; QACS BaseCase Power Flow Solution; 3 Substation Contingency; Gen. & Load/100 Optimal Dispatch; Dispatch Results; Shed Load for Low V; Network Damage Summary; Estimated Service Areas (Potential); Estimated Outage Areas (potential).

  20. Deletion of histone deacetylase 3 reveals critical roles in S phase progression and DNA damage control.

    PubMed

    Bhaskara, Srividya; Chyla, Brenda J; Amann, Joseph M; Knutson, Sarah K; Cortez, David; Sun, Zu-Wen; Hiebert, Scott W

    2008-04-11

    Histone deacetylases (HDACs) are enzymes that modify key residues in histones to regulate chromatin architecture, and they play a vital role in cell survival, cell-cycle progression, and tumorigenesis. To understand the function of Hdac3, a critical component of the N-CoR/SMRT repression complex, a conditional allele of Hdac3 was engineered. Cre-recombinase-mediated inactivation of Hdac3 led to a delay in cell-cycle progression, cell-cycle-dependent DNA damage, and apoptosis in mouse embryonic fibroblasts (MEFs). While no overt defects in mitosis were observed in Hdac3-/- MEFs, including normal H3Ser10 phosphorylation, DNA damage was observed in Hdac3-/- interphase cells, which appears to be associated with defective DNA double-strand break repair. Moreover, we noted that Hdac3-/- MEFs were protected from DNA damage when quiescent, which may provide a mechanistic basis for the action of HDAC inhibitors on cycling tumor cells.

  1. Development of synthetic flood damage curve by explicit costs analysis

    NASA Astrophysics Data System (ADS)

    Martina, Mario; Molinari, Daniela; Dottori, Francesco; Scorzini, Annarita

    2015-04-01

    characteristics. Such functions were developed using a what-if analysis using data collected after the 2012 flood in the Umbria Region in Central Italy, as well as authors' experience, as reference to understand damage mechanisms. Observed damage data were also used to calibrate the functions.

  2. Transmission Bearing Damage Detection Using Decision Fusion Analysis

    NASA Technical Reports Server (NTRS)

    Dempsey, Paula J.; Lewicki, David G.; Decker, Harry J.

    2004-01-01

    A diagnostic tool was developed for detecting fatigue damage to rolling element bearings in an OH-58 main rotor transmission. Two different monitoring technologies, oil debris analysis and vibration, were integrated using data fusion into a health monitoring system for detecting bearing surface fatigue pitting damage. This integrated system showed improved detection and decision-making capabilities as compared to using individual monitoring technologies. This diagnostic tool was evaluated by collecting vibration and oil debris data from tests performed in the NASA Glenn 500 hp Helicopter Transmission Test Stand. Data was collected during experiments performed in this test rig when two unanticipated bearing failures occurred. Results show that combining the vibration and oil debris measurement technologies improves the detection of pitting damage on spiral bevel gears duplex ball bearings and spiral bevel pinion triplex ball bearings in a main rotor transmission.

  3. Tapered Roller Bearing Damage Detection Using Decision Fusion Analysis

    NASA Technical Reports Server (NTRS)

    Dempsey, Paula J.; Kreider, Gary; Fichter, Thomas

    2006-01-01

    A diagnostic tool was developed for detecting fatigue damage of tapered roller bearings. Tapered roller bearings are used in helicopter transmissions and have potential for use in high bypass advanced gas turbine aircraft engines. A diagnostic tool was developed and evaluated experimentally by collecting oil debris data from failure progression tests conducted using health monitoring hardware. Failure progression tests were performed with tapered roller bearings under simulated engine load conditions. Tests were performed on one healthy bearing and three pre-damaged bearings. During each test, data from an on-line, in-line, inductance type oil debris sensor and three accelerometers were monitored and recorded for the occurrence of bearing failure. The bearing was removed and inspected periodically for damage progression throughout testing. Using data fusion techniques, two different monitoring technologies, oil debris analysis and vibration, were integrated into a health monitoring system for detecting bearing surface fatigue pitting damage. The data fusion diagnostic tool was evaluated during bearing failure progression tests under simulated engine load conditions. This integrated system showed improved detection of fatigue damage and health assessment of the tapered roller bearings as compared to using individual health monitoring technologies.

  4. Lightning Strike Ablation Damage Influence Factors Analysis of Carbon Fiber/Epoxy Composite Based on Coupled Electrical-Thermal Simulation

    NASA Astrophysics Data System (ADS)

    Yin, J. J.; Chang, F.; Li, S. L.; Yao, X. L.; Sun, J. R.; Xiao, Y.

    2016-12-01

    According to the mathematical analysis model constructed on the basis of energy-balance relationship in lightning strike, and accompany with the simplified calculation strategy of composite resin pyrolysis degree dependent electrical conductivity, an effective three dimensional thermal-electrical coupling analysis finite element model of composite laminate suffered from lightning current was established based on ABAQUS, to elucidate the effects of lighting current waveform parameters and thermal/electrical properties of composite laminate on the extent of ablation damage. Simulated predictions agree well with the composite lightning strike directed effect experimental data, illustrating the potential accuracy of the constructed model. The analytical results revealed that extent of composite lightning strike ablation damage can be characterized by action integral validly, there exist remarkable power function relationships between action integral and visual damage area, projected damage area, maximum damage depth and damage volume of ablation damage, and enhancing the electrical conductivity and specific heat of composite, ablation damage will be descended obviously, power function relationships also exist between electrical conductivity, specific heat and ablation damage, however, the impact of thermal conductivity on the extent of ablation damage is not notable. The conclusions obtained provide some guidance for composite anti-lightning strike structure-function integration design.

  5. The Nature of Macular Damage in Glaucoma as Revealed by Averaging Optical Coherence Tomography Data

    PubMed Central

    Hood, Donald C.; Raza, Ali S.; de Moraes, Carlos Gustavo V.; Johnson, Chris A.; Liebmann, Jeffrey M.; Ritch, Robert

    2012-01-01

    Purpose To better understand the nature of glaucomatous damage, especially to the macula, the inner retinal thickness maps obtained with frequency domain optical coherence tomography (fdOCT) were averaged. Methods Frequency domain optical coherence tomography macular and optic disc cube scans were obtained from 54 healthy eyes and 156 eyes with glaucomatous optic neuropathy. A manually corrected algorithm was used for layer segmentation. Patients' eyes were grouped both by mean deviation (MD) and hemifield classification using standard categories and 24-2 (6° grid) visual fields (VFs). To obtain average difference maps, the thickness of retinal nerve fiber (RNF) and retinal ganglion cell plus inner plexiform (RGC+) layers were averaged and subtracted from the average control values. Results On the average difference maps, RGC+ and RNF layer thinning was seen in the patient groups with VFs classified as normal. The pattern of the thinning was the same, but the degree of thinning increased with decreased MD and with classification category (from normal to arcuate). This RGC+ thinning was largely within the central four points of the 24-2 (6° grid) field, after correcting for RGC displacement. Conclusion 1. VF categories represent different degrees of the same pattern of RGC+ and RNFL layer thinning. 2. RGC+ damage occurs in the central macula even in patients with VFs classified as normal. 3. The 6° grid (24-2) pattern is not optimally designed to detect macular damage. 4. A schematic model of RGC projections is proposed to explain the pattern of macular loss, including the greater vulnerability of the inferior retinal region. Translational relevance The 24-2 is not an optimal test pattern for detecting or following glaucomatous damage. Further, we suggest clinical fdOCT reports include RGC+ and RNFL probability plots combined with VF information. PMID:23626924

  6. Analysis Methods for Progressive Damage of Composite Structures

    NASA Technical Reports Server (NTRS)

    Rose, Cheryl A.; Davila, Carlos G.; Leone, Frank A.

    2013-01-01

    This document provides an overview of recent accomplishments and lessons learned in the development of general progressive damage analysis methods for predicting the residual strength and life of composite structures. These developments are described within their State-of-the-Art (SoA) context and the associated technology barriers. The emphasis of the authors is on developing these analysis tools for application at the structural level. Hence, modeling of damage progression is undertaken at the mesoscale, where the plies of a laminate are represented as a homogenous orthotropic continuum. The aim of the present effort is establish the ranges of validity of available models, to identify technology barriers, and to establish the foundations of the future investigation efforts. Such are the necessary steps towards accurate and robust simulations that can replace some of the expensive and time-consuming "building block" tests that are currently required for the design and certification of aerospace structures.

  7. Visualization and Analysis of Impact Damage in Sapphire

    DTIC Science & Technology

    2011-11-01

    Analysis of Impact Damage in Sapphire Elmar Strassburger Fraunhofer-Institut für Kurzzeitdynamik, Ernst - Mach -Institut (EMI) Parimal Patel and...Miami, FL, 12–16 September 2011. *Fraunhofer-Institut für Kurzzeitdynamik, Ernst - Mach -Institut (EMI), Am Christianswuhr 2, 79400 Kandern, Germany 14...ABSTRACT This report reviews work carried out with the fully instrumented Edge-on Impact (EOI) facility at the Ernst - Mach -Institute (EMI), using a

  8. Lightning Strike Ablation Damage Characteristic Analysis for Carbon Fiber/Epoxy Composite Laminate with Fastener

    NASA Astrophysics Data System (ADS)

    Yin, J. J.; Li, S. L.; Yao, X. L.; Chang, F.; Li, L. K.; Zhang, X. H.

    2016-08-01

    In order to analyze the lightning strike ablation damage characteristic of composite laminate with fastener, based on the energy-balance relationship in lightning strike, mathematical analysis model of ablation damage of composite laminate with fastener was constructed. According to the model, an effective three dimensional thermal-electrical coupling analysis finite element model of composite laminate with fastener suffered from lightning current was established based on ABAQUS, and lightning strike ablation damage characteristic was analyzed. Analytical results reveal that lightning current could conduct through the thickness direction of the laminate due to the existence of metallic fastener, and then distribute to all layers, finally conducted in-the-plane of each layer, conductive ability of different layup orientations depend on potential distribution and in-the-plane electrical conductivity along potential gradient declining direction; different potential boundaries correspond to different potential distribution in each layer, and result in conductive ability of different layup orientations was changed, then caused different lightning strike ablation damage distribution. According to the investigation in this paper, we can recognize the lightning strike ablation damage characteristic of composite laminate with fastener qualitatively.

  9. Image Science and Analysis Group Spacecraft Damage Detection/Characterization

    NASA Technical Reports Server (NTRS)

    Wheaton, Ira M., Jr.

    2010-01-01

    This project consisted of several tasks that could be served by an intern to assist the ISAG in detecting damage to spacecrafts during missions. First, this project focused on supporting the Micrometeoroid Orbital Debris (MMOD) damage detection and assessment for the Hubble Space Telescope (HST) using imagery from the last two HST Shuttle servicing missions. In this project, we used coordinates of two windows on the Shuttle Aft flight deck from where images were taken and the coordinates of three ID points in order to calculate the distance from each window to the three points. Then, using the specifications from the camera used, we calculated the image scale in pixels per inch for planes parallel to and planes in the z-direction to the image plane (shown in Table 1). This will help in the future for calculating measurements of objects in the images. Next, tabulation and statistical analysis were conducted for screening results (shown in Table 2) of imagery with Orion Thermal Protection System (TPS) damage. Using the Microsoft Excel CRITBINOM function and Goal Seek, the probabilities of detection of damage to different shuttle tiles were calculated as shown in Table 3. Using developed measuring tools, volume and area measurements will be created from 3D models of Orion TPS damage. Last, mathematical expertise was provided to the Photogrammetry Team. These mathematical tasks consisted of developing elegant image space error equations for observations along 3D lines, circles, planes, etc. and checking proofs for minimal sets of sufficient multi-linear constraints. Some of the processes and resulting equations are displayed in Figure 1.

  10. Metabolic network analysis revealed distinct routes of deletion effects between essential and non-essential genes.

    PubMed

    Ma, Jing; Zhang, Xun; Ung, Choong Yong; Chen, Yu Zong; Li, Baowen

    2012-04-01

    Interest in essential genes has arisen recently given their importance in antimicrobial drug development. Although knockouts of essential genes are commonly known to cause lethal phenotypes, there is insufficient understanding on the intermediate changes followed by genetic perturbation and to what extent essential genes correlate to other genes. Here, we characterized the gene knockout effects by using a list of affected genes, termed as 'damage lists'. These damage lists were identified through a refined cascading failure approach that was based on a previous topological flux balance analysis. Using an Escherichia coli metabolic network, we incorporated essentiality information into damage lists and revealed that the knockout of an essential gene mainly affects a large range of other essential genes whereas knockout of a non-essential gene only interrupts other non-essential genes. Also, genes sharing common damage lists tend to have the same essentiality. We extracted 72 core functional modules from the common damage lists of essential genes and demonstrated their ability to halt essential metabolites production. Overall, our network analysis revealed that essential and non-essential genes propagated their deletion effects via distinct routes, conferring mechanistic explanation to the observed lethality phenotypes of essential genes.

  11. Quantitative interactome analysis reveals a chemoresistant edgotype

    PubMed Central

    Chavez, Juan D.; Schweppe, Devin K.; Eng, Jimmy K.; Zheng, Chunxiang; Taipale, Alex; Zhang, Yiyi; Takara, Kohji; Bruce, James E.

    2015-01-01

    Chemoresistance is a common mode of therapy failure for many cancers. Tumours develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine structural and protein interaction changes on a proteomic scale. Here, chemical crosslinking and mass spectrometry were employed to quantify changes in protein structures and interactions in multidrug-resistant human carcinoma cells. Quantitative analysis of the largest crosslinking-derived, protein interaction network comprising 1,391 crosslinked peptides allows for ‘edgotype' analysis in a cell model of chemoresistance. We detect consistent changes to protein interactions and structures, including those involving cytokeratins, topoisomerase-2-alpha, and post-translationally modified histones, which correlate with a chemoresistant phenotype. PMID:26235782

  12. Identification and analysis of damaged or porous hair.

    PubMed

    Hill, Virginia; Loni, Elvan; Cairns, Thomas; Sommer, Jonathan; Schaffer, Michael

    2014-06-01

    Cosmetic hair treatments have been referred to as 'the pitfall' of hair analysis. However, most cosmetic treatments, when applied to the hair as instructed by the product vendors, do not interfere with analysis, provided such treatments can be identified by the laboratory and the samples analyzed and reported appropriately for the condition of the hair. This paper provides methods for identifying damaged or porous hair samples using digestion rates of hair in dithiothreitol with and without proteinase K, as well as a protein measurement method applied to dithiothreitol-digested samples. Extremely damaged samples may be unsuitable for analysis. Aggressive and extended aqueous washing of hair samples is a proven method for removing or identifying externally derived drug contamination of hair. In addition to this wash procedure, we have developed an alternative wash procedure using 90% ethanol for washing damaged or porous hair. The procedure, like the aqueous wash procedure, requires analysis of the last of five washes to evaluate the effectiveness of the washing procedure. This evaluation, termed the Wash Criterion, is derived from studies of the kinetics of washing of hair samples that have been experimentally contaminated and of hair from drug users. To study decontamination methods, in vitro contaminated drug-negative hair samples were washed by both the aqueous buffer method and a 90% ethanol method. Analysis of cocaine and methamphetamine was by liquid chromatography-tandem mass spectrometry (LC/MS/MS). Porous hair samples from drug users, when washed in 90% ethanol, pass the wash criterion although they may fail the aqueous wash criterion. Those samples that fail both the ethanolic and aqueous wash criterion are not reported as positive for ingestion. Similar ratios of the metabolite amphetamine relative to methamphetamine in the last wash and the hair is an additional criterion for assessing contamination vs. ingestion of methamphetamine.

  13. Finite element stress analysis of idealized composite damage zones

    NASA Technical Reports Server (NTRS)

    Obrien, D.; Herakovich, C. T.

    1978-01-01

    A quasi three dimensional finite element stress analysis of idealized damage zones in composite laminates is presented. The damage zones consist of a long centered groove or cutout extending one or two layers in depth from both top and bottom surfaces of a thin composite laminate. Elastic results are presented for compressive loading of four and eight layer laminates. It is shown that a boundary layer exists near the cutout edge similar to that previously shown to exist along free edges. The cutout is shown to produce significant interlaminar stresses in the interior of the laminate away from free cutout edges. The interlaminar stresses are also shown to contribute to failure which is defined using the Tsai-Wu failure criteria.

  14. Spiral-Bevel-Gear Damage Detected Using Decision Fusion Analysis

    NASA Technical Reports Server (NTRS)

    Dempsey, Paula J.; Handschuh, Robert F.

    2003-01-01

    Helicopter transmission integrity is critical to helicopter safety because helicopters depend on the power train for propulsion, lift, and flight maneuvering. To detect impending transmission failures, the ideal diagnostic tools used in the health-monitoring system would provide real-time health monitoring of the transmission, demonstrate a high level of reliable detection to minimize false alarms, and provide end users with clear information on the health of the system without requiring them to interpret large amounts of sensor data. A diagnostic tool for detecting damage to spiral bevel gears was developed. (Spiral bevel gears are used in helicopter transmissions to transfer power between nonparallel intersecting shafts.) Data fusion was used to integrate two different monitoring technologies, oil debris analysis and vibration, into a health-monitoring system for detecting surface fatigue pitting damage on the gears.

  15. Subsurface damage detection and damage mechanism analysis of chemical-mechanical polished optics

    NASA Astrophysics Data System (ADS)

    Ye, Hui; Yang, Wei; Bi, Guo; Yang, Ping; Guo, Yinbiao

    2014-09-01

    Detection of the subsurface damage depth in optical elements has significance on the subsequent material removal amount and improving element surface quality. The paper focuses on the subsurface damage of chemical-mechanical polished K9 specimen, and analyses the chemical-mechanical polishing mechanism and the cause of subsurface damage. A most suitable etchant is chosen and the step-by-step etching method is applied to measure the subsurface damage depth. A microscope is used to detect the damage morphology and the variation trend at different depth. Research shows that the subsurface damage caused by chemical-mechanical polishing is Hertz scratch, and the scratch quantity below surface presents a variation of zero-more-less-disappeared. The K9 specimen is polished for 3 min under the pressure of 2.5 Kgf and the spindle speed of 43139 r/min, thus resulting in a subsurface damage depth 15.3μm.

  16. Fatigue Crack Growth Database for Damage Tolerance Analysis

    NASA Technical Reports Server (NTRS)

    Forman, R. G.; Shivakumar, V.; Cardinal, J. W.; Williams, L. C.; McKeighan, P. C.

    2005-01-01

    The objective of this project was to begin the process of developing a fatigue crack growth database (FCGD) of metallic materials for use in damage tolerance analysis of aircraft structure. For this initial effort, crack growth rate data in the NASGRO (Registered trademark) database, the United States Air Force Damage Tolerant Design Handbook, and other publicly available sources were examined and used to develop a database that characterizes crack growth behavior for specific applications (materials). The focus of this effort was on materials for general commercial aircraft applications, including large transport airplanes, small transport commuter airplanes, general aviation airplanes, and rotorcraft. The end products of this project are the FCGD software and this report. The specific goal of this effort was to present fatigue crack growth data in three usable formats: (1) NASGRO equation parameters, (2) Walker equation parameters, and (3) tabular data points. The development of this FCGD will begin the process of developing a consistent set of standard fatigue crack growth material properties. It is envisioned that the end product of the process will be a general repository for credible and well-documented fracture properties that may be used as a default standard in damage tolerance analyses.

  17. Diagnosis of Lung Cancer by Fractal Analysis of Damaged DNA

    PubMed Central

    Namazi, Hamidreza; Kiminezhadmalaie, Mona

    2015-01-01

    Cancer starts when cells in a part of the body start to grow out of control. In fact cells become cancer cells because of DNA damage. A DNA walk of a genome represents how the frequency of each nucleotide of a pairing nucleotide couple changes locally. In this research in order to study the cancer genes, DNA walk plots of genomes of patients with lung cancer were generated using a program written in MATLAB language. The data so obtained was checked for fractal property by computing the fractal dimension using a program written in MATLAB. Also, the correlation of damaged DNA was studied using the Hurst exponent measure. We have found that the damaged DNA sequences are exhibiting higher degree of fractality and less correlation compared with normal DNA sequences. So we confirmed this method can be used for early detection of lung cancer. The method introduced in this research not only is useful for diagnosis of lung cancer but also can be applied for detection and growth analysis of different types of cancers. PMID:26539245

  18. Deep rock damage in the San Andreas Fault revealed by P- and S-type fault-zone-guided waves

    USGS Publications Warehouse

    Ellsworth, William L.; Malin, Peter E.

    2011-01-01

    Damage to fault-zone rocks during fault slip results in the formation of a channel of low seismic-wave velocities. Within such channels guided seismic waves, denoted by Fg, can propagate. Here we show with core samples, well logs and Fg-waves that such a channel is crossed by the SAFOD (San Andreas Fault Observatory at Depth) borehole at a depth of 2.7 km near Parkfield, California, USA. This laterally extensive channel extends downwards to at least half way through the seismogenic crust, more than about 7 km. The channel supports not only the previously recognized Love-type- (FL) and Rayleigh-type- (FR) guided waves, but also a new fault-guided wave, which we name FF. As recorded 2.7 km underground, FF is normally dispersed, ends in an Airy phase, and arrives between the P- and S-waves. Modelling shows that FF travels as a leaky mode within the core of the fault zone. Combined with the drill core samples, well logs and the two other types of guided waves, FF at SAFOD reveals a zone of profound, deep, rock damage. Originating from damage accumulated over the recent history of fault movement, we suggest it is maintained either by fracturing near the slip surface of earthquakes, such as the 1857 Fort Tejon M 7.9, or is an unexplained part of the fault-creep process known to be active at this site.

  19. Micromechanical Continuum Damage Analysis of Plain Woven Composites

    NASA Astrophysics Data System (ADS)

    Li, L.; Aliabadi, F.; Wen, P. H.

    2015-01-01

    Application of meshfree Galerkin method to homogenization and Continuum Damage Mechanics (CDM) analysis of plain woven composites is presented. Three types of meshfree formulations are developed and include: radial basis function, moving least squares and moving Kriging. Three benchmark examples are used to demonstrated the efficiency of the meshfree formulation as well as compare the performance of the three shape functions. Non-linear stress-strain relationhip of unit cellusing the three shape functions are assessed with two benchmark examples of CDM model.

  20. Chromosome Model reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-domains

    NASA Technical Reports Server (NTRS)

    Costes, Sylvain V.; Ponomarev, Artem; Chen, James L.; Cucinotta, Francis A.; Barcellos-Hoff, Helen

    2007-01-01

    Several proteins involved in the response to DNA double strand breaks (DSB) form microscopically visible nuclear domains, or foci, after exposure to ionizing radiation. Radiation-induced foci (RIF) are believed to be located where DNA damage is induced. To test this assumption, we analyzed the spatial distribution of 53BP1, phosphorylated ATM and gammaH2AX RIF in cells irradiated with high linear energy transfer (LET) radiation. Since energy is randomly deposited along high-LET particle paths, RIF along these paths should also be randomly distributed. The probability to induce DSB can be derived from DNA fragment data measured experimentally by pulsed-field gel electrophoresis. We used this probability in Monte Carlo simulations to predict DSB locations in synthetic nuclei geometrically described by a complete set of human chromosomes, taking into account microscope optics from real experiments. As expected, simulations produced DNA-weighted random (Poisson) distributions. In contrast, the distributions of RIF obtained as early as 5 min after exposure to high LET (1 GeV/amu Fe) were non-random. This deviation from the expected DNA-weighted random pattern can be further characterized by relative DNA image measurements. This novel imaging approach shows that RIF were located preferentially at the interface between high and low DNA density regions, and were more frequent in regions with lower density DNA than predicted. This deviation from random behavior was more pronounced within the first 5 min following irradiation for phosphorylated ATM RIF, while gammaH2AX and 53BP1 RIF showed very pronounced deviation up to 30 min after exposure. These data suggest the existence of repair centers in mammalian epithelial cells. These centers would be nuclear sub-domains where DNA lesions would be collected for more efficient repair.

  1. Impact damage analysis of balsawood sandwich composite materials

    NASA Astrophysics Data System (ADS)

    Abdalslam, Suof Omran

    In this study, a new composite sandwich structure with a balsa wood core (end grain and regular balsa) in conjunction with E-glass/epoxy face sheets was proposed, fabricated, impact tested, and modeled. The behavior of the sandwich structure under low velocity impact and compression after impact was investigated. Low velocity impact tests were carried out by drop-weight impact tower at different energy levels (8J-35J) to evaluate the impact response of the sandwich structure. Visual inspection, destructive and non destructive evaluation methods have been conducted. For the sandwich plate with end grain core, the damage was very clear and can be visually detected. However, the damage in regular balsa core was not clearly visible and destructive evaluation method was used. Compression testing was done after subjecting the specimens to impact testing. Impact test results; load-time, load-deflection history and energy absorption for sandwich composites with two different cores, end grain and regular balsa were compared and they were investigated at three different impact energies. The results show that the sandwich structures with end grain core are able to withstand impact loading better than the regular balsa core because the higher stiffness of end grain core informs of sustaining higher load and higher overall energy. The results obtained from compression after impact testing show that the strengths of sandwich composites with end grain and regular balsa cores were reduced about 40% and 52%, respectively, after impact. These results were presented in terms of stress-strain curves for both damaged and undamaged specimens. Finite element analysis was conducted on the sandwich composite structure using LS-DYNA code to simulate impact test. A 3- D finite element model was developed and appropriate material properties were given to each component. The computational model was developed to predict the response of sandwich composite under dynamic loading. The experimental

  2. Structural damage identification using multifunctional Bragg grating sensors: II. Damage detection results and analysis

    NASA Astrophysics Data System (ADS)

    Betz, Daniel C.; Staszewski, Wieslaw J.; Thursby, Graham; Culshaw, Brian

    2006-10-01

    Damage detection is an important issue in structural health monitoring. Lamb waves are the most widely used acousto-ultrasonic guided waves for damage detection. This paper gives the results of experiments carried out to study the identification of damage using Bragg grating sensors as ultrasonic receivers of Lamb waves. The experiments involve a rectangular aluminium plate. Damage was introduced into the plate by drilling a hole into the centre of the plate. In order to obtain different severity of damage, the hole diameter was increased step by step. Several signal processing tools are presented and then applied to the Lamb wave signals in order to find a parameter that corresponds to the severity of damage. The parameter that serves as the damage index has to have small cross-sensitivity to other physical parameters, e.g. temperature. Therefore, additional experiments have been carried out to study the temperature dependence of the Lamb wave signals. In order to determine the influence of the temperature on the damage detection results, the cross-sensitivity is studied within this paper.

  3. Nanoscale histone localization in live cells reveals reduced chromatin mobility in response to DNA damage

    PubMed Central

    Liu, Jing; Vidi, Pierre-Alexandre; Lelièvre, Sophie A.; Irudayaraj, Joseph M. K.

    2015-01-01

    ABSTRACT Nuclear functions including gene expression, DNA replication and genome maintenance intimately rely on dynamic changes in chromatin organization. The movements of chromatin fibers might play important roles in the regulation of these fundamental processes, yet the mechanisms controlling chromatin mobility are poorly understood owing to methodological limitations for the assessment of chromatin movements. Here, we present a facile and quantitative technique that relies on photoactivation of GFP-tagged histones and paired-particle tracking to measure chromatin mobility in live cells. We validate the method by comparing live cells to ATP-depleted cells and show that chromatin movements in mammalian cells are predominantly energy dependent. We also find that chromatin diffusion decreases in response to DNA breaks induced by a genotoxic drug or by the ISceI meganuclease. Timecourse analysis after cell exposure to ionizing radiation indicates that the decrease in chromatin mobility is transient and precedes subsequent increased mobility. Future applications of the method in the DNA repair field and beyond are discussed. PMID:25501817

  4. PCR-based analysis of mitochondrial DNA copy number, mitochondrial DNA damage, and nuclear DNA damage

    PubMed Central

    Gonzalez-Hunt, Claudia P.; Rooney, John P.; Ryde, Ian T.; Anbalagan, Charumathi; Joglekar, Rashmi

    2016-01-01

    Because of the role DNA damage and depletion play in human disease, it is important to develop and improve tools to assess these endpoints. This unit describes PCR-based methods to measure nuclear and mitochondrial DNA damage and copy number. Long amplicon quantitative polymerase chain reaction (LA-QPCR) is used to detect DNA damage by measuring the number of polymerase-inhibiting lesions present based on the amount of PCR amplification; real-time PCR (RT-PCR) is used to calculate genome content. In this unit we provide step-by-step instructions to perform these assays in Homo sapiens, Mus musculus, Rattus norvegicus, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Oryzias latipes, Fundulus grandis, and Fundulus heteroclitus, and discuss the advantages and disadvantages of these assays. PMID:26828332

  5. Lightning damage to a general aviation aircraft: Description and analysis

    NASA Technical Reports Server (NTRS)

    Hacker, P. T.

    1974-01-01

    The damage sustained by a Beechcraft King Air Model B90 aircraft by a single lightning discharge is presented and analyzed. The incident occurred during landing approach at Jackson, Michigan, on Feb. 19, 1971. In addition to the usual melted-metal damage at the lightning attachment points, there was severe implosion-type damage over a large area on the lower right side of the aircraft and impact- and crushing-type damage on the upper and lower surfaces on the left wingtip near the trailing edge. Analyses indicate that the implosion-type damage was probably caused by lightning-generated shock waves, that the impact-and crushing-type damage was caused by magnetic forces, and that the lightning discharge was a multiple strike with at least 11 strokes separated in time by about 4.5 milliseconds. The evidence indicates that the lightning discharge was rather different from the average in character severity.

  6. Non-Harmonic Fourier Analysis for bladed wheels damage detection

    NASA Astrophysics Data System (ADS)

    Neri, P.; Peeters, B.

    2015-11-01

    The interaction between bladed wheels and the fluid distributed by the stator vanes results in cyclic loading of the rotating components. Compressors and turbines wheels are subject to vibration and fatigue issues, especially when resonance conditions are excited. Even if resonance conditions can be often predicted and avoided, high cycle fatigue failures can occur, causing safety issues and economic loss. Rigorous maintenance programs are then needed, forcing the system to expensive shut-down. Blade crack detection methods are beneficial for condition-based maintenance. While contact measurement systems are not always usable in exercise conditions (e.g. high temperature), non-contact methods can be more suitable. One (or more) stator-fixed sensor can measure all the blades as they pass by, in order to detect the damaged ones. The main drawback in this situation is the short acquisition time available for each blade, which is shortened by the high rotational speed of the components. A traditional Discrete Fourier Transform (DFT) analysis would result in a poor frequency resolution. A Non-Harmonic Fourier Analysis (NHFA) can be executed with an arbitrary frequency resolution instead, allowing to obtain frequency information even with short-time data samples. This paper shows an analytical investigation of the NHFA method. A data processing algorithm is then proposed to obtain frequency shift information from short time samples. The performances of this algorithm are then studied by experimental and numerical tests.

  7. Structural Damage Prediction and Analysis for Hypervelocity Impact

    NASA Technical Reports Server (NTRS)

    Elfer, Norman

    1995-01-01

    It is necessary to integrate a wide variety of technical disciplines to provide an analysis of structural damage to a spacecraft due to hypervelocity impact. There are many uncertainties, and more detailed investigation is warranted, in each technical discipline. However, a total picture of the debris and meteoroid hazard is required to support manned spaceflight in general, and the international Space Station in particular. In the performance of this contract, besides producing a handbook, research and development was conducted in several different areas. The contract was broken into six separate tasks. Each task objectives and accomplishments will be reviewed in the following sections. The Handbook and separate task reports are contained as attachments to the final report. The final section summarizes all of the recommendations coming out of this study. The analyses and comments are general design guidelines and not necessarily applicable to final Space Station designs since several configuration and detailed design changes were being made during the course of this contract. Rather, the analyses and comments may indicate either a point-in-time concept analysis, available test data, or desirable protection goals, not hindered by the design and operation constraints faced by Space Station designers.

  8. Analysis Concerning the Inspection Threshold for Multi-Site Damage

    DTIC Science & Technology

    1993-12-01

    uL 200 words) Periodic inspections, at a prescribed interval, for Multi-Site Damage (MSD) in longitudinal fuselage lap-joints start when the aircraft ...at a prescribed interval, for Multi-Site Damage (MSD) in longitudinal fuselage lap-joints start when the aircraft has accumulated a certain number of...viii 1. INTRODUCTION AND SCOPE The cumulative probability of detection of Multi-Site Damage (MSD) in fuselage lap-joints of aging aircraft was assessed

  9. Damage Analysis of Rectangular Section Composite Beam under Pure Bending

    NASA Astrophysics Data System (ADS)

    Liu, Yiping; Xiao, Fan; Liu, Zejia; Tang, Liqun; Fang, Daining

    2013-02-01

    Laminated composite beams are commonly used in engineering applications involving macro to nano structures. Based on the assumption that plain sections remain plain after deformation, this paper analyzes stress distributions in cross-ply laminated composite beams with rectangular cross-sections, and formulates the basic damage equations through Kachanov's damage definition and Janson's failure criterion. The location of the neutral axis and the ultimate bending moment are obtained for pure bending cases. The effect of the elastic modulus of the two layers on the damage evolution is analyzed; a reasonable damage composite beam model is proposed to predict the ultimate bending moment.

  10. Damage Assessment Using Vibration Analysis on the Z24-BRIDGE

    NASA Astrophysics Data System (ADS)

    Maeck, J.; de Roeck, G.

    2003-01-01

    Vibration monitoring is a useful evaluation tool in the development of a non-destructive damage-identification technique, and relies on the fact that occurrence of damage in a structural system leads to changes in its dynamic properties. It can give global information of a structure, and the location of the damage has not to be known in advance. The damage-identification technique is based on the observed shifts in eigenfrequencies and modeshapes and relate the dynamic characteristics to a damage pattern of the structure. The presented technique makes use of the calculation of modal bending moments and curvatures to derive the bending stiffness at each location. The basic assumption is that damage can be directly related to a decrease of stiffness in the structure. Damage-assessment techniques are validated on the progressively damaged prestressed concrete bridge Z24 in Switzerland, tested in the framework of the Brite Euram project SIMCES. A series of full modal surveys are carried out on the bridge before and after applying a number of damage scenarios.

  11. Mechanistic Analysis of Rock Damage Anisotropy and Rotation Around Circular Cavities

    NASA Astrophysics Data System (ADS)

    Xu, Hao; Arson, Chloé

    2015-11-01

    We used the differential stress-induced damage (DSID) model to predict anisotropic crack propagation under tensile and shear stress. The damage variable is similar to a crack density tensor. The damage function and the damage potential are expressed as functions of the energy release rate, defined as the thermodynamic force that is work-conjugate to damage. Contrary to the previous damage models, flow rules are obtained by deriving dissipation functions by the energy release rate, and thermodynamic consistency is ensured. The damage criterion is adapted from the Drucker-Prager yield function. Simulations of biaxial stress tests showed that: (1) three-dimensional states of damage can be obtained for three-dimensional states of stress; (2) no damage propagates under isotropic compression; (3) crack planes propagate in the direction parallel to major compression stress; (4) damage propagation hardens the material; (5) stiffness and deformation anisotropy result from the anisotropy of damage. There is no one-to-one relationship between stress and damage. We demonstrated the effect of the loading sequence in a two-step simulation (a shear loading phase and a compression loading phase): the current state of stress and damage can be used to track the effect of stress history on damage rotation. We finally conducted a sensitivity analysis with the finite element method, to explore the stress conditions in which damage is expected to rotate around a circular cavity subject to pressurization or depressurization. Simulation results showed that: (1) before damage initiation, the DSID model matches the analytical solution of stress distribution obtained with the theory of elasticity; (2) the DSID model can predict the extent of the tensile damage zone at the crown, and that of the compressive damage zone at the sidewalls; (3) damage generated during a vertical far-field compression followed by a depressurization of the cavity is more intense than that generated during a

  12. Quantitative phosphoproteomics reveals genistein as a modulator of cell cycle and DNA damage response pathways in triple-negative breast cancer cells

    PubMed Central

    FANG, YI; ZHANG, QIAN; WANG, XIN; YANG, XUE; WANG, XIANGYU; HUANG, ZHEN; JIAO, YUCHEN; WANG, JING

    2016-01-01

    Around one sixth of breast cancer cases are classified as triple-negative breast cancer (TNBC), named after the absence of the expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2); however, patients with TNBC suffer from poor clinical outcome and shortage of targeted therapy. Genistein, an estrogenic soy isoflavone, shows anticancer effects in TNBC cells such as inducing G2/M cell cycle arrest and apoptosis. However, the underlying mechanism of its anticancer effects is poorly understood and its elucidation can help the development of novel therapeutic strategies for TNBC. In this study, by combining isobaric tag-based TMT labeling with titanium dioxide-based phosphopeptide enrichment, we quantitated 5,445 phosphorylation sites on 2,008 phosphoproteins in the TNBC cell line MDA-MB-231, upon genistein treatment. Our analysis revealed 332 genistein-regulated phosphorylation sites on 226 proteins. Our data show that genistein can regulate several biological processes during the cell cycle, including DNA replication, cohesin complex cleavage, and kinetochore formation. Furthermore, genistein can also activate DNA damage response, including activation of ATR and BRCA1 complex. Overall, our study presents evidence at a phosphoproteomic level that genistein is able to inhibit TNBC cell growth by regulating the cell cycle and DNA damage response in a more complex manner. Our findings help elucidate the mechanisms through which genistein exerts its anticancer effects in TNBC cells. PMID:26783066

  13. A Histomorphometric Analysis of Radiation Damage in an Isogenic Murine Model of Distraction Osteogenesis

    PubMed Central

    Zheutlin, Alexander R.; Deshpande, Sagar S.; Nelson, Noah S.; Polyatskaya, Yekaterina; Rodriguez, Jose J.; Donneys, Alexis; Buchman, Steven R.

    2015-01-01

    Purpose The devastation radiation therapy (XRT) causes to endogenous tissue in head and neck cancer (HNC) patients can be a prohibitive obstacle in reconstruction of the mandible, demanding a better understanding of XRT-induced damage and options for reconstruction. Our study investigates the cellular damage caused by radiation in an isogenic murine model of mandibular distraction osteogenesis (DO). We posit that radiation will result in reduced osteocytes, with elevated empty lacunae and immature osteoid. Methods Twenty Lewis rats were randomly assigned to two groups: DO (n=10) and XRT/DO (n=10). Both groups underwent an osteotomy and mandibular DO across a 5.1 mm gap. XRT was administered to the XRT/DO group at a fractionated, human equivalent dose of 35 Gy prior to surgery. Animals were sacrificed on postoperative day 40 and mandibles were harvested and sectioned for histological analysis. Results Bone that underwent radiation revealed a significantly decreased osteocyte count and complementary increase in empty lacunae when compared to non-XRT bone (p=0.019, p=0.000). Additionally, XRT bone demonstrated increased immature osteoid and decreased mature woven bone when compared to non-radiated bone (p=0.001 and p=0.003, respectively). Furthermore, analysis of the ratio of immature osteoid to woven bone volume exhibited a significant increase in the XRT bone, further revealing the devastating damage brought by XRT (p=0.001). Conclusion These results clearly demonstrate the cellular diminution that occurs as a result of radiation. This foundational study provides the groundwork upon which to investigate cellular therapies in an immunoprivileged model of mandibular DO. PMID:26341682

  14. Structure of C-terminal Tandem BRCT Repeats of Rtt107 Protein Reveals Critical Role in Interaction with Phosphorylated Histone H2A during DNA Damage Repair*

    PubMed Central

    Li, Xinxin; Liu, Kaixian; Li, Fudong; Wang, Juncheng; Huang, Hongda; Wu, Jihui; Shi, Yunyu

    2012-01-01

    Rtt107 (regulator of Ty1 transposition 107; Esc4) is a DNA repair protein from Saccharomyces cerevisiae that can restore stalled replication forks following DNA damage. There are six BRCT (BRCA1 C-terminal) domains in Rtt107 that act as binding sites for other recruited proteins during DNA repair. Several Rtt107 binding partners have been identified, including Slx4, Rtt101, Rad55, and the Smc5/6 (structural maintenance of chromosome) protein complex. Rtt107 can reportedly be recruited to chromatin in the presence of Rtt101 and Rtt109 upon DNA damage, but the chromatin-binding site of Rtt107 has not been identified. Here, we report our investigation of the interaction between phosphorylated histone H2A (γH2A) and the C-terminal tandem BRCT repeats (BRCT5-BRCT6) of Rtt107. The crystal structures of BRCT5-BRCT6 alone and in a complex with γH2A reveal the molecular basis of the Rtt107-γH2A interaction. We used in vitro mutagenesis and a fluorescence polarization assay to confirm the location of the Rtt107 motif that is crucial for this interaction. In addition, these assays indicated that this interaction requires the phosphorylation of H2A. An in vivo phenotypic analysis in yeast demonstrated the critical role of BRCT5-BRCT6 and its interaction with γH2A during the DNA damage response. Our results shed new light on the molecular mechanism by which Rtt107 is recruited to chromatin in response to stalled DNA replication forks. PMID:22262834

  15. Damage Tolerance Analysis of a Pressurized Liquid Oxygen Tank

    NASA Technical Reports Server (NTRS)

    Forth, Scott C.; Harvin, Stephen F.; Gregory, Peyton B.; Mason, Brian H.; Thompson, Joe E.; Hoffman, Eric K.

    2006-01-01

    A damage tolerance assessment was conducted of an 8,000 gallon pressurized Liquid Oxygen (LOX) tank. The LOX tank is constructed of a stainless steel pressure vessel enclosed by a thermal-insulating vacuum jacket. The vessel is pressurized to 2,250 psi with gaseous nitrogen resulting in both thermal and pressure stresses on the tank wall. Finite element analyses were performed on the tank to characterize the stresses from operation. Engineering material data was found from both the construction of the tank and the technical literature. An initial damage state was assumed based on records of a nondestructive inspection performed on the tank. The damage tolerance analyses were conducted using the NASGRO computer code. This paper contains the assumptions, and justifications, made for the input parameters to the damage tolerance analyses and the results of the damage tolerance analyses with a discussion on the operational safety of the LOX tank.

  16. Historic Earthquake Damage for Buildings and Damage Estimated by the Rapid Seismic Analysis Procedure: A Comparison.

    DTIC Science & Technology

    1986-03-01

    the 1971 San Fernando earthquake and later code changes to reflect these -. lessons. Criteria 2 and 5 eliminate the smaller buildings in the 2,500... Fernando earthquake. The spurious peak was caused by the amplification of the base motion through the rock ridge and the fracturing of the ridge... Fernando earthquake (Ref 12). For pre-1933 buildings, the damage threshold is 0.15g. Maximum ground accelerations of 0.3g or greater are associated

  17. Analysis of shape memory alloy sensory particles for damage detection via substructure and continuum damage modeling

    NASA Astrophysics Data System (ADS)

    Bielefeldt, Brent R.; Benzerga, A. Amine; Hartl, Darren J.

    2016-04-01

    The ability to monitor and predict the structural health of an aircraft is of growing importance to the aerospace industry. Currently, structural inspections and maintenance are based upon experiences with similar aircraft operating in similar conditions. While effective, these methods are time-intensive and unnecessary if the aircraft is not in danger of structural failure. It is imagined that future aircraft will utilize non-destructive evaluation methods, allowing for the near real-time monitoring of structural health. A particularly interesting method involves utilizing the unique transformation response of shape memory alloy (SMA) particles embedded in an aircraft structure. By detecting changes in the mechanical and/or electromagnetic responses of embedded particles, operators could detect the formation or propagation of fatigue cracks in the vicinity of these particles. This work focuses on a finite element model of SMA particles embedded in an aircraft wing using a substructure modeling approach in which degrees of freedom are retained only at specified points of connection to other parts or the application of boundary conditions, greatly reducing computational cost. Previous work evaluated isolated particle response to a static crack to numerically demonstrate and validate this damage detection method. This paper presents the implementation of a damage model to account for crack propagation and examine for the first time the effect of particle configuration and/or relative placement with respect to the ability to detect damage.

  18. On damage detection in wind turbine gearboxes using outlier analysis

    NASA Astrophysics Data System (ADS)

    Antoniadou, Ifigeneia; Manson, Graeme; Dervilis, Nikolaos; Staszewski, Wieslaw J.; Worden, Keith

    2012-04-01

    The proportion of worldwide installed wind power in power systems increases over the years as a result of the steadily growing interest in renewable energy sources. Still, the advantages offered by the use of wind power are overshadowed by the high operational and maintenance costs, resulting in the low competitiveness of wind power in the energy market. In order to reduce the costs of corrective maintenance, the application of condition monitoring to gearboxes becomes highly important, since gearboxes are among the wind turbine components with the most frequent failure observations. While condition monitoring of gearboxes in general is common practice, with various methods having been developed over the last few decades, wind turbine gearbox condition monitoring faces a major challenge: the detection of faults under the time-varying load conditions prevailing in wind turbine systems. Classical time and frequency domain methods fail to detect faults under variable load conditions, due to the temporary effect that these faults have on vibration signals. This paper uses the statistical discipline of outlier analysis for the damage detection of gearbox tooth faults. A simplified two-degree-of-freedom gearbox model considering nonlinear backlash, time-periodic mesh stiffness and static transmission error, simulates the vibration signals to be analysed. Local stiffness reduction is used for the simulation of tooth faults and statistical processes determine the existence of intermittencies. The lowest level of fault detection, the threshold value, is considered and the Mahalanobis squared-distance is calculated for the novelty detection problem.

  19. Multi-frequency local wavenumber analysis and ply correlation of delamination damage.

    PubMed

    Juarez, Peter D; Leckey, Cara A C

    2015-09-01

    Wavenumber domain analysis through use of scanning laser Doppler vibrometry has been shown to be effective for non-contact inspection of damage in composites. Qualitative and semi-quantitative local wavenumber analysis of realistic delamination damage and quantitative analysis of idealized damage scenarios (Teflon inserts) have been performed previously in the literature. This paper presents a new methodology based on multi-frequency local wavenumber analysis for quantitative assessment of multi-ply delamination damage in carbon fiber reinforced polymer (CFRP) composite specimens. The methodology is presented and applied to a real world damage scenario (impact damage in an aerospace CFRP composite). The methodology yields delamination size and also correlates local wavenumber results from multiple excitation frequencies to theoretical dispersion curves in order to robustly determine the delamination ply depth. Results from the wavenumber based technique are validated against a traditional nondestructive evaluation method.

  20. ANALYSIS OF IMPACT DAMAGE USING LINE SCANNING THERMOGRAPHY

    SciTech Connect

    Ley, O.; Valatka, T.; Godinez, V.; Chung, S.; Schutte, J.; Dunne, K.; Caiazzo, A.; Bandos, B.

    2010-02-22

    Impact damage in a composite shaft was studied using Line Scanning Thermography (LST), a novel dynamic thermography technique capable of inspecting large areas in short times. It is expected that projectile impact in a laminate composite will generate a discontinuity that affects heat propagation. Therefore, as heat is deposited over the impacted region, a hot spot will be observed. In this study several impact points were evaluated using UT and LST. Experiments show that assessing impact damage using LST is a dynamic process, which should be accounted for when using dynamic thermography to quantify impact damage extension and severity. The LST images provided information about the region affected by impact damage, which was consistent with the damage region determined using UT. It is seen that the damage areas obtained at early observation time after heat application show small areas with severe damage; and for further times after heat application, the temperature of the hot spots drops and the size of the region affected increases with time following a linear relationship with the observation time.

  1. Analysis of damage in composite laminates under bending

    NASA Astrophysics Data System (ADS)

    Kuriakose, Sunil

    The focus of this research was damage formation in composite laminates subjected to bending. Matrix cracking and internal delamination are common damage modes before final failure for a composite laminate under thermo-mechanical loading. Two configurations of cross-ply laminates, namely [0m/90 n]s and [90m/0n]s, were considered for the study. Approximate analytical solutions for the stress states in the two laminates subjected to constant bending moment, with matrix cracks in the 90° layers, were derived using a variational approach. The evolution of matrix cracking under monotonically increasing load was studied for a number of composite materials. The analytical predictions showed an initial stage of rapid matrix crack multiplication followed by a slowing down in the crack multiplication. In the case of [0m/90n] s laminate, 0° ply failure in tension or compression was found to be likely even at the initial stages of matrix cracking for laminates with thin 90° layer. The 0° ply failure is delayed for laminates with thicker 90° layer. The analytical model for the stress state in the [90m/0 n]s laminate was extended to include delamination from the matrix crack-tip along the 0/90 interface. The bending moment required to initiate crack-tip delamination was computed as a function of the crack density. By comparing this result with matrix crack evolution, the relative dominance of the two modes of damage could be determined. The critical crack density beyond which delamination dominates matrix cracking is obtained from the analysis. The critical crack density is interpreted as the stage beyond which growth of delamination rather than matrix cracking is likely to occur. Parametric studies conducted by varying the laminate configuration showed that the critical crack density for delamination onset strongly depends on the thickness of the 90° layer and the distance of the 90° layer from the laminate mid-plane. Quasi-static growth of delamination under monotonic

  2. TSS tether cable meteoroid/orbital debris damage analysis

    NASA Technical Reports Server (NTRS)

    Hayashida, K. B.; Robinson, J. H.

    1993-01-01

    This report summarizes the damage analyses performed on the tether cable used for the tethered satellite system (TSS), for the damage that could be caused by meteoroid or orbital debris impacts. The TSS consists of a tethered satellite deployer and a tethered satellite. The analytical studies were performed at Marshall Space Flight Center (MSFC) with the results from the following tests: (1) hypervelocity impact tests to determine the 'critical' meteoroid particle diameter, i.e., the maximum size of a meteoroid particle which can impact the tether cable without causing 'failure'; (2) electrical resistance tests on the damaged and undamaged tether cable to determine if degradation of current flow occurred through the damaged tether cables; and (3) tensile load tests to verify the load carrying capability of the damaged tether cables. Finally, the HULL hydrodynamic computer code was used to simulate the hypervelocity impact of the tether cable by particles at velocities higher than can be tested, to determine the extent of the expected tether damage.

  3. Numerical analysis of laser ablation and damage in glass with multiple picosecond laser pulses.

    PubMed

    Sun, Mingying; Eppelt, Urs; Russ, Simone; Hartmann, Claudia; Siebert, Christof; Zhu, Jianqiang; Schulz, Wolfgang

    2013-04-08

    This study presents a novel numerical model for laser ablation and laser damage in glass including beam propagation and nonlinear absorption of multiple incident ultrashort laser pulses. The laser ablation and damage in the glass cutting process with a picosecond pulsed laser was studied. The numerical results were in good agreement with our experimental observations, thereby revealing the damage mechanism induced by laser ablation. Beam propagation effects such as interference, diffraction and refraction, play a major role in the evolution of the crater structure and the damage region. There are three different damage regions, a thin layer and two different kinds of spikes. Moreover, the electronic damage mechanism was verified and distinguished from heat modification using the experimental results with different pulse spatial overlaps.

  4. Statistical analysis of vibration-induced bone and joint damages.

    PubMed

    Schenk, T

    1995-01-01

    Vibration-induced damages to bones and joints are still occupational diseases with insufficient knowledge about causing and moderating factors and resulting damages. For a better understanding of these relationships also retrospective analyses of already acknowledged occupational diseases may be used. Already recorded detailed data for 203 in 1970 to 1979 acknowledged occupational diseases in the building industry and the building material industry of the GDR are the basis for the here described investigations. The data were gathered from the original documents of the occupational diseases and scaled in cooperation of an industrial engineer and an industrial physician. For the purposes of this investigations the data are to distinguish between data which describe the conditions of the work place (e.g. material, tools and posture), the exposure parameters (e.g. beginning of exposure and latency period) and the disease (e.g. anamnestical and radiological data). These data are treated for the use with sophisticated computerized statistical methods. The following analyses were carried out. Investigation of the connections between the several characteristics, which describe the occupational disease (health damages), including the comparison of the severity of the damages at the individual joints. Investigation of the side dependence of the damages. Investigation of the influence of the age at the beginning of the exposure and the age at the acknowledgement of the occupational disease and herewith of the exposure duration. Investigation of the effect of different occupational and exposure conditions.

  5. Multiomic Analysis of the UV-Induced DNA Damage Response.

    PubMed

    Boeing, Stefan; Williamson, Laura; Encheva, Vesela; Gori, Ilaria; Saunders, Rebecca E; Instrell, Rachael; Aygün, Ozan; Rodriguez-Martinez, Marta; Weems, Juston C; Kelly, Gavin P; Conaway, Joan W; Conaway, Ronald C; Stewart, Aengus; Howell, Michael; Snijders, Ambrosius P; Svejstrup, Jesper Q

    2016-05-11

    In order to facilitate the identification of factors and pathways in the cellular response to UV-induced DNA damage, several descriptive proteomic screens and a functional genomics screen were performed in parallel. Numerous factors could be identified with high confidence when the screen results were superimposed and interpreted together, incorporating biological knowledge. A searchable database, bioLOGIC, which provides access to relevant information about a protein or process of interest, was established to host the results and facilitate data mining. Besides uncovering roles in the DNA damage response for numerous proteins and complexes, including Integrator, Cohesin, PHF3, ASC-1, SCAF4, SCAF8, and SCAF11, we uncovered a role for the poorly studied, melanoma-associated serine/threonine kinase 19 (STK19). Besides effectively uncovering relevant factors, the multiomic approach also provides a systems-wide overview of the diverse cellular processes connected to the transcription-related DNA damage response.

  6. Statistical multi-site fatigue damage analysis model

    NASA Astrophysics Data System (ADS)

    Wang, G. S.

    1995-02-01

    A statistical model has been developed to evaluate fatigue damage at multi-sites in complex joints based on coupon test data and fracture mechanics methods. The model is similar to the USAF model, but modified by introducing a failure criterion and a probability of fatal crack occurrence to account for the multiple site damage phenomenon. The involvement of NDI techniques has been included in the model which can be used to evaluate the structural reliability, the detectability of fatigue damage (cracks), and the risk of failure based on NDI results taken from samples. A practical example is provided for rivet fasteners and bolted fasteners. It is shown that the model can be used even if it is based on conventional S-N coupon experiments should further fractographic inspections be made for cracks on the broken surfaces of specimens.

  7. Numerical analysis of a quasistatic piezoelectric problem with damage*

    NASA Astrophysics Data System (ADS)

    Fernández, José R.; Martínez, Rebeca; Stavroulakis, Georgios E.

    2008-07-01

    The quasistatic evolution of the mechanical state of a piezoelectric body with damage is numerically studied in this paper. Both damage and piezoelectric effects are included into the model. The variational formulation leads to a coupled system composed of two linear variational equations for the displacement field and the electric potential, and a nonlinear parabolic variational equation for the damage field. The existence of a unique weak solution is stated. Then, a fully discrete scheme is introduced by using a finite element method to approximate the spatial variable and an Euler scheme to discretize the time derivatives. Error estimates are derived on the approximate solutions, from which the linear convergence of the algorithm is deduced under suitable regularity conditions. Finally, a two-dimensional example is presented to demonstrate the behaviour of the solution. To cite this article: J.R. Fernández et al., C. R. Mecanique 336 (2008).

  8. Thermomechanics of damageable materials under diffusion: modelling and analysis

    NASA Astrophysics Data System (ADS)

    Roubíček, Tomáš; Tomassetti, Giuseppe

    2015-12-01

    We propose a thermodynamically consistent general-purpose model describing diffusion of a solute or a fluid in a solid undergoing possible phase transformations and damage, beside possible visco-inelastic processes. Also heat generation/consumption/transfer is considered. Damage is modelled as rate-independent. The applications include metal-hydrogen systems with metal/hydride phase transformation, poroelastic rocks, structural and ferro/para-magnetic phase transformation, water and heat transport in concrete, and if diffusion is neglected, plasticity with damage and viscoelasticity, etc. For the ensuing system of partial differential equations and inclusions, we prove existence of solutions by a carefully devised semi-implicit approximation scheme of the fractional-step type.

  9. Surface crack analysis applied to impact damage in a thick graphite-epoxy composite

    NASA Technical Reports Server (NTRS)

    Poe, C. C., Jr.; Harris, C. E.; Morris, D. H.

    1988-01-01

    The residual tensile strength of a thick graphite/epoxy composite with impact damage was predicted using surface crack analysis. The damage was localized to a region directly beneath the impact site and extended only part way through the laminate. The damaged region contained broken fibers, and the locus of breaks in each layer resembled a crack perpendicular to the direction of the fibers. In some cases, the impacts broke fibers without making a visible crater. The impact damage was represented as a semi-elliptical surface crack with length and depth equal to that of the impact damage. The maximum length and depth of the damage were predicted with a stress analysis and a maximum shear stress criterion. The predictions and measurements of strength were in good agreement.

  10. Invoking Thomas Kuhn: What Citation Analysis Reveals about Science Education

    NASA Astrophysics Data System (ADS)

    Loving, Cathleen C.; Cobern, William W.

    This paper analyzes how Thomas Kuhn's writings are used by others, especially science education researchers. Previous research in citation analysis is used to frame questions related to who cites Kuhn, in what manner and why. Research questions first focus on the variety of disciplines invoking Kuhn and to what extent Structure of Scientific Revolutions (SSR) is cited. The Web of Science database provides material from 1982 for this analysis. The science education literature is analyzed using back issues from 1985 of the Journal of Research in Science Teaching and Science Education. An article analysis reveals trends in terms of what Kuhnian ideas are most frequently invoked. Results indicate a wide array of disciplines from beekeeping to law cite Kuhn - especially generic citations to SSR. The science education journal analysis reveals pervasive use of the term paradigm, although use is quite varied. The two areas of research in science education most impacted by Kuhn appear to be conceptual change theory and constructivist epistemologies. Additional uses of Kuhn are discussed. The degree to which Kuhn is invoked in ways supporting the theoretical framework of citation analysis, whether his work is misappropriated, and the impact of Kuhn are discussed.

  11. Hybrid molecular dynamics simulation for plasma induced damage analysis

    NASA Astrophysics Data System (ADS)

    Matsukuma, Masaaki

    2016-09-01

    In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam

  12. UAV-based urban structural damage assessment using object-based image analysis and semantic reasoning

    NASA Astrophysics Data System (ADS)

    Fernandez Galarreta, J.; Kerle, N.; Gerke, M.

    2014-09-01

    Structural damage assessment is critical after disasters but remains a challenge. Many studies have explored the potential of remote sensing data, but limitations of vertical data persist. Oblique imagery has been identified as more useful, though the multi-angle imagery also adds a new dimension of complexity. This paper addresses damage assessment based on multi-perspective, overlapping, very high resolution oblique images obtained with unmanned aerial vehicles (UAVs). 3-D point-cloud assessment for the entire building is combined with detailed object-based image analysis (OBIA) of façades and roofs. This research focuses not on automatic damage assessment, but on creating a methodology that supports the often ambiguous classification of intermediate damage levels, aiming at producing comprehensive per-building damage scores. We identify completely damaged structures in the 3-D point cloud, and for all other cases provide the OBIA-based damage indicators to be used as auxiliary information by damage analysts. The results demonstrate the usability of the 3-D point-cloud data to identify major damage features. Also the UAV-derived and OBIA-processed oblique images are shown to be a suitable basis for the identification of detailed damage features on façades and roofs. Finally, we also demonstrate the possibility of aggregating the multi-perspective damage information at building level.

  13. UAV-based urban structural damage assessment using object-based image analysis and semantic reasoning

    NASA Astrophysics Data System (ADS)

    Fernandez Galarreta, J.; Kerle, N.; Gerke, M.

    2015-06-01

    Structural damage assessment is critical after disasters but remains a challenge. Many studies have explored the potential of remote sensing data, but limitations of vertical data persist. Oblique imagery has been identified as more useful, though the multi-angle imagery also adds a new dimension of complexity. This paper addresses damage assessment based on multi-perspective, overlapping, very high resolution oblique images obtained with unmanned aerial vehicles (UAVs). 3-D point-cloud assessment for the entire building is combined with detailed object-based image analysis (OBIA) of façades and roofs. This research focuses not on automatic damage assessment, but on creating a methodology that supports the often ambiguous classification of intermediate damage levels, aiming at producing comprehensive per-building damage scores. We identify completely damaged structures in the 3-D point cloud, and for all other cases provide the OBIA-based damage indicators to be used as auxiliary information by damage analysts. The results demonstrate the usability of the 3-D point-cloud data to identify major damage features. Also the UAV-derived and OBIA-processed oblique images are shown to be a suitable basis for the identification of detailed damage features on façades and roofs. Finally, we also demonstrate the possibility of aggregating the multi-perspective damage information at building level.

  14. USAF Damage Tolerant Design Handbook: Guidelines for the analysis and Design of Damage Tolerant Aircraft Structures. Revision A

    DTIC Science & Technology

    1979-03-01

    710 5O• Figure 2.2 (Con’t) IwSCAIorn MOu.&m uwi.z, AS io ameow A S*I tw aeK WL I N uaA AULSKtI o~ SSDUTT AL SARM I SIOU L - -I ~ 7 I 01.3) PY...POINT 0.005, FOR REMAINING STRUCTURE TYPICAL DAMAGE ANALYSIS MFG. DAMAGE 0 20 40 60 80 100 120 140 PER CENT OF DESIGN LIFETIME Figure 2.29 Development...71.; - 94 444.6.444in 140 2024-T3 120 8 W 80 in.4 0 G O - 40- 4 o With buckling plates K value for 20 * Without buckling plates thick plate OL I 1 I

  15. Towards a Fuzzy Bayesian Network Based Approach for Safety Risk Analysis of Tunnel-Induced Pipeline Damage.

    PubMed

    Zhang, Limao; Wu, Xianguo; Qin, Yawei; Skibniewski, Miroslaw J; Liu, Wenli

    2016-02-01

    Tunneling excavation is bound to produce significant disturbances to surrounding environments, and the tunnel-induced damage to adjacent underground buried pipelines is of considerable importance for geotechnical practice. A fuzzy Bayesian networks (FBNs) based approach for safety risk analysis is developed in this article with detailed step-by-step procedures, consisting of risk mechanism analysis, the FBN model establishment, fuzzification, FBN-based inference, defuzzification, and decision making. In accordance with the failure mechanism analysis, a tunnel-induced pipeline damage model is proposed to reveal the cause-effect relationships between the pipeline damage and its influential variables. In terms of the fuzzification process, an expert confidence indicator is proposed to reveal the reliability of the data when determining the fuzzy probability of occurrence of basic events, with both the judgment ability level and the subjectivity reliability level taken into account. By means of the fuzzy Bayesian inference, the approach proposed in this article is capable of calculating the probability distribution of potential safety risks and identifying the most likely potential causes of accidents under both prior knowledge and given evidence circumstances. A case concerning the safety analysis of underground buried pipelines adjacent to the construction of the Wuhan Yangtze River Tunnel is presented. The results demonstrate the feasibility of the proposed FBN approach and its application potential. The proposed approach can be used as a decision tool to provide support for safety assurance and management in tunnel construction, and thus increase the likelihood of a successful project in a complex project environment.

  16. FRP/steel composite damage acoustic emission monitoring and analysis

    NASA Astrophysics Data System (ADS)

    Li, Dongsheng; Chen, Zhi

    2015-04-01

    FRP is a new material with good mechanical properties, such as high strength of extension, low density, good corrosion resistance and anti-fatigue. FRP and steel composite has gotten a wide range of applications in civil engineering because of its good performance. As the FRP/steel composite get more and more widely used, the monitor of its damage is also getting more important. To monitor this composite, acoustic emission (AE) is a good choice. In this study, we prepare four identical specimens to conduct our test. During the testing process, the AE character parameters and mechanics properties were obtained. Damaged properties of FRP/steel composite were analyzed through acoustic emission (AE) signals. By the growing trend of AE accumulated energy, the severity of the damage made on FRP/steel composite was estimated. The AE sentry function has been successfully used to study damage progression and fracture emerge release rate of composite laminates. This technique combines the cumulative AE energy with strain energy of the material rather than analyzes the AE information and mechanical separately.

  17. Clothing damage analysis in alleged sexual assaults--the need for a systematic approach.

    PubMed

    Boland, C A; McDermott, S D; Ryan, J

    2007-04-11

    Clothing damage analysis is an integral part of the examinations carried out in sexual assault type cases. This analysis can be used to corroborate different versions of events and is at its most powerful in elucidating false allegation cases and consent cases. The purpose of this study was to determine to what extent people with varying levels of forensic awareness, experience and training could correctly carry out damage analysis. Two participant groups were asked to take part in this study. Group A ('forensic group') comprised participants at a forensic science conference, and Group B ('student group') comprised students undertaking a degree course in Forensic Science. Each group was given a practical workshop consisting of a lecture outlining common fabric types and general features observed in different damage types. Each participant was subsequently shown 25 pieces of 'damage' and asked to identify both the type of fabric construction (knit or weave) and the type of damage (cut, tear, rip, wear and tear). The ability to identify fabric construction and damage types varied within the two groups studied and across the groups. The forensic group performed better both in fabric and damage assessment than the student group. This paper suggests a systematic approach to clothing damage analysis to maximise the benefits that can be obtained from this area of forensic science and to minimise the subjectivity within the field.

  18. Development of an engineering analysis of progressive damage in composites during low velocity impact

    NASA Technical Reports Server (NTRS)

    Humphreys, E. A.

    1981-01-01

    A computerized, analytical methodology was developed to study damage accumulation during low velocity lateral impact of layered composite plates. The impact event was modeled as perfectly plastic with complete momentum transfer to the plate structure. A transient dynamic finite element approach was selected to predict the displacement time response of the plate structure. Composite ply and interlaminar stresses were computed at selected time intervals and subsequently evaluated to predict layer and interlaminar damage. The effects of damage on elemental stiffness were then incorporated back into the analysis for subsequent time steps. Damage predicted included fiber failure, matrix ply failure and interlaminar delamination.

  19. A damage analysis for brittle materials using stochastic micro-structural information

    NASA Astrophysics Data System (ADS)

    Lin, Shih-Po; Chen, Jiun-Shyan; Liang, Shixue

    2016-03-01

    In this work, a micro-crack informed stochastic damage analysis is performed to consider the failures of material with stochastic microstructure. The derivation of the damage evolution law is based on the Helmholtz free energy equivalence between cracked microstructure and homogenized continuum. The damage model is constructed under the stochastic representative volume element (SRVE) framework. The characteristics of SRVE used in the construction of the stochastic damage model have been investigated based on the principle of the minimum potential energy. The mesh dependency issue has been addressed by introducing a scaling law into the damage evolution equation. The proposed methods are then validated through the comparison between numerical simulations and experimental observations of a high strength concrete. It is observed that the standard deviation of porosity in the microstructures has stronger effect on the damage states and the peak stresses than its effect on the Young's and shear moduli in the macro-scale responses.

  20. Structure Inventory for Damage Analysis (SID). User’s Manual

    DTIC Science & Technology

    1989-03-01

    identifier, damage category, a percentage of total structure value. and location); monetary values (building, contents and other items, i.e...since some measures may not be regulatory development policies , and physically feasible for the feet of protection temporary emergency elevation of...target protection elevation is structures or future structures under flood 425.5 feet. The difference in water surface plain regulatory policies is

  1. Fatigue Damage Analysis of an Elastomeric Tank Track Component

    DTIC Science & Technology

    2012-02-22

    hyperelastic law has been selected to represent the rubber’s stress-strain behavior on first extension (i.e. the primary stress-strain curve), and the Ogden...precursor that exists in this material prior to any damage accumulation. The crack precursor size depends on the microstructure of the polymer /filler... Polymer Science 8, 707, 1964. 2. Mars W. V., Cracking Energy Density as a predictor of fatigue life under multiaxial conditions, Rubber Chemistry

  2. Application of outlier analysis for baseline-free damage diagnosis

    NASA Astrophysics Data System (ADS)

    Kim, Seung Dae; In, Chi Won; Cronin, Kelly E.; Sohn, Hoon; Harries, Kent

    2006-03-01

    As carbon fiber-reinforced polymer (CFRP) laminates have been widely accepted as valuable materials for retrofitting civil infrastructure systems, an appropriate assessment of bonding conditions between host structures and CFRP laminates becomes a critical issue to guarantee the performance of CFRP strengthened structures. This study attempts to develop a continuous performance monitoring system for CFRP strengthened structures by autonomously inspecting the bonding conditions between the CFRP layers and the host structure. The uniqueness of this study is to develop a new concept and theoretical framework of nondestructive testing (NDT), in which debonding is detected "without using past baseline data." The proposed baseline-free damage diagnosis is achieved in two stages. In the first step, features sensitive to debonding of the CFPR layers but insensitive to loading conditions are extracted based on a concept referred to as a time reversal process. This time reversal process allows extracting damage-sensitive features without direct comparison with past baseline data. Then, a statistical damage classifier will be developed in the second step to make a decision regarding the bonding condition of the CFRP layers. The threshold necessary for decision making will be adaptively determined without predetermined threshold values. Monotonic and fatigue load tests of full-scale CFRP strengthened RC beams are conducted to demonstrate the potential of the proposed reference-free debonding monitoring system.

  3. Creep Damage Analysis of a Lattice Truss Panel Structure

    NASA Astrophysics Data System (ADS)

    Jiang, Wenchun; Li, Shaohua; Luo, Yun; Xu, Shugen

    2017-01-01

    The creep failure for a lattice truss sandwich panel structure has been predicted by finite element method (FEM). The creep damage is calculated by three kinds of stresses: as-brazed residual stress, operating thermal stress and mechanical load. The creep damage at tensile and compressive loads have been calculated and compared. The creep rate calculated by FEM, Gibson-Ashby and Hodge-Dunand models have been compared. The results show that the creep failure is located at the fillet at both tensile and creep loads. The damage rate at the fillet at tensile load is 50 times as much as that at compressive load. The lattice truss panel structure has a better creep resistance to compressive load than tensile load, because the creep and stress triaxiality at the fillet has been decreased at compressive load. The maximum creep strain at the fillet and the equivalent creep strain of the panel structure increase with the increase of applied load. Compared with Gibson-Ashby model and Hodge-Dunand models, the modified Gibson-Ashby model has a good prediction result compared with FEM. However, a more accurate model considering the size effect of the structure still needs to be developed.

  4. Chaotic and ambient vibration analysis of composite lap joint damage

    NASA Astrophysics Data System (ADS)

    Pecora, Lou; Nichols, Jon; Seaver, Mark; Trickey, Steve; Motley, Sara

    2007-04-01

    We examined strain time series from fiber Bragg gratings sensors located in various positions on a composite material beam attached to a steel plate by a lap joint. The beam was vibrated using both broad-band chaotic signals (Lorenz system), and a narrow band signal conforming to the Pierson-Moskowitz frequency distribution for wave height (ambient excitation). The system was damaged by decreasing the torque on instrumented bolts in the lap joint from very tight all the way through to a joint with a gap and slippage. We analyzed the strain data by reconstructing the attractor of the system in the case of chaotic forcing and a pseudo-attractor in the case of sea-wave forcing. Using the highest torque case as an "undamaged" baseline, we calculated the continuity statistic between the baseline attractor and the attractors of the various damage levels for both forcing cases. We show where one can and cannot say that the functional relationship between the attractors changes and how those changes are related to damage levels.

  5. Rate process analysis of thermal damage in cartilage.

    PubMed

    Díaz, Sergio H; Nelson, J Stuart; Wong, Brian J F

    2003-01-07

    Cartilage laser thermoforming (CLT) is a new surgical procedure that allows in situ treatment of deformities in the head and neck with less morbidity than traditional approaches. While some animal and human studies have shown promising results, the clinical feasibility of CLT depends on preservation of chondrocyte viability, which has not been extensively studied. The present paper characterizes cellular damage due to heat in rabbit nasal cartilage. Damage was modelled as a first orderrate process for which two experimentally derived coefficients, A = 1.2 x 10(70) s(-1) and Ea = 4.5 x 10(5) J mole(-1), were determined by quantifying the decrease in concentration of healthy chondrocytes in tissue samples as a function of exposure time to constant-temperature water baths. After immersion, chondrocytes were enzymatically isolated from the matrix and stained with a two-component fluorescent dye. The dye binds nuclear DNA differentially depending upon chondrocyte viability. A flow cytometer was used to detect differential cell fluorescence to determine the percentage of live and dead cells in each sample. As a result, a damage kinetic model was obtained that can be used to predict the onset, extent and severity of cellular injury to thermal exposure.

  6. Rate process analysis of thermal damage in cartilage

    NASA Astrophysics Data System (ADS)

    Díaz, Sergio H.; Nelson, J. Stuart; Wong, Brian J. F.

    2003-01-01

    Cartilage laser thermoforming (CLT) is a new surgical procedure that allows in situ treatment of deformities in the head and neck with less morbidity than traditional approaches. While some animal and human studies have shown promising results, the clinical feasibility of CLT depends on preservation of chondrocyte viability, which has not been extensively studied. The present paper characterizes cellular damage due to heat in rabbit nasal cartilage. Damage was modelled as a first order rate process for which two experimentally derived coefficients, A = 1.2 × 1070 s-1 and Ea = 4.5 × 105 J mole-1, were determined by quantifying the decrease in concentration of healthy chondrocytes in tissue samples as a function of exposure time to constant-temperature water baths. After immersion, chondrocytes were enzymatically isolated from the matrix and stained with a two-component fluorescent dye. The dye binds nuclear DNA differentially depending upon chondrocyte viability. A flow cytometer was used to detect differential cell fluorescence to determine the percentage of live and dead cells in each sample. As a result, a damage kinetic model was obtained that can be used to predict the onset, extent and severity of cellular injury to thermal exposure.

  7. Having a direct look: analysis of DNA damage and repair mechanisms by next generation sequencing.

    PubMed

    Meier, Bettina; Gartner, Anton

    2014-11-15

    Genetic information is under constant attack from endogenous and exogenous sources, and the use of model organisms has provided important frameworks to understand how genome stability is maintained and how various DNA lesions are repaired. The advance of high throughput next generation sequencing (NGS) provides new inroads for investigating mechanisms needed for genome maintenance. These emerging studies, which aim to link genetic toxicology and mechanistic analyses of DNA repair processes in vivo, rely on defining mutational signatures caused by faulty replication, endogenous DNA damaging metabolites, or exogenously applied genotoxins; the analysis of their nature, their frequency and distribution. In contrast to classical studies, where DNA repair deficiency is assessed by reduced cellular survival, the localization of DNA repair factors and their interdependence as well as limited analysis of single locus reporter assays, NGS based approaches reveal the direct, quantal imprint of mutagenesis genome-wide, at the DNA sequence level. As we will show, such investigations require the analysis of DNA derived from single genotoxin treated cells, or DNA from cell populations regularly passaged through single cell bottlenecks when naturally occurring mutation accumulation is investigated. We will argue that the life cycle of the nematode Caenorhabditis elegans, its genetic malleability combined with whole genome sequencing provides an exciting model system to conduct such analysis.

  8. Having a direct look: Analysis of DNA damage and repair mechanisms by next generation sequencing

    PubMed Central

    Meier, Bettina; Gartner, Anton

    2014-01-01

    Genetic information is under constant attack from endogenous and exogenous sources, and the use of model organisms has provided important frameworks to understand how genome stability is maintained and how various DNA lesions are repaired. The advance of high throughput next generation sequencing (NGS) provides new inroads for investigating mechanisms needed for genome maintenance. These emerging studies, which aim to link genetic toxicology and mechanistic analyses of DNA repair processes in vivo, rely on defining mutational signatures caused by faulty replication, endogenous DNA damaging metabolites, or exogenously applied genotoxins; the analysis of their nature, their frequency and distribution. In contrast to classical studies, where DNA repair deficiency is assessed by reduced cellular survival, the localization of DNA repair factors and their interdependence as well as limited analysis of single locus reporter assays, NGS based approaches reveal the direct, quantal imprint of mutagenesis genome-wide, at the DNA sequence level. As we will show, such investigations require the analysis of DNA derived from single genotoxin treated cells, or DNA from cell populations regularly passaged through single cell bottlenecks when naturally occurring mutation accumulation is investigated. We will argue that the life cycle of the nematode Caenorhabditis elegans, its genetic malleability combined with whole genome sequencing provides an exciting model system to conduct such analysis. PMID:25131498

  9. Damage and fracture loci for a dual-phase steel and a high-strength low-alloyed steel: Revealing the different plastic localization-damage-ductile fracture pattern

    NASA Astrophysics Data System (ADS)

    Lian, Junhe; Münstermann, Sebastian; Bleck, Wolfgang

    2016-10-01

    The ductile fracture locus has been developed in the recent years as a relevant tool to predict the ductile fracture and assess the structure safety. In the various developed models, the occurrence of the final fracture or the initiation of the fracture is considered as the critical phase of deformation for materials or structures. However, in the application of high-strength steels, the damage onset and evolution are of significant importance in the forming processes, as they are naturally interacting with the plastic localization and ductile fracture and eventually creating various possible failure patterns. The present study contributes to a demonstration of the differences of these features in different steels by quantitatively comparing the material parameters of a hybrid damage mechanics model. A dual-phase steel sheet (DP600) and a high-strength low-alloy steel plate (S355J2+N), which show very different relation patterns between damage and fracture, are investigated. The aim of this study is to compare the plastic localization, damage and fracture loci of them and reveal the differences in their localization-damage initiation-ductile fracture patterns. The reasons for the observed different patterns are discussed and it is concluded that the microstructural features are ultimately contributing to the different patterns and the criteria for evaluating the cold formability of these steels shall be varied depending on their failure patterns.

  10. Aging and DNA damage in humans: a meta-analysis study

    PubMed Central

    Soares, Jorge Pinto; Cortinhas, António; Bento, Teresa; Leitão, José Carlos; Collins, Andrew R.; Gaivã, Isabel; Mota, Maria Paula

    2014-01-01

    Age-related DNA damage is regarded as one of the possible explanations of aging. Although a generalized idea about the accumulation of DNA damage with age exists, results found in the literature are inconsistent. To better understand the question of age-related DNA damage in humans and to identify possible moderator variables, a meta-analysis was conducted. Electronic databases and bibliographies for studies published since 2004 were searched. Summary odds ratios (ORs) and 95% confidence intervals (CIs) for age-related DNA damage were calculated in a random-effects model. A total of 76 correlations from 36 studies with 4676 participants were included. Based on our analysis, a correlation between age and DNA damage was found (r = 0.230, p = 0.000; 95% confidence interval = 0.111 - 0.342). The test for heterogeneity of variance indicates that the study´s results are significantly high (Q (75) = 1754.831, p = 0.000). Moderator variables such as smoking habits, technique used, and the tissue/sample analyzed, are shown to influence age-related DNA damage (p=0.026; p=0.000; p=0.000, respectively). Nevertheless, sex did not show any influence on this relation (p=0.114). In conclusion, this meta-analysis showed an association between age and DNA damage in humans. It was also found that smoking habits, the technique used, and tissue/sample analyzed, are important moderator variables in age-related DNA damage. PMID:25140379

  11. Mathematical Analysis of Biomolecular Network Reveals Connections Between Diseases

    NASA Astrophysics Data System (ADS)

    Wang, Guanyu

    2012-02-01

    Connections between cancer and metabolic diseases may consist in the complex network of interactions among a common set of biomolecules. By applying singularity and bifurcation analysis, the phenotypes constrained by the AKT signaling pathway are identified and mapped onto the parameter space, which include cancer and certain metabolic diseases. By considering physiologic properties (sensitivity, robustness and adaptivity) the AKT pathway must possess in order to efficiently sense growth factors and nutrients, the region of normal responses is located. The analysis illuminates the parameter space and reveals system-level mechanisms in regulating biological functions (cell growth, survival, proliferation and metabolism) and how their deregulation may lead to the development of diseases. The analytical expressions summarize the synergistic interactions among many molecules, which provides valuable insights into therapeutic interventions.

  12. Tyndall AFB Bomb Damage Repair Field Test, Documentation and Analysis

    DTIC Science & Technology

    1975-10-01

    was not tested, as bping Irrele- vant to these tests. Simulation of this event was not attempted because it would have provided little or no...Richardson, Texas, Report No. AFWL-TR-71-42, October 1971. 11. Bussone, P.S., B.J. Bottomley, and G.C. Hoff , Rapid Repair of Bomb- Damaged Runways...Airfield Runways, Air Force Weapons Laboratory, Klrtland AFB, New Mexico, Report No. AFWL-TR-73-214, February 1974. 19. Hoff , George C, Investigation of

  13. Hierarchical nanoreinforced composites: Computational analysis of damage mechanisms

    NASA Astrophysics Data System (ADS)

    Mishnaevsky, Leon, Jr.; Pontefisso, Alessandro; Dai, Gaoming

    2016-07-01

    The potential of hierarchical composites with secondary nanoreinforcement is discussed and analysed on the basis of the computational modelling. The concept of nanostructuring of interfaces as an important reserve of the improvement of the composite properties is discussed. The influence of distribution, shape, orientation of nanoparticles (carbon nanotube, graphene) in unidirectional polymer matrix composites on the strength and damage resistance of the composites is studied in computational studies. The possible directions of the improvement of nanoreinforced composites by controlling shapes, localization and other parameters of nanoreinforcements are reviewed.

  14. Spatial Fourier Analysis of a Free-Free Beam for Structural Damage Detection

    NASA Astrophysics Data System (ADS)

    Bhagat, Mihir; Ganguli, Ranjan

    2014-07-01

    Free-free beams (FFB) are used to model many structures, such as missiles, rockets, MEMS (Micro Electro Mechanical Systems), etc. This paper aims to illustrate a novel structural health monitoring method-Fourier analysis of mode shapes of damaged beams-and extend it to the case of FFB. The damaged mode shapes of FFB are obtained by a finite element model and then studied using spatial Fourier analysis. The effect of noise in the mode shape data is considered and it is found that the Fourier coefficients provide a useful indication about the location and size of damage.

  15. Far Forward Anesthesia and Massive Blood Transfusion: Two Cases Revealing the Challenge of Damage Control Resuscitation in an Austere Environment.

    PubMed

    Gaskin, David; Kroll, Nicholas A; Ochs, Alyson A; Schreiber, Martin A; Pandalai, Prakash K

    2015-10-01

    Since the beginning of Operation Enduring Freedom and Operation Iraqi Freedom, the US military has treated more than 51,000 casualties and sustained more than 6,600 deaths. The past decade of conflict has solidified major advances in the use of blood component therapy and the liberal use of fresh whole blood during damage control resuscitation. This resuscitation strategy, combined with far forward damage control surgery, rapid aeromedical evacuation, and major improvements in critical care air transportation and personal protective equipment has led to a 90% to 92% survival rate in US casualties. We describe 2 cases treated by a Forward Surgical Team serving in Afghanistan during Operation Enduring Freedom in 2014. Both patients suffered severe trauma and required massive blood transfusion and damage control surgery. In describing these 2 cases, we wish to share our experience with damage control, resuscitation in an austere environment, as well as advocate for the critical role of the Certified Registered Nurse Anesthetist in advancing the knowledge and execution of this lifesaving strategy in both military and civilian trauma centers. In addition, we suggest alternatives to the current transfusion strategy, which will mitigate limitations currently encountered.

  16. Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling

    PubMed Central

    Chaki, Moumita; Airik, Rannar; Ghosh, Amiya K.; Giles, Rachel H.; Chen, Rui; Slaats, Gisela G.; Wang, Hui; Hurd, Toby W.; Zhou, Weibin; Cluckey, Andrew; Gee, Heon-Yung; Ramaswami, Gokul; Hong, Chen-Jei; Hamilton, Bruce A.; Červenka, Igor; Ganji, Ranjani Sri; Bryja, Vitezslav; Arts, Heleen H.; van Reeuwijk, Jeroen; Oud, Machteld M.; Letteboer, Stef J.F.; Roepman, Ronald; Husson, Hervé; Ibraghimov-Beskrovnaya, Oxana; Ysunaga, Takayuki; Walz, Gerd; Eley, Lorraine; Sayer, John A.; Schermer, Bernhard; Liebau, Max C.; Benzing, Thomas; Le Corre, Stephanie; Drummond, Iain; Joles, Jaap A.; Janssen, Sabine; Allen, Susan J.; Natarajan, Sivakumar; O Toole, John F.; Attanasio, Massimo; Saunier, Sophie; Antignac, Corinne; Koenekoop, Robert K.; Ren, Huanan; Lopez, Irma; Nayir, Ahmet; Stoetzel, Corinne; Dollfus, Helene; Massoudi, Rustin; Gleeson, Joseph G.; Andreoli, Sharon P.; Doherty, Dan G.; Lindstrad, Anna; Golzio, Christelle; Katsanis, Nicholas; Pape, Lars; Abboud, Emad B.; Al-Rajhi, Ali A.; Lewis, Richard A.; Lupski, James R.; Omran, Heymut; Lee, Eva; Wang, Shaohui; Sekiguchi, JoAnn M.; Saunders, Rudel; Johnson, Colin A.; Garner, Elizabeth; Vanselow, Katja; Andersen, Jens S.; Shlomai, Joseph; Nurnberg, Gudrun; Nurnberg, Peter; Levy, Shawn; Smogorzewska, Agata; Otto, Edgar A.; Hildebrandt, Friedhelm

    2012-01-01

    SUMMARY Nephronophthisis-related ciliopathies (NPHP-RC) are degenerative recessive diseases that affect kidney, retina and brain. Genetic defects in NPHP gene products that localize to cilia and centrosomes defined them as ‘ciliopathies’. However, disease mechanisms remain poorly understood. Here we identify by whole exome resequencing, mutations of MRE11, ZNF423, and CEP164 as causing NPHP-RC. All three genes function within the DNA damage response (DDR) pathway, hitherto not implicated in ciliopathies. We demonstrate that, upon induced DNA damage, the NPHP-RC proteins ZNF423, CEP164 and NPHP10 colocalize to nuclear foci positive for TIP60, known to activate ATM at sites of DNA damage. We show that knockdown of CEP164 or ZNF423 causes sensitivity to DNA damaging agents, and that cep164 knockdown in zebrafish results in dysregulated DDR and an NPHP-RC phenotype. We identify TTBK2, CCDC92, NPHP3 and DVL3 as novel CEP164 interaction partners. Our findings link degenerative diseases of kidney and retina, disorders of increasing prevalence, to mechanisms of DDR. PMID:22863007

  17. INSYDE: a synthetic, probabilistic flood damage model based on explicit cost analysis

    NASA Astrophysics Data System (ADS)

    Dottori, Francesco; Figueiredo, Rui; Martina, Mario L. V.; Molinari, Daniela; Scorzini, Anna Rita

    2016-12-01

    Methodologies to estimate economic flood damages are increasingly important for flood risk assessment and management. In this work, we present a new synthetic flood damage model based on a component-by-component analysis of physical damage to buildings. The damage functions are designed using an expert-based approach with the support of existing scientific and technical literature, loss adjustment studies, and damage surveys carried out for past flood events in Italy. The model structure is designed to be transparent and flexible, and therefore it can be applied in different geographical contexts and adapted to the actual knowledge of hazard and vulnerability variables. The model has been tested in a recent flood event in northern Italy. Validation results provided good estimates of post-event damages, with similar or superior performances when compared with other damage models available in the literature. In addition, a local sensitivity analysis was performed in order to identify the hazard variables that have more influence on damage assessment results.

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

    PubMed

    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.

  19. Analysis of spatial correlations between patterns of DNA damage response and DNA replication in nuclei of cells subjected to replication stress or oxidative damage.

    PubMed

    Bernas, Tytus; Berniak, Krzysztof; Rybak, Paulina; Zarębski, Mirosław; Zhao, Hong; Darzynkiewicz, Zbigniew; Dobrucki, Jerzy W

    2013-10-01

    Sites of DNA replication (EdU incorporation) and DNA damage signaling (γH2AX) induced by camptothecin (Cpt) or hydrogen peroxide (H2O2) form characteristic patterns of foci in cell nuclei. The overlap between these patterns is a function of the number of DNA double strand breaks (DSBs) formed in replication sites. The goal of this study was to optimize a method of quantitative assessment of a degree of correlation between these two patterns. Such a correlation can be used to estimate a probability of inducing damage in sections of replicating DNA. The damage and replication foci are imaged in 3D with confocal microscopy and their respective positions within nuclei are determined with adaptive image segmentation. Using correlation functions spatial proximity of the resultant point patterns is quantified over the range of distances in cells in early-, mid- and late S-phase. As the numbers (and nuclear densities) of γH2AX and replication foci differ significantly in the subsequent substages of S phase, the detected association values were corrected for the expected random overlap between both classes of foci. Thus, the probability of their nonrandom association was estimated. Moreover, self association (clustering) of DNA replication sites in different stages of S-phase of the cell cycle was detected and accounted for. While the analysis revealed a strong correlation between the γH2AX foci and the sites of DNA replication in cells treated with Cpt, only a low correlation was apparent in cells exposed to H2O2. © 2013 International Society for Advancement of Cytometry.

  20. In situ micropillar compression reveals superior strength and ductility but an absence of damage in lamellar bone

    NASA Astrophysics Data System (ADS)

    Schwiedrzik, Jakob; Raghavan, Rejin; Bürki, Alexander; Lenader, Victor; Wolfram, Uwe; Michler, Johann; Zysset, Philippe

    2014-07-01

    Ageing societies suffer from an increasing incidence of bone fractures. Bone strength depends on the amount of mineral measured by clinical densitometry, but also on the micromechanical properties of the hierarchical organization of bone. Here, we investigate the mechanical response under monotonic and cyclic compression of both single osteonal lamellae and macroscopic samples containing numerous osteons. Micropillar compression tests in a scanning electron microscope, microindentation and macroscopic compression tests were performed on dry ovine bone to identify the elastic modulus, yield stress, plastic deformation, damage accumulation and failure mechanisms. We found that isolated lamellae exhibit a plastic behaviour, with higher yield stress and ductility but no damage. In agreement with a proposed rheological model, these experiments illustrate a transition from a ductile mechanical behaviour of bone at the microscale to a quasi-brittle response driven by the growth of cracks along interfaces or in the vicinity of pores at the macroscale.

  1. GENETIC AND MOLECULAR ANALYSIS OF DNA DAMAGE REPAIR AND TOLERANCE PATHWAYS.

    SciTech Connect

    SUTHERLAND, B.M.

    2001-07-26

    Radiation can damage cellular components, including DNA. Organisms have developed a panoply of means of dealing with DNA damage. Some repair paths have rather narrow substrate specificity (e.g. photolyases), which act on specific pyrimidine photoproducts in a specific type (e.g., DNA) and conformation (double-stranded B conformation) of nucleic acid. Others, for example, nucleotide excision repair, deal with larger classes of damages, in this case bulky adducts in DNA. A detailed discussion of DNA repair mechanisms is beyond the scope of this article, but one can be found in the excellent book of Friedberg et al. [1] for further detail. However, some DNA damages and paths for repair of those damages important for photobiology will be outlined below as a basis for the specific examples of genetic and molecular analysis that will be presented below.

  2. Cohesive Laws and Progressive Damage Analysis of Composite Bonded Joints, a Combined Numerical/Experimental Approach

    NASA Technical Reports Server (NTRS)

    Girolamo, Donato; Davila, Carlos G.; Leone, Frank A.; Lin, Shih-Yung

    2015-01-01

    The results of an experimental/numerical campaign aimed to develop progressive damage analysis (PDA) tools for predicting the strength of a composite bonded joint under tensile loads are presented. The PDA is based on continuum damage mechanics (CDM) to account for intralaminar damage, and cohesive laws to account for interlaminar and adhesive damage. The adhesive response is characterized using standard fracture specimens and digital image correlation (DIC). The displacement fields measured by DIC are used to calculate the J-integrals, from which the associated cohesive laws of the structural adhesive can be derived. A finite element model of a sandwich conventional splice joint (CSJ) under tensile loads was developed. The simulations, in agreement with experimental tests, indicate that the model is capable of predicting the interactions of damage modes that lead to the failure of the joint.

  3. Damage localization in linear-form structures based on sensitivity investigation for principal component analysis

    NASA Astrophysics Data System (ADS)

    Viet Ha, Nguyen; Golinval, Jean-Claude

    2010-10-01

    This paper addresses the problem of damage detection and localization in linear-form structures. Principal component analysis (PCA) is a popular technique for dynamic system investigation. The aim of the paper is to present a damage diagnosis method based on sensitivities of PCA results in the frequency domain. Starting from frequency response functions (FRFs) measured at different locations on the structure; PCA is performed to determine the main features of the signals. Sensitivities of principal directions obtained from PCA to structural parameters are then computed and inspected according to the location of sensors; their variation from the healthy state to the damaged state indicates damage locations. It is worth noting that damage localization is performed without the need of modal identification. Influences of some features as noise, choice of parameter and number of sensors are discussed. The efficiency and limitations of the proposed method are illustrated using numerical and real-world examples.

  4. Systematic analysis of axonal damage and inflammatory response in different white matter tracts of acutely injured rat spinal cord.

    PubMed

    Gomes-Leal, W; Corkill, D J; Picanço-Diniz, C W

    2005-12-20

    The mechanisms of white matter (WM) damage during secondary degeneration are a fundamental issue in the pathophysiology of central nervous system (CNS) diseases. Our main goal was to describe the pattern of an acute inflammatory response and secondary damage to axons in different WM tracts of acutely injured rat spinal cord. Adult rats were deeply anesthetized and injected with 20 nmol of NMDA into the spinal cord ventral horn on T7. Animals were perfused after survival times of 1 day, 3 days and 7 days. Ten micrometer sections were submitted to immunocytochemical analysis for activated macrophages/microglia, neutrophils and damaged axons. There were inflammatory response and progressive tissue destruction of ventral WM (VWM) with formation of microcysts in both VWM and lateral WM (LWM). In the VWM, the number of beta-amyloid precursor protein (beta-APP) end-bulbs increased from 1 day with a peak at 3 days, decreasing by 7 days following the injection. APP end-bulbs were present in the dorsal WM (DWM) at 3 days survival time but were not in the LWM. Electron microscopic analysis revealed different degrees of myelin disruption and axonal pathology in the vacuolated WM up to 14 mm along the rostrocaudal axis. Quantitative analysis revealed a significant loss of medium and large axons (P < 0.05), but not of small axons (P > 0.05). Our results suggest that bystander axonal damage and myelin vacuolation are important secondary component of the pathology of WM tracts following rat SCI. Further studies are needed to understand the mechanisms of these pathological events.

  5. Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites

    PubMed Central

    Wu, Qian; Paul, Atanu; Su, Dan; Mehmood, Shahid; Foo, Tzeh Keong; Ochi, Takashi; Bunting, Emma L.; Xia, Bing; Robinson, Carol V.; Wang, Bin; Blundell, Tom L.

    2016-01-01

    Summary BRCA1 accumulation at DNA damage sites is an important step for its function in the DNA damage response and in DNA repair. BRCA1-BRCT domains bind to proteins containing the phosphorylated serine-proline-x-phenylalanine (pSPxF) motif including Abraxas, Bach1/FancJ, and CtIP. In this study, we demonstrate that ionizing radiation (IR)-induces ATM-dependent phosphorylation of serine 404 (S404) next to the pSPxF motif. Crystal structures of BRCT/Abraxas show that phosphorylation of S404 is important for extensive interactions through the N-terminal sequence outside the pSPxF motif and leads to formation of a stable dimer. Mutation of S404 leads to deficiency in BRCA1 accumulation at DNA damage sites and cellular sensitivity to IR. In addition, two germline mutations of BRCA1 are found to disrupt the dimer interface and dimer formation. Thus, we demonstrate a mechanism involving IR-induced phosphorylation and dimerization of the BRCT/Abraxas complex for regulating Abraxas-mediated recruitment of BRCA1 in response to IR. PMID:26778126

  6. Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites.

    PubMed

    Wu, Qian; Paul, Atanu; Su, Dan; Mehmood, Shahid; Foo, Tzeh Keong; Ochi, Takashi; Bunting, Emma L; Xia, Bing; Robinson, Carol V; Wang, Bin; Blundell, Tom L

    2016-02-04

    BRCA1 accumulation at DNA damage sites is an important step for its function in the DNA damage response and in DNA repair. BRCA1-BRCT domains bind to proteins containing the phosphorylated serine-proline-x-phenylalanine (pSPxF) motif including Abraxas, Bach1/FancJ, and CtIP. In this study, we demonstrate that ionizing radiation (IR)-induces ATM-dependent phosphorylation of serine 404 (S404) next to the pSPxF motif. Crystal structures of BRCT/Abraxas show that phosphorylation of S404 is important for extensive interactions through the N-terminal sequence outside the pSPxF motif and leads to formation of a stable dimer. Mutation of S404 leads to deficiency in BRCA1 accumulation at DNA damage sites and cellular sensitivity to IR. In addition, two germline mutations of BRCA1 are found to disrupt the dimer interface and dimer formation. Thus, we demonstrate a mechanism involving IR-induced phosphorylation and dimerization of the BRCT/Abraxas complex for regulating Abraxas-mediated recruitment of BRCA1 in response to IR.

  7. Chemical proteomics reveals a γH2AX-53BP1 interaction in the DNA damage response

    PubMed Central

    Kleiner, Ralph E.; Verma, Priyanka; Molloy, Kelly R.; Chait, Brian T.; Kapoor, Tarun M.

    2015-01-01

    DNA double-strand break repair involves phosphorylation of histone variant H2AX (‘γH2AX’), which accumulates in foci at sites of damage. In current models, the recruitment of multiple DNA repair proteins to γH2AX foci depends mainly on recognition of this ‘mark’ by a single protein, MDC1. However, DNA repair proteins accumulate at γH2AX sites without MDC1, suggesting that other ‘readers’ exist. Here, we use a quantitative chemical proteomics approach to profile direct, phospho-selective γH2AX binders in native proteomes. We identify γH2AX binders, including the DNA repair mediator, 53BP1, which we show recognizes γH2AX through its BRCT domains. Furthermore, we investigate targeting of wild-type 53BP1 or a mutant form deficient in γH2AX binding, to chromosomal breaks resulting from endogenous and exogenous DNA damage. Our results show how direct recognition of γH2AX modulates protein localization at DNA damage sites, and suggest how specific chromatin ‘mark’-‘reader’ interactions contribute to essential mechanisms ensuring genome stability. PMID:26344695

  8. A registry analysis of damage to the deceased donor pancreas during procurement.

    PubMed

    Ausania, F; Drage, M; Manas, D; Callaghan, C J

    2015-11-01

    Surgical injury to the pancreas is thought to occur commonly during procurement. The UK Transplant Registry was analyzed to determine the frequency of pancreatic injuries, identify factors associated with damage, and assess the impact of injuries on graft survival. Twelve hundred ninety-six pancreata were procured from donation after brain death donors, with 314 (19.5%) from donation after circulatory death donors. More than 50% of recovered pancreata had at least one injury, most commonly a short portal vein (21.5%). Liver donation, procurement team origin, hepatic artery (HA) arising from the superior mesenteric artery (SMA), and increasing donor BMI were associated with increased rates of pancreas damage on univariate analyses; on multivariate analysis only the presence of an HA from the SMA remained significant (p = 0.02). Six hundred forty solid organ pancreas transplants were performed; 238 had some form of damage. Overall, there was no difference in graft survival between damaged and undamaged organs (p = 0.28); however, graft loss was significantly more frequent in pancreata with arterial damage (p = 0.04) and in those with parenchymal damage (p = 0.05). Damage to the pancreas during organ recovery is more common than other organs, and meticulous surgical technique and awareness of damage risk factors are essential to reduce rates of procurement-related injuries.

  9. Structural damage localization by outlier analysis of signal-processed mode shapes - Analytical and experimental validation

    NASA Astrophysics Data System (ADS)

    Ulriksen, M. D.; Damkilde, L.

    2016-02-01

    Contrary to global modal parameters such as eigenfrequencies, mode shapes inherently provide structural information on a local level. Therefore, this particular modal parameter and its derivatives are utilized extensively for damage identification. Typically, more or less advanced mathematical methods are employed to identify damage-induced discontinuities in the spatial mode shape signals, hereby, potentially, facilitating damage detection and/or localization. However, by being based on distinguishing damage-induced discontinuities from other signal irregularities, an intrinsic deficiency in these methods is the high sensitivity towards measurement noise. In the present paper, a damage localization method which, compared to the conventional mode shape-based methods, has greatly enhanced robustness towards measurement noise is proposed. The method is based on signal processing of a spatial mode shape by means of continuous wavelet transformation (CWT) and subsequent application of a generalized discrete Teager-Kaiser energy operator (GDTKEO) to identify damage-induced mode shape discontinuities. In order to evaluate whether the identified discontinuities are in fact damage-induced, outlier analysis is conducted by applying the Mahalanobis metric to major principal scores of the sensor-located bands of the signal-processed mode shape. The method is tested analytically and benchmarked with other mode shape-based damage localization approaches on the basis of a free-vibrating beam and validated experimentally in the context of a residential-sized wind turbine blade subjected to an impulse load.

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

    PubMed

    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.

  11. Acoustic Emission Analysis of Damage Progression in Thermal Barrier Coatings Under Thermal Cyclic Conditions

    NASA Technical Reports Server (NTRS)

    Appleby, Matthew; Zhu, Dongming; Morscher, Gregory

    2015-01-01

    Damage evolution of electron beam-physical vapor deposited (EBVD-PVD) ZrO2-7 wt.% Y2O3 thermal barrier coatings (TBCs) under thermal cyclic conditions was monitored using an acoustic emission (AE) technique. The coatings were heated using a laser heat flux technique that yields a high reproducibility in thermal loading. Along with AE, real-time thermal conductivity measurements were also taken using infrared thermography. Tests were performed on samples with induced stress concentrations, as well as calcium-magnesium-alumino-silicate (CMAS) exposure, for comparison of damage mechanisms and AE response to the baseline (as-produced) coating. Analysis of acoustic waveforms was used to investigate damage development by comparing when events occurred, AE event frequency, energy content and location. The test results have shown that AE accumulation correlates well with thermal conductivity changes and that AE waveform analysis could be a valuable tool for monitoring coating degradation and provide insight on specific damage mechanisms.

  12. Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage.

    PubMed

    Kennedy, Scott R; Salk, Jesse J; Schmitt, Michael W; Loeb, Lawrence A

    2013-01-01

    Mitochondrial DNA (mtDNA) is believed to be highly vulnerable to age-associated damage and mutagenesis by reactive oxygen species (ROS). However, somatic mtDNA mutations have historically been difficult to study because of technical limitations in accurately quantifying rare mtDNA mutations. We have applied the highly sensitive Duplex Sequencing methodology, which can detect a single mutation among >10(7) wild type molecules, to sequence mtDNA purified from human brain tissue from both young and old individuals with unprecedented accuracy. We find that the frequency of point mutations increases ~5-fold over the course of 80 years of life. Overall, the mutation spectra of both groups are comprised predominantly of transition mutations, consistent with misincorporation by DNA polymerase γ or deamination of cytidine and adenosine as the primary mutagenic events in mtDNA. Surprisingly, G → T mutations, considered the hallmark of oxidative damage to DNA, do not significantly increase with age. We observe a non-uniform, age-independent distribution of mutations in mtDNA, with the D-loop exhibiting a significantly higher mutation frequency than the rest of the genome. The coding regions, but not the D-loop, exhibit a pronounced asymmetric accumulation of mutations between the two strands, with G → A and T → C mutations occurring more often on the light strand than the heavy strand. The patterns and biases we observe in our data closely mirror the mutational spectrum which has been reported in studies of human populations and closely related species. Overall our results argue against oxidative damage being a major driver of aging and suggest that replication errors by DNA polymerase γ and/or spontaneous base hydrolysis are responsible for the bulk of accumulating point mutations in mtDNA.

  13. Full-length high-temperature severe fuel damage test No. 2. Final safety analysis

    SciTech Connect

    Hesson, G.M.; Lombardo, N.J.; Pilger, J.P.; Rausch, W.N.; King, L.L.; Hurley, D.E.; Parchen, L.J.; Panisko, F.E.

    1993-09-01

    Hazardous conditions associated with performing the Full-Length High- Temperature (FLHT). Severe Fuel Damage Test No. 2 experiment have been analyzed. Major hazards that could cause harm or damage are (1) radioactive fission products, (2) radiation fields, (3) reactivity changes, (4) hydrogen generation, (5) materials at high temperature, (6) steam explosion, and (7) steam pressure pulse. As a result of this analysis, it is concluded that with proper precautions the FLHT- 2 test can be safely conducted.

  14. Molecular analysis of aggressive renal cell carcinoma with unclassified histology reveals distinct subsets

    PubMed Central

    Chen, Ying-Bei; Xu, Jianing; Skanderup, Anders Jacobsen; Dong, Yiyu; Brannon, A. Rose; Wang, Lu; Won, Helen H.; Wang, Patricia I.; Nanjangud, Gouri J.; Jungbluth, Achim A.; Li, Wei; Ojeda, Virginia; Hakimi, A. Ari; Voss, Martin H.; Schultz, Nikolaus; Motzer, Robert J.; Russo, Paul; Cheng, Emily H.; Giancotti, Filippo G.; Lee, William; Berger, Michael F.; Tickoo, Satish K.; Reuter, Victor E.; Hsieh, James J.

    2016-01-01

    Renal cell carcinomas with unclassified histology (uRCC) constitute a significant portion of aggressive non-clear cell renal cell carcinomas that have no standard therapy. The oncogenic drivers in these tumours are unknown. Here we perform a molecular analysis of 62 high-grade primary uRCC, incorporating targeted cancer gene sequencing, RNA sequencing, single-nucleotide polymorphism array, fluorescence in situ hybridization, immunohistochemistry and cell-based assays. We identify recurrent somatic mutations in 29 genes, including NF2 (18%), SETD2 (18%), BAP1 (13%), KMT2C (10%) and MTOR (8%). Integrated analysis reveals a subset of 26% uRCC characterized by NF2 loss, dysregulated Hippo–YAP pathway and worse survival, whereas 21% uRCC with mutations of MTOR, TSC1, TSC2 or PTEN and hyperactive mTORC1 signalling are associated with better clinical outcome. FH deficiency (6%), chromatin/DNA damage regulator mutations (21%) and ALK translocation (2%) distinguish additional cases. Altogether, this study reveals distinct molecular subsets for 76% of our uRCC cohort, which could have diagnostic and therapeutic implications. PMID:27713405

  15. Applying robust variant of Principal Component Analysis as a damage detector in the presence of outliers

    NASA Astrophysics Data System (ADS)

    Gharibnezhad, Fahit; Mujica, Luis E.; Rodellar, José

    2015-01-01

    Using Principal Component Analysis (PCA) for Structural Health Monitoring (SHM) has received considerable attention over the past few years. PCA has been used not only as a direct method to identify, classify and localize damages but also as a significant primary step for other methods. Despite several positive specifications that PCA conveys, it is very sensitive to outliers. Outliers are anomalous observations that can affect the variance and the covariance as vital parts of PCA method. Therefore, the results based on PCA in the presence of outliers are not fully satisfactory. As a main contribution, this work suggests the use of robust variant of PCA not sensitive to outliers, as an effective way to deal with this problem in SHM field. In addition, the robust PCA is compared with the classical PCA in the sense of detecting probable damages. The comparison between the results shows that robust PCA can distinguish the damages much better than using classical one, and even in many cases allows the detection where classic PCA is not able to discern between damaged and non-damaged structures. Moreover, different types of robust PCA are compared with each other as well as with classical counterpart in the term of damage detection. All the results are obtained through experiments with an aircraft turbine blade using piezoelectric transducers as sensors and actuators and adding simulated damages.

  16. Phosphoproteomic Analysis Reveals Regulatory Mechanisms at the Kidney Filtration Barrier

    PubMed Central

    Rinschen, Markus M.; Wu, Xiongwu; König, Tim; Pisitkun, Trairak; Hagmann, Henning; Pahmeyer, Caroline; Lamkemeyer, Tobias; Kohli, Priyanka; Schnell, Nicole; Schermer, Bernhard; Dryer, Stuart; Brooks, Bernard R.; Beltrao, Pedro; Krueger, Marcus

    2014-01-01

    Diseases of the kidney filtration barrier are a leading cause of ESRD. Most disorders affect the podocytes, polarized cells with a limited capacity for self-renewal that require tightly controlled signaling to maintain their integrity, viability, and function. Here, we provide an atlas of in vivo phosphorylated, glomerulus-expressed proteins, including podocyte-specific gene products, identified in an unbiased tandem mass spectrometry–based approach. We discovered 2449 phosphorylated proteins corresponding to 4079 identified high-confidence phosphorylated residues and performed a systematic bioinformatics analysis of this dataset. We discovered 146 phosphorylation sites on proteins abundantly expressed in podocytes. The prohibitin homology domain of the slit diaphragm protein podocin contained one such site, threonine 234 (T234), located within a phosphorylation motif that is mutated in human genetic forms of proteinuria. The T234 site resides at the interface of podocin dimers. Free energy calculation through molecular dynamic simulations revealed a role for T234 in regulating podocin dimerization. We show that phosphorylation critically regulates formation of high molecular weight complexes and that this may represent a general principle for the assembly of proteins containing prohibitin homology domains. PMID:24511133

  17. Fatigue damage evaluation of plain woven carbon fiber reinforced plastic (CFRP) modified with MFC (micro-fibrillated cellulose) by thermo-elastic damage analysis (TDA)

    NASA Astrophysics Data System (ADS)

    Aoyama, Ryohei; Okubo, Kazuya; Fujii, Toru

    2013-04-01

    The aim of this study is to investigate characteristics of fatigue damage of CFRP modified with MFC by TDA under tensile cyclic loading. In this paper, fatigue life of CFRP modified with MFC was investigated under cyclic loading. Characteristics of fatigue damage of CFRP modified with MFC were evaluated by thermo-elastic damage analysis. Maximum improvement in fatigue life was also obtained under cyclic loading when epoxy matrix was enhanced with 0.3wt% of MFC as well as under static loading. Result of TDA showed same tendency as the result of fatigue test, and the result of TDA well expressed the fatigue damage behavior of plain woven CFRP plate. Eventually, TDA was effective for clear understanding the degree of fatigue damage progression of CFRP modified with MFC.

  18. Fatigue analysis of multiple site damage at a row of holes in a wide panel

    NASA Technical Reports Server (NTRS)

    Buhler, Kimberley; Grandt, Alten F., Jr.; Moukawsher, E. J.

    1994-01-01

    This paper is concerned with predicting the fatigue life of unstiffened panels which contain multiple site damage (MSD). The initial damage consists of through-the-thickness cracks emanating from a row of holes in the center of a finite width panel. A fracture mechanics analysis has been developed to predict the growth, interaction, and coalescence of the various cracks which propagate in the panel. A strain-life analysis incorporating Neuber's rule for notches, and Miner's rule for cumulative damage, is also employed to predict crack initiation for holes without initial cracking. This analysis is compared with the results of a series of fatigue tests on 2024-T3 aluminum panels, and is shown to do an excellent job of predicting the influence of MSD on the fatigue life of nine inch wide specimens. Having established confidence in the ability to analyze the influence of MSD on fatigue life, a parametric study is conducted to examine the influence of various MSD scenarios in an unstiffened panel. The numerical study considered 135 cases in all, with the parametric variables being the applied cyclic stress level, the lead crack geometry, and the number and location of MSD cracks. The numerical analysis provides details for the manner in which lead cracks and MSD cracks grow and coalesce leading to final failure. The results indicate that MSD located adjacent to lead cracks is the most damaging configuration, while for cases without lead cracks, MSD clusters which are not separated by uncracked holes are most damaging.

  19. Detection of bearing damage by statistic vibration analysis

    NASA Astrophysics Data System (ADS)

    Sikora, E. A.

    2016-04-01

    The condition of bearings, which are essential components in mechanisms, is crucial to safety. The analysis of the bearing vibration signal, which is always contaminated by certain types of noise, is a very important standard for mechanical condition diagnosis of the bearing and mechanical failure phenomenon. In this paper the method of rolling bearing fault detection by statistical analysis of vibration is proposed to filter out Gaussian noise contained in a raw vibration signal. The results of experiments show that the vibration signal can be significantly enhanced by application of the proposed method. Besides, the proposed method is used to analyse real acoustic signals of a bearing with inner race and outer race faults, respectively. The values of attributes are determined according to the degree of the fault. The results confirm that the periods between the transients, which represent bearing fault characteristics, can be successfully detected.

  20. Oxidative damage induced by copper in mouse primary hepatocytes by single-cell analysis.

    PubMed

    Jing, Mingyang; Liu, Yang; Song, Wei; Yan, Yunxing; Yan, Wenbao; Liu, Rutao

    2016-01-01

    Copper can disturb the intracellular redox balance, induce oxidative stress, and subsequently cause irreversible damage, leading to a variety of diseases. In the present study, mouse primary hepatocytes were chosen to elucidate the in vitro oxidative damage of short-term copper exposure (10-200 μM) by single-cell analysis. We evaluated the toxicity of copper by reactive oxygen species (ROS), glutathione (GSH), and oxidative DNA damage at the single-cell level. Oxidative damage induced by copper was verified by the morphological changes, persistent elevations of excessive ROS and malondialdehyde (MDA), a decrease in GSH level, and the oxidative DNA damage. Furthermore, the average ROS generation, GSH consumption, and the indicators in DNA damage did not significantly change at relatively low concentrations (10 or 50 μM), but we can find the alterations of parameters in some single cells clearly. Emphasis on the analysis of single cells is conducive to gain a better understanding on the toxicity of copper. This study will also complement studies on the environmental risk assessment of copper pollution.

  1. High performance implementation of probabilistic damage tolerance analysis

    NASA Astrophysics Data System (ADS)

    Crosby, Nathan

    A number of recent studies have demonstrated that large-scale extratropical wave activity is characterized by quasi-periodic behavior on timescales of 20-30 days, particularly in the Southern Hemisphere. This phenomenon has been termed the Baroclinic Annular Mode (BAM), and is responsible for the modulation of eddy heat fluxes, eddy kinetic energy, and precipitation on large scales. However, the extent to which this periodic modulation is discernable or significant on smaller spatial scales had not yet been established. Using data from the ECMWF Interim Reanalysis for the period 1979-2014, this study extensively examines the spatial structure of the BAM. Spectral analyses reveal the spatial limitations of the periodic behavior, while lag-correlation analyses reveal the patterns of propagation and development of anomalies that give rise to the observed periodicity. Periodic behavior is more robust in the Southern Hemisphere than in the Northern Hemisphere, but filtering out low wavenumbers from NH data helps clarify the BAM signal. Additionally, it is demonstrated that the BAM appears very differently in two relatively similar global climate models, suggesting further study is needed to determine how modern GCMs capture the BAM. Supplementing our analyses of observed and modeled data is a simple two-way linear feedback model, which is utilized to demonstrate the principal mechanism underlying periodic behavior in the BAM. The model makes it apparent that the BAM can be modeled as a simple linear feedback between baroclinicity and eddy heat fluxes. The periodicity seen on larger scales is a product of differential advection rates affecting the development of spatially overlapping, out-of-phase anomalies. The large-scale nature of the periodic behavior, however, makes it difficult to draw conclusions about the potential utility of the BAM for weather analysts and forecasters, and the limitations of this study limit our ability to describe its role in the climate

  2. Comparison of Damage Path Predictions for Composite Laminates by Explicit and Standard Finite Element Analysis Tools

    NASA Technical Reports Server (NTRS)

    Bogert, Philip B.; Satyanarayana, Arunkumar; Chunchu, Prasad B.

    2006-01-01

    Splitting, ultimate failure load and the damage path in center notched composite specimens subjected to in-plane tension loading are predicted using progressive failure analysis methodology. A 2-D Hashin-Rotem failure criterion is used in determining intra-laminar fiber and matrix failures. This progressive failure methodology has been implemented in the Abaqus/Explicit and Abaqus/Standard finite element codes through user written subroutines "VUMAT" and "USDFLD" respectively. A 2-D finite element model is used for predicting the intra-laminar damages. Analysis results obtained from the Abaqus/Explicit and Abaqus/Standard code show good agreement with experimental results. The importance of modeling delamination in progressive failure analysis methodology is recognized for future studies. The use of an explicit integration dynamics code for simple specimen geometry and static loading establishes a foundation for future analyses where complex loading and nonlinear dynamic interactions of damage and structure will necessitate it.

  3. A fracture mechanics analysis of impact damage in a thick composite laminate

    NASA Technical Reports Server (NTRS)

    Poe, C. C., Jr.

    1985-01-01

    Graphite/epoxy filament-wound cases (FWC) for the solid rocket motors of the space shuttle are being made by NASA. The FWC cases are wound with AS4W graphite fiber impregnated with an epoxy resin and are about 1.4 inches or more thick. Graphite-epoxy composite laminates, unlike metals, can be damaged easily by low velocity impacts of objects like dropped tools. The residual tension strength of the FWC laminate, after impact, is being studied at Langley Research Center. The conditions that give minimum visual evidence of damage are being emphasized. A fracture mechanics analysis was developed to predict the residual strength, after impact, using radiographs to measure the size of the damage and an equivalent surface crack to represent the damage.

  4. Analysis about factors affecting the degree of damage of buildings in earthquake

    NASA Astrophysics Data System (ADS)

    Jia, Jing; Yan, Jinghong

    2015-07-01

    Earthquakes have been affecting human's safety through human's history. Previous studies on earthquake, mostly, focused on the performance of buildings or evaluating damages. This paper, however, compares different factors that have influence on the damage of buildings with a case study in Wenchuan earthquake, using multiple linear regression methodology, so as to identify to what extend this factors influence the buildings’ damages, then give the rank of importance of these factors. In this process, authors take the type of structure as a dummy variable to compare the degree of damages caused by different types of structure, which were barely studied before. Besides, Factor Analysis Methodology(FA) will be adapted to classify factors, the results of which will simplify later study. The outcome of this study would make a big difference in optimizing the seismic design and improving residential seismic quality.

  5. Duplication and analysis of meteoroid damage on LDEF and advanced spacecraft materials

    NASA Technical Reports Server (NTRS)

    Hill, David C.; Rose, M. Frank

    1995-01-01

    The analysis of exposed surfaces on LDEF since its retrieval in 1990 has revealed a wide range of meteoroid and debris (M&D) impact features in the sub-micron to millimeter size range, ranging from quasi-infinite target cratering in LDEF metallic structural members (e.g. inter-costals, tray clamps, etc.) to non-marginal perforations in metallic experimental surfaces (e.g. thin foil detectors, etc.). Approximately 34,000 impact features are estimated to exist on the exposed surfaces of LDEF. The vast majority of impact craters in metal substrates exhibit circular footprints, with approximately 50 percent retaining impactor residues in varying states of shock processing. The fundamental goals of this project were to duplicate and analyze meteoroid impact damage on spacecraft metallic materials with a view to quantifying the residue retention and oblique impact morphology characteristics. Using the hypervelocity impact test facility established at Auburn University a series of impact tests (normal and oblique incidence) were executed producing consistently high (11-12 km/s) peak impact velocities, the results of which were subsequently analyzed using Scanning Electron Microscope (SEM) and Energy Dispersive X-ray Spectroscopy (EDXS) facilities at Auburn University.

  6. A limit analysis approach to derive a thermodynamic damage potential for non-linear geomaterials

    NASA Astrophysics Data System (ADS)

    Karrech, A.; Poulet, T.; Regenauer-Lieb, K.

    2012-10-01

    This paper introduces a mathematical model which describes the continuum damage of non-linear geo-materials. The model accounts for full thermo-mechanical coupling as well as irreversible failure and its effect on shear heating. It involves multi-mechanisms creep to describe the material rheology depending on time, temperature, pressure and water content. This coupled thermo-mechanical model combined with the upper bound theory is used to formulate a potential capable of predicting the damage evolution. The model is implemented and applied to a cross-sectional geological layer subjected to extension. It reveals that damage accelerates the creation of faults and accentuates the localization of shear zones, thereby competing with the increase in material rigidity due to rate dependency, especially at high temperature.

  7. Evaluation of Progressive Failure Analysis and Modeling of Impact Damage in Composite Pressure Vessels

    NASA Technical Reports Server (NTRS)

    Sanchez, Christopher M.

    2011-01-01

    NASA White Sands Test Facility (WSTF) is leading an evaluation effort in advanced destructive and nondestructive testing of composite pressure vessels and structures. WSTF is using progressive finite element analysis methods for test design and for confirmation of composite pressure vessel performance. Using composite finite element analysis models and failure theories tested in the World-Wide Failure Exercise, WSTF is able to estimate the static strength of composite pressure vessels. Additionally, test and evaluation on composites that have been impact damaged is in progress so that models can be developed to estimate damage tolerance and the degradation in static strength.

  8. Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison.

    PubMed

    Forgacs, David; Wallen, Rick L; Dobson, Lauren K; Derr, James N

    2016-01-01

    Yellowstone National Park is home to one of the only plains bison populations that have continuously existed on their present landscape since prehistoric times without evidence of domestic cattle introgression. Previous studies characterized the relatively high levels of nuclear genetic diversity in these bison, but little is known about their mitochondrial haplotype diversity. This study assessed mitochondrial genomes from 25 randomly selected Yellowstone bison and found 10 different mitochondrial haplotypes with a haplotype diversity of 0.78 (± 0.06). Spatial analysis of these mitochondrial DNA (mtDNA) haplotypes did not detect geographic population subdivision (FST = -0.06, p = 0.76). However, we identified two independent and historically important lineages in Yellowstone bison by combining data from 65 bison (defined by 120 polymorphic sites) from across North America representing a total of 30 different mitochondrial DNA haplotypes. Mitochondrial DNA haplotypes from one of the Yellowstone lineages represent descendants of the 22 indigenous bison remaining in central Yellowstone in 1902. The other mitochondrial DNA lineage represents descendants of the 18 females introduced from northern Montana in 1902 to supplement the indigenous bison population and develop a new breeding herd in the northern region of the park. Comparing modern and historical mitochondrial DNA diversity in Yellowstone bison helps uncover a historical context of park restoration efforts during the early 1900s, provides evidence against a hypothesized mitochondrial disease in bison, and reveals the signature of recent hybridization between American plains bison (Bison bison bison) and Canadian wood bison (B. b. athabascae). Our study demonstrates how mitochondrial DNA can be applied to delineate the history of wildlife species and inform future conservation actions.

  9. Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison

    PubMed Central

    Derr, James N.

    2016-01-01

    Yellowstone National Park is home to one of the only plains bison populations that have continuously existed on their present landscape since prehistoric times without evidence of domestic cattle introgression. Previous studies characterized the relatively high levels of nuclear genetic diversity in these bison, but little is known about their mitochondrial haplotype diversity. This study assessed mitochondrial genomes from 25 randomly selected Yellowstone bison and found 10 different mitochondrial haplotypes with a haplotype diversity of 0.78 (± 0.06). Spatial analysis of these mitochondrial DNA (mtDNA) haplotypes did not detect geographic population subdivision (FST = -0.06, p = 0.76). However, we identified two independent and historically important lineages in Yellowstone bison by combining data from 65 bison (defined by 120 polymorphic sites) from across North America representing a total of 30 different mitochondrial DNA haplotypes. Mitochondrial DNA haplotypes from one of the Yellowstone lineages represent descendants of the 22 indigenous bison remaining in central Yellowstone in 1902. The other mitochondrial DNA lineage represents descendants of the 18 females introduced from northern Montana in 1902 to supplement the indigenous bison population and develop a new breeding herd in the northern region of the park. Comparing modern and historical mitochondrial DNA diversity in Yellowstone bison helps uncover a historical context of park restoration efforts during the early 1900s, provides evidence against a hypothesized mitochondrial disease in bison, and reveals the signature of recent hybridization between American plains bison (Bison bison bison) and Canadian wood bison (B. b. athabascae). Our study demonstrates how mitochondrial DNA can be applied to delineate the history of wildlife species and inform future conservation actions. PMID:27880780

  10. Quantitative flux analysis reveals folate-dependent NADPH production

    NASA Astrophysics Data System (ADS)

    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.

  11. Applications of a damage tolerance analysis methodology in aircraft design and production

    NASA Technical Reports Server (NTRS)

    Woodward, M. R.; Owens, S. D.; Law, G. E.; Mignery, L. A.

    1992-01-01

    Objectives of customer mandated aircraft structural integrity initiatives in design are to guide material selection, to incorporate fracture resistant concepts in the design, to utilize damage tolerance based allowables and planned inspection procedures necessary to enhance the safety and reliability of manned flight vehicles. However, validated fracture analysis tools for composite structures are needed to accomplish these objectives in a timely and economical manner. This paper briefly describes the development, validation, and application of a damage tolerance methodology for composite airframe structures. A closed-form analysis code, entitled SUBLAM was developed to predict the critical biaxial strain state necessary to cause sublaminate buckling-induced delamination extension in an impact damaged composite laminate. An embedded elliptical delamination separating a thin sublaminate from a thick parent laminate is modelled. Predicted failure strains were correlated against a variety of experimental data that included results from compression after impact coupon and element tests. An integrated analysis package was developed to predict damage tolerance based margin-of-safety (MS) using NASTRAN generated loads and element information. Damage tolerance aspects of new concepts are quickly and cost-effectively determined without the need for excessive testing.

  12. Analysis of chromosome damage for biodosimetry using imaging flow cytometry.

    PubMed

    Beaton, L A; Ferrarotto, C; Kutzner, B C; McNamee, J P; Bellier, P V; Wilkins, R C

    2013-08-30

    The dicentric chromosome assay (DCA), which involves counting the frequency of dicentric chromosomes in mitotic lymphocytes and converting it to a dose-estimation for ionizing radiation exposure, is considered to be the gold standard for radiation biodosimetry. Furthermore, for emergency response, the DCA has been adapted for triage by simplifying the scoring method [1]. With the development of new technologies such as the imaging flow cytometer, it may now be possible to adapt this microscope-based method to an automated cytometry method. This technology allows the sensitivity of microscopy to be maintained while adding the increased throughput of flow cytometry. A new protocol is being developed to adapt the DCA to the imaging cytometer in order to further increase the rapid determination of a biological dose. Peripheral blood mononuclear cells (PBMC) were isolated from ex vivo irradiated whole blood samples using a density gradient separation method and cultured with PHA and Colcemid. After 48h incubation, the chromosomes were isolated, stained for DNA content with propidium iodide (PI) and labelled with a centromere marker. Stained chromosomes were then analyzed on the ImageStream(×) (EMD-Millipore, Billerica, MA). Preliminary results indicate that individual chromosomes can be identified and mono- and dicentric chromosomes can be differentiated by imaging cytometry. A dose response curve was generated using this technology. The details of the method and the dose response curve are presented and compared to traditional microscope scoring. Imaging cytometry is a new technology which enables the rapid, automated analysis of fluorescently labelled chromosomes. Adapting the dicentric assay to this technology has the potential for high throughput analysis for mass casualty events.

  13. Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family

    PubMed Central

    Trempe, Jean-François; Šašková, Klára Grantz; Sivá, Monika; Ratcliffe, Colin D. H.; Veverka, Václav; Hoegl, Annabelle; Ménade, Marie; Feng, Xin; Shenker, Solomon; Svoboda, Michal; Kožíšek, Milan; Konvalinka, Jan; Gehring, Kalle

    2016-01-01

    The eukaryotic Ddi1 family is defined by a conserved retroviral aspartyl protease-like (RVP) domain found in association with a ubiquitin-like (UBL) domain. Ddi1 from Saccharomyces cerevisiae additionally contains a ubiquitin-associated (UBA) domain. The substrate specificity and role of the protease domain in the biological functions of the Ddi family remain unclear. Yeast Ddi1 has been implicated in the regulation of cell cycle progression, DNA-damage repair, and exocytosis. Here, we investigated the multi-domain structure of yeast Ddi1 using X-ray crystallography, nuclear magnetic resonance, and small-angle X-ray scattering. The crystal structure of the RVP domain sheds light on a putative substrate recognition site involving a conserved loop. Isothermal titration calorimetry confirms that both UBL and UBA domains bind ubiquitin, and that Ddi1 binds K48-linked diubiquitin with enhanced affinity. The solution NMR structure of a helical domain that precedes the protease displays tertiary structure similarity to DNA-binding domains from transcription regulators. Our structural studies suggest that the helical domain could serve as a landing platform for substrates in conjunction with attached ubiquitin chains binding to the UBL and UBA domains. PMID:27646017

  14. Comparing monofractal and multifractal analysis of corrosion damage evolution in reinforcing bars.

    PubMed

    Xu, Yidong; Qian, Chunxiang; Pan, Lei; Wang, Bingbing; Lou, Chi

    2012-01-01

    Based on fractal theory and damage mechanics, the aim of this paper is to describe the monofractal and multifractal characteristics of corrosion morphology and develop a new approach to characterize the nonuniform corrosion degree of reinforcing bars. The relationship between fractal parameters and tensile strength of reinforcing bars are discussed. The results showed that corrosion mass loss ratio of a bar cannot accurately reflect the damage degree of the bar. The corrosion morphology of reinforcing bars exhibits both monofractal and multifractal features. The fractal dimension and the tensile strength of corroded steel bars exhibit a power function relationship, while the width of multifractal spectrum and tensile strength of corroded steel bars exhibit a linear relationship. By comparison, using width of multifractal spectrum as multifractal damage variable not only reflects the distribution of corrosion damage in reinforcing bars, but also reveals the influence of nonuniform corrosion on the mechanical properties of reinforcing bars. The present research provides a new approach for the establishment of corrosion damage constitutive models of reinforcing bars.

  15. Comparing Monofractal and Multifractal Analysis of Corrosion Damage Evolution in Reinforcing Bars

    PubMed Central

    Xu, Yidong; Qian, Chunxiang; Pan, Lei; Wang, Bingbing; Lou, Chi

    2012-01-01

    Based on fractal theory and damage mechanics, the aim of this paper is to describe the monofractal and multifractal characteristics of corrosion morphology and develop a new approach to characterize the nonuniform corrosion degree of reinforcing bars. The relationship between fractal parameters and tensile strength of reinforcing bars are discussed. The results showed that corrosion mass loss ratio of a bar cannot accurately reflect the damage degree of the bar. The corrosion morphology of reinforcing bars exhibits both monofractal and multifractal features. The fractal dimension and the tensile strength of corroded steel bars exhibit a power function relationship, while the width of multifractal spectrum and tensile strength of corroded steel bars exhibit a linear relationship. By comparison, using width of multifractal spectrum as multifractal damage variable not only reflects the distribution of corrosion damage in reinforcing bars, but also reveals the influence of nonuniform corrosion on the mechanical properties of reinforcing bars. The present research provides a new approach for the establishment of corrosion damage constitutive models of reinforcing bars. PMID:22238682

  16. Analysis of the epithelial damage produced by Entamoeba histolytica infection.

    PubMed

    Betanzos, Abigail; Schnoor, Michael; Javier-Reyna, Rosario; García-Rivera, Guillermina; Bañuelos, Cecilia; Pais-Morales, Jonnatan; Orozco, Esther

    2014-06-12

    Entamoeba histolytica is the causative agent of human amoebiasis, a major cause of diarrhea and hepatic abscess in tropical countries. Infection is initiated by interaction of the pathogen with intestinal epithelial cells. This interaction leads to disruption of intercellular structures such as tight junctions (TJ). TJ ensure sealing of the epithelial layer to separate host tissue from gut lumen. Recent studies provide evidence that disruption of TJ by the parasitic protein EhCPADH112 is a prerequisite for E. histolytica invasion that is accompanied by epithelial barrier dysfunction. Thus, the analysis of molecular mechanisms involved in TJ disassembly during E. histolytica invasion is of paramount importance to improve our understanding of amoebiasis pathogenesis. This article presents an easy model that allows the assessment of initial host-pathogen interactions and the parasite invasion potential. Parameters to be analyzed include transepithelial electrical resistance, interaction of EhCPADH112 with epithelial surface receptors, changes in expression and localization of epithelial junctional markers and localization of parasite molecules within epithelial cells.

  17. Analysis of cavitation damage on the Space Shuttle main engine high pressure oxidizer turbopump

    NASA Technical Reports Server (NTRS)

    Stinebring, D. R.

    1985-01-01

    The performance of the Space Shuttle Main Engines (SSME) has met or exceeded specifications. However, the durability for selected components has not met the desired lifetime criteria. Thus, the High-Pressure Oxidizer Turbopump (HPOTP) has experienced cavitation erosion problems in a number of locations in the pump. An investigation was conducted, taking into account an analysis of the cavitation damage, the development of a flow model for the pump, and the recommendation of design changes which would increase the life expectancy of the unit. The present paper is concerned with the cavitation damage analysis. A model is presented which relates the heavy damage on the housing and over the inducer blades to unsteady blade surface cavitation. This cavitation occurs on the inducer blades in the wakes downstream of the pump inlet housing vanes.

  18. Retinal damage in chloroquine maculopathy, revealed by high resolution imaging: a case report utilizing adaptive optics scanning laser ophthalmoscopy.

    PubMed

    Bae, Eun Jin; Kim, Kyoung Rae; Tsang, Stephen H; Park, Sung Pyo; Chang, Stanley

    2014-02-01

    A 53-year-old Asian woman was treated with hydroxychloroquine and chloroquine for lupus erythematosus. Within a few years, she noticed circle-shaped shadows in her central vision. Upon examination, the patient's visual acuity was 20 / 25 in both eyes. Humphrey visual field (HVF) testing revealed a central visual defect, and fundoscopy showed a ring-shaped area of parafoveal retinal pigment epithelium depigmentation. Fundus autofluorescence imaging showed a hypofluorescent lesion consistent with bull's eye retinopathy. Adaptive optics scanning laser ophthalmoscope (AO-SLO) revealed patch cone mosaic lesions, in which cones were missing or lost. In addition, the remaining cones consisted of asymmetrical shapes and sizes that varied in brightness. Unlike previous studies employing deformable mirrors for wavefront aberration correction, our AO-SLO approach utilized dual liquid crystal on silicon spatial light modulators. Thus, by using AO-SLO, we were able to create a photographic montage consisting of high quality images. Disrupted cone AO-SLO images were matched with visual field test results and functional deficits were associated with a precise location on the montage, which allowed correlation of histological findings with functional changes determined by HVF. We also investigated whether adaptive optics imaging was more sensitive to anatomical changes compared with spectral-domain optical coherence tomography.

  19. Meta-analysis of attitudes toward damage-causing mammalian wildlife.

    PubMed

    Kansky, Ruth; Kidd, Martin; Knight, Andrew T

    2014-08-01

    Many populations of threatened mammals persist outside formally protected areas, and their survival depends on the willingness of communities to coexist with them. An understanding of the attitudes, and specifically the tolerance, of individuals and communities and the factors that determine these is therefore fundamental to designing strategies to alleviate human-wildlife conflict. We conducted a meta-analysis to identify factors that affected attitudes toward 4 groups of terrestrial mammals. Elephants (65%) elicited the most positive attitudes, followed by primates (55%), ungulates (53%), and carnivores (44%). Urban residents presented the most positive attitudes (80%), followed by commercial farmers (51%) and communal farmers (26%). A tolerance to damage index showed that human tolerance of ungulates and primates was proportional to the probability of experiencing damage while elephants elicited tolerance levels higher than anticipated and carnivores elicited tolerance levels lower than anticipated. Contrary to conventional wisdom, experiencing damage was not always the dominant factor determining attitudes. Communal farmers had a lower probability of being positive toward carnivores irrespective of probability of experiencing damage, while commercial farmers and urban residents were more likely to be positive toward carnivores irrespective of damage. Urban residents were more likely to be positive toward ungulates, elephants, and primates when probability of damage was low, but not when it was high. Commercial and communal farmers had a higher probability of being positive toward ungulates, primates, and elephants irrespective of probability of experiencing damage. Taxonomic bias may therefore be important. Identifying the distinct factors explaining these attitudes and the specific contexts in which they operate, inclusive of the species causing damage, will be essential for prioritizing conservation investments.

  20. Nonlinear dynamic analysis of damaged Reddy-Bickford beams supported on an elastic Pasternak foundation

    NASA Astrophysics Data System (ADS)

    Stojanović, Vladimir; Petković, Marko D.

    2016-12-01

    Geometrically nonlinear free and forced vibrations of damaged high order shear deformable beams resting on a nonlinear Pasternak foundation are investigated in this paper. Equations of motion are derived for the beam which is under subjected combined action of arbitrarily distributed or concentrated transverse loading as well as axial loading. To account for shear deformations, the concept of high order shear deformation is used in comparison with the concept of first order shear deformation theory. Analyses are performed to investigate the effects of the specific stiffness of the foundation on the damaged beam frequencies and displacements with the aim of equalising the response of a damaged and an intact beam. According to that, functions of the foundation stiffness are determined depending on the location and size of the damage as a result of the possibility for the damaged beam to behave like one that is intact. An advanced p-version of the finite element method is developed for geometrically nonlinear vibrations of damaged Reddy-Bickford beams. The present study gives a clear view of the nonlinear dynamical behaviour of four types of beams according to high order shear deformation theory - an intact beam, a damaged beam, a damaged beam on an elastic foundation and intact beam on elastic foundation. The paper also presents the derivation of a new set of two nonlinear partial differential equations where only the transverse and axial displacements figure. The forced nonlinear vibrations problem is solved in the time domain using the Newmark integration method. Free vibration analysis carried out by harmonic balance and the use of continuation methods and backbone curves are constructed.

  1. Analysis of Radiation Damage in Light Water Reactors: Comparison of Cluster Analysis Methods for the Analysis of Atom Probe Data.

    PubMed

    Hyde, Jonathan M; DaCosta, Gérald; Hatzoglou, Constantinos; Weekes, Hannah; Radiguet, Bertrand; Styman, Paul D; Vurpillot, Francois; Pareige, Cristelle; Etienne, Auriane; Bonny, Giovanni; Castin, Nicolas; Malerba, Lorenzo; Pareige, Philippe

    2017-01-30

    Irradiation of reactor pressure vessel (RPV) steels causes the formation of nanoscale microstructural features (termed radiation damage), which affect the mechanical properties of the vessel. A key tool for characterizing these nanoscale features is atom probe tomography (APT), due to its high spatial resolution and the ability to identify different chemical species in three dimensions. Microstructural observations using APT can underpin development of a mechanistic understanding of defect formation. However, with atom probe analyses there are currently multiple methods for analyzing the data. This can result in inconsistencies between results obtained from different researchers and unnecessary scatter when combining data from multiple sources. This makes interpretation of results more complex and calibration of radiation damage models challenging. In this work simulations of a range of different microstructures are used to directly compare different cluster analysis algorithms and identify their strengths and weaknesses.

  2. A new hand-held microfluidic cytometer for evaluating irradiation damage by analysis of the damaged cells distribution

    PubMed Central

    Wang, Junsheng; Fan, Zhiqiang; Zhao, Yile; Song, Younan; Chu, Hui; Song, Wendong; Song, Yongxin; Pan, Xinxiang; Sun, Yeqing; Li, Dongqing

    2016-01-01

    Space radiation brings uneven damages to cells. The detection of the distribution of cell damage plays a very important role in radiation medicine and the related research. In this paper, a new hand-held microfluidic flow cytometer was developed to evaluate the degree of radiation damage of cells. The device we propose overcomes the shortcomings (e.g., large volume and high cost) of commercial flow cytometers and can evaluate the radiation damage of cells accurately and quickly with potential for onsite applications. The distribution of radiation-damaged cells is analyzed by a simultaneous detection of immunofluorescence intensity of γ-H2AX and resistance pulse sensor (RPS) signal. The γ-H2AX fluorescence intensity provides information of the degree of radiation damage in cells. The ratio of the number of cells with γ-H2AX fluorescence signals to the total numbers of cells detected by RPS indicates the percentage of the cells that are damaged by radiation. The comparison experiment between the developed hand-held microfluidic flow cytometer and a commercial confocal microscope indicates a consistent and comparable detection performance. PMID:26983800

  3. Chromatin Dynamics during DNA Repair Revealed by Pair Correlation Analysis of Molecular Flow in the Nucleus

    PubMed Central

    Hinde, Elizabeth; Kong, Xiangduo; Yokomori, Kyoko; Gratton, Enrico

    2014-01-01

    Chromatin dynamics modulate DNA repair factor accessibility throughout the DNA damage response. The spatiotemporal scale upon which these dynamics occur render them invisible to live cell imaging. Here we present a believed novel assay to monitor the in vivo structural rearrangements of chromatin during DNA repair. By pair correlation analysis of EGFP molecular flow into chromatin before and after damage, this assay measures millisecond variations in chromatin compaction with submicron resolution. Combined with laser microirradiation we employ this assay to monitor the real-time accessibility of DNA at the damage site. We find from comparison of EGFP molecular flow with a molecule that has an affinity toward double-strand breaks (Ku-EGFP) that DNA damage induces a transient decrease in chromatin compaction at the damage site and an increase in compaction to adjacent regions, which together facilitate DNA repair factor recruitment to the lesion with high spatiotemporal control. PMID:24988341

  4. Damage detection of engine bladed-disks using multivariate statistical analysis

    NASA Astrophysics Data System (ADS)

    Fang, X.; Tang, J.

    2006-03-01

    The timely detection of damage in aero-engine bladed-disks is an extremely important and challenging research topic. Bladed-disks have high modal density and, particularly, their vibration responses are subject to significant uncertainties due to manufacturing tolerance (blade-to-blade difference or mistuning), operating condition change and sensor noise. In this study, we present a new methodology for the on-line damage detection of engine bladed-disks using their vibratory responses during spin-up or spin-down operations which can be measured by blade-tip-timing sensing technique. We apply a principle component analysis (PCA)-based approach for data compression, feature extraction, and denoising. The non-model based damage detection is achieved by analyzing the change between response features of the healthy structure and of the damaged one. We facilitate such comparison by incorporating the Hotelling's statistic T2 analysis, which yields damage declaration with a given confidence level. The effectiveness of the method is demonstrated by case studies.

  5. Conversation after Right Hemisphere Brain Damage: Motivations for Applying Conversation Analysis

    ERIC Educational Resources Information Center

    Barnes, Scott; Armstrong, Elizabeth

    2010-01-01

    Despite the well documented pragmatic deficits that can arise subsequent to Right Hemisphere Brain Damage (RHBD), few researchers have directly studied everyday conversations involving people with RHBD. In recent years, researchers have begun applying Conversation Analysis (CA) to the everyday talk of people with aphasia. This research programme…

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Independent component analysis of DTI data reveals white matter covariances in Alzheimer's disease

    NASA Astrophysics Data System (ADS)

    Ouyang, Xin; Sun, Xiaoyu; Guo, Ting; Sun, Qiaoyue; Chen, Kewei; Yao, Li; Wu, Xia; Guo, Xiaojuan

    2014-03-01

    Alzheimer's disease (AD) is a progressive neurodegenerative disease with the clinical symptom of the continuous deterioration of cognitive and memory functions. Multiple diffusion tensor imaging (DTI) indices such as fractional anisotropy (FA) and mean diffusivity (MD) can successfully explain the white matter damages in AD patients. However, most studies focused on the univariate measures (voxel-based analysis) to examine the differences between AD patients and normal controls (NCs). In this investigation, we applied a multivariate independent component analysis (ICA) to investigate the white matter covariances based on FA measurement from DTI data in 35 AD patients and 45 NCs from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. We found that six independent components (ICs) showed significant FA reductions in white matter covariances in AD compared with NC, including the genu and splenium of corpus callosum (IC-1 and IC-2), middle temporal gyral of temporal lobe (IC-3), sub-gyral of frontal lobe (IC-4 and IC-5) and sub-gyral of parietal lobe (IC-6). Our findings revealed covariant white matter loss in AD patients and suggest that the unsupervised data-driven ICA method is effective to explore the changes of FA in AD. This study assists us in understanding the mechanism of white matter covariant reductions in the development of AD.

  8. A Finite Element Analysis for Predicting the Residual Compressive Strength of Impact-Damaged Sandwich Panels

    NASA Technical Reports Server (NTRS)

    Ratcliffe, James G.; Jackson, Wade C.

    2008-01-01

    A simple analysis method has been developed for predicting the residual compressive strength of impact-damaged sandwich panels. The method is tailored for honeycomb core-based sandwich specimens that exhibit an indentation growth failure mode under axial compressive loading, which is driven largely by the crushing behavior of the core material. The analysis method is in the form of a finite element model, where the impact-damaged facesheet is represented using shell elements and the core material is represented using spring elements, aligned in the thickness direction of the core. The nonlinear crush response of the core material used in the analysis is based on data from flatwise compression tests. A comparison with a previous analysis method and some experimental data shows good agreement with results from this new approach.

  9. A Finite Element Analysis for Predicting the Residual Compression Strength of Impact-Damaged Sandwich Panels

    NASA Technical Reports Server (NTRS)

    Ratcliffe, James G.; Jackson, Wade C.

    2008-01-01

    A simple analysis method has been developed for predicting the residual compression strength of impact-damaged sandwich panels. The method is tailored for honeycomb core-based sandwich specimens that exhibit an indentation growth failure mode under axial compression loading, which is driven largely by the crushing behavior of the core material. The analysis method is in the form of a finite element model, where the impact-damaged facesheet is represented using shell elements and the core material is represented using spring elements, aligned in the thickness direction of the core. The nonlinear crush response of the core material used in the analysis is based on data from flatwise compression tests. A comparison with a previous analysis method and some experimental data shows good agreement with results from this new approach.

  10. [Chlorophyll fluorescence spectrum analysis of greenhouse cucumber disease and insect damage].

    PubMed

    Sui, Yuan-yuan; Yu, Hai-ye; Zhang, Lei; Luo, Han; Ren, Shun; Zhao, Guo-gang

    2012-05-01

    The present paper is based on chlorophyll fluorescence spectrum analysis. The wavelength 685 nm was determined as the primary characteristic point for the analysis of healthy or disease and insect damaged leaf by spectrum configuration. Dimensionality reduction of the spectrum was achieved by combining simple intercorrelation bands selection and principal component analysis (PCA). The principal component factor was reduced from 10 to 5 while the spectrum information was kept reaching 99.999%. By comparing and analysing three modeling methods, namely the partial least square regression (PLSR), BP neural network (BP) and least square support vector machine regression (LSSVMR), regarding correlation coefficient of true value and predicted value as evaluation criterion, eventually, LSSVMR was confirmed as the appropriate method for modeling of greenhouse cucumber disease and insect damage chlorophyll fluorescence spectrum analysis.

  11. Analysis of damaging effects of laser-plasma accelerated shrapnels on protecting glass shield

    NASA Astrophysics Data System (ADS)

    Martinkova, Michaela; Kalal, Milan; Shmatov, Mikhail L.

    2013-11-01

    Analysis of the damage caused by laser plasma accelerated fragments of metal target was performed. Measured as well as calculated parameters of craters and shrapnel found in BK7 glass blastshield are presented. Method applied for the measurement of parameters of craters is described. Potential damage of optical elements by the so-called striking cores (high-velocity stable objects arising due to collapse of cones or some other target parts toward their axes) that can be generated in IFE related experiments is evaluated.

  12. Tornado risk analysis at Savannah River Plant using windspeed damage thresholds and single building strike frequencies

    SciTech Connect

    Taylor, D.H.; McDonald, J.R.; Twisdale, L.A.

    1985-01-01

    In order to evaluate the safety of existing structures and properly design new structures, an analysis of tornado resistance was conducted on each process building at SRP and other buildings by type. Damage estimates were cataloged for each Fujita class windspeed interval and windspeeds were cataloged as a function of increased levels of damage. The probability, for any structure, of a tornado exceeding each windspeed threshold was calculated using the TORRISK computer code which was developed for calculating the probability of a tornado strike on nuclear power generating plants.

  13. Decision-tree analysis of factors influencing rainfall-related building structure and content damage

    NASA Astrophysics Data System (ADS)

    Spekkers, M. H.; Kok, M.; Clemens, F. H. L. R.; ten Veldhuis, J. A. E.

    2014-09-01

    Flood-damage prediction models are essential building blocks in flood risk assessments. So far, little research has been dedicated to damage from small-scale urban floods caused by heavy rainfall, while there is a need for reliable damage models for this flood type among insurers and water authorities. The aim of this paper is to investigate a wide range of damage-influencing factors and their relationships with rainfall-related damage, using decision-tree analysis. For this, district-aggregated claim data from private property insurance companies in the Netherlands were analysed, for the period 1998-2011. The databases include claims of water-related damage (for example, damages related to rainwater intrusion through roofs and pluvial flood water entering buildings at ground floor). Response variables being modelled are average claim size and claim frequency, per district, per day. The set of predictors include rainfall-related variables derived from weather radar images, topographic variables from a digital terrain model, building-related variables and socioeconomic indicators of households. Analyses were made separately for property and content damage claim data. Results of decision-tree analysis show that claim frequency is most strongly associated with maximum hourly rainfall intensity, followed by real estate value, ground floor area, household income, season (property data only), buildings age (property data only), a fraction of homeowners (content data only), a and fraction of low-rise buildings (content data only). It was not possible to develop statistically acceptable trees for average claim size. It is recommended to investigate explanations for the failure to derive models. These require the inclusion of other explanatory factors that were not used in the present study, an investigation of the variability in average claim size at different spatial scales, and the collection of more detailed insurance data that allows one to distinguish between the

  14. ANALYSIS OF DAMAGE TO WASTE PACKAGES CAUSED BY SEISMIC EVENTS DURING POST-CLOSURE

    SciTech Connect

    Alves, S W; Blair, S C; Carlson, S R; Gerhard, M; Buscheck, T A

    2008-05-27

    This paper presents methodology and results of an analysis of damage due to seismic ground motion for waste packages emplaced in a nuclear waste repository at Yucca Mountain, Nevada. A series of three-dimensional rigid body kinematic simulations of waste packages, pallets, and drip shields subjected to seismic ground motions was performed. The simulations included strings of several waste packages and were used to characterize the number, location, and velocity of impacts that occur during seismic ground motion. Impacts were categorized as either waste package-to-waste package (WP-WP) or waste package-to-pallet (WP-P). In addition, a series of simulations was performed for WP-WP and WP-P impacts using a detailed representation of a single waste package. The detailed simulations were used to determine the amount of damage from individual impacts, and to form a damage catalog, indexed according to the type, angle, location and force/velocity of the impact. Finally, the results from the two analyses were combined to estimate the total damage to a waste package that may occur during an episode of seismic ground motion. This study addressed two waste package types, four levels of peak ground velocity (PGV), and 17 ground motions at each PGV. Selected aspects of waste package degradation, such as effective wall thickness and condition of the internals, were also considered. As expected, increasing the PGV level of the vibratory ground motion increases the damage to the waste packages. Results show that most of the damage is caused by WP-P impacts. TAD-bearing waste packages with intact internals are highly resistant to damage, even at a PGV of 4.07 m/s, which is the highest level analyzed.

  15. Damage and Failure Analysis of AZ31 Alloy Sheet in Warm Stamping Processes

    NASA Astrophysics Data System (ADS)

    Zhao, P. J.; Chen, Z. H.; Dong, C. F.

    2016-07-01

    In this study, a combined experimental-numerical investigation on the failure of AZ31 Mg alloy sheet in the warm stamping process was carried out based on modified GTN damage model which integrated Yld2000 anisotropic yield criterion. The constitutive equations of material were implemented into a VUMAT subroutine for solver ABAQUS/Explicit and applied to the formability analysis of mobile phone shell. The morphology near the crack area was observed using SEM, and the anisotropic damage evolution at various temperatures was simulated. The distributions of plastic strain, damage evolution, thickness, and fracture initiation obtained from FE simulation were analyzed. The corresponding forming limit diagrams were worked out, and the comparison with the experimental data showed a good agreement.

  16. Multimodal, multiphoton microscopy and image correlation analysis for characterizing corneal thermal damage

    NASA Astrophysics Data System (ADS)

    Lo, Wen; Chang, Yu-Lin; Liu, Jia-Shiu; Hseuh, Chiu-Mei; Hovhannisyan, Vladimir; Chen, Shean-Jen; Tan, Hsin-Yuan; Dong, Chen-Yuan

    2009-09-01

    We used the combination of multiphoton autofluorescence (MAF), forward second-harmonic generation (FWSHG), and backward second-harmonic generation (BWSHG) imaging for the qualitative and quantitative characterization of thermal damage of ex vivo bovine cornea. We attempt to characterize the structural alterations by qualitative MAF, FWSHG, and BWSHG imaging in the temperature range of 37 to 90°C. In addition to measuring the absolute changes in the three types of signals at the stromal surface, we also performed image correlation analysis between FWSHG and BWSHG and demonstrate that with increasing thermal damage, image correlation between FWSHG and BWSHG significantly increases. Our results show that while MAF and BWSHG intensities may be used as preliminary indicators of the extent of corneal thermal damage, the most sensitive measures are provided by the decay in FWSHG intensity and the convergence of FWSHG and BWSHG images.

  17. Regularized discriminant analysis for multi-sensor decision fusion and damage detection with Lamb waves

    NASA Astrophysics Data System (ADS)

    Mishra, Spandan; Vanli, O. Arda; Huffer, Fred W.; Jung, Sungmoon

    2016-04-01

    In this study we propose a regularized linear discriminant analysis approach for damage detection which does not require an intermediate feature extraction step and therefore more efficient in handling data with high-dimensionality. A robust discriminant model is obtained by shrinking of the covariance matrix to a diagonal matrix and thresholding redundant predictors without hurting the predictive power of the model. The shrinking and threshold parameters of the discriminant function (decision boundary) are estimated to minimize the classification error. Furthermore, it is shown how the damage classification achieved by the proposed method can be extended to multiple sensors by following a Bayesian decision-fusion formulation. The detection probability of each sensor is used as a prior condition to estimate the posterior detection probability of the entire network and the posterior detection probability is used as a quantitative basis to make the final decision about the damage.

  18. Consequence analysis to determine the damage to humans from vapour cloud explosions using characteristic curves.

    PubMed

    Alonso, Fernando Díaz; Ferradás, Enrique González; Sánchez, Teresa de Jesús Jiménez; Aznar, Agustín Miñana; Gimeno, José Ruiz; Alonso, Jesús Martínez

    2008-01-15

    The aim of this paper is to provide a methodology to facilitate consequence analysis for vapour cloud explosions (VCE). Firstly, the main PROBIT equations to evaluate direct damage on humans from those accidents (eardrum rupture, death due to skull fracture, death due to whole body impact and lung damage) are discussed and the most suitable ones are selected. Secondly, a new methodology is developed to relate characteristic overpressure-impulse-distance curves for VCE, obtained in a previous paper (F. Diaz Alonso et al., Characteristic overpressure-impulse-distance curves for vapour cloud explosions using the TNO Multi-Energy model, J. Hazard. Mater. A137 (2006) 734-741) with the selected PROBIT equations. This methodology allows the determination of damage as a function of distance to the accident's origin in only one step, using explosion energy and VCE Multi-Energy charge strength as input parameters.

  19. Transmission electron microscopy analysis of mechanical polishing-related damage in silicon carbide wafers

    NASA Astrophysics Data System (ADS)

    Grim, J. R.; Benamara, M.; Skowronski, M.; Everson, W. J.; Heydemann, V. D.

    2006-12-01

    The subsurface damage generated by mechanical polishing of silicon carbide wafers was investigated and quantified by plan view transmission electron microscopy (TEM) and atomic force microscopy (AFM). Damage generated during polishing using diamond abrasives with 0.5 µm particle size consists of dislocation loops with length up to 400 nm from the scratches. The total dislocation density was estimated at 5 × 1010 dislocations cm-2. TEM analysis of the Burgers vectors indicates that the initial perfect dislocations have a Burgers vector of b = a/3 lang11-20rang-type with many dislocation dissociated into two partials with b = a/3 lang1-100rang. The depth of damage was estimated to be up to 50 nm. 4H-SiC homoepitaxial layers grown on mechanically polished substrates without further surface treatment exhibit threading dislocation density along scratches in the order of 105 cm-1.

  20. Progressive damage analysis of carbon/epoxy laminates under couple laser and mechanical loading

    NASA Astrophysics Data System (ADS)

    Liu, Wanlei; Chang, Xinlong; Zhang, Xiaojun; Zhang, Youhong

    A multiscale model based bridge theory is proposed for the progressive damage analysis of carbon/epoxy laminates under couple laser and mechanical loading. The ablation model is adopted to calculate ablation temperature changing and ablation surface degradation. The polynomial strengthening model of matrix is used to improve bridging model for reducing parameter input. Stiffness degradation methods of bridging model are also improved in order to analyze the stress redistribution more accurately when the damage occurs. Thermal-mechanical analyses of the composite plate are performed using the ABAQUS/Explicit program with the developed model implemented in the VUMAT. The simulation results show that this model can be used to proclaim the mesoscale damage mechanism of composite laminates under coupled loading.

  1. A padding method to reduce edge effects for enhanced damage identification using wavelet analysis

    NASA Astrophysics Data System (ADS)

    Montanari, Lorenzo; Basu, Biswajit; Spagnoli, Andrea; Broderick, Brian M.

    2015-02-01

    Vibration response based structural damage identification by spatial wavelet analysis is widely considered a powerful tool in Structural Health Monitoring (SHM). This work deals with the issue of border distortions in wavelet transform that can mask tiny damages close to the boundary of a structure. Since traditional padding methods (e.g., zero-padding, symmetric padding, linear padding) are often not satisfactory, a simple and computationally inexpensive signal extension method, based on fitting polynomial functions and continuity conditions at the extrema, is proposed. The method is applied to analyze noisy mode shapes and static deflection of cracked cantilever and simply supported beams. The effectiveness and the versatility of the method in localizing tiny damages close to clamped, free or hinged beam boundaries is demonstrated. Furthermore, an extensive comparison with the linear padding method and Messina's isomorphism methods is carried out.

  2. Modal analysis of a cantilever beam by use of the slope-assisted BOTDA method for damage identification

    NASA Astrophysics Data System (ADS)

    Minardo, A.; Coscetta, A.; Pirozzi, S.; Bernini, R.; Zeni, L.

    2013-05-01

    We report an experimental study on a cantilever beam, aimed to verify the feasibility of modal analysis by distributed Brillouin sensing for structural damage identification. Damage identification was carried out for three defect cases, analyzing the changes of the natural frequencies and mode shapes of the first two bending modes. Comparison with finite element method (FEM) analysis shows that the damage can be detected and localized, within the limitation dictated by the spatial resolution (30 cm) of our sensor.

  3. Numerical analysis for structural health monitoring of a damaged composite panel using PZT actuators and sensors

    NASA Astrophysics Data System (ADS)

    Nagabhushana, A.; Spiegel, M.; Adu, S.; Hayes, N.; Paul, D.; Trivedi, K.; Fairbee, B.; Zheng, H.; Gerrity, A.; Kotru, S.; Roy, S.; Barkey, M.; Burkett, S. L.

    2012-04-01

    Reliable damage detection is crucial for assessing the integrity of a structure. In this paper, a numerical study of a composite panel fabricated to simulate a crack is undertaken using finite element methods (FEM). The damage to be considered is a transverse crack which pre-exists in the structure. The finite element models are developed for an undamaged and a damaged composite panel to compute the change in Lamb wave response due to the existence of a crack. The model is validated using shear lag analysis applied at the crack. The results are verified experimentally by comparing the results for an undamaged composite panel and a composite panel fabricated with a simulated crack using the vacuum assisted resin transfer molding (VARTM) process. The responses for each panel are obtained using surface mounted lead zirconate titanate (PZT) actuators and sensors. PZT is used to generate Lamb waves which produce stress throughout the panel thickness. Propagation characteristics of Lamb waves are varied by the presence of damage. The sensor data provide reliable information about the integrity of the structure. Numerical results are compared to the sensor output to ensure accuracy of the damage detection system.

  4. Advanced Damage Tolerance Analysis of International Space Station Pressure Wall Welds

    NASA Technical Reports Server (NTRS)

    Allen, Phillip A.

    2006-01-01

    EM20/MSFC has sponsored technology in the area of advanced damage tolerance analysis tools used to analyze the International Space Station (ISS) pressure wall welds. The ISS European modules did not receive non-destructive evaluation (NDE) inspection after proof test. In final assembly configuration, most welds could only be inspected from one side, and some welds were uninspectible. Therefore, advanced damage tolerance analysis was required to determine the critical initial flaw sizes and predicted safe life for the pressure wall welds. EM20 sponsored the development of a new finite element tools using FEA-Crack and WARP3D to solve the problem. This presentation gives a brief overview of the new analytical tools and the analysis results.

  5. Comprehensive SNP scan of DNA repair and DNA damage response genes reveal multiple susceptibility loci conferring risk to tobacco associated leukoplakia and oral cancer.

    PubMed

    Mondal, Pinaki; Datta, Sayantan; Maiti, Guru Prasad; Baral, Aradhita; Jha, Ganga Nath; Panda, Chinmay Kumar; Chowdhury, Shantanu; Ghosh, Saurabh; Roy, Bidyut; Roychoudhury, Susanta

    2013-01-01

    Polymorphic variants of DNA repair and damage response genes play major role in carcinogenesis. These variants are suspected as predisposition factors to Oral Squamous Cell Carcinoma (OSCC). For identification of susceptible variants affecting OSCC development in Indian population, the "maximally informative" method of SNP selection from HapMap data to non-HapMap populations was applied. Three hundred twenty-five SNPs from 11 key genes involved in double strand break repair, mismatch repair and DNA damage response pathways were genotyped on a total of 373 OSCC, 253 leukoplakia and 535 unrelated control individuals. The significantly associated SNPs were validated in an additional cohort of 144 OSCC patients and 160 controls. The rs12515548 of MSH3 showed significant association with OSCC both in the discovery and validation phases (discovery P-value: 1.43E-05, replication P-value: 4.84E-03). Two SNPs (rs12360870 of MRE11A, P-value: 2.37E-07 and rs7003908 of PRKDC, P-value: 7.99E-05) were found to be significantly associated only with leukoplakia. Stratification of subjects based on amount of tobacco consumption identified SNPs that were associated with either high or low tobacco exposed group. The study reveals a synergism between associated SNPs and lifestyle factors in predisposition to OSCC and leukoplakia.

  6. Kinetic Modeling Reveals the Roles of Reactive Oxygen Species Scavenging and DNA Repair Processes in Shaping the Dose-Response Curve of KBrO₃-Induced DNA Damage.

    PubMed

    Spassova, Maria A; Miller, David J; Nikolov, Alexander S

    2015-01-01

    We have developed a kinetic model to investigate how DNA repair processes and scavengers of reactive oxygen species (ROS) can affect the dose-response shape of prooxidant induced DNA damage. We used as an example chemical KBrO3 which is activated by glutathione and forms reactive intermediates that directly interact with DNA to form 8-hydroxy-2-deoxyguanosine DNA adducts (8-OH-dG). The single strand breaks (SSB) that can result from failed base excision repair of these adducts were considered as an effect downstream from 8-OH-dG. We previously demonstrated that, in the presence of effective base excision repair, 8-OH-dG can exhibit threshold-like dose-response dependence, while the downstream SSB can still exhibit a linear dose-response. Here we demonstrate that this result holds for a variety of conditions, including low levels of GSH, the presence of additional SSB repair mechanisms, or a scavenger. It has been shown that melatonin, a terminal scavenger, inhibits KBrO3-caused oxidative damage. Our modeling revealed that sustained exposure to KBrO3 can lead to fast scavenger exhaustion, in which case the dose-response shapes for both endpoints are not substantially affected. The results are important to consider when forming conclusions on a chemical's toxicity dose dependence based on the dose-response of early genotoxic events.

  7. Analysis of core damage frequency from internal events: Peach Bottom, Unit 2

    SciTech Connect

    Kolaczkowski, A.M.; Lambright, J.A.; Ferrell, W.L.; Cathey, N.G.; Najafi, B.; Harper, F.T.

    1986-10-01

    This document contains the internal event initiated accident sequence analyses for Peach Bottom, Unit 2; one of the reference plants being examined as part of the NUREG-1150 effort by the Nuclear Regulatory Commission. NUREG-1150 will document the risk of a selected group of nuclear power plants. As part of that work, this report contains the overall core damage frequency estimate for Peach Bottom, Unit 2, and the accompanying plant damage state frequencies. Sensitivity and uncertainty analyses provided additional insights regarding the dominant contributors to the Peach Bottom core damage frequency estimate. The mean core damage frequency at Peach Bottom was calculated to be 8.2E-6. Station blackout type accidents (loss of all ac power) were found to dominate the overall results. Anticipated Transient Without Scram accidents were also found to be non-negligible contributors. The numerical results are largely driven by common mode failure probability estimates and to some extent, human error. Because of significant data and analysis uncertainties in these two areas (important, for instance, to the most dominant scenario in this study), it is recommended that the results of the uncertainty and sensitivity analyses be considered before any actions are taken based on this analysis.

  8. Decision tree analysis of factors influencing rainfall-related building damage

    NASA Astrophysics Data System (ADS)

    Spekkers, M. H.; Kok, M.; Clemens, F. H. L. R.; ten Veldhuis, J. A. E.

    2014-04-01

    Flood damage prediction models are essential building blocks in flood risk assessments. Little research has been dedicated so far to damage of small-scale urban floods caused by heavy rainfall, while there is a need for reliable damage models for this flood type among insurers and water authorities. The aim of this paper is to investigate a wide range of damage-influencing factors and their relationships with rainfall-related damage, using decision tree analysis. For this, district-aggregated claim data from private property insurance companies in the Netherlands were analysed, for the period of 1998-2011. The databases include claims of water-related damage, for example, damages related to rainwater intrusion through roofs and pluvial flood water entering buildings at ground floor. Response variables being modelled are average claim size and claim frequency, per district per day. The set of predictors include rainfall-related variables derived from weather radar images, topographic variables from a digital terrain model, building-related variables and socioeconomic indicators of households. Analyses were made separately for property and content damage claim data. Results of decision tree analysis show that claim frequency is most strongly associated with maximum hourly rainfall intensity, followed by real estate value, ground floor area, household income, season (property data only), buildings age (property data only), ownership structure (content data only) and fraction of low-rise buildings (content data only). It was not possible to develop statistically acceptable trees for average claim size, which suggest that variability in average claim size is related to explanatory variables that cannot be defined at the district scale. Cross-validation results show that decision trees were able to predict 22-26% of variance in claim frequency, which is considerably better compared to results from global multiple regression models (11-18% of variance explained). Still, a

  9. Global Phospholipidomics Analysis Reveals Selective Pulmonary Peroxidation Profiles Upon Inhalation of Single Walled Carbon Nanotubes

    PubMed Central

    Tyurina, Yulia Y.; Kisin, Elena R.; Murray, Ashley; Tyurin, Vladimir A.; Kapralova, Valentina I.; Sparvero, Louis J.; Amoscato, Andrew A.; Samhan-Arias, Alejandro K.; Swedin, Linda; Lahesmaa, Riitta; Fadeel, Bengt; Shvedova, Anna A.; Kagan, Valerian E.

    2011-01-01

    It is commonly believed that nanomaterials cause non-specific oxidative damage. Our mass spectrometry-based oxidative lipidomics analysis of all major phospholipid classes revealed highly selective patterns of pulmonary peroxidation after inhalation exposure of mice to single-walled carbon nanotubes. No oxidized molecular species were found in two most abundant phospholipid classes – phosphatidylcholine and phosphatidylethanolamine. Peroxidation products were identified in three relatively minor classes of anionic phospholipids, cardiolipin, phosphatidylserine and phosphatidylinositol whereby oxygenation of polyunsaturated fatty acid residues also showed unusual substrate specificity. This non-random peroxidation coincided with the accumulation of apoptotic cells in the lung. A similar selective phospholipid peroxidation profile was detected upon incubation of a mixture of total lung lipids with H2O2/cytochrome c known to catalyze cardiolipin and phosphatidylserine peroxidation in apoptotic cells. The characterized specific phospholipid peroxidation signaling pathways indicate new approaches to the development of mitochondria targeted regulators of cardiolipin peroxidation to protect against deleterious effects of pro-apoptotic effects of single-walled carbon nanotubes in the lung. PMID:21800898

  10. Large-scale transient sensitivity analysis of a radiation damaged bipolar junction transistor.

    SciTech Connect

    Hoekstra, Robert John; Gay, David M.; Bartlett, Roscoe Ainsworth; Phipps, Eric Todd

    2007-11-01

    Automatic differentiation (AD) is useful in transient sensitivity analysis of a computational simulation of a bipolar junction transistor subject to radiation damage. We used forward-mode AD, implemented in a new Trilinos package called Sacado, to compute analytic derivatives for implicit time integration and forward sensitivity analysis. Sacado addresses element-based simulation codes written in C++ and works well with forward sensitivity analysis as implemented in the Trilinos time-integration package Rythmos. The forward sensitivity calculation is significantly more efficient and robust than finite differencing.

  11. Integrated analysis considered mitigation cost, damage cost and adaptation cost in Northeast Asia

    NASA Astrophysics Data System (ADS)

    Park, J. H.; Lee, D. K.; Kim, H. G.; Sung, S.; Jung, T. Y.

    2015-12-01

    Various studies show that raising the temperature as well as storms, cold snap, raining and drought caused by climate change. And variety disasters have had a damage to mankind. The world risk report(2012, The Nature Conservancy) and UNU-EHS (the United Nations University Institute for Environment and Human Security) reported that more and more people are exposed to abnormal weather such as floods, drought, earthquakes, typhoons and hurricanes over the world. In particular, the case of Korea, we influenced by various pollutants which are occurred in Northeast Asian countries, China and Japan, due to geographical meteorological characteristics. These contaminants have had a significant impact on air quality with the pollutants generated in Korea. Recently, around the world continued their effort to reduce greenhouse gas and to improve air quality in conjunction with the national or regional development goals priority. China is also working on various efforts in accordance with the international flows to cope with climate change and air pollution. In the future, effect of climate change and air quality in Korea and Northeast Asia will be change greatly according to China's growth and mitigation policies. The purpose of this study is to minimize the damage caused by climate change on the Korean peninsula through an integrated approach taking into account the mitigation and adaptation plan. This study will suggest a climate change strategy at the national level by means of a comprehensive economic analysis of the impacts and mitigation of climate change. In order to quantify the impact and damage cost caused by climate change scenarios in a regional scale, it should be priority variables selected in accordance with impact assessment of climate change. The sectoral impact assessment was carried out on the basis of selected variables and through this, to derive the methodology how to estimate damage cost and adaptation cost. And then, the methodology was applied in Korea

  12. Development of tools to automate quantitative analysis of radiation damage in SAXS experiments

    PubMed Central

    Brooks-Bartlett, Jonathan C.; Batters, Rebecca A.; Bury, Charles S.; Lowe, Edward D.; Ginn, Helen Mary; Round, Adam; Garman, Elspeth F.

    2017-01-01

    Biological small-angle X-ray scattering (SAXS) is an increasingly popular technique used to obtain nanoscale structural information on macromolecules in solution. However, radiation damage to the samples limits the amount of useful data that can be collected from a single sample. In contrast to the extensive analytical resources available for macromolecular crystallography (MX), there are relatively few tools to quantitate radiation damage for SAXS, some of which require a significant level of manual characterization, with the potential of leading to conflicting results from different studies. Here, computational tools have been developed to automate and standardize radiation damage analysis for SAXS data. RADDOSE-3D, a dose calculation software utility originally written for MX experiments, has been extended to account for the cylindrical geometry of the capillary tube, the liquid composition of the sample and the attenuation of the beam by the capillary material to allow doses to be calculated for many SAXS experiments. Furthermore, a library has been written to visualize and explore the pairwise similarity of frames. The calculated dose for the frame at which three subsequent frames are determined to be dissimilar is defined as the radiation damage onset threshold (RDOT). Analysis of RDOTs has been used to compare the efficacy of radioprotectant compounds to extend the useful lifetime of SAXS samples. Comparison of the RDOTs shows that, for radioprotectant compounds at 5 and 10 mM concentration, glycerol is the most effective compound. However, at 1 and 2 mM concentrations, di­thio­threitol (DTT) appears to be most effective. Our newly developed visualization library contains methods that highlight the unusual radiation damage results given by SAXS data collected using higher concentrations of DTT: these observations should pave the way to the development of more sophisticated frame merging strategies. PMID:28009547

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

    NASA Astrophysics Data System (ADS)

    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 (<2% of row-crop land), the extent of highly unprofitable land increased to 2.5 Mha, or 27% of row-crop land, in the 2015 projection. Aggregation of these areas to the township level revealed ‘hotspots’ for potential management change in Western, Central, and Northeast Iowa. In these least 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.

  14. Trophic hierarchies revealed via amino acid isotopic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Despite the potential of isotopic methods to illuminate trophic function, accurate estimates of lifetime feeding tendencies have remained elusive. A relatively new approach—referred to as compound-specific isotopic analysis (CSIA)—has emerged, centering on the measurement of 15N:14N ratios in amino ...

  15. Analysis of copy number variations reveals differences among cattle breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in the modern domesticated cattle using array comparative genomic hybridization (array CGH) and quanti...

  16. A Coupled/Uncoupled Computational Scheme for Deformation and Fatigue Damage Analysis of Unidirectional Metal-Matrix Composites

    NASA Technical Reports Server (NTRS)

    Wilt, Thomas E.; Arnold, Steven M.; Saleeb, Atef F.

    1997-01-01

    A fatigue damage computational algorithm utilizing a multiaxial, isothermal, continuum-based fatigue damage model for unidirectional metal-matrix composites has been implemented into the commercial finite element code MARC using MARC user subroutines. Damage is introduced into the finite element solution through the concept of effective stress that fully couples the fatigue damage calculations with the finite element deformation solution. Two applications using the fatigue damage algorithm are presented. First, an axisymmetric stress analysis of a circumferentially reinforced ring, wherein both the matrix cladding and the composite core were assumed to behave elastic-perfectly plastic. Second, a micromechanics analysis of a fiber/matrix unit cell using both the finite element method and the generalized method of cells (GMC). Results are presented in the form of S-N curves and damage distribution plots.

  17. Continuum Damage Mechanics Models for the Analysis of Progressive Failure in Open-Hole Tension Laminates

    NASA Technical Reports Server (NTRS)

    Song, Kyonchan; Li, Yingyong; Rose, Cheryl A.

    2011-01-01

    The performance of a state-of-the-art continuum damage mechanics model for interlaminar damage, coupled with a cohesive zone model for delamination is examined for failure prediction of quasi-isotropic open-hole tension laminates. Limitations of continuum representations of intra-ply damage and the effect of mesh orientation on the analysis predictions are discussed. It is shown that accurate prediction of matrix crack paths and stress redistribution after cracking requires a mesh aligned with the fiber orientation. Based on these results, an aligned mesh is proposed for analysis of the open-hole tension specimens consisting of different meshes within the individual plies, such that the element edges are aligned with the ply fiber direction. The modeling approach is assessed by comparison of analysis predictions to experimental data for specimen configurations in which failure is dominated by complex interactions between matrix cracks and delaminations. It is shown that the different failure mechanisms observed in the tests are well predicted. In addition, the modeling approach is demonstrated to predict proper trends in the effect of scaling on strength and failure mechanisms of quasi-isotropic open-hole tension laminates.

  18. Development of DNA Damage Response Signaling Biomarkers using Automated, Quantitative Image Analysis

    PubMed Central

    Nikolaishvilli-Feinberg, Nana; Cohen, Stephanie M.; Midkiff, Bentley; Zhou, Yingchun; Olorvida, Mark; Ibrahim, Joseph G.; Omolo, Bernard; Shields, Janiel M.; Thomas, Nancy E.; Groben, Pamela A.; Kaufmann, William K.

    2014-01-01

    The DNA damage response (DDR) coordinates DNA repair with cell cycle checkpoints to ameliorate or mitigate the pathological effects of DNA damage. Automated quantitative analysis (AQUA) and Tissue Studio are commercial technologies that use digitized immunofluorescence microscopy images to quantify antigen expression in defined tissue compartments. Because DDR is commonly activated in cancer and may reflect genetic instability within the lesion, a method to quantify DDR in cancer offers potential diagnostic and/or prognostic value. In this study, both AQUA and Tissue Studio algorithms were used to quantify the DDR in radiation-damaged skin fibroblasts, melanoma cell lines, moles, and primary and metastatic melanomas. Digital image analysis results for three markers of DDR (γH2AX, P-ATM, P-Chk2) correlated with immunoblot data for irradiated fibroblasts, whereas only γH2AX and P-Chk2 correlated with immunoblot data in melanoma cell lines. Melanoma cell lines displayed substantial variation in γH2AX and P-Chk2 expression, and P-Chk2 expression was significantly correlated with radioresistance. Moles, primary melanomas, and melanoma metastases in brain, lung and liver displayed substantial variation in γH2AX expression, similar to that observed in melanoma cell lines. Automated digital analysis of immunofluorescent images stained for DDR biomarkers may be useful for predicting tumor response to radiation and chemotherapy. PMID:24309508

  19. Frequencies and Flutter Speed Estimation for Damaged Aircraft Wing Using Scaled Equivalent Plate Analysis

    NASA Technical Reports Server (NTRS)

    Krishnamurthy, Thiagarajan

    2010-01-01

    Equivalent plate analysis is often used to replace the computationally expensive finite element analysis in initial design stages or in conceptual design of aircraft wing structures. The equivalent plate model can also be used to design a wind tunnel model to match the stiffness characteristics of the wing box of a full-scale aircraft wing model while satisfying strength-based requirements An equivalent plate analysis technique is presented to predict the static and dynamic response of an aircraft wing with or without damage. First, a geometric scale factor and a dynamic pressure scale factor are defined to relate the stiffness, load and deformation of the equivalent plate to the aircraft wing. A procedure using an optimization technique is presented to create scaled equivalent plate models from the full scale aircraft wing using geometric and dynamic pressure scale factors. The scaled models are constructed by matching the stiffness of the scaled equivalent plate with the scaled aircraft wing stiffness. It is demonstrated that the scaled equivalent plate model can be used to predict the deformation of the aircraft wing accurately. Once the full equivalent plate geometry is obtained, any other scaled equivalent plate geometry can be obtained using the geometric scale factor. Next, an average frequency scale factor is defined as the average ratio of the frequencies of the aircraft wing to the frequencies of the full-scaled equivalent plate. The average frequency scale factor combined with the geometric scale factor is used to predict the frequency response of the aircraft wing from the scaled equivalent plate analysis. A procedure is outlined to estimate the frequency response and the flutter speed of an aircraft wing from the equivalent plate analysis using the frequency scale factor and geometric scale factor. The equivalent plate analysis is demonstrated using an aircraft wing without damage and another with damage. Both of the problems show that the scaled

  20. Bird impact at aircraft structure - Damage analysis using Coupled Euler Lagrangian Approach

    NASA Astrophysics Data System (ADS)

    Smojver, I.; Ivancevic, D.

    2010-06-01

    Numerical bird strike damage prediction procedure has been applied on the very detailed large airplane secondary structure consisting of sandwich, composite and metallic structural items. The impacted inboard flap finite element model is modelled using 3D, shell and continuum shell elements, coupled with appropriate kinematic constraints. The bird has been modelled using Coupled Euler Lagrangian approach, in order to avoid the numerical difficulties connected with mesh distortion. Various failure modes, such as Carbon Fibre Reinforced Plastics (CFRP) face layer rupture, failure of composite matrix, damage initiation / evolution in the sandwich structure Nomex core and elastoplastic failure of a metallic structure have been investigated. Besides, general contact has been applied as to efficiently capture the contact between Eulerian bird material and the structure, as well as large deformations of the different structural components. Compared to the classic Lagrangian modelling of the bird, the analysis has proven to be more stable, and the results, such as damage areas, physically more realistic. The impact has been applied in the area that is the most probably subjected to the impact damage during exploitation.

  1. Vibration-based damage detection in plates by using time series analysis

    NASA Astrophysics Data System (ADS)

    Trendafilova, Irina; Manoach, Emil

    2008-07-01

    This paper deals with the problem of vibration health monitoring (VHM) in structures with nonlinear dynamic behaviour. It aims to introduce two viable VHM methods that use large amplitude vibrations and are based on nonlinear time series analysis. The methods suggested explore some changes in the state space geometry/distribution of the structural dynamic response with damage and their use for damage detection purposes. One of the methods uses the statistical distribution of state space points on the attractor of a vibrating structure, while the other one is based on the Poincaré map of the state space projected dynamic response. In this paper both methods are developed and demonstrated for a thin vibrating plate. The investigation is based on finite element modelling of the plate vibration response. The results obtained demonstrate the influence of damage on the local dynamic attractor of the plate state space and the applicability of the proposed strategies for damage assessment. The approach taken in this study and the suggested VHM methods are rather generic and permit development and applications for other more complex nonlinear structures.

  2. Fuselage Versus Subcomponent Panel Response Correlation Based on ABAQUS Explicit Progressive Damage Analysis Tools

    NASA Technical Reports Server (NTRS)

    Gould, Kevin E.; Satyanarayana, Arunkumar; Bogert, Philip B.

    2016-01-01

    Analysis performed in this study substantiates the need for high fidelity vehicle level progressive damage analyses (PDA) structural models for use in the verification and validation of proposed sub-scale structural models and to support required full-scale vehicle level testing. PDA results are presented that capture and correlate the responses of sub-scale 3-stringer and 7-stringer panel models and an idealized 8-ft diameter fuselage model, which provides a vehicle level environment for the 7-stringer sub-scale panel model. Two unique skin-stringer attachment assumptions are considered and correlated in the models analyzed: the TIE constraint interface versus the cohesive element (COH3D8) interface. Evaluating different interfaces allows for assessing a range of predicted damage modes, including delamination and crack propagation responses. Damage models considered in this study are the ABAQUS built-in Hashin procedure and the COmplete STress Reduction (COSTR) damage procedure implemented through a VUMAT user subroutine using the ABAQUS/Explicit code.

  3. Chromosomal damage and apoptosis analysis in exfoliated oral epithelial cells from mouthwash and alcohol users

    PubMed Central

    Rocha, Rodrigo dos Santos; Meireles, José Roberto Cardoso; de Moraes Marcílio Cerqueira, Eneida

    2014-01-01

    Chromosomal damage and apoptosis were analyzed in users of mouthwash and/or alcoholic beverages, using the micronucleus test on exfoliated oral mucosa cells. Samples from four groups of 20 individuals each were analyzed: three exposed groups (EG1, EG2 and EG3) and a control group (CG). EG1 comprised mouthwash users; EG2 comprised drinkers, and EG3 users of both mouthwashes and alcoholic beverages. Cell material was collected by gently scraping the insides of the cheeks. Then the cells were fixed in a methanol/acetic acid (3:1) solution and stained and counterstained, respectively, with Schiff reactive and fast green. Endpoints were computed on 2,000 cells in a blind test. Statistical analysis showed that chromosomal damage and apoptosis were significantly higher in individuals of groups EG1 and EG3 than in controls (p < 0.005 and p < 0.001, respectively). No significant difference in chromosomal damage and apoptosis was observed between the exposed groups. In EG2, only the occurrence of apoptosis was significantly higher than in the controls. These results suggest that mouthwashes alone or in association with alcoholic drinks induce genotoxic effects, manifested as chromosomal damage and apoptosis. They also suggest that alcoholic drinks are effective for stimulating the process of apoptosis. However, these data need to be confirmed in larger samples. PMID:25505845

  4. Towards a canonical elastoplastic damage model

    NASA Astrophysics Data System (ADS)

    Taher, Salah El-Din F.; Baluch, Mohammed H.; Al-Gadhib, Ali H.

    1994-05-01

    Fundamental aspects of elastoplastic damage are outlined. Time-independent isotropic damage is considered in order to study material degradation. By splitting the total strain tensor into its components of elastic damage and plastic damage and using recoverable energy equivalence, three distinct modes of behavior are particularized. For each mode of behavior, a suitable damage variable is culled. An in-depth analysis of this formulation reveals a certain incongruity in the assumptions postulated in some of the previously proposed models. The suggested generalized concepts are supported by experimental evidence.

  5. Interindividual variability in auditory scene analysis revealed by confidence judgements.

    PubMed

    Pelofi, C; de Gardelle, V; Egré, P; Pressnitzer, D

    2017-02-19

    Because musicians are trained to discern sounds within complex acoustic scenes, such as an orchestra playing, it has been hypothesized that musicianship improves general auditory scene analysis abilities. Here, we compared musicians and non-musicians in a behavioural paradigm using ambiguous stimuli, combining performance, reaction times and confidence measures. We used 'Shepard tones', for which listeners may report either an upward or a downward pitch shift for the same ambiguous tone pair. Musicians and non-musicians performed similarly on the pitch-shift direction task. In particular, both groups were at chance for the ambiguous case. However, groups differed in their reaction times and judgements of confidence. Musicians responded to the ambiguous case with long reaction times and low confidence, whereas non-musicians responded with fast reaction times and maximal confidence. In a subsequent experiment, non-musicians displayed reduced confidence for the ambiguous case when pure-tone components of the Shepard complex were made easier to discern. The results suggest an effect of musical training on scene analysis: we speculate that musicians were more likely to discern components within complex auditory scenes, perhaps because of enhanced attentional resolution, and thus discovered the ambiguity. For untrained listeners, stimulus ambiguity was not available to perceptual awareness.This article is part of the themed issue 'Auditory and visual scene analysis'.

  6. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis.

    PubMed

    Weinberg, Zasha; Perreault, Jonathan; Meyer, Michelle M; Breaker, Ronald R

    2009-12-03

    Estimates of the total number of bacterial species indicate that existing DNA sequence databases carry only a tiny fraction of the total amount of DNA sequence space represented by this division of life. Indeed, environmental DNA samples have been shown to encode many previously unknown classes of proteins and RNAs. Bioinformatics searches of genomic DNA from bacteria commonly identify new noncoding RNAs (ncRNAs) such as riboswitches. In rare instances, RNAs that exhibit more extensive sequence and structural conservation across a wide range of bacteria are encountered. Given that large structured RNAs are known to carry out complex biochemical functions such as protein synthesis and RNA processing reactions, identifying more RNAs of great size and intricate structure is likely to reveal additional biochemical functions that can be achieved by RNA. We applied an updated computational pipeline to discover ncRNAs that rival the known large ribozymes in size and structural complexity or that are among the most abundant RNAs in bacteria that encode them. These RNAs would have been difficult or impossible to detect without examining environmental DNA sequences, indicating that numerous RNAs with extraordinary size, structural complexity, or other exceptional characteristics remain to be discovered in unexplored sequence space.

  7. Proteomic Analysis of Hylocereus polyrhizus Reveals Metabolic Pathway Changes

    PubMed Central

    Hua, Qingzhu; Zhou, Qianjun; Gan, Susheng; Wu, Jingyu; Chen, Canbin; Li, Jiaqiang; Ye, Yaoxiong; Zhao, Jietang; Hu, Guibing; Qin, Yonghua

    2016-01-01

    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. PMID:27690004

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

    PubMed Central

    Ray, Ann; Kinch, Lisa N.; de Souza Santos, Marcela; Grishin, Nick V.

    2016-01-01

    ABSTRACT 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. PMID:27460800

  9. Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

    PubMed Central

    Dephoure, Noah; Hwang, Sunyoung; O'Sullivan, Ciara; Dodgson, Stacie E; Gygi, Steven P; Amon, Angelika; Torres, Eduardo M

    2014-01-01

    Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive oxygen species (ROS). Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains. Our results show that aneuploidy causes alterations in metabolism and redox homeostasis. Cells respond to these alterations through both transcriptional and posttranscriptional mechanisms. DOI: http://dx.doi.org/10.7554/eLife.03023.001 PMID:25073701

  10. Integrative network analysis reveals molecular mechanisms of blood pressure regulation

    PubMed Central

    Huan, Tianxiao; Meng, Qingying; Saleh, Mohamed A; Norlander, Allison E; Joehanes, Roby; Zhu, Jun; Chen, Brian H; Zhang, Bin; Johnson, Andrew D; Ying, Saixia; Courchesne, Paul; Raghavachari, Nalini; Wang, Richard; Liu, Poching; O'Donnell, Christopher J; Vasan, Ramachandran; Munson, Peter J; Madhur, Meena S; Harrison, David G; Yang, Xia; Levy, Daniel

    2015-01-01

    Genome-wide association studies (GWAS) have identified numerous loci associated with blood pressure (BP). The molecular mechanisms underlying BP regulation, however, remain unclear. We investigated BP-associated molecular mechanisms by integrating BP GWAS with whole blood mRNA expression profiles in 3,679 individuals, using network approaches. BP transcriptomic signatures at the single-gene and the coexpression network module levels were identified. Four coexpression modules were identified as potentially causal based on genetic inference because expression-related SNPs for their corresponding genes demonstrated enrichment for BP GWAS signals. Genes from the four modules were further projected onto predefined molecular interaction networks, revealing key drivers. Gene subnetworks entailing molecular interactions between key drivers and BP-related genes were uncovered. As proof-of-concept, we validated SH2B3, one of the top key drivers, using Sh2b3−/− mice. We found that a significant number of genes predicted to be regulated by SH2B3 in gene networks are perturbed in Sh2b3−/− mice, which demonstrate an exaggerated pressor response to angiotensin II infusion. Our findings may help to identify novel targets for the prevention or treatment of hypertension. PMID:25882670

  11. Genomic analysis reveals selection in Chinese native black pig

    PubMed Central

    Fu, Yuhua; Li, Cencen; Tang, Qianzi; Tian, Shilin; Jin, Long; Chen, Jianhai; Li, Mingzhou; Li, Changchun

    2016-01-01

    Identification of genomic signatures that help reveal mechanisms underlying desirable traits in domesticated pigs is of significant biological, agricultural and medical importance. To identify the genomic footprints left by selection during domestication of the Enshi black pig, a typical native and meat-lard breed in China, we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations. Combining this data with the available whole genomes of 13 Chinese wild boars, we identified 417 protein-coding genes embedded in the selected regions of Enshi black pigs. These genes are mainly involved in developmental and metabolic processes, response to stimulus, and other biological processes. Signatures of selection were detected in genes involved in body size and immunity (RPS10 and VASN), lipid metabolism (GSK3), male fertility (INSL6) and developmental processes (TBX19). These findings provide a window into the potential genetic mechanism underlying development of desirable phenotypes in Enshi black pigs during domestication and subsequent artificial selection. Thus, our results illustrate how domestication has shaped patterns of genetic variation in Enshi black pigs and provide valuable genetic resources that enable effective use of pigs in agricultural production. PMID:27808243

  12. Multiple etiologies for Alzheimer disease are revealed by segregation analysis

    SciTech Connect

    Rao, V.S.; Connor-Lacke, L.; Cupplies, L.A.; Growdon, J.H.; Farrer, L.A.; Duijn, C.M. van

    1994-11-01

    We have evaluated several transmission models for Alzheimer disease (AD), using the logistic regressive approach in 401 nuclear families of consecutively ascertained and rigorously diagnosed probands. Models postulating no major gene effect, random environmental transmission, recessive inheritance, and sporadic occurrence were rejected under varied assumptions regarding the associations among sex, age, and major gene susceptibility. Transmission of the disorder was not fully explained by a single Mendelian model for all families. Stratification of families as early- and late-onset by using the median of family mean onset ages showed that, regardless of the model studied, two groups of families fit better than a single group. AD in early-onset families is transmitted as an autosomal dominant trait with full penetrance in both sexes and has a gene frequency of 1.5%. Dominant inheritance also gave the best fit of the data in late-onset families, but this hypothesis was rejected, suggesting the presence of heterogeneity within this subset. Our study also revealed that genetically nonsusceptible males and females develop AD, indicating the presence of phenocopies within early-onset and late-onset groups. Moreover, our results suggest that the higher risk to females is not solely due to their increased longevity. 50 refs., 5 tabs.

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

    PubMed Central

    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. PMID:28337181

  14. Proteomic Analysis of Hylocereus polyrhizus Reveals Metabolic Pathway Changes.

    PubMed

    Hua, Qingzhu; Zhou, Qianjun; Gan, Susheng; Wu, Jingyu; Chen, Canbin; Li, Jiaqiang; Ye, Yaoxiong; Zhao, Jietang; Hu, Guibing; Qin, Yonghua

    2016-09-28

    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.

  15. Global Analysis of ATM Polymorphism Reveals Significant Functional Constraint

    PubMed Central

    Thorstenson, Yvonne R.; Shen, Peidong; Tusher, Virginia G.; Wayne, Tierney L.; Davis, Ronald W.; Chu, Gilbert; Oefner, Peter J.

    2001-01-01

    ATM, the gene that is mutated in ataxia-telangiectasia, is associated with cerebellar degeneration, abnormal proliferation of small blood vessels, and cancer. These clinically important manifestations have stimulated interest in defining the sequence variation in the ATM gene. Therefore, we undertook a comprehensive survey of sequence variation in ATM in diverse human populations. The protein-encoding exons of the gene (9,168 bp) and the adjacent intron and untranslated sequences (14,661 bp) were analyzed in 93 individuals from seven major human populations. In addition, the coding sequence was analyzed in one chimpanzee, one gorilla, one orangutan, and one Old World monkey. In human ATM, 88 variant sites were discovered by denaturing high-performance liquid chromatography, which is 96%–100% sensitive for detection of DNA sequence variation. ATM was compared to 14 other autosomal genes for nucleotide diversity. The noncoding regions of ATM had diversity values comparable to other genes, but the coding regions had very low diversity, especially in the last 29% of the protein sequence. A test of the neutral evolution hypothesis, through use of the Hudson/Kreitman/Aguadé statistic, revealed that this region of the human ATM gene was significantly constrained relative to that of the orangutan, the Old World monkey, and the mouse, but not relative to that of the chimpanzee or the gorilla. ATM displayed extensive linkage disequilibrium, consistent with suppression of meiotic recombination at this locus. Seven haplotypes were defined. Two haplotypes accounted for 82% of all chromosomes analyzed in all major populations; two others carrying the same D126E missense polymorphism accounted for 33% of chromosomes in Africa but were never observed outside of Africa. The high frequency of this polymorphism may be due either to a population expansion within Africa or to selective pressure. PMID:11443540

  16. Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes

    PubMed Central

    Liem, Michael; Fonseka, Pamali; Atukorala, Ishara; Ozcitti, Cemil; Mechler, Adam; Adda, Christopher G.; Ang, Ching-Seng; Mathivanan, Suresh

    2015-01-01

    Extracellular vesicles (EVs) include the exosomes (30-100 nm) that are produced through the endocytic pathway via the multivesicular bodies and the ectosomes (100-1000 nm) that are released through the budding of the plasma membrane. Despite the differences in the mode of biogenesis and size, reliable markers that can distinguish between exosomes and ectosomes are non-existent. Moreover, the precise functional differences between exosomes and ectosomes remains poorly characterised. Here, using label-free quantitative proteomics, we highlight proteins that could be exploited as markers to discriminate between exosomes and ectosomes. For the first time, a global proteogenomics analysis unveiled the secretion of mutant proteins that are implicated in cancer progression through tumor-derived EVs. Follow up integrated bioinformatics analysis highlighted the enrichment of oncogenic cargo in exosomes and ectosomes. Interestingly, exosomes induced significant cell proliferation and migration in recipient cells compared to ectosomes confirming the oncogenic nature of exosomes. These findings ascertain that cancer cells facilitate oncogenesis by the secretion of mutant and oncoproteins into the tumor microenvironment via exosomes and ectosomes. The integrative proteogenomics approach utilized in this study has the potential to identify disease biomarker candidates which can be later assayed in liquid biopsies obtained from cancer patients. PMID:25944692

  17. Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes.

    PubMed

    Keerthikumar, Shivakumar; Gangoda, Lahiru; Liem, Michael; Fonseka, Pamali; Atukorala, Ishara; Ozcitti, Cemil; Mechler, Adam; Adda, Christopher G; Ang, Ching-Seng; Mathivanan, Suresh

    2015-06-20

    Extracellular vesicles (EVs) include the exosomes (30-100 nm) that are produced through the endocytic pathway via the multivesicular bodies and the ectosomes (100-1000 nm) that are released through the budding of the plasma membrane. Despite the differences in the mode of biogenesis and size, reliable markers that can distinguish between exosomes and ectosomes are non-existent. Moreover, the precise functional differences between exosomes and ectosomes remains poorly characterised. Here, using label-free quantitative proteomics, we highlight proteins that could be exploited as markers to discriminate between exosomes and ectosomes. For the first time, a global proteogenomics analysis unveiled the secretion of mutant proteins that are implicated in cancer progression through tumor-derived EVs. Follow up integrated bioinformatics analysis highlighted the enrichment of oncogenic cargo in exosomes and ectosomes. Interestingly, exosomes induced significant cell proliferation and migration in recipient cells compared to ectosomes confirming the oncogenic nature of exosomes. These findings ascertain that cancer cells facilitate oncogenesis by the secretion of mutant and oncoproteins into the tumor microenvironment via exosomes and ectosomes. The integrative proteogenomics approach utilized in this study has the potential to identify disease biomarker candidates which can be later assayed in liquid biopsies obtained from cancer patients.

  18. Network analysis reveals potential markers for pediatric adrenocortical carcinoma

    PubMed Central

    Kulshrestha, Anurag; Suman, Shikha; Ranjan, Rakesh

    2016-01-01

    Pediatric adrenocortical carcinoma (ACC) is a rare malignancy with a poor outcome. Molecular mechanisms of pediatric ACC oncogenesis and advancement are not well understood. Accurate and timely diagnosis of the disease requires identification of new markers for pediatric ACC. Differentially expressed genes (DEGs) were identified from the gene expression profile of pediatric ACC and obtained from Gene Expression Omnibus. Gene Ontology functional and pathway enrichment analysis was implemented to recognize the functions of DEGs. A protein–protein interaction (PPI) and gene–gene functional interaction (GGI) network of DEGs was constructed. Hub gene detection and enrichment analysis of functional modules were performed. Furthermore, a gene regulatory network incorporating DEGs–microRNAs–transcription factors was constructed and analyzed. A total of 431 DEGs including 228 upregulated and 203 downregulated DEGs were screened. These genes were largely involved in cell cycle, steroid biosynthesis, and p53 signaling pathways. Upregulated genes, CDK1, CCNB1, CDC20, and BUB1B, were identified as the common hubs of PPI and GGI networks. All the four common hub genes were also part of modules of the PPI network. Moreover, all the four genes were also present in the largest module of GGI network. A gene regulatory network consisting of 82 microRNAs and 100 transcription factors was also constructed. CDK1, CCNB1, CDC20, and BUB1B may serve as potential biomarker of pediatric ACC and as potential targets for therapeutic approach, although experimental studies are required to authenticate our findings. PMID:27555782

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

    NASA Astrophysics Data System (ADS)

    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.

  20. Genomic analysis of regulatory network dynamics reveals large topological changes

    NASA Astrophysics Data System (ADS)

    Luscombe, Nicholas M.; Madan Babu, M.; Yu, Haiyuan; Snyder, Michael; Teichmann, Sarah A.; Gerstein, Mark

    2004-09-01

    Network analysis has been applied widely, providing a unifying language to describe disparate systems ranging from social interactions to power grids. It has recently been used in molecular biology, but so far the resulting networks have only been analysed statically. Here we present the dynamics of a biological network on a genomic scale, by integrating transcriptional regulatory information and gene-expression data for multiple conditions in Saccharomyces cerevisiae. We develop an approach for the statistical analysis of network dynamics, called SANDY, combining well-known global topological measures, local motifs and newly derived statistics. We uncover large changes in underlying network architecture that are unexpected given current viewpoints and random simulations. In response to diverse stimuli, transcription factors alter their interactions to varying degrees, thereby rewiring the network. A few transcription factors serve as permanent hubs, but most act transiently only during certain conditions. By studying sub-network structures, we show that environmental responses facilitate fast signal propagation (for example, with short regulatory cascades), whereas the cell cycle and sporulation direct temporal progression through multiple stages (for example, with highly inter-connected transcription factors). Indeed, to drive the latter processes forward, phase-specific transcription factors inter-regulate serially, and ubiquitously active transcription factors layer above them in a two-tiered hierarchy. We anticipate that many of the concepts presented here-particularly the large-scale topological changes and hub transience-will apply to other biological networks, including complex sub-systems in higher eukaryotes.

  1. Genomic analysis of regulatory network dynamics reveals large topological changes.

    PubMed

    Luscombe, Nicholas M; Babu, M Madan; Yu, Haiyuan; Snyder, Michael; Teichmann, Sarah A; Gerstein, Mark

    2004-09-16

    Network analysis has been applied widely, providing a unifying language to describe disparate systems ranging from social interactions to power grids. It has recently been used in molecular biology, but so far the resulting networks have only been analysed statically. Here we present the dynamics of a biological network on a genomic scale, by integrating transcriptional regulatory information and gene-expression data for multiple conditions in Saccharomyces cerevisiae. We develop an approach for the statistical analysis of network dynamics, called SANDY, combining well-known global topological measures, local motifs and newly derived statistics. We uncover large changes in underlying network architecture that are unexpected given current viewpoints and random simulations. In response to diverse stimuli, transcription factors alter their interactions to varying degrees, thereby rewiring the network. A few transcription factors serve as permanent hubs, but most act transiently only during certain conditions. By studying sub-network structures, we show that environmental responses facilitate fast signal propagation (for example, with short regulatory cascades), whereas the cell cycle and sporulation direct temporal progression through multiple stages (for example, with highly inter-connected transcription factors). Indeed, to drive the latter processes forward, phase-specific transcription factors inter-regulate serially, and ubiquitously active transcription factors layer above them in a two-tiered hierarchy. We anticipate that many of the concepts presented here--particularly the large-scale topological changes and hub transience--will apply to other biological networks, including complex sub-systems in higher eukaryotes.

  2. A secretomics analysis reveals major differences in the macrophage responses towards different types of carbon nanotubes.

    PubMed

    Palomäki, Jaana; Sund, Jukka; Vippola, Minnamari; Kinaret, Pia; Greco, Dario; Savolainen, Kai; Puustinen, Anne; Alenius, Harri

    2015-01-01

    Certain types of carbon nanotubes (CNT) can evoke inflammation, fibrosis and mesothelioma in vivo, raising concerns about their potential health effects. It has been recently postulated that NLRP3 inflammasome activation is important in the CNT-induced toxicity. However, more comprehensive studies of the protein secretion induced by CNT can provide new information about their possible pathogenic mechanisms. Here, we studied protein secretion from human macrophages with a proteomic approach in an unbiased way. Human monocyte-derived macrophages (MDM) were exposed to tangled or rigid, long multi-walled CNT (MWCNT) or crocidolite asbestos for 6 h. The growth media was concentrated and secreted proteins were analyzed using 2D-DIGE and DeCyder software. Subsequently, significantly up- or down-regulated protein spots were in-gel digested and identified with an LC-MS/MS approach. Bioinformatics analysis was performed to reveal the different patterns of protein secretion induced by these materials. The results show that both long rigid MWCNT and asbestos elicited ample and highly similar protein secretion. In contrast, exposure to long tangled MWCNT induced weaker protein secretion with a more distinct profile. Secretion of lysosomal proteins followed the exposure to all materials, suggesting lysosomal damage. However, only long rigid MWCNT was associated with apoptosis. This analysis suggests that the CNT toxicity in human MDM is mediated via vigorous secretion of inflammation-related proteins and apoptosis. This study provides new insights into the mechanisms of toxicity of high aspect ratio nanomaterials and indicates that not all types of CNT are as hazardous as asbestos fibers.

  3. Analysis of Discrete-Source Damage Progression in a Tensile Stiffened Composite Panel

    NASA Technical Reports Server (NTRS)

    Wang, John T.; Lotts, Christine G.; Sleight, David W.

    1999-01-01

    This paper demonstrates the progressive failure analysis capability in NASA Langley s COMET-AR finite element analysis code on a large-scale built-up composite structure. A large-scale five stringer composite panel with a 7-in. long discrete source damage was analyzed from initial loading to final failure including the geometric and material nonlinearities. Predictions using different mesh sizes, different saw cut modeling approaches, and different failure criteria were performed and assessed. All failure predictions have a reasonably good correlation with the test result.

  4. Failure mechanism analysis of electromigration dominated damage in TiSi2 nanowires

    NASA Astrophysics Data System (ADS)

    Zou, Chen-Xia; Xu, Jun; Zhang, Xin-Zheng; Song, Xue-Feng; Yu, Da-Peng

    2009-06-01

    Electromigration-induced damage has been an important concern in very large scale integrated circuit design for a long time and will be a major road block in the pursuit of nanoelectronics devices and next generation power electronics. In this letter, the failure mechanism analysis on two-terminal TiSi2 nanowire devices was reported. Electromigration dominant mass migration is observed and verified by energy dispersive spectroscopy. The contribution of thermomigration is discussed based on temperature simulation. This work provides useful reference for future devices and the failure analysis on nanostructures.

  5. Development of advanced structural analysis methodologies for predicting widespread fatigue damage in aircraft structures

    NASA Technical Reports Server (NTRS)

    Harris, Charles E.; Starnes, James H., Jr.; Newman, James C., Jr.

    1995-01-01

    NASA is developing a 'tool box' that includes a number of advanced structural analysis computer codes which, taken together, represent the comprehensive fracture mechanics capability required to predict the onset of widespread fatigue damage. These structural analysis tools have complementary and specialized capabilities ranging from a finite-element-based stress-analysis code for two- and three-dimensional built-up structures with cracks to a fatigue and fracture analysis code that uses stress-intensity factors and material-property data found in 'look-up' tables or from equations. NASA is conducting critical experiments necessary to verify the predictive capabilities of the codes, and these tests represent a first step in the technology-validation and industry-acceptance processes. NASA has established cooperative programs with aircraft manufacturers to facilitate the comprehensive transfer of this technology by making these advanced structural analysis codes available to industry.

  6. Progressive Damage Analysis of Laminated Composite (PDALC)-A Computational Model Implemented in the NASA COMET Finite Element Code

    NASA Technical Reports Server (NTRS)

    Lo, David C.; Coats, Timothy W.; Harris, Charles E.; Allen, David H.

    1996-01-01

    A method for analysis of progressive failure in the Computational Structural Mechanics Testbed is presented in this report. The relationship employed in this analysis describes the matrix crack damage and fiber fracture via kinematics-based volume-averaged variables. Damage accumulation during monotonic and cyclic loads is predicted by damage evolution laws for tensile load conditions. The implementation of this damage model required the development of two testbed processors. While this report concentrates on the theory and usage of these processors, a complete list of all testbed processors and inputs that are required for this analysis are included. Sample calculations for laminates subjected to monotonic and cyclic loads were performed to illustrate the damage accumulation, stress redistribution, and changes to the global response that occur during the load history. Residual strength predictions made with this information compared favorably with experimental measurements.

  7. Genome analysis of the platypus reveals unique signatures of evolution.

    PubMed

    Warren, Wesley C; Hillier, LaDeana W; Marshall Graves, Jennifer A; Birney, Ewan; Ponting, Chris P; Grützner, Frank; Belov, Katherine; Miller, Webb; Clarke, Laura; Chinwalla, Asif T; Yang, Shiaw-Pyng; Heger, Andreas; Locke, Devin P; Miethke, Pat; Waters, Paul D; Veyrunes, Frédéric; Fulton, Lucinda; Fulton, Bob; Graves, Tina; Wallis, John; Puente, Xose S; López-Otín, Carlos; Ordóñez, Gonzalo R; Eichler, Evan E; Chen, Lin; Cheng, Ze; Deakin, Janine E; Alsop, Amber; Thompson, Katherine; Kirby, Patrick; Papenfuss, Anthony T; Wakefield, Matthew J; Olender, Tsviya; Lancet, Doron; Huttley, Gavin A; Smit, Arian F A; Pask, Andrew; Temple-Smith, Peter; Batzer, Mark A; Walker, Jerilyn A; Konkel, Miriam K; Harris, Robert S; Whittington, Camilla M; Wong, Emily S W; Gemmell, Neil J; Buschiazzo, Emmanuel; Vargas Jentzsch, Iris M; Merkel, Angelika; Schmitz, Juergen; Zemann, Anja; Churakov, Gennady; Kriegs, Jan Ole; Brosius, Juergen; Murchison, Elizabeth P; Sachidanandam, Ravi; Smith, Carly; Hannon, Gregory J; Tsend-Ayush, Enkhjargal; McMillan, Daniel; Attenborough, Rosalind; Rens, Willem; Ferguson-Smith, Malcolm; Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R; Ray, David A; Kube, Michael; Reinhardt, Richard; Pringle, Thomas H; Taylor, James; Jones, Russell C; Nixon, Brett; Dacheux, Jean-Louis; Niwa, Hitoshi; Sekita, Yoko; Huang, Xiaoqiu; Stark, Alexander; Kheradpour, Pouya; Kellis, Manolis; Flicek, Paul; Chen, Yuan; Webber, Caleb; Hardison, Ross; Nelson, Joanne; Hallsworth-Pepin, Kym; Delehaunty, Kim; Markovic, Chris; Minx, Pat; Feng, Yucheng; Kremitzki, Colin; Mitreva, Makedonka; Glasscock, Jarret; Wylie, Todd; Wohldmann, Patricia; Thiru, Prathapan; Nhan, Michael N; Pohl, Craig S; Smith, Scott M; Hou, Shunfeng; Nefedov, Mikhail; de Jong, Pieter J; Renfree, Marilyn B; Mardis, Elaine R; Wilson, Richard K

    2008-05-08

    We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

  8. Image analysis of weaverbird nests reveals signature weave textures.

    PubMed

    Bailey, Ida E; Backes, André; Walsh, Patrick T; Morgan, Kate V; Meddle, Simone L; Healy, Susan D

    2015-06-01

    In nature, many animals build structures that can be readily measured at the scale of their gross morphology (e.g. length, volume and weight). Capturing individuality as can be done with the structures designed and built by human architects or artists, however, is more challenging. Here, we tested whether computer-aided image texture classification approaches can be used to describe textural variation in the nests of weaverbirds (Ploceus species) in order to attribute nests to the individual weaverbird that built them. We found that a computer-aided texture analysis approach does allow the assignment of a signature to weaverbirds' nests. We suggest that this approach will be a useful tool with which to examine individual variation across a range of animal constructions, not just for nests.

  9. Image analysis of weaverbird nests reveals signature weave textures

    PubMed Central

    Bailey, Ida E.; Backes, André; Walsh, Patrick T.; Morgan, Kate V.; Meddle, Simone L.; Healy, Susan D.

    2015-01-01

    In nature, many animals build structures that can be readily measured at the scale of their gross morphology (e.g. length, volume and weight). Capturing individuality as can be done with the structures designed and built by human architects or artists, however, is more challenging. Here, we tested whether computer-aided image texture classification approaches can be used to describe textural variation in the nests of weaverbirds (Ploceus species) in order to attribute nests to the individual weaverbird that built them. We found that a computer-aided texture analysis approach does allow the assignment of a signature to weaverbirds' nests. We suggest that this approach will be a useful tool with which to examine individual variation across a range of animal constructions, not just for nests. PMID:26543586

  10. Genome analysis of the platypus reveals unique signatures of evolution

    PubMed Central

    Warren, Wesley C.; Hillier, LaDeana W.; Marshall Graves, Jennifer A.; Birney, Ewan; Ponting, Chris P.; Grützner, Frank; Belov, Katherine; Miller, Webb; Clarke, Laura; Chinwalla, Asif T.; Yang, Shiaw-Pyng; Heger, Andreas; Locke, Devin P.; Miethke, Pat; Waters, Paul D.; Veyrunes, Frédéric; Fulton, Lucinda; Fulton, Bob; Graves, Tina; Wallis, John; Puente, Xose S.; López-Otín, Carlos; Ordóñez, Gonzalo R.; Eichler, Evan E.; Chen, Lin; Cheng, Ze; Deakin, Janine E.; Alsop, Amber; Thompson, Katherine; Kirby, Patrick; Papenfuss, Anthony T.; Wakefield, Matthew J.; Olender, Tsviya; Lancet, Doron; Huttley, Gavin A.; Smit, Arian F. A.; Pask, Andrew; Temple-Smith, Peter; Batzer, Mark A.; Walker, Jerilyn A.; Konkel, Miriam K.; Harris, Robert S.; Whittington, Camilla M.; Wong, Emily S. W.; Gemmell, Neil J.; Buschiazzo, Emmanuel; Vargas Jentzsch, Iris M.; Merkel, Angelika; Schmitz, Juergen; Zemann, Anja; Churakov, Gennady; Kriegs, Jan Ole; Brosius, Juergen; Murchison, Elizabeth P.; Sachidanandam, Ravi; Smith, Carly; Hannon, Gregory J.; Tsend-Ayush, Enkhjargal; McMillan, Daniel; Attenborough, Rosalind; Rens, Willem; Ferguson-Smith, Malcolm; Lefèvre, Christophe M.; Sharp, Julie A.; Nicholas, Kevin R.; Ray, David A.; Kube, Michael; Reinhardt, Richard; Pringle, Thomas H.; Taylor, James; Jones, Russell C.; Nixon, Brett; Dacheux, Jean-Louis; Niwa, Hitoshi; Sekita, Yoko; Huang, Xiaoqiu; Stark, Alexander; Kheradpour, Pouya; Kellis, Manolis; Flicek, Paul; Chen, Yuan; Webber, Caleb; Hardison, Ross; Nelson, Joanne; Hallsworth-Pepin, Kym; Delehaunty, Kim; Markovic, Chris; Minx, Pat; Feng, Yucheng; Kremitzki, Colin; Mitreva, Makedonka; Glasscock, Jarret; Wylie, Todd; Wohldmann, Patricia; Thiru, Prathapan; Nhan, Michael N.; Pohl, Craig S.; Smith, Scott M.; Hou, Shunfeng; Renfree, Marilyn B.; Mardis, Elaine R.; Wilson, Richard K.

    2009-01-01

    We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation. PMID:18464734

  11. Time-Frequency Analysis Reveals Pairwise Interactions in Insect Swarms

    NASA Astrophysics Data System (ADS)

    Puckett, James G.; Ni, Rui; Ouellette, Nicholas T.

    2015-06-01

    The macroscopic emergent behavior of social animal groups is a classic example of dynamical self-organization, and is thought to arise from the local interactions between individuals. Determining these interactions from empirical data sets of real animal groups, however, is challenging. Using multicamera imaging and tracking, we studied the motion of individual flying midges in laboratory mating swarms. By performing a time-frequency analysis of the midge trajectories, we show that the midge behavior can be segmented into two distinct modes: one that is independent and composed of low-frequency maneuvers, and one that consists of higher-frequency nearly harmonic oscillations conducted in synchrony with another midge. We characterize these pairwise interactions, and make a hypothesis as to their biological function.

  12. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

    PubMed Central

    Irie, Naoki; Kuratani, Shigeru

    2011-01-01

    One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates. PMID:21427719

  13. Kidney tumor biomarkers revealed by simultaneous multiple matrix metabolomics analysis.

    PubMed

    Ganti, Sheila; Taylor, Sandra L; Abu Aboud, Omran; Yang, Joy; Evans, Christopher; Osier, Michael V; Alexander, Danny C; Kim, Kyoungmi; Weiss, Robert H

    2012-07-15

    Metabolomics is increasingly being used in cancer biology for biomarker discovery and identification of potential novel therapeutic targets. However, a systematic metabolomics study of multiple biofluids to determine their interrelationships and to describe their use as tumor proxies is lacking. Using a mouse xenograft model of kidney cancer, characterized by subcapsular implantation of Caki-1 clear cell human kidney cancer cells, we examined tissue, serum, and urine all obtained simultaneously at baseline (urine) and at, or close to, animal sacrifice (urine, tissue, and plasma). Uniform metabolomics analysis of all three "matrices" was accomplished using gas chromatography- and liquid chromatography-mass spectrometry. Of all the metabolites identified (267 in tissue, 246 in serum, and 267 in urine), 89 were detected in all 3 matrices, and the majority was altered in the same direction. Heat maps of individual metabolites showed that alterations in serum were more closely related to tissue than was urine. Two metabolites, cinnamoylglycine and nicotinamide, were concordantly and significantly (when corrected for multiple testing) altered in tissue and serum, and cysteine-glutathione disulfide showed the highest change (232.4-fold in tissue) of any metabolite. On the basis of these and other considerations, three pathways were chosen for biologic validation of the metabolomic data, resulting in potential therapeutic target identification. These data show that serum metabolomics analysis is a more accurate proxy for tissue changes than urine and that tryptophan degradation (yielding anti-inflammatory metabolites) is highly represented in renal cell carcinoma, and support the concept that PPAR-α antagonism may be a potential therapeutic approach for this disease.

  14. Characterization of impact damage in composite laminates using guided wavefield imaging and local wavenumber domain analysis.

    PubMed

    Rogge, Matthew D; Leckey, Cara A C

    2013-09-01

    Delaminations in composite laminates resulting from impact events may be accompanied by minimal indication of damage at the surface. As such, inspections are required to ensure defects are within allowable limits. Conventional ultrasonic scanning techniques have been shown to effectively characterize the size and depth of delaminations but require physical contact with the structure and considerable setup time. Alternatively, a non-contact scanning laser vibrometer may be used to measure guided wave propagation in the laminate structure generated by permanently bonded transducers. A local Fourier domain analysis method is presented for processing guided wavefield data to estimate spatially dependent wavenumber values, which can be used to determine delamination depth. The technique is applied to simulated wavefields and results are analyzed to determine limitations of the technique with regards to determining defect size and depth. Based on simulation results, guidelines for application of the technique are developed. Finally, experimental wavefield data is obtained in quasi-isotropic carbon fiber reinforced polymer (CFRP) laminates with impact damage. The recorded wavefields are analyzed and wavenumber is measured to an accuracy of up to 8.5% in the region of shallow delaminations. These results show the promise of local wavenumber domain analysis to characterize the depth of delamination damage in composite laminates. The technique can find application in automated vehicle health assurance systems with potential for high detection rates and greatly reduced operator effort and setup time.

  15. Displacement damage analysis and modified electrical equivalent circuit for electron and photon-irradiated silicon solar cells

    NASA Astrophysics Data System (ADS)

    Arjhangmehr, Afshin; Feghhi, Seyed Amir Hossein

    2014-10-01

    Solar modules and arrays are the conventional energy resources of space satellites. Outside the earth's atmosphere, solar panels experience abnormal radiation environments and because of incident particles, photovoltaic (PV) parameters degrade. This article tries to analyze the electrical performance of electron and photon-irradiated mono-crystalline silicon (mono-Si) solar cells. PV cells are irradiated by mono-energetic electrons and poly-energetic photons and immediately characterized after the irradiation. The mean degradation of the maximum power (Pmax) of silicon solar cells is presented and correlated using the displacement damage dose (Dd) methodology. This method simplifies evaluation of cell performance in space radiation environments and produces a single characteristic curve for Pmax degradation. Furthermore, complete analysis of the results revealed that the open-circuit voltage (Voc) and the filling factor of mono-Si cells did not significantly change during the irradiation and were independent of the radiation type and fluence. Moreover, a new technique is developed that adapts the irradiation-induced effects in a single-cell equivalent electrical circuit and adjusts its elements. The "modified circuit" is capable of modeling the "radiation damage" in the electrical behavior of mono-Si solar cells and simplifies the designing of the compensation circuits.

  16. Proteomic and phosphoproteomic analysis of renal cortex in a salt-load rat model of advanced kidney damage

    PubMed Central

    Jiang, Shaoling; He, Hanchang; Tan, Lishan; Wang, Liangliang; Su, Zhengxiu; Liu, Yufeng; Zhu, Hongguo; Zhang, Menghuan; Hou, Fan Fan; Li, Aiqing

    2016-01-01

    Salt plays an essential role in the progression of chronic kidney disease and hypertension. However, the mechanisms underlying pathogenesis of salt-induced kidney damage remain largely unknown. Here, Sprague-Dawley rats, that underwent 5/6 nephrectomy (5/6Nx, a model of advanced kidney damage) or sham operation, were treated for 2 weeks with a normal or high-salt diet. We employed aTiO2 enrichment, iTRAQ labeling and liquid-chromatography tandem mass spectrometry strategy for proteomic and phosphoproteomic profiling of the renal cortex. We found 318 proteins differentially expressed in 5/6Nx group relative to sham group, and 310 proteins significantly changed in response to salt load in 5/6Nx animals. Totally, 1810 unique phosphopeptides corresponding to 550 phosphoproteins were identified. We identified 113 upregulated and 84 downregulated phosphopeptides in 5/6Nx animals relative to sham animals. Salt load induced 78 upregulated and 91 downregulated phosphopeptides in 5/6Nx rats. The differentially expressed phospholproteins are important transporters, structural molecules, and receptors. Protein-protein interaction analysis revealed that the differentially phosphorylated proteins in 5/6Nx group, Polr2a, Srrm1, Gsta2 and Pxn were the most linked. Salt-induced differential phosphoproteins, Myh6, Lmna and Des were the most linked. Altered phosphorylation levels of lamin A and phospholamban were validated. This study will provide new insight into pathogenetic mechanisms of chronic kidney disease and salt sensitivity. PMID:27775022

  17. Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis

    PubMed Central

    Cao, Mu-Shui; Liu, Bing-Ya; Dai, Wen-Tao; Zhou, Wei-Xin; Li, Yi-Xue; Li, Yuan-Yuan

    2015-01-01

    Gastric Carcinoma is one of the most common cancers in the world. A large number of differentially expressed genes have been identified as being associated with gastric cancer progression, however, little is known about the underlying regulatory mechanisms. To address this problem, we developed a differential networking approach that is characterized by including a nascent methodology, differential coexpression analysis (DCEA), and two novel quantitative methods for differential regulation analysis. We first applied DCEA to a gene expression dataset of gastric normal mucosa, adenoma and carcinoma samples to identify gene interconnection changes during cancer progression, based on which we inferred normal, adenoma, and carcinoma-specific gene regulation networks by using linear regression model. It was observed that cancer genes and drug targets were enriched in each network. To investigate the dynamic changes of gene regulation during carcinogenesis, we then designed two quantitative methods to prioritize differentially regulated genes (DRGs) and gene pairs or links (DRLs) between adjacent stages. It was found that known cancer genes and drug targets are significantly higher ranked. The top 4% normal vs. adenoma DRGs (36 genes) and top 6% adenoma vs. carcinoma DRGs (56 genes) proved to be worthy of further investigation to explore their association with gastric cancer. Out of the 16 DRGs involved in two top-10 DRG lists of normal vs. adenoma and adenoma vs. carcinoma comparisons, 15 have been reported to be gastric cancer or cancer related. Based on our inferred differential networking information and known signaling pathways, we generated testable hypotheses on the roles of GATA6, ESRRG and their signaling pathways in gastric carcinogenesis. Compared with established approaches which build genome-scale GRNs, or sub-networks around differentially expressed genes, the present one proved to be better at enriching cancer genes and drug targets, and prioritizing

  18. Modeling technical change in climate analysis: evidence from agricultural crop damages.

    PubMed

    Ahmed, Adeel; Devadason, Evelyn S; Al-Amin, Abul Quasem

    2017-03-29

    This study accounts for the Hicks neutral technical change in a calibrated model of climate analysis, to identify the optimum level of technical change for addressing climate changes. It demonstrates the reduction to crop damages, the costs to technical change, and the net gains for the adoption of technical change for a climate-sensitive Pakistan economy. The calibrated model assesses the net gains of technical change for the overall economy and at the agriculture-specific level. The study finds that the gains of technical change are overwhelmingly higher than the costs across the agriculture subsectors. The gains and costs following technical change differ substantially for different crops. More importantly, the study finds a cost-effective optimal level of technical change that potentially reduces crop damages to a minimum possible level. The study therefore contends that the climate policy for Pakistan should consider the role of technical change in addressing climate impacts on the agriculture sector.

  19. A Neural Network/Acoustic Emission Analysis of Impact Damaged Graphite/Epoxy Pressure Vessels

    NASA Technical Reports Server (NTRS)

    Walker, James L.; Hill, Erik v. K.; Workman, Gary L.; Russell, Samuel S.

    1995-01-01

    Acoustic emission (AE) signal analysis has been used to measure the effects of impact damage on burst pressure in 5.75 inch diameter, inert propellant filled, filament wound pressure vessels. The AE data were collected from fifteen graphite/epoxy pressure vessels featuring five damage states and three resin systems. A burst pressure prediction model was developed by correlating the AE amplitude (frequency) distribution, generated during the first pressure ramp to 800 psig (approximately 25% of the average expected burst pressure for an undamaged vessel) to known burst pressures using a four layered back propagation neural network. The neural network, trained on three vessels from each resin system, was able to predict burst pressures with a worst case error of 5.7% for the entire fifteen bottle set.

  20. [Applications of habitat equivalency analysis in ecological damage assessment of oil spill incident].

    PubMed

    Yang, Yin; Han, Da-xiong; Wang, Hai-yan

    2011-08-01

    Habitat equivalency analysis (HEA) is one of the methods commonly used by U.S. National Oceanic and Atmospheric Administration in natural resources damage assessment, but rarely applied in China. Based on the theory of HEA and the assessment practices of domestic oil spill incidents, a modification on the HEA was made in this paper, and applied to calculate the habitat value in oil spill incidents. According to the data collected from an oil spill incident in China, the modified HEA was applied in a case study to scale the compensatory-restoration. By introducing the ecological service equivalent factor to transfer various habitats, it was achieved to value of the injured habitats in ecological damage assessment of oil spill incident.

  1. An acoustic emission and acousto-ultrasonic analysis of impact damaged composite pressure vessels

    NASA Technical Reports Server (NTRS)

    Workman, Gary L. (Principal Investigator); Walker, James L.

    1996-01-01

    The use of acoustic emission to characterize impact damage in composite structures is being performed on composite bottles wrapped with graphite epoxy and kevlar bottles. Further development of the acoustic emission methodology will include neural net analysis and/or other multivariate techniques to enhance the capability of the technique to identify dominant failure mechanisms during fracture. The acousto-ultrasonics technique will also continue to be investigated to determine its ability to predict regions prone to failure prior to the burst tests. Characterization of the stress wave factor before, and after impact damage will be useful for inspection purposes in manufacturing processes. The combination of the two methods will also allow for simple nondestructive tests capable of predicting the performance of a composite structure prior to its being placed in service and during service.

  2. Phylogenetic analysis reveals a scattered distribution of autumn colours

    PubMed Central

    Archetti, Marco

    2009-01-01

    Background and Aims Leaf colour in autumn is rarely considered informative for taxonomy, but there is now growing interest in the evolution of autumn colours and different hypotheses are debated. Research efforts are hindered by the lack of basic information: the phylogenetic distribution of autumn colours. It is not known when and how autumn colours evolved. Methods Data are reported on the autumn colours of 2368 tree species belonging to 400 genera of the temperate regions of the world, and an analysis is made of their phylogenetic relationships in order to reconstruct the evolutionary origin of red and yellow in autumn leaves. Key Results Red autumn colours are present in at least 290 species (70 genera), and evolved independently at least 25 times. Yellow is present independently from red in at least 378 species (97 genera) and evolved at least 28 times. Conclusions The phylogenetic reconstruction suggests that autumn colours have been acquired and lost many times during evolution. This scattered distribution could be explained by hypotheses involving some kind of coevolutionary interaction or by hypotheses that rely on the need for photoprotection. PMID:19126636

  3. A graphical analysis revealed frailty deficits aggregate and are multidimensional

    PubMed Central

    Sourial, Nadia; Wolfson, Christina; Bergman, Howard; Zhu, Bin; Karunananthan, Sathya; Quail, Jacqueline; Fletcher, John; Weiss, Deborah; Bandeen-Roche, Karen; Béland, François

    2013-01-01

    Objective To examine the relationships among seven frailty domains: nutrition, physical activity, mobility, strength, energy, cognition, and mood, using data from three studies. Study Design and Setting Data from three studies were separately analyzed using Multiple Correspondence Analysis (MCA). The graphical output of MCA was used to assess 1) if the presence of deficits in the frailty domains separate from the absence of deficits on the graph, 2) the dimensionality of the domains, 3) the clustering of domains within each dimension and 4) their relationship with age, sex and disability. Results were compared across the studies. Results In two studies, presence of deficits for all domains separated from absence of deficits. In the third study, there was separation in all domains except cognition. Three main dimensions were retained in each study however assigned dimensionality of domains differed. The clustering of mobility with energy and/or strength was consistent across studies. Deficits were associated with older age, female sex and disability. Conclusion Our results suggest that frailty is a multidimensional concept for which the relationships among domains differ according to the population characteristics. These domains, with the possible exception of cognition, appear to aggregate together and share a common underlying construct. PMID:19880286

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

    PubMed

    Hall, David P; MacCormick, Ian J C; Phythian-Adams, Alex T; Rzechorzek, Nina M; Hope-Jones, David; Cosens, Sorrel; Jackson, Stewart; Bates, Matthew G D; Collier, David J; Hume, David A; Freeman, Thomas; Thompson, A A Roger; Baillie, John Kenneth

    2014-01-01

    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.

  5. Network Analysis Reveals Distinct Clinical Syndromes Underlying Acute Mountain Sickness

    PubMed Central

    Hall, David P.; MacCormick, Ian J. C.; Phythian-Adams, Alex T.; Rzechorzek, Nina M.; Hope-Jones, David; Cosens, Sorrel; Jackson, Stewart; Bates, Matthew G. D.; Collier, David J.; Hume, David A.; Freeman, Thomas; Thompson, A. A. Roger; Baillie, John Kenneth

    2014-01-01

    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. PMID:24465370

  6. Differential Network Analysis Reveals Genetic Effects on Catalepsy Modules

    PubMed Central

    Iancu, Ovidiu D.; Oberbeck, Denesa; Darakjian, Priscila; Kawane, Sunita; Erk, Jason; McWeeney, Shannon; Hitzemann, Robert

    2013-01-01

    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. PMID:23555609

  7. Bioimage analysis of Shigella infection reveals targeting of colonic crypts.

    PubMed

    Arena, Ellen T; Campbell-Valois, Francois-Xavier; Tinevez, Jean-Yves; Nigro, Giulia; Sachse, Martin; Moya-Nilges, Maryse; Nothelfer, Katharina; Marteyn, Benoit; Shorte, Spencer L; Sansonetti, Philippe J

    2015-06-23

    Few studies within the pathogenic field have used advanced imaging and analytical tools to quantitatively measure pathogenicity in vivo. In this work, we present a novel approach for the investigation of host-pathogen processes based on medium-throughput 3D fluorescence imaging. The guinea pig model for Shigella flexneri invasion of the colonic mucosa was used to monitor the infectious process over time with GFP-expressing S. flexneri. A precise quantitative imaging protocol was devised to follow individual S. flexneri in a large tissue volume. An extensive dataset of confocal images was obtained and processed to extract specific quantitative information regarding the progression of S. flexneri infection in an unbiased and exhaustive manner. Specific parameters included the analysis of S. flexneri positions relative to the epithelial surface, S. flexneri density within the tissue, and volume of tissue destruction. In particular, at early time points, there was a clear association of S. flexneri with crypts, key morphological features of the colonic mucosa. Numerical simulations based on random bacterial entry confirmed the bias of experimentally measured S. flexneri for early crypt targeting. The application of a correlative light and electron microscopy technique adapted for thick tissue samples further confirmed the location of S. flexneri within colonocytes at the mouth of crypts. This quantitative imaging approach is a novel means to examine host-pathogen systems in a tailored and robust manner, inclusive of the infectious agent.

  8. Consanguinity and late fertility: spatial analysis reveals positive association patterns.

    PubMed

    Lisa, Antonella; Astolfi, Paola; Zei, Gianna; Tentoni, Stefania

    2015-01-01

    The role of consanguinity on human complex traits is an important and controversial issue. In this work we focused on the Sardinian population and examined the effect of consanguineous unions on late female fertility. During the last century the island has been characterized by a high incidence of marriages between relatives, favoured by socio economic conditions and geographical isolation, and by high fertility despite a widespread tendency to delay reproduction. Through spatial analysis techniques, we explored the geographical heterogeneity of consanguinity and late fertility, and identified in Central-Eastern Sardinia a common area with an excess of both traits, where the traits are positively associated. We found that their association did not significantly affect women's fertility in the area, despite the expected negative role of both traits. Intriguingly, this critical zone corresponds well to areas reported by previous studies as being peculiar for a high frequency of centenarians and for lower risk in pregnancy outcome. The proposed approach can be generally exploited to identify target populations on which socioeconomic, biodemographic and genetic data can be collected at the individual level, and deeper analyses carried out to disentangle the determinants of complex biological traits and to investigate their association.

  9. Layered Social Network Analysis Reveals Complex Relationships in Kindergarteners

    PubMed Central

    Golemiec, Mireille; Schneider, Jonathan; Boyce, W. Thomas; Bush, Nicole R.; Adler, Nancy; Levine, Joel D.

    2016-01-01

    The interplay between individuals forms building blocks for social structure. Here, we examine the structure of behavioral interactions among kindergarten classroom with a hierarchy-neutral approach to examine all possible underlying patterns in the formation of layered networks of “reciprocal” interactions. To understand how these layers are coordinated, we used a layered motif approach. Our dual layered motif analysis can therefore be thought of as the dynamics of smaller groups that tile to create the group structure, or alternatively they provide information on what the average child would do in a given local social environment. When we examine the regulated motifs in layered networks, we find that transitivity is at least partially involved in the formation of these layered network structures. We also found complex combinations of the expected reciprocal interactions. The mechanisms used to understand social networks of kindergarten children here are also applicable on a more general scale to any group of individuals where interactions and identities can be readily observed and scored. PMID:26973572

  10. Quantifying clustered DNA damage induction and repair by gel electrophoresis, electronic imaging and number average length analysis

    NASA Technical Reports Server (NTRS)

    Sutherland, Betsy M.; Georgakilas, Alexandros G.; Bennett, Paula V.; Laval, Jacques; Sutherland, John C.; Gewirtz, A. M. (Principal Investigator)

    2003-01-01

    Assessing DNA damage induction, repair and consequences of such damages requires measurement of specific DNA lesions by methods that are independent of biological responses to such lesions. Lesions affecting one DNA strand (altered bases, abasic sites, single strand breaks (SSB)) as well as damages affecting both strands (clustered damages, double strand breaks) can be quantified by direct measurement of DNA using gel electrophoresis, gel imaging and number average length analysis. Damage frequencies as low as a few sites per gigabase pair (10(9)bp) can be quantified by this approach in about 50ng of non-radioactive DNA, and single molecule methods may allow such measurements in DNA from single cells. This review presents the theoretical basis, biochemical requirements and practical aspects of this approach, and shows examples of their applications in identification and quantitation of complex clustered damages.

  11. Functional Tissue Analysis Reveals Successful Cryopreservation of Human Osteoarthritic Synovium

    PubMed Central

    de Vries, Marieke; Bennink, Miranda B.; van Lent, Peter L. E. M.; van der Kraan, Peter M.; Koenders, Marije I.; Thurlings, Rogier M.; van de Loo, Fons A. J.

    2016-01-01

    Osteoarthritis (OA) is a degenerative joint disease affecting cartilage and is the most common form of arthritis worldwide. One third of OA patients have severe synovitis and less than 10% have no evidence of synovitis. Moreover, synovitis is predictive for more severe disease progression. This offers a target for therapy but more research on the pathophysiological processes in the synovial tissue of these patients is needed. Functional studies performed with synovial tissue will be more approachable when this material, that becomes available by joint replacement surgery, can be stored for later use. We set out to determine the consequences of slow-freezing of human OA synovial tissue. Therefore, we validated a method that can be applied in every routine laboratory and performed a comparative study of five cryoprotective agent (CPA) solutions. To determine possible deleterious cryopreservation-thaw effects on viability, the synovial tissue architecture, metabolic activity, RNA quality, expression of cryopreservation associated stress genes, and expression of OA characteristic disease genes was studied. Furthermore, the biological activity of the cryopreserved tissue was determined by measuring cytokine secretion induced by the TLR ligands lipopolysaccharides and Pam3Cys. Compared to non frozen synovium, no difference in cell and tissue morphology could be identified in the conditions using the CS10, standard and CryoSFM CPA solution for cryopreservation. However, we observed significantly lower preservation of tissue morphology with the Biofreeze and CS2 media. The other viability assays showed trends in the same direction but were not sensitive enough to detect significant differences between conditions. In all assays tested a clearly lower viability was detected in the condition in which synovium was frozen without CPA solution. This detailed analysis showed that OA synovial tissue explants can be cryopreserved while maintaining the morphology, viability and

  12. Neuronal Networks during Burst Suppression as Revealed by Source Analysis

    PubMed Central

    Reinicke, Christine; Moeller, Friederike; Anwar, Abdul Rauf; Mideksa, Kidist Gebremariam; Pressler, Ronit; Deuschl, Günther; Stephani, Ulrich; Siniatchkin, Michael

    2015-01-01

    Introduction Burst-suppression (BS) is an electroencephalography (EEG) pattern consisting of alternant periods of slow waves of high amplitude (burst) and periods of so called flat EEG (suppression). It is generally associated with coma of various etiologies (hypoxia, drug-related intoxication, hypothermia, and childhood encephalopathies, but also anesthesia). Animal studies suggest that both the cortex and the thalamus are involved in the generation of BS. However, very little is known about mechanisms of BS in humans. The aim of this study was to identify the neuronal network underlying both burst and suppression phases using source reconstruction and analysis of functional and effective connectivity in EEG. Material/Methods Dynamic imaging of coherent sources (DICS) was applied to EEG segments of 13 neonates and infants with burst and suppression EEG pattern. The brain area with the strongest power in the analyzed frequency (1–4 Hz) range was defined as the reference region. DICS was used to compute the coherence between this reference region and the entire brain. The renormalized partial directed coherence (RPDC) was used to describe the informational flow between the identified sources. Results/Conclusion Delta activity during the burst phases was associated with coherent sources in the thalamus and brainstem as well as bilateral sources in cortical regions mainly frontal and parietal, whereas suppression phases were associated with coherent sources only in cortical regions. Results of the RPDC analyses showed an upwards informational flow from the brainstem towards the thalamus and from the thalamus to cortical regions, which was absent during the suppression phases. These findings may support the theory that a “cortical deafferentiation” between the cortex and sub-cortical structures exists especially in suppression phases compared to burst phases in burst suppression EEGs. Such a deafferentiation may play a role in the poor neurological outcome of

  13. Network analysis reveals multiscale controls on streamwater chemistry

    USGS Publications Warehouse

    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.

  14. Conformational diversity analysis reveals three functional mechanisms in proteins

    PubMed Central

    Fornasari, María Silvina

    2017-01-01

    Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call “rigid” (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions. PMID:28192432

  15. Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

    NASA Astrophysics Data System (ADS)

    Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2014-12-01

    Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine

  16. Mutant Analysis Reveals Allosteric Regulation of ClpB Disaggregase

    PubMed Central

    Franke, Kamila B.; Bukau, Bernd; Mogk, Axel

    2017-01-01

    The members of the hexameric AAA+ disaggregase of E. coli and S. cerevisiae, ClpB, and Hsp104, cooperate with the Hsp70 chaperone system in the solubilization of aggregated proteins. Aggregate solubilization relies on a substrate threading activity of ClpB/Hsp104 fueled by ATP hydrolysis in both ATPase rings (AAA-1, AAA-2). ClpB/Hsp104 ATPase activity is controlled by the M-domains, which associate to the AAA-1 ring to downregulate ATP hydrolysis. Keeping M-domains displaced from the AAA-1 ring by association with Hsp70 increases ATPase activity due to enhanced communication between protomers. This communication involves conserved arginine fingers. The control of ClpB/Hsp104 activity is crucial, as hyperactive mutants with permanently dissociated M-domains exhibit cellular toxicity. Here, we analyzed AAA-1 inter-ring communication in relation to the M-domain mediated ATPase regulation, by subjecting a conserved residue of the AAA-1 domain subunit interface of ClpB (A328) to mutational analysis. While all A328X mutants have reduced disaggregation activities, their ATPase activities strongly differed. ClpB-A328I/L mutants have reduced ATPase activity and when combined with the hyperactive ClpB-K476C M-domain mutation, suppress cellular toxicity. This underlines that ClpB ATPase activation by M-domain dissociation relies on increased subunit communication. The ClpB-A328V mutant in contrast has very high ATPase activity and exhibits cellular toxicity on its own, qualifying it as novel hyperactive ClpB mutant. ClpB-A328V hyperactivity is however, different from that of M-domain mutants as M-domains stay associated with the AAA-1 ring. The high ATPase activity of ClpB-A328V primarily relies on the AAA-2 ring and correlates with distinct conformational changes in the AAA-2 catalytic site. These findings characterize the subunit interface residue A328 as crucial regulatory element to control ATP hydrolysis in both AAA rings. PMID:28275610

  17. Mutant Analysis Reveals Allosteric Regulation of ClpB Disaggregase.

    PubMed

    Franke, Kamila B; Bukau, Bernd; Mogk, Axel

    2017-01-01

    The members of the hexameric AAA+ disaggregase of E. coli and S. cerevisiae, ClpB, and Hsp104, cooperate with the Hsp70 chaperone system in the solubilization of aggregated proteins. Aggregate solubilization relies on a substrate threading activity of ClpB/Hsp104 fueled by ATP hydrolysis in both ATPase rings (AAA-1, AAA-2). ClpB/Hsp104 ATPase activity is controlled by the M-domains, which associate to the AAA-1 ring to downregulate ATP hydrolysis. Keeping M-domains displaced from the AAA-1 ring by association with Hsp70 increases ATPase activity due to enhanced communication between protomers. This communication involves conserved arginine fingers. The control of ClpB/Hsp104 activity is crucial, as hyperactive mutants with permanently dissociated M-domains exhibit cellular toxicity. Here, we analyzed AAA-1 inter-ring communication in relation to the M-domain mediated ATPase regulation, by subjecting a conserved residue of the AAA-1 domain subunit interface of ClpB (A328) to mutational analysis. While all A328X mutants have reduced disaggregation activities, their ATPase activities strongly differed. ClpB-A328I/L mutants have reduced ATPase activity and when combined with the hyperactive ClpB-K476C M-domain mutation, suppress cellular toxicity. This underlines that ClpB ATPase activation by M-domain dissociation relies on increased subunit communication. The ClpB-A328V mutant in contrast has very high ATPase activity and exhibits cellular toxicity on its own, qualifying it as novel hyperactive ClpB mutant. ClpB-A328V hyperactivity is however, different from that of M-domain mutants as M-domains stay associated with the AAA-1 ring. The high ATPase activity of ClpB-A328V primarily relies on the AAA-2 ring and correlates with distinct conformational changes in the AAA-2 catalytic site. These findings characterize the subunit interface residue A328 as crucial regulatory element to control ATP hydrolysis in both AAA rings.

  18. Multi scale analysis by acoustic emission of damage mechanisms in natural fibre woven fabrics/epoxy composites.

    NASA Astrophysics Data System (ADS)

    Bonnafous, C.; Touchard, F.; Chocinski-Arnault, L.

    2010-06-01

    This paper proposes to develop an experimental program to characterize the type and the development of damage in composite with complex microstructure. A multi-scale analysis by acoustic emission has been developed and applied to hemp fibre woven fabrics/epoxy composite. The experimental program consists of tensile tests performed on single yarn, neat epoxy resin and composite materials to identify their AE amplitude signatures. A statistical analysis of AE amplitude signals has been realised and correlated with microscopic observations. Results have enabled to identify three types of damage in composites and their associated AE amplitudes: matrix cracking, interfacial debonding and reinforcement damage and fracture. Tracking of these damage mechanisms in hemp/epoxy composites has been performed to show the process of damage development in natural fibre reinforced composites.

  19. Visualization of co-localization in Aβ42-administered neuroblastoma cells reveals lysosome damage and autophagosome accumulation related to cell death.

    PubMed

    Soura, Violetta; Stewart-Parker, Maris; Williams, Thomas L; Ratnayaka, Arjuna; Atherton, Joe; Gorringe, Kirsti; Tuffin, Jack; Darwent, Elisabeth; Rambaran, Roma; Klein, William; Lacor, Pascale; Staras, Kevin; Thorpe, Julian; Serpell, Louise C

    2012-01-15

    Aβ42 [amyloid-β peptide-(1-42)] plays a central role in Alzheimer's disease and is known to have a detrimental effect on neuronal cell function and survival when assembled into an oligomeric form. In the present study we show that administration of freshly prepared Aβ42 oligomers to a neuroblastoma (SH-SY5Y) cell line results in a reduction in survival, and that Aβ42 enters the cells prior to cell death. Immunoconfocal and immunogold electron microscopy reveal the path of the Aβ42 with time through the endosomal system and shows that it accumulates in lysosomes. A 24 h incubation with Aβ results in cells that have damaged lysosomes showing signs of enzyme leakage, accumulate autophagic vacuoles and exhibit severely disrupted nuclei. Endogenous Aβ is evident in the cells and the results of the present study suggest that the addition of Aβ oligomers disrupts a crucial balance in Aβ conformation and concentration inside neuronal cells, resulting in catastrophic effects on cellular function and, ultimately, in cell death.

  20. Gastric Tissue Damage Analysis Generated by Ischemia: Bioimpedance, Confocal Endomicroscopy, and Light Microscopy

    PubMed Central

    Beltran, Nohra E.; Garcia, Laura E.; Garcia-Lorenzana, Mario

    2013-01-01

    The gastric mucosa ischemic tissular damage plays an important role in critical care patients' outcome, because it is the first damaged tissue by compensatory mechanism during shock. The aim of the study is to relate bioimpedance changes with tissular damage level generated by ischemia by means of confocal endomicroscopy and light microscopy. Bioimpedance of the gastric mucosa and confocal images were obtained from Wistar male rats during basal and ischemia conditions. They were anesthetized, and stain was applied (fluorescein and/or acriflavine). The impedance spectroscopy catheter was inserted and then confocal endomicroscopy probe. After basal measurements and biopsy, hepatic and gastric arteries clamping induced ischemia. Finally, pyloric antrum tissue was preserved in buffered formaldehyde (10%) for histology processing using light microscopy. Confocal images were equalized, binarized, and boundary defined, and infiltrations were quantified. Impedance and infiltrations increased with ischemia showing significant changes between basal and ischemia conditions (P < 0.01). Light microscopy analysis allows detection of general alterations in cellular and tissular integrity, confirming gastric reactance and confocal images quantification increments obtained during ischemia. PMID:23841094

  1. Damage detection and quantification in a structural model under seismic excitation using time-frequency analysis

    NASA Astrophysics Data System (ADS)

    Chan, Chun-Kai; Loh, Chin-Hsiung; Wu, Tzu-Hsiu

    2015-04-01

    In civil engineering, health monitoring and damage detection are typically carry out by using a large amount of sensors. Typically, most methods require global measurements to extract the properties of the structure. However, some sensors, like LVDT, cannot be used due to in situ limitation so that the global deformation remains unknown. An experiment is used to demonstrate the proposed algorithms: a one-story 2-bay reinforce concrete frame under weak and strong seismic excitation. In this paper signal processing techniques and nonlinear identification are used and applied to the response measurements of seismic response of reinforced concrete structures subject to different level of earthquake excitations. Both modal-based and signal-based system identification and feature extraction techniques are used to study the nonlinear inelastic response of RC frame using both input and output response data or output only measurement. From the signal-based damage identification method, which include the enhancement of time-frequency analysis of acceleration responses and the estimation of permanent deformation using directly from acceleration response data. Finally, local deformation measurement from dense optical tractor is also use to quantify the damage of the RC frame structure.

  2. Genome wide analysis of Silurana (Xenopus) tropicalis development reveals dynamic expression using network enrichment analysis.

    PubMed

    Langlois, Valérie S; Martyniuk, Christopher J

    2013-01-01

    Development involves precise timing of gene expression and coordinated pathways for organogenesis and morphogenesis. Functional and sub-network enrichment analysis provides an integrated approach for identifying networks underlying development. The objectives of this study were to characterize early gene regulatory networks over Silurana tropicalis development from NF stage 2 to 46 using a custom Agilent 4×44K microarray. There were >8000 unique gene probes that were differentially expressed between Nieuwkoop-Faber (NF) stage 2 and stage 16, and >2000 gene probes differentially expressed between NF 34 and 46. Gene ontology revealed that genes involved in nucleosome assembly, cell division, pattern specification, neurotransmission, and general metabolism were increasingly regulated throughout development, consistent with active development. Sub-network enrichment analysis revealed that processes such as membrane hyperpolarisation, retinoic acid, cholesterol, and dopamine metabolic gene networks were activated/inhibited over time. This study identifies RNA transcripts that are potentially maternally inherited in an anuran species, provides evidence that the expression of genes involved in retinoic acid receptor signaling may increase prior to those involved in thyroid receptor signaling, and characterizes novel gene expression networks preceding organogenesis which increases understanding of the spatiotemporal embryonic development in frogs.

  3. Transcriptomic Analysis of Carboxylic Acid Challenge in Escherichia coli: Beyond Membrane Damage

    PubMed Central

    Royce, Liam A.; Boggess, Erin; Fu, Yao; Liu, Ping; Shanks, Jacqueline V.; Dickerson, Julie; Jarboe, Laura R.

    2014-01-01

    Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0 to probe mechanisms of toxicity. This analysis highlights the intracellular acidification and membrane damage caused by C8 challenge. Network component analysis identified transcription factors with altered activity including GadE, the activator of the glutamate-dependent acid resistance system (AR2) and Lrp, the amino acid biosynthesis regulator. The intracellular acidification was quantified during exogenous challenge, but was not observed in a carboxylic acid producing strain, though this may be due to lower titers than those used in our exogenous challenge studies. We developed a framework for predicting the proton motive force during adaptation to strong inorganic acids and carboxylic acids. This model predicts that inorganic acid challenge is mitigated by cation accumulation, but that carboxylic acid challenge inverts the proton motive force and requires anion accumulation. Utilization of native acid resistance systems was not useful in terms of supporting growth or alleviating intracellular acidification. AR2 was found to be non-functional, possibly due to membrane damage. We proposed that interaction of Lrp and C8 resulted in repression of amino acid biosynthesis. However, this hypothesis was not supported by perturbation of lrp expression or amino acid supplementation. E. coli strains were also engineered for altered cyclopropane fatty acid content in the membrane, which had a dramatic effect on membrane properties, though C8 tolerance was not increased. We conclude that achieving higher production titers requires circumventing the membrane damage. As higher titers are achieved, acidification may become problematic. PMID:24586888

  4. Time-frequency vibration analysis for the detection of motor damages caused by bearing currents

    NASA Astrophysics Data System (ADS)

    Prudhom, Aurelien; Antonino-Daviu, Jose; Razik, Hubert; Climente-Alarcon, Vicente

    2017-02-01

    Motor failure due to bearing currents is an issue that has drawn an increasing industrial interest over recent years. Bearing currents usually appear in motors operated by variable frequency drives (VFD); these drives may lead to common voltage modes which cause currents induced in the motor shaft that are discharged through the bearings. The presence of these currents may lead to the motor bearing failure only few months after system startup. Vibration monitoring is one of the most common ways for detecting bearing damages caused by circulating currents; the evaluation of the amplitudes of well-known characteristic components in the vibration Fourier spectrum that are associated with race, ball or cage defects enables to evaluate the bearing condition and, hence, to identify an eventual damage due to bearing currents. However, the inherent constraints of the Fourier transform may complicate the detection of the progressive bearing degradation; for instance, in some cases, other frequency components may mask or be confused with bearing defect-related while, in other cases, the analysis may not be suitable due to the eventual non-stationary nature of the captured vibration signals. Moreover, the fact that this analysis implies to lose the time-dimension limits the amount of information obtained from this technique. This work proposes the use of time-frequency (T-F) transforms to analyse vibration data in motors affected by bearing currents. The experimental results obtained in real machines show that the vibration analysis via T-F tools may provide significant advantages for the detection of bearing current damages; among other, these techniques enable to visualise the progressive degradation of the bearing while providing an effective discrimination versus other components that are not related with the fault. Moreover, their application is valid regardless of the operation regime of the machine. Both factors confirm the robustness and reliability of these tools

  5. DNA Damage Analysis in Children with Non-syndromic Developmental Delay by Comet Assay

    PubMed Central

    Chand, Parkash; Ballambattu, Vishnu Bhat; Hanumanthappa, Nandeesha; Veeramani, Raveendranath

    2016-01-01

    Introduction Majority of the developmental delays in children are non-syndromic and they are believed to have an underlying DNA damage, though not well substantiated. Hence the present study was carried out to find out if there is any increased DNA damage in children with non-syndromic developmental delay by using the comet assay. Aim The present case-control study was undertaken to assess the level of DNA damage in children with non syndromic developmental delay and compare the same with that of age and sex matched controls using submarine gel electrophoresis (Comet Assay). Materials and Methods The blood from clinically diagnosed children with non syndromic developmental delay and controls were subjected for alkaline version of comet assay – Single cell gel electrophoresis using lymphocytes isolated from the peripheral blood. The comets were observed under a bright field microscope; photocaptured and scored using the Image J image quantification software. Comet parameters were compared between the cases and controls and statistical analysis and interpretation of results was done using the statistical software SPSS version 20. Results The mean comet tail length in cases and control was 20.77+7.659μm and 08.97+4.398μm respectively which was statistically significant (p<0.001). Other comet parameters like total comet length and % DNA in tail also showed a statistically significant difference (p < 0.001) between cases and controls. Conclusion The current investigation unraveled increased levels of DNA damage in children with non syndromic developmental delay when compared to the controls. PMID:27437200

  6. Full-Length High-Temperature Severe Fuel Damage Test No. 5: Final safety analysis

    SciTech Connect

    Lanning, D.D.; Lombardo, N.J.; Panisko, F.E.

    1993-09-01

    This report presents the final safety analysis for the preparation, conduct, and post-test discharge operation for the Full-Length High Temperature Experiment-5 (FLHT-5) to be conducted in the L-24 position of the National Research Universal (NRU) Reactor at Chalk River Nuclear Laboratories (CRNL), Ontario, Canada. The test is sponsored by an international group organized by the US Nuclear Regulatory Commission. The test is designed and conducted by staff from Pacific Northwest Laboratory with CRNL staff support. The test will study the consequences of loss-of-coolant and the progression of severe fuel damage.

  7. The Comet-FISH assay for the analysis of DNA damage and repair.

    PubMed

    Spivak, Graciela

    2010-01-01

    In this chapter, I describe the alkaline single-cell gel electrophoresis (Comet assay) combined with fluorescence in situ hybridization (FISH) technology, used in our laboratory, to study the incidence and repair of lesions induced in human cells by ultraviolet light. The Comet-FISH method permits the simultaneous and comparative analysis of DNA damage and its repair throughout the genome and in defined chromosomal regions. This very sensitive approach can be applied to any lesion, such as those induced by chemical carcinogens and products of cellular metabolism that can be converted to DNA single- or double-strand breaks. The unique advantages and limitations of the method for particular applications are discussed.

  8. Oxidative Damage Induced by Arsenic in Mice or Rats: A Systematic Review and Meta-Analysis.

    PubMed

    Xu, Mengchuan; Rui, Dongsheng; Yan, Yizhong; Xu, Shangzhi; Niu, Qiang; Feng, Gangling; Wang, Yan; Li, Shugang; Jing, Mingxia

    2017-03-01

    In this meta-analysis, studies reporting arsenic-induced oxidative damage in mouse models were systematically evaluated to provide a scientific understanding of oxidative stress mechanisms associated with arsenic poisoning. Fifty-eight relevant peer-reviewed publications were identified through exhaustive database searching. Oxidative stress indexes assessed included superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), glutathione peroxidase (GPx), glutathione-s-transferase (GST), glutathione reductase (GR), oxidized glutathione (GSSG), malondialdehyde (MDA), and reactive oxygen species (ROS). Our meta-analysis showed that arsenic exposure generally suppressed measured levels of the antioxidants, SOD, CAT, GSH, GPx, GST, and GR, but increased levels of the oxidants, GSSG, MDA, and ROS. Arsenic valence was important and GR and MDA levels increased to a significantly (P < 0.05) greater extent upon exposure to As(3+) than to As(5+). Other factors that contributed to a greater overall oxidative effect from arsenic exposure included intervention time, intervention method, dosage, age of animals, and the sample source from which the indexes were estimated. Our meta-analysis effectively summarized a wide range of studies and detected a positive relationship between arsenic exposure and oxidative damage. These data provide a scientific basis for the prevention and treatment of arsenic poisoning.

  9. Analysis of core damage frequency: Peach Bottom, Unit 2 internal events appendices

    SciTech Connect

    Kolaczkowski, A.M.; Cramond, W.R.; Sype, T.T.; Maloney, K.J.; Wheeler, T.A.; Daniel, S.L.; Sandia National Labs., Albuquerque, NM )

    1989-08-01

    This document contains the appendices for the accident sequence analysis of internally initiated events for the Peach Bottom, Unit 2 Nuclear Power Plant. This is one of the five plant analyses conducted as part of the NUREG-1150 effort for the Nuclear Regulatory Commission. The work performed and described here is an extensive reanalysis of that published in October 1986 as NUREG/CR-4550, Volume 4. It addresses comments from numerous reviewers and significant changes to the plant systems and procedures made since the first report. The uncertainty analysis and presentation of results are also much improved, and considerable effort was expended on an improved analysis of loss of offsite power. The content and detail of this report is directed toward PRA practitioners who need to know how the work was done and the details for use in further studies. The mean core damage frequency is 4.5E-6 with 5% and 95% uncertainty bounds of 3.5E-7 and 1.3E-5, respectively. Station blackout type accidents (loss of all ac power) contributed about 46% of the core damage frequency with Anticipated Transient Without Scram (ATWS) accidents contributing another 42%. The numerical results are driven by loss of offsite power, transients with the power conversion system initially available operator errors, and mechanical failure to scram. 13 refs., 345 figs., 171 tabs.

  10. Damage Tolerance Analysis of Space Shuttle External Tank Lug Fillet Welds Using NASGRO

    NASA Technical Reports Server (NTRS)

    Allen, Phillip A.

    2006-01-01

    The damage tolerance of the External Tank (ET) lug welds were reassessed because of an increase in the loads due to the removal of the protuberance air load (PAT.,) ramp. The analysis methods included detailed finite element analysis (FEA) of the ET welded lugs and FEA of the lug weld test configuration. The FEA results were used as input to the crack growth analysis code NASGRO to calculate the mission life capability of the ET lug welds and to predict the number of cycles to failure in the lug weld testing. The presentation presents the method of transferring the FEM results to the NASGRO model and gives correlations between FEM and NASGRO stress intensity calculations.

  11. Full-Scale Test and Analysis of a PRSEUS Fuselage Panel to Assess Damage-Containment Features

    NASA Technical Reports Server (NTRS)

    Bergan, Andrew; Bakuckas, John G.; Lovejoy, Andrew E.; Jegley, Dawn C.; Linton, Kim A.; Korkosz, Gregory; Awerbuch, Jonathan; Tan, Tein-Min

    2011-01-01

    Stitched composite technology has the potential to substantially decrease structural weight through enhanced damage containment capabilities. The most recent generation of stitched composite technology, the Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) concept, has been shown to successfully arrest damage at the sub-component level through tension testing of a three stringer panel with damage in the form of a two-bay notch. In a joint effort undertaken by the National Aeronautics and Space Administration (NASA), the Federal Aviation Administration (FAA), and the Boeing Company, further studies are being conducted to characterize the damage containment features of the PRSEUS concept. A full-scale residual strength test will be performed on a fuselage panel to determine if the load capacity will meet strength, deformation, and damage tolerance requirements. A curved panel was designed, fabricated, and prepared for residual strength testing. A pre-test Finite Element Model (FEM) was developed using design allowables from previous test programs to predict test panel deformation characteristics and margins of safety. Three phases of testing with increasing damage severity include: (1) as manufactured; (2) barely visible impact damage (BVID) and visible impact damage (VID); and (3) discrete source damage (DSD) where the panel will be loaded to catastrophic failure. This paper presents the background information, test plan, and experimental procedure. This paper is the first of several future articles reporting the test preparations, results, and analysis conducted in the test program.

  12. Damage analysis of CFRP-confined circular concrete-filled steel tubular columns by acoustic emission techniques

    NASA Astrophysics Data System (ADS)

    Li, Dongsheng; Chen, Zhi; Feng, Quanming; Wang, Yanlei

    2015-08-01

    Damage properties of carbon fiber-reinforced polymer (CFRP) confined circular concrete-filled steel tubular (CCFT) columns were analyzed through acoustic emission (AE) signals. AE characteristic parameters were obtained through axial compression tests. The severity of damage to CFRP-CCFT columns was estimated using the growing trend of AE accumulated energy as basis. The bearing capacity of CFRP-CCFT columns and AE accumulated energy improved as CFRP layers increased. The damage process was studied using a number of crucial AE parameters. The cracks’ mode can be differentiated through the ratio of the rise time to the waveform amplitude and through average frequency analysis. With the use of intensity signal analysis, the damage process of the CFRP-CCFT columns can be classified into three levels that represent different degrees. Based on b-value analysis, the development of the obtained cracks can be defined. Thus, identifying an initial yielding and providing early warning is possible.

  13. Analysis of Individual Molecular Events of DNA Damage Response by Flow and Image Assisted Cytometry

    PubMed Central

    Darzynkiewicz, Zbigniew; Traganos, Frank; Zhao, Hong; Halicka, H. Dorota; Skommer, Joanna; Wlodkowic, Donald

    2010-01-01

    This chapter describes molecular mechanisms of DNA damage response (DDR) and presents flow- and image-assisted cytometric approaches to assess these mechanisms and measure the extent of DDR in individual cells. DNA damage was induced by cell treatment with oxidizing agents, UV light, DNA topoisomerase I or II inhibitors, cisplatin, tobacco smoke, and by exogenous and endogenous oxidants. Chromatin relaxation (decondensation) is an early event of DDR chromatin that involves modification of high mobility group proteins (HMGs) and histone H1 and was detected by cytometry by analysis of the susceptibility of DNA in situ to denaturation using the metachromatic fluorochrome acridine orange. Translocation of the MRN complex consisting of Meiotic Recombination 11 Homolog A (Mre11), Rad50 homolog and Nijmegen Breakage Syndrome 1 (NMR1) into DNA damage sites was assessed by laser scanning cytometry as the increase in the intensity of maximal pixel as well as integral value of Mre11 immunofluorescence. Examples of cytometric detection of activation of Ataxia telangiectasia mutated (ATM), and Check 2 (Chk2) protein kinases using phospho-specific Abs targeting Ser1981 and Thr68 of these proteins, respectively are also presented. We also discuss approaches to correlate activation of ATM and Chk2 with phosphorylation of p53 on Ser15 and histone H2AX on Ser139 as well as with cell cycle position and DNA replication. The capability of laser scanning cytometry to quantify individual foci of phosphorylated H2AX and/or ATM that provides more dependable assessment of the presence of DNA double-strand breaks is outlined. The new microfluidic Lab-on-a-Chip platforms for interrogation of individual cells offer a novel approach for DDR cytometric analysis. PMID:21722802

  14. Micromechanics Fatigue Damage Analysis Modeling for Fabric Reinforced Ceramic Matrix Composites

    NASA Technical Reports Server (NTRS)

    Min, J. B.; Xue, D.; Shi, Y.

    2013-01-01

    A micromechanics analysis modeling method was developed to analyze the damage progression and fatigue failure of fabric reinforced composite structures, especially for the brittle ceramic matrix material composites. A repeating unit cell concept of fabric reinforced composites was used to represent the global composite structure. The thermal and mechanical properties of the repeating unit cell were considered as the same as those of the global composite structure. The three-phase micromechanics, the shear-lag, and the continuum fracture mechanics models were integrated with a statistical model in the repeating unit cell to predict the progressive damages and fatigue life of the composite structures. The global structure failure was defined as the loss of loading capability of the repeating unit cell, which depends on the stiffness reduction due to material slice failures and nonlinear material properties in the repeating unit cell. The present methodology is demonstrated with the analysis results evaluated through the experimental test performed with carbon fiber reinforced silicon carbide matrix plain weave composite specimens.

  15. Stress analysis and damage evaluation of flawed composite laminates by hybrid-numerical methods

    NASA Technical Reports Server (NTRS)

    Yang, Yii-Ching

    1992-01-01

    Structural components in flight vehicles is often inherited flaws, such as microcracks, voids, holes, and delamination. These defects will degrade structures the same as that due to damages in service, such as impact, corrosion, and erosion. It is very important to know how a structural component can be useful and survive after these flaws and damages. To understand the behavior and limitation of these structural components researchers usually do experimental tests or theoretical analyses on structures with simulated flaws. However, neither approach has been completely successful. As Durelli states that 'Seldom does one method give a complete solution, with the most efficiency'. Examples of this principle is seen in photomechanics which additional strain-gage testing can only average stresses at locations of high concentration. On the other hand, theoretical analyses including numerical analyses are implemented with simplified assumptions which may not reflect actual boundary conditions. Hybrid-Numerical methods which combine photomechanics and numerical analysis have been used to correct this inefficiency since 1950's. But its application is limited until 1970's when modern computer codes became available. In recent years, researchers have enhanced the data obtained from photoelasticity, laser speckle, holography and moire' interferometry for input of finite element analysis on metals. Nevertheless, there is only few of literature being done on composite laminates. Therefore, this research is dedicated to this highly anisotropic material.

  16. Finite Elements Analysis of a Composite Semi-Span Test Article With and Without Discrete Damage

    NASA Technical Reports Server (NTRS)

    Lovejoy, Andrew E.; Jegley, Dawn C. (Technical Monitor)

    2000-01-01

    AS&M Inc. performed finite element analysis, with and without discrete damage, of a composite semi-span test article that represents the Boeing 220-passenger transport aircraft composite semi-span test article. A NASTRAN bulk data file and drawings of the test mount fixtures and semi-span components were utilized to generate the baseline finite element model. In this model, the stringer blades are represented by shell elements, and the stringer flanges are combined with the skin. Numerous modeling modifications and discrete source damage scenarios were applied to the test article model throughout the course of the study. This report details the analysis method and results obtained from the composite semi-span study. Analyses were carried out for three load cases: Braked Roll, LOG Down-Bending and 2.5G Up-Bending. These analyses included linear and nonlinear static response, as well as linear and nonlinear buckling response. Results are presented in the form of stress and strain plots. factors of safety for failed elements, buckling loads and modes, deflection prediction tables and plots, and strainage prediction tables and plots. The collected results are presented within this report for comparison to test results.

  17. Testing and Analysis of a Composite Non-Cylindrical Aircraft Fuselage Structure . Part II; Severe Damage

    NASA Technical Reports Server (NTRS)

    Przekop, Adam; Jegley, Dawn C.; Lovejoy, Andrew E.; Rouse, Marshall; Wu, Hsi-Yung T.

    2016-01-01

    The Environmentally Responsible Aviation Project aimed to develop aircraft technologies enabling significant fuel burn and community noise reductions. Small incremental changes to the conventional metallic alloy-based 'tube and wing' configuration were not sufficient to achieve the desired metrics. One airframe concept identified by the project as having the potential to dramatically improve aircraft performance was a composite-based hybrid wing body configuration. Such a concept, however, presented inherent challenges stemming from, among other factors, the necessity to transfer wing loads through the entire center fuselage section which accommodates a pressurized cabin confined by flat or nearly flat panels. This paper discusses a finite element analysis and the testing of a large-scale hybrid wing body center section structure developed and constructed to demonstrate that the Pultruded Rod Stitched Efficient Unitized Structure concept can meet these challenging demands of the next generation airframes. Part II of the paper considers the final test to failure of the test article in the presence of an intentionally inflicted severe discrete source damage under the wing up-bending loading condition. Finite element analysis results are compared with measurements acquired during the test and demonstrate that the hybrid wing body test article was able to redistribute and support the required design loads in a severely damaged condition.

  18. Seismic damage analysis of the outlet piers of arch dams using the finite element sub-model method

    NASA Astrophysics Data System (ADS)

    Song, Liangfeng; Wu, Mingxin; Wang, Jinting; Xu, Yanjie

    2016-09-01

    This study aims to analyze seismic damage of reinforced outlet piers of arch dams by the nonlinear finite element (FE) sub-model method. First, the dam-foundation system is modeled and analyzed, in which the effects of infinite foundation, contraction joints, and nonlinear concrete are taken into account. The detailed structures of the outlet pier are then simulated with a refined FE model in the sub-model analysis. In this way the damage mechanism of the plain (unreinforced) outlet pier is analyzed, and the effects of two reinforcement measures (i.e., post-tensioned anchor cables and reinforcing bar) on the dynamic damage to the outlet pier are investigated comprehensively. Results show that the plain pier is damaged severely by strong earthquakes while implementation of post-tensioned anchor cables strengthens the pier effectively. In addition, radiation damping strongly alleviates seismic damage to the piers.

  19. Advanced Durability and Damage Tolerance Design and Analysis Methods for Composite Structures: Lessons Learned from NASA Technology Development Programs

    NASA Technical Reports Server (NTRS)

    Harris, Charles E.; Starnes, James H., Jr.; Shuart, Mark J.

    2003-01-01

    Aerospace vehicles are designed to be durable and damage tolerant. Durability is largely an economic life-cycle design consideration whereas damage tolerance directly addresses the structural airworthiness (safety) of the vehicle. However, both durability and damage tolerance design methodologies must address the deleterious effects of changes in material properties and the initiation and growth of microstructural damage that may occur during the service lifetime of the vehicle. Durability and damage tolerance design and certification requirements are addressed for commercial transport aircraft and NASA manned spacecraft systems. The state-of-the-art in advanced design and analysis methods is illustrated by discussing the results of several recently completed NASA technology development programs. These programs include the NASA Advanced Subsonic Technology Program demonstrating technologies for large transport aircraft and the X-33 hypersonic test vehicle demonstrating technologies for a single-stage-to-orbit space launch vehicle.

  20. Microtexture Analysis and Modeling of Ambient Fatigue and Creep-Fatigue Damages in Ti-6Al-4V Alloy

    NASA Astrophysics Data System (ADS)

    Kumar, Jalaj; Singh, A. K.; Raman, S. Ganesh Sundara; Kumar, Vikas

    2017-02-01

    In the present investigation, microtexture analysis using electron back-scattered diffraction technique has been performed to study fatigue- and creep-fatigue damages and associated deformation structures in Ti-6Al-4V alloy. Special emphasis has been given to low-angle grain boundary configuration and its possible application as a damage indicator. Damage is mostly present in the form of voids as investigated through scanning electron microscopy. Stored deformation energies have been evaluated for the strain-controlled fatigue-, the stress-controlled fatigue-, and the creep-fatigue-tested samples. Stored deformation energies have also been analyzed vis-à-vis total damage energies to quantify the contribution of damages to various samples. A relation between the stored deformation energy and the applied strain amplitude has been proposed in this study.

  1. Advances in Structural Integrity Analysis Methods for Aging Metallic Airframe Structures with Local Damage

    NASA Technical Reports Server (NTRS)

    Starnes, James H., Jr.; Newman, James C., Jr.; Harris, Charles E.; Piascik, Robert S.; Young, Richard D.; Rose, Cheryl A.

    2003-01-01

    Analysis methodologies for predicting fatigue-crack growth from rivet holes in panels subjected to cyclic loads and for predicting the residual strength of aluminum fuselage structures with cracks and subjected to combined internal pressure and mechanical loads are described. The fatigue-crack growth analysis methodology is based on small-crack theory and a plasticity induced crack-closure model, and the effect of a corrosive environment on crack-growth rate is included. The residual strength analysis methodology is based on the critical crack-tip-opening-angle fracture criterion that characterizes the fracture behavior of a material of interest, and a geometric and material nonlinear finite element shell analysis code that performs the structural analysis of the fuselage structure of interest. The methodologies have been verified experimentally for structures ranging from laboratory coupons to full-scale structural components. Analytical and experimental results based on these methodologies are described and compared for laboratory coupons and flat panels, small-scale pressurized shells, and full-scale curved stiffened panels. The residual strength analysis methodology is sufficiently general to include the effects of multiple-site damage on structural behavior.

  2. Microstructural analysis of MTR fuel plates damaged by a coolant flow blockage

    NASA Astrophysics Data System (ADS)

    Leenaers, A.; Joppen, F.; Van den Berghe, S.

    2009-10-01

    In 1975, as a result of a blockage of the coolant inlet flow, two plates of a fuel element of the BR2 reactor of the Belgian Nuclear Research Centre (SCK•CEN) were partially melted. The fuel element consisted of Al-clad plates with 90% 235U enriched UAl x fuel dispersed in an Al matrix. The element had accumulated a burn up of 21% 235U before it was removed from the reactor. Recently, the damaged fuel plates were sent to the hot laboratory for detailed PIE. Microstructural changes and associated temperature markers were used to identify several stages in the progression to fuel melting. It was found that the temperature in the center of the fuel plate had increased above 900-950 °C before the reactor was scrammed. In view of the limited availability of such datasets, the results of this microstructural analysis provide valuable input in the analysis of accident scenarios for research reactors.

  3. Evaluation of skin damage caused by percutaneous absorption enhancers using fractal analysis.

    PubMed

    Obata, Y; Sesumi, T; Takayama, K; Isowa, K; Grosh, S; Wick, S; Sitz, R; Nagai, T

    2000-04-01

    Fractal analysis of the cross-sectional morphology of rat skin was conducted to evaluate pathologic changes evoked by percutaneous absorption enhancers. Male hairless rats (WBN/Ht-ILA), 8 weeks old, weighing 160 to 180 g were used. Under anesthetization, glass cells (10-mm inner diameter) were attached to the rats' abdomens, and test solutions containing various mixtures of the percutaneous absorption enhancers, sodium lauryl sulfate, isopropanol, 2-methyl-1-butanol, and sodium myristate were applied. Six hours after application, the solutions were removed and the abdominal skin was excised. Skin cross sections were analyzed with a charge-coupled device (CCD) camera. Image data taken by the CCD camera were fed into a desktop digital computer; then the fractal dimension of each skin cross section was determined on the basis of the box-counting algorithm. A pathologic study was also performed on the skin treated with the test solution. All sections of skin were examined with an optical photo microscope. Pathologic findings were classified into five levels. The total irritation score (TIS) was defined as the summation of damage levels in all regions. Only with the administration of hydrogel containing 2-methyl-1-butanol or sodium lauryl sulfate were positive values of TIS observed. However, the TIS values were independent of the concentration of these components. The most severe skin damage was evoked by application of sodium lauryl sulfate. Noticeable skin damage was also seen with 2-methyl-1-butanol. No irritation to the skin resulted from treatment with isopropanol or sodium myristate. When test solution containing sodium lauryl sulfate was applied to the skin, a remarkable increment in fractal dimensions was noted. This may suggest that the structure of the skin was greatly compromised as a result of sodium lauryl sulfate application. Although no change in fractal dimension was observed as a result of application of the test solution containing only 25

  4. Lost ecosystem services as a measure of oil spill damages: a conceptual analysis of the importance of baselines.

    PubMed

    Kennedy, Chris J; Cheong, So-Min

    2013-10-15

    The assessment and quantification of damages resulting from marine oil spills is typically coordinated by NOAA, and has historically utilized Habitat Equivalency Analysis (HEA) to estimate damages. Resource economists and others have called for the damage assessment process to instead estimate injuries through the valuation of lost ecosystem services. Our conceptual analysis explores ecosystem service valuation from the perspective of "baselines," which are a fundamental component of both primary and compensatory restoration activities. In practice, baselines have been defined in ecological terms, with minimal consideration of the socioeconomic side of ecosystem service provision. We argue that, for the purposes of scaling compensatory restoration, it is more appropriate to characterize baselines in value terms, thereby integrating non-market valuation approaches from the onset of the damage assessment process. Benefits and challenges of this approach are discussed, along with guidelines for practitioners to identify circumstances in which socioeconomic variables are likely to be important for baseline characterization.

  5. Failure Analysis of Discrete Damaged Tailored Extension-Shear-Coupled Stiffened Composite Panels

    NASA Technical Reports Server (NTRS)

    Baker, Donald J.

    2005-01-01

    The results of an analytical and experimental investigation of the failure of composite is tiffener panels with extension-shear coupling are presented. This tailored concept, when used in the cover skins of a tiltrotor aircraft wing has the potential for increasing the aeroelastic stability margins and improving the aircraft productivity. The extension-shear coupling is achieved by using unbalanced 45 plies in the skin. The failure analysis of two tailored panel configurations that have the center stringer and adjacent skin severed is presented. Finite element analysis of the damaged panels was conducted using STAGS (STructural Analysis of General Shells) general purpose finite element program that includes a progressive failure capability for laminated composite structures that is based on point-stress analysis, traditional failure criteria, and ply discounting for material degradation. The progressive failure predicted the path of the failure and maximum load capability. There is less than 12 percent difference between the predicted failure load and experimental failure load. There is a good match of the panel stiffness and strength between the progressive failure analysis and the experimental results. The results indicate that the tailored concept would be feasible to use in the wing skin of a tiltrotor aircraft.

  6. Integrative proteome analysis of Brachypodium distachyon roots and leaves reveals a synergetic responsive network under H2O2 stress.

    PubMed

    Bian, Yan-Wei; Lv, Dong-Wen; Cheng, Zhi-Wei; Gu, Ai-Qin; Cao, Hui; Yan, Yue-Ming

    2015-10-14

    The plant oxidative stress response is vital for defense against various abiotic and biotic stresses. In this study, ultrastructural changes and the proteomic response to H2O2 stress in roots and leaves of the model plant Brachypodium distachyon were studied. Transmission electron microscopy (TEM) showed that the ultrastructural damage in roots was more serious than in leaves. Particularly, the ultrastructures of organelles and the nucleus in root tip cells were damaged, leading to the inhibition of normal biological activities of roots, which then spread throughout the plant. Based on two-dimensional electrophoresis (2-DE) and MALDI-TOF/TOF-MS, 84 and 53 differentially accumulated protein (DAP) spots representing 75 and 45 unique proteins responsive to H2O2 stress in roots and leaves, respectively, were identified. These protein species were mainly involved in signal transduction, energy metabolism, redox homeostasis/stress defense, protein folding/degradation, and cell wall/cell structure. Interestingly, two 14-3-3 proteins (GF14-B and GF14-D) were identified as DAPs in both roots and leaves. Protein-protein interaction (PPI) analysis revealed a synergetic H2O2-responsive network.

  7. Damage detection method for wind turbine blades based on dynamics analysis and mode shape difference curvature information

    NASA Astrophysics Data System (ADS)

    Wang, Yanfeng; Liang, Ming; Xiang, Jiawei

    2014-10-01

    Blades are among the key components of wind turbines. Blade damage is one of the most common types of structural defects and can cause catastrophic structural failure. Therefore, it is highly desirable to detect and diagnose blade damage as early as possible. In this paper, we propose a method for blade damage detection and diagnosis. This method incorporates finite element method (FEM) for dynamics analysis (modal analysis and response analysis) and the mode shape difference curvature (MSDC) information for damage detection/diagnosis. Finite element models of wind turbine blades have been built and modified via frequency comparison with experimental data and the formula for the model updating technique. Our numerical simulation results have demonstrated that the proposed technique can detect the spatial locations of damages for wind turbine blades. Changes in natural frequencies and modes for smaller size blades with damage are found to occur at lower frequencies and lower modes than in the larger sized blade case. The relationship between modal parameters and damage information (location, size) is very complicated especially for larger size blades. Moreover, structure and dynamic characters for larger size blades are different from those for smaller sized blades. Therefore, dynamic response analysis for a larger sized wind turbine blade with a multi-layer composite material based on aerodynamic loads’ (including lift forces and drag forces) calculation has been carried out and improved the efficiency and precision to damage detection by combining (MSDC) information. This method provides a low cost and efficient non-destructive tool for wind turbine blade condition monitoring.

  8. Treatment and Analysis of a Paint Chip from "Water Lilies": A Fire Damaged Monet

    NASA Technical Reports Server (NTRS)

    Miller, Sharon K. R.; Banks, Bruce A.; Tollis, Greg

    2001-01-01

    A museum fire in 1958 severely damaged a Monet 'Water Lilies' (1916-1926) painting that was on display. The surface of the painting is very dark with areas of blistering and charring. Over the years, traditional techniques have been found to be ineffective at removal of the soot and char from the surface. The painting, which is now in the care of the New York University (NYU) Conservation Center of the Institute of Fine Arts, was the subject of a study to determine if atomic oxygen treatment could remove the soot and char without damaging the fragile painting underneath. For test purposes, a small chip of paint was removed from the edge of the painting by a conservator at NYU and supplied to NASA Glenn Research Center for atomic oxygen treatment and analysis. The diffuse spectral reflectance, at three locations on the paint chip, was monitored at intervals during the atomic oxygen treatment process. Photo documentation of the chip during treatment was also performed. The color contrast was calculated from the spectral reflectance data as a function of treatment duration. Results of the testing indicated that the contrast improved as a result of the treatment, and the differentiation of colors on the surface was significantly improved. Soot and char could be removed without visibly affecting the gross surface features such as impasto areas. These results indicate the feasibility for the treatment of the 'Water Lilies' painting.

  9. Fourier spectral-based modal curvature analysis and its application to damage detection in beams

    NASA Astrophysics Data System (ADS)

    Yang, Zhi-Bo; Radzienski, Maciej; Kudela, Pawel; Ostachowicz, Wieslaw

    2017-02-01

    In this paper, a simple Fourier spectral-based method is proposed to calculate the modal curvature (MC) of beams instead of the traditional central difference method. Based on the present method, damages in beam-like structures are localized. The present method provides an alternative selection to estimate MC in damage detection. There are two advantages of the present method. Firstly, the spectral calculation of spatial derivatives is conducted globally, which provides the suppression for noise. In addition, signal processing in the wavenumber domain provides an alternative choice for spatial filtering for mode shapes. Secondly, the proposed method provides a precise estimation of the MC which is related to original definition. With the absence of numerical derivative, the estimated results can be more stable and robust. Statistical analysis is conducted to show the effectiveness and noise immunity of the proposed method. In order to obtain the better identification, the MC calculated by the proposed method is employed as the input of continuous wavelet transform, and then the hybrid method is generated. The validations of the present method and comparison with the traditional central difference method are numerically and experimentally demonstrated.

  10. Analysis of Beam-Induced Damage to the SLC Positron Production Target

    SciTech Connect

    Bharadwaj, Vinod

    2002-08-20

    The nominal Next Linear Collider (NLC) positron production design is based on extrapolation of the existing SLAC Linear Collider (SLC) positron production system. Given that the SLC positron production target failed during a run, it is necessary to analyze the beam-induced damage to the target in order to validate the extrapolations on which the NLC target is based. The failed SLC target and its associated housing were sent to existing ''hot-cell'' facilities at LANL for analysis. The target material, a tungsten-rhenium ''puck'', was removed from the housing and photographed and x-rayed. Leak-checking on the cooling system was performed. Sections were then removed from the target to determine the extent of internal damage to the material. High resolution photographs were taken and extensive hardness tests were performed on the irradiated and non-irradiated areas of the target material. The results of these analyses and conclusions applicable to the NLC target design are presented in this paper.

  11. Spectrophotometric analysis of flavonoid-DNA interactions and DNA damaging/protecting and cytotoxic potential of flavonoids in human peripheral blood lymphocytes.

    PubMed

    Rusak, Gordana; Piantanida, Ivo; Masić, Lozika; Kapuralin, Katarina; Durgo, Ksenija; Kopjar, Nevenka

    2010-10-06

    The ability of luteolin, kaempferol and apigenin to bind to calf thymus (ct)-DNA, mode of action and stability of flavonoids in buffer were investigated. Spectrophotometric analysis revealed a rapid degradation of apigenin in an aqueous medium, while kaempferol and luteolin were stable for 24h upon dissolution in water. Spectrophotometric study of the interactions of kaempferol and luteolin with calf thymus DNA suggests classic intercalation as their dominant binding mode to DNA. Cytotoxicity/genotoxicity and cytoprotective/genoprotective effects of flavonoids in non-stressed and hydrogen peroxide stressed human peripheral lymphocytes were investigated using the fluorescent dye exclusion method and alkaline comet assay. Flavonoids revealed significant genoprotective effects in hydrogen peroxide stressed cells and in cells submitted to longer incubation in the cell culture medium. Luteolin, followed by apigenin and kaempferol, was shown to be the most effective in protecting DNA from oxidative damage induced by hydrogen peroxide. However, the investigated flavonoids also induced DNA damage, indicating their prooxidative capacity. The balance between the protection of DNA from oxidative damage and prooxidative effects was strongly dependent on flavonoid concentration and the incubation period.

  12. USAF Damage Tolerant Design Handbook: Guidelines for the Analysis and Design of Damage Tolerant Aircraft Structures. Revision B

    DTIC Science & Technology

    1984-05-01

    Applied Mechanics, Vol. 24 (1957), p. 109. 3. I. N. Sneddon and M. Lowengrub, Crack Problems in the Classical Theory of Elasticity, New York: John ... Wilhem , "Fracture Mechanics Guidelines for Aircraft Structural Applications," AFFDL-TR-69-111, Feb. 1970. 20. A. P. Parker, The Mechanics of Fracture and...Toughness, ASTM STP 514, (1972), pp. 1-20. 99. Verette, R., and Wilhem , D. P., "Development & Evaluation of Methods of Plane Stress Fracture Analysis

  13. Development of synthetic velocity - depth damage curves using a Weighted Monte Carlo method and Logistic Regression analysis

    NASA Astrophysics Data System (ADS)

    Vozinaki, Anthi Eirini K.; Karatzas, George P.; Sibetheros, Ioannis A.; Varouchakis, Emmanouil A.

    2014-05-01

    Damage curves are the most significant component of the flood loss estimation models. Their development is quite complex. Two types of damage curves exist, historical and synthetic curves. Historical curves are developed from historical loss data from actual flood events. However, due to the scarcity of historical data, synthetic damage curves can be alternatively developed. Synthetic curves rely on the analysis of expected damage under certain hypothetical flooding conditions. A synthetic approach was developed and presented in this work for the development of damage curves, which are subsequently used as the basic input to a flood loss estimation model. A questionnaire-based survey took place among practicing and research agronomists, in order to generate rural loss data based on the responders' loss estimates, for several flood condition scenarios. In addition, a similar questionnaire-based survey took place among building experts, i.e. civil engineers and architects, in order to generate loss data for the urban sector. By answering the questionnaire, the experts were in essence expressing their opinion on how damage to various crop types or building types is related to a range of values of flood inundation parameters, such as floodwater depth and velocity. However, the loss data compiled from the completed questionnaires were not sufficient for the construction of workable damage curves; to overcome this problem, a Weighted Monte Carlo method was implemented, in order to generate extra synthetic datasets with statistical properties identical to those of the questionnaire-based data. The data generated by the Weighted Monte Carlo method were processed via Logistic Regression techniques in order to develop accurate logistic damage curves for the rural and the urban sectors. A Python-based code was developed, which combines the Weighted Monte Carlo method and the Logistic Regression analysis into a single code (WMCLR Python code). Each WMCLR code execution

  14. Damage analysis and fundamental studies. Quarterly progress report, April-June 1980

    SciTech Connect

    Not Available

    1980-08-01

    The DAFS program element is a national effort composed of contributions from a number of National Laboratories and other government laboratories, universities, and industrial laboratories. It was organized by the Materials and Radiation Effects Branch, Office of Fusion Energy, DOE, and a Task Group on Damage Analysis and Fundamental Studies which operates under the auspices of that Branch. The purpose of this series of reports is to provide a working technical record of that effort for the use of the program participants, for the fusion energy program in general, and for the Department of Energy. This report is organized along topical lines in parallel to a Program Plan of the same title so that activities and accomplishments may be followed readily, relative to that Program Plan.

  15. Damage analysis and fundamental studies. Quarterly progress report, January-March 1980

    SciTech Connect

    Not Available

    1980-05-01

    The DAFS program element is a national effort composed of contributions from a number of National Laboratories and other government laboratories, universities, and industrial laboratories. It was organized by the Materials and Radiation Effects Branch, Office of Fusion Energy, DOE, and a Task Group on Damage Analysis and Fundamental Studies which operates under the auspices of that Branch. The purpose of this series of reports is to provide a working technical record of that effort for the use of the program participants, for the fusion energy program in general, and for the Department of Energy. This report is organized along topical lines in parallel to a Program Plan of the same title so that activities and accomplishments may be followed readily, relative to that Program Plan. Thus, the work of a given laboratory may appear throughout the report. The Table of Contents is annotated for the convenience of the reader.

  16. Structural damage detection in an aeronautical panel using analysis of variance

    NASA Astrophysics Data System (ADS)

    Gonsalez, Camila Gianini; da Silva, Samuel; Brennan, Michael J.; Lopes Junior, Vicente

    2015-02-01

    This paper describes a procedure for structural health assessment based on one-way analysis of variance (ANOVA) together with Tukey's multiple comparison test, to determine whether the results are statistically significant. The feature indices are obtained from electromechanical impedance measurements using piezoceramic sensor/actuator patches bonded to the structure. Compared to the classical approach based on a simple change of the observed signals, using for example root mean square responses, the decision procedure in this paper involves a rigorous statistical test. Experimental tests were carried out on an aeronautical panel in the laboratory to validate the approach. In order to include uncontrolled variability in the dynamic responses, the measurements were taken over several days in different environmental conditions using all eight sensor/actuator patches. The damage was simulated by controlling the tightness and looseness of the bolts and was correctly diagnosed. The paper discusses the strengths and weakness of the approach in light of the experimental results.

  17. Biomechanics Analysis of Pressure Ulcer Using Damaged Interface Model between Bone and Muscle in the Human Buttock

    NASA Astrophysics Data System (ADS)

    Slamet, Samuel Susanto; Takano, Naoki; Tanabe, Yoshiyuki; Hatano, Asako; Nagasao, Tomohisa

    This paper aims at building up a computational procedure to study the bio-mechanism of pressure ulcer using the finite element method. Pressure ulcer is a disease that occurs in the human body after 2 hours of continuous external force. In the very early stage of pressure ulcer, it is found that the tissues inside the body are damaged, even though skin surface looks normal. This study assumes that tension and/or shear strain will cause damage to loose fibril tissue between the bone and muscle and that propagation of damaged area will lead to fatal stage. Analysis was performed using the finite element method by modeling the damaged fibril tissue as a cutout. By varying the loading directions and watching both tensile and shear strains, the risk of fibril tissue damage and propagation of the damaged area is discussed, which may give new insight for the careful nursing for patients, particularly after surgical treatment. It was found that the pressure ulcer could reoccur for a surgical flap treatment. The bone cut and surgical flap surgery is not perfect to prevent the bone-muscle interfacial damage.

  18. The perception of positive and negative facial expressions in unilateral brain-damaged patients: A meta-analysis.

    PubMed

    Abbott, Jacenta D; Cumming, Geoff; Fidler, Fiona; Lindell, Annukka K

    2013-01-01

    How the brain is lateralised for emotion processing remains a key question in contemporary neuropsychological research. The right hemisphere hypothesis asserts that the right hemisphere dominates emotion processing, whereas the valence hypothesis holds that positive emotion is processed in the left hemisphere and negative emotion is controlled by the right hemisphere. A meta-analysis was conducted to assess unilateral brain-damaged individuals' performance on tasks of facial emotion perception according to valence. A systematic search of the literature identified seven articles that met the conservative selection criteria and could be included in a meta-analysis. A total of 12 meta-analyses of facial expression perception were constructed assessing identification and labelling tasks according to valence and the side of brain damage. The results demonstrated that both left and right hemisphere damage leads to impairments in emotion perception (identification and labelling) irrespective of valence. Importantly, right hemisphere damage prompted more pronounced emotion perception impairment than left hemisphere damage, across valence, suggesting right hemisphere dominance for emotion perception. Furthermore, right hemisphere damage was associated with a larger tendency for impaired perception of negative than positive emotion across identification and labelling tasks. Overall the findings support Adolphs, Jansari, and Tranel (2001) model whereby the right hemisphere preferentially processes negative facial expressions and both hemispheres process positive facial expressions.

  19. Bladed wheels damage detection through Non-Harmonic Fourier Analysis improved algorithm

    NASA Astrophysics Data System (ADS)

    Neri, P.

    2017-05-01

    Recent papers introduced the Non-Harmonic Fourier Analysis for bladed wheels damage detection. This technique showed its potential in estimating the frequency of sinusoidal signals even when the acquisition time is short with respect to the vibration period, provided that some hypothesis are fulfilled. Anyway, previously proposed algorithms showed severe limitations in cracks detection at their early stage. The present paper proposes an improved algorithm which allows to detect a blade vibration frequency shift due to a crack whose size is really small compared to the blade width. Such a technique could be implemented for condition-based maintenance, allowing to use non-contact methods for vibration measurements. A stator-fixed laser sensor could monitor all the blades as they pass in front of the spot, giving precious information about the wheel health. This configuration determines an acquisition time for each blade which become shorter as the machine rotational speed increases. In this situation, traditional Discrete Fourier Transform analysis results in poor frequency resolution, being not suitable for small frequency shift detection. Non-Harmonic Fourier Analysis instead showed high reliability in vibration frequency estimation even with data samples collected in a short time range. A description of the improved algorithm is provided in the paper, along with a comparison with the previous one. Finally, a validation of the method is presented, based on finite element simulations results.

  20. Finite element method for viscoelastic medium with damage and the application to structural analysis of solid rocket motor grain

    NASA Astrophysics Data System (ADS)

    Deng, Bin; Shen, ZhiBin; Duan, JingBo; Tang, GuoJin

    2014-05-01

    This paper studies the damage-viscoelastic behavior of composite solid propellants of solid rocket motors (SRM). Based on viscoelastic theories and strain equivalent hypothesis in damage mechanics, a three-dimensional (3-D) nonlinear viscoelastic constitutive model incorporating with damage is developed. The resulting viscoelastic constitutive equations are numerically discretized by integration algorithm, and a stress-updating method is presented by solving nonlinear equations according to the Newton-Raphson method. A material subroutine of stress-updating is made up and embedded into commercial code of Abaqus. The material subroutine is validated through typical examples. Our results indicate that the finite element results are in good agreement with the analytical ones and have high accuracy, and the suggested method and designed subroutine are efficient and can be further applied to damage-coupling structural analysis of practical SRM grain.

  1. Review Article: Economic evaluation of flood damage to agriculture - review and analysis of existing methods

    NASA Astrophysics Data System (ADS)

    Brémond, P.; Grelot, F.; Agenais, A.-L.

    2013-10-01

    In Europe, economic evaluation of flood management projects is increasingly used to help decision making. At the same time, the management of flood risk is shifting towards new concepts such as giving more room to water by restoring floodplains. Agricultural areas are particularly targeted by projects following those concepts since they are frequently located in floodplain areas and since the potential damage to such areas is expected to be lower than to cities or industries for example. Additional or avoided damage to agriculture may have a major influence on decisions concerning these projects and the economic evaluation of flood damage to agriculture is thus an issue that needs to be tackled. The question of flood damage to agriculture can be addressed in different ways. This paper reviews and analyzes existing studies which have developed or used damage functions for agriculture in the framework of an economic appraisal of flood management projects. A conceptual framework of damage categories is proposed for the agricultural sector. The damage categories were used to structure the review. Then, a total of 42 studies are described, with a detailed review of 26 of them, based on the following criteria: types of damage considered, the influential flood parameters chosen, and monetized damage indicators used. The main recommendations resulting from this review are that even if existing methods have already focused on damage to crops, still some improvement is needed for crop damage functions. There is also a need to develop damage functions for other agricultural damage categories, including farm buildings and their contents. Finally, to cover all possible agricultural damage, and in particular loss of activity, a farm scale approach needs to be used.

  2. Influence of Corrosion Damage on Prediction of Residual Strength Capacities - An Experimental Analysis

    NASA Astrophysics Data System (ADS)

    Appuhamy, Jayasinghe Mudalige Ruwan Sanjeewa; Ohga, Mitao; Kaita, Tatsumasa; Chun, Pang-Jo; Fujii, Katashi; Dissanayake, Ranjith

    Civil infrastructure systems are prone to age related deterioration due to the exposure to aggressive environmental conditions and inadequate maintenance, and often causes reduction of their carrying capacities. Designing these systems for a particular service life and maintaining them in a safe condition during their entire service life have been recognized as very critical issues worldwide. There have been many damage examples of older steel bridge structures due to corrosion around the world during past few decades and they intensified the importance of attention to the careful evaluation of existing structures for the feasibility of current usage and strengthening them by retrofitting some selected corroded members to ensure the public safety. Therefore, a simple and accurate method to calculate the remaining yield and tensile strength by using a concept of representative effective thickness with correlation of initial thickness and the maximum corroded depth is proposed in this study, based on the results of many tensile coupon tests conducted on corroded specimens cut from a steel girder used for about hundred years with severe corrosion. The proposed methodology revealed more accurate and reliable estimation for the maintenance management of existing corroded steel structures.

  3. Meta-Analysis of Attitudes toward Damage-Causing Mammalian Wildlife

    PubMed Central

    KANSKY, RUTH; KIDD, MARTIN; KNIGHT, ANDREW T

    2014-01-01

    Many populations of threatened mammals persist outside formally protected areas, and their survival depends on the willingness of communities to coexist with them. An understanding of the attitudes, and specifically the tolerance, of individuals and communities and the factors that determine these is therefore fundamental to designing strategies to alleviate human-wildlife conflict. We conducted a meta-analysis to identify factors that affected attitudes toward 4 groups of terrestrial mammals. Elephants (65%) elicited the most positive attitudes, followed by primates (55%), ungulates (53%), and carnivores (44%). Urban residents presented the most positive attitudes (80%), followed by commercial farmers (51%) and communal farmers (26%). A tolerance to damage index showed that human tolerance of ungulates and primates was proportional to the probability of experiencing damage while elephants elicited tolerance levels higher than anticipated and carnivores elicited tolerance levels lower than anticipated. Contrary to conventional wisdom, experiencing damage was not always the dominant factor determining attitudes. Communal farmers had a lower probability of being positive toward carnivores irrespective of probability of experiencing damage, while commercial farmers and urban residents were more likely to be positive toward carnivores irrespective of damage. Urban residents were more likely to be positive toward ungulates, elephants, and primates when probability of damage was low, but not when it was high. Commercial and communal farmers had a higher probability of being positive toward ungulates, primates, and elephants irrespective of probability of experiencing damage. Taxonomic bias may therefore be important. Identifying the distinct factors explaining these attitudes and the specific contexts in which they operate, inclusive of the species causing damage, will be essential for prioritizing conservation investments. Meta-Análisis de las Posturas hacia la Mam

  4. Damage-Resistant Composites Using Electrospun Nanofibers: A Multiscale Analysis of the Toughening Mechanisms.

    PubMed

    Daelemans, Lode; van der Heijden, Sam; De Baere, Ives; Rahier, Hubert; Van Paepegem, Wim; De Clerck, Karen

    2016-05-11

    nanofiber bridging mechanism expresses itself is different for each scale and dependent on parameters linked to a certain scale. The multiscale analysis of the toughening mechanisms reported in this paper is therefore crucial for understanding the behavior of nanofiber toughened composites, and as such allows for designing novel, damage-resistant, nanofiber-toughened materials.

  5. Scaling craters in carbonates: Electron paramagnetic resonance analysis of shock damage

    NASA Technical Reports Server (NTRS)

    Polanskey, Carol A.; Ahrens, Thomas J.

    1994-01-01

    Carbonate samples from the 8.9-Mt nuclear (near-surface explosion) crater, OAK, and a terrestrial impact crater, Meteor Crater, were analyzed for shock damage using electron paramagnetic resonance (EPR). Samples from below the OAK apparent crater floor were obtained from six boreholes, as well as ejecta recovered from the crater floor. The degree of shock damage in the carbonate material was assessed by comparing the sample spectra to the spectra of Solenhofen and Kaibab limestone, which had been skocked to known pressures. Analysis of the OAK Crater borehole samples has identified a thin zone of allocthonous highly shocked (10-13 GPa) carbonate material underneath the apparent crater floor. This approx. 5- to 15-m-thick zone occurs at a maximum depth of approx. 125 m below current seafloor at the borehole, sited at the initial position of the OAK explosive, and decreases in depth towards the apparent crater edge. Because this zone of allocthonous shocked rock delineates deformed rock below, and a breccia of mobilized sand and collapse debris above, it appears to outline the transient crater. The transient crater volume inferred in this way is found to by 3.2 +/- 0.2 times 10(exp 6)cu m, which is in good agreement with a volume of 5.3 times 10(exp 6)cu m inferred from gravity scaling of laboratory experiments. A layer of highly shocked material is also found near the surface outside the crater. The latter material could represent a fallout ejecta layer. The ejecta boulders recovered from the present crater floor experienced a range of shock pressures from approx. 0 to 15 GPa with the more heavily shocked samples all occurring between radii of 360 and approx. 600 m. Moreover, the fossil content, lithology and Sr isotopic composition all demonstrate that the initial position of the bulk of the heavily shocked rock ejecta sampled was originally near surface rock at initial depths in the 32 to 45-m depth (below sea level) range. The EPR technique is also sensitive to

  6. Quantitative Proteomic Analysis Reveals Populus cathayana Females Are More Sensitive and Respond More Sophisticatedly to Iron Deficiency than Males.

    PubMed

    Zhang, Sheng; Zhang, Yunxiang; Cao, Yanchun; Lei, Yanbao; Jiang, Hao

    2016-03-04

    Previous studies have shown that there are significant sexual differences in the morphological and physiological responses of Populus cathayana Rehder to nitrogen and phosphorus deficiencies, but little is known about the sex-specific differences in responses to iron deficiency. In this study, the effects of iron deficiency on the morphology, physiology, and proteome of P. cathayana males and females were investigated. The results showed that iron deficiency (25 days) significantly decreased height growth, photosynthetic rate, chlorophyll content, and tissue iron concentration in both sexes. A comparison between the sexes indicated that iron-deficient males had less height inhibition and photosynthesis system II or chloroplast ultrastructural damage than iron-deficient females. iTRAQ-based quantitative proteomic analysis revealed that 144 and 68 proteins were decreased in abundance (e.g., proteins involved in photosynthesis, carbohydrate and energy metabolism, and gene expression regulation) and 78 and 39 proteins were increased in abundance (e.g., proteins involved in amino acid metabolism and stress response) according to the criterion of ratio ≥1.5 in females and males, respectively. A comparison between the sexes indicated that iron-deficient females exhibited a greater change in the proteins involved in photosynthesis, carbon and energy metabolism, the redox system, and stress responsive proteins. This study reveals females are more sensitive and have a more sophisticated response to iron deficiency compared with males and provides new insights into differential sexual responses to nutrient deficiency.

  7. Does Plant Origin Influence the Fitness Impact of Flower Damage? A Meta-Analysis

    PubMed Central

    González-Browne, Catalina; Murúa, Maureen M.; Navarro, Luis; Medel, Rodrigo

    2016-01-01

    Herbivory has been long considered an important component of plant-animal interactions that influences the success of invasive species in novel habitats. One of the most important hypotheses linking herbivory and invasion processes is the enemy-release hypothesis, in which exotic plants are hypothesized to suffer less herbivory and fitness-costs in their novel ranges as they leave behind their enemies in the original range. Most evidence, however, comes from studies on leaf herbivory, and the importance of flower herbivory for the invasion process remains largely unknown. Here we present the results of a meta-analysis of the impact of flower herbivory on plant reproductive success, using as moderators the type of damage caused by floral herbivores and the residence status of the plant species. We found 51 papers that fulfilled our criteria. We also included 60 records from unpublished data of the laboratory, gathering a total of 143 case studies. The effects of florivory and nectar robbing were both negative on plant fitness. The methodology employed in studies of flower herbivory influenced substantially the outcome of flower damage. Experiments using natural herbivory imposed a higher fitness cost than simulated herbivory, such as clipping and petal removal, indicating that studies using artificial herbivory as surrogates of natural herbivory underestimate the real fitness impact of flower herbivory. Although the fitness cost of floral herbivory was high both in native and exotic plant species, floral herbivores had a three-fold stronger fitness impact on exotic than native plants, contravening a critical element of the enemy-release hypothesis. Our results suggest a critical but largely unrecognized role of floral herbivores in preventing the spread of introduced species into newly colonized areas. PMID:26785039

  8. Strain-Based Damage Determination Using Finite Element Analysis for Structural Health Management

    NASA Technical Reports Server (NTRS)

    Hochhalter, Jacob D.; Krishnamurthy, Thiagaraja; Aguilo, Miguel A.

    2016-01-01

    A damage determination method is presented that relies on in-service strain sensor measurements. The method employs a gradient-based optimization procedure combined with the finite element method for solution to the forward problem. It is demonstrated that strains, measured at a limited number of sensors, can be used to accurately determine the location, size, and orientation of damage. Numerical examples are presented to demonstrate the general procedure. This work is motivated by the need to provide structural health management systems with a real-time damage characterization. The damage cases investigated herein are characteristic of point-source damage, which can attain critical size during flight. The procedure described can be used to provide prognosis tools with the current damage configuration.

  9. Empirical Fragility Analysis of Buildings and Boats Damaged By the 2011 Great East Japan Tsunami and Their Practical Application

    NASA Astrophysics Data System (ADS)

    Suppasri, A.; Charvet, I.; Leelawat, N.; Fukutani, Y.; Muhari, A.; Futami, T.; Imamura, F.

    2014-12-01

    This study focused in turn on detailed data of buildings and boats damage caused by the 2011 tsunami in order to understand its main causes and provide damage probability estimates. Tsunami-induced building damage data was collected from field surveys, and includes inundation depth, building material, number of stories and occupancy type for more than 80,000 buildings. Numerical simulations with high resolution bathymetry and topography data were conducted to obtain characteristic tsunami measures such as flow velocity. These data were analyzed using advanced statistical methods, ordinal regression analysis to create not only empirical 2D tsunami fragility curves, but also 3D tsunami fragility surfaces for the first time. The effect of floating debris was also considered, by using a binary indicator of debris impact based on the proximity of a structure from a debris source (i.e. washed away building). Both the 2D and 3D fragility analyses provided results for each different building damage level, and different topography. While 2D fragility curves provide easily interpretable results relating tsunami flow depth to damage probability for different damage levels, 3D fragility surfaces allow for several influential tsunami parameters to be taken into account thus reduce uncertainty in the probability estimations. More than 20,000 damaged boats were used in the analysis similar to the one carried out on the buildings. Detailed data for each boat comprises information on the damage ratio (paid value over insured value), tonnage, engine type, material type and damage classification. The 2D and 3D fragility analyses were developed using representative tsunami heights for each port obtained from field surveys and flow velocities obtained from the aforementioned simulations. The results are currently being adapted for practical disaster mitigation. They are being integrated with the probabilistic tsunami hazard analysis, in order to create offshore and onshore

  10. Spatio-temporal flow analysis in bileaflet heart valve hinge regions: potential analysis for blood element damage.

    PubMed

    Simon, Hélène A; Dasi, Lakshmi P; Leo, Hwa-Liang; Yoganathan, Ajit P

    2007-08-01

    Point-wise velocity measurements have been traditionally acquired to estimate blood damage potential induced by prosthetic heart valves with emphasis on peak values of velocity magnitude and Reynolds stresses. However, the inherently Lagrangian nature of platelet activation and hemolysis makes such measurements of limited predictive value. This study provides a refined fluid mechanical analysis, including blood element paths and stress exposure times, of the hinge flows of a CarboMedics bileaflet mechanical heart valve placed under both mitral and aortic conditions and a St Jude Medical bileaflet valve placed under aortic conditions. The hinge area was partitioned into characteristic regions based on dominant flow structures and spatio-temporal averaging was performed on the measured velocities and Reynolds shear stresses to estimate the average bulk stresses acting on blood elements transiting through the hinge. A first-order estimate of viscous stress levels and exposure times were computed. Both forward and leakage flow phases were characterized in each partition by dynamic flows dependent on subtle leaflet movements and transvalvular pressure fluctuations. Blood elements trapped in recirculation regions may experience exposure times as long as the entire forward flow phase duration. Most calculated stresses were below the accepted blood damage threshold. Estimates of the stress levels indicate that the flow conditions within the boundary layers near the hinge and leaflet walls may be more detrimental to blood cells than bulk flow conditions, while recirculation regions may promote thrombus buildup.

  11. Failure Analysis Study and Long-Term Reliability of Optical Assemblies with End-Face Damage

    NASA Technical Reports Server (NTRS)

    Kichak, Robert A.; Ott, Melanie N.; Leidecker, Henning W.; Chuska, Richard F.; Greenwell, Christopher J.

    2008-01-01

    In June 2005, the NESC received a multi-faceted request to determine the long term reliability of fiber optic termini on the ISS that exhibited flaws not manufactured to best workmanship practices. There was a lack of data related to fiber optic workmanship as it affects the long term reliability of optical fiber assemblies in a harsh environment. A fiber optic defect analysis was requested which would find and/or create various types of chips, spalls, scratches, etc., that were identified by the ISS personnel. Once the defects and causes were identified the next step would be to perform long term reliability testing of similar assemblies with similar defects. The goal of the defect analysis would be for the defects to be observed and documented for deterioration of fiber optic performance. Though this report mostly discusses what has been determined as evidence of poor manufacturing processes, it also concludes the majority of the damage could have been avoided with a rigorous process in place.

  12. Assessment of Damage Tolerance Requirements and Analysis - Task 1 report. Volume 2. Analytical Methods

    DTIC Science & Technology

    1986-03-31

    always smaller than kt; and for the same kt, kN decreases with decreasing p . Such a relationship conforms with the empirical observa- tion that the...predict fatigue crack initiation under spectrum loading, cumulative damage computations must be performed. The Palmgren -Miner approach of linear...the Palmgren -Miner approach, the cumulative damage is, nk -Zdn - Df J 0 \\dn / i i (19) When cumulative damage equals a predetermined value of Df, a

  13. Analysis of core damage frequency due to external events at the DOE (Department of Energy) N-Reactor

    SciTech Connect

    Lambright, J.A.; Bohn, M.P.; Daniel, S.L. ); Baxter, J.T. ); Johnson, J.J.; Ravindra, M.K.; Hashimoto, P.O.; Mraz, M.J.; Tong, W.H.; Conoscente, J.P. ); Brosseau, D.A. )

    1990-11-01

    A complete external events probabilistic risk assessment has been performed for the N-Reactor power plant, making full use of all insights gained during the past ten years' developments in risk assessment methodologies. A detailed screening analysis was performed which showed that all external events had negligible contribution to core damage frequency except fires, seismic events, and external flooding. A limited scope analysis of the external flooding risk indicated that it is not a major risk contributor. Detailed analyses of the fire and seismic risks resulted in total (mean) core damage frequencies of 1.96E-5 and 4.60E-05 per reactor year, respectively. Detailed uncertainty analyses were performed for both fire and seismic risks. These results show that the core damage frequency profile for these events is comparable to that found for existing commercial power plants if proposed fixes are completed as part of the restart program. 108 refs., 85 figs., 80 tabs.

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

    PubMed Central

    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

  15. Damage detection of metro tunnel structure through transmissibility function and cross correlation analysis using local excitation and measurement

    NASA Astrophysics Data System (ADS)

    Feng, Lei; Yi, Xiaohua; Zhu, Dapeng; Xie, Xiongyao; Wang, Yang

    2015-08-01

    In a modern metropolis, metro rail systems have become a dominant mode for mass transportation. The structural health of a metro tunnel is closely related to public safety. Many vibration-based techniques for detecting and locating structural damage have been developed in the past several decades. However, most damage detection techniques and validation tests are focused on bridge and building structures; very few studies have been reported on tunnel structures. Among these techniques, transmissibility function and cross correlation analysis are two well-known diagnostic approaches. The former operates in frequency domain and the latter in time domain. Both approaches can be applied to detect and locate damage through acceleration data obtained from sensor arrays. Furthermore, the two approaches can directly utilize structural response data without requiring excitation measurement, which offers advantages in field testing on a large structure. In this research, a numerical finite element model of a metro tunnel is built and different types of structural defects are introduced at multiple locations of the tunnel. Transmissibility function and cross correlation analysis are applied to perform structural damage detection and localization, based on simulated structural vibration data. Numerical results demonstrate that the introduced defects can be successfully identified and located. The sensitivity and feasibility of the two approaches have been verified when sufficient distribution of measurement locations is available. Damage detection results of the two different approaches are compared and discussed.

  16. Crack Growth Prediction Methodology for Multi-Site Damage: Layered Analysis and Growth During Plasticity

    NASA Technical Reports Server (NTRS)

    James, Mark Anthony

    1999-01-01

    A finite element program has been developed to perform quasi-static, elastic-plastic crack growth simulations. The model provides a general framework for mixed-mode I/II elastic-plastic fracture analysis using small strain assumptions and plane stress, plane strain, and axisymmetric finite elements. Cracks are modeled explicitly in the mesh. As the cracks propagate, automatic remeshing algorithms delete the mesh local to the crack tip, extend the crack, and build a new mesh around the new tip. State variable mapping algorithms transfer stresses and displacements from the old mesh to the new mesh. The von Mises material model is implemented in the context of a non-linear Newton solution scheme. The fracture criterion is the critical crack tip opening displacement, and crack direction is predicted by the maximum tensile stress criterion at the crack tip. The implementation can accommodate multiple curving and interacting cracks. An additional fracture algorithm based on nodal release can be used to simulate fracture along a horizontal plane of symmetry. A core of plane strain elements can be used with the nodal release algorithm to simulate the triaxial state of stress near the crack tip. Verification and validation studies compare analysis results with experimental data and published three-dimensional analysis results. Fracture predictions using nodal release for compact tension, middle-crack tension, and multi-site damage test specimens produced accurate results for residual strength and link-up loads. Curving crack predictions using remeshing/mapping were compared with experimental data for an Arcan mixed-mode specimen. Loading angles from 0 degrees to 90 degrees were analyzed. The maximum tensile stress criterion was able to predict the crack direction and path for all loading angles in which the material failed in tension. Residual strength was also accurately predicted for these cases.

  17. Analysis of damaging hydrogeological events: the case of the Calabria Region (Southern Italy).

    PubMed

    Petrucci, O; Polemio, M; Pasqua, A A

    2009-03-01

    A period of bad weather conditions due to prolonged intense rainfall and strong winds can trigger landslides, floods, secondary floods (accumulation of rain on surfaces with low permeability), and sea storms, causing damage to humans and infrastructure. As a whole, these periods of bad weather and triggered phenomena can be defined as damaging hydrogeological events (DHEs). We define a methodological approach based on seven simple indexes to analyze such events. The indexes describe the return period (T) and trend of rainfall, the extent of hit areas, and the level of damages; they can be considered attributes of georeferenced features and analyzed with GIS techniques. We tested our method in an Italian region frequently hit by DHEs. In a period of 10 years, 747 damaging phenomena (landslides, 43%; floods, 38%) and 94 DHEs have been classified. The road network and housing areas are the most frequently damaged elements, threatened by all types of damaging phenomena. T classes are almost in accordance with the level of damage. These results can be used to outline warning levels for civil protection purposes, to forecast the areas most likely to be hit and the potential ensuing damage, to disseminate information concerning vulnerable areas, and to increase people's awareness of risk.

  18. Pulse Frequency Effect on Neutron Damage in -Iron: A KMC Analysis

    SciTech Connect

    Perlado, J M; Lodi, D; Dominguez, E; Ogando, F; Prieto, J; Diaz de la Rubia, T; Caturla, J

    2001-05-01

    The pulsed nature of the irradiation and the high neutron dose are the critical factors in an Inertial Fusion Energy reactor (IFE). The damage that structural materials suffer under these extremes conditions require a careful study and assessment. The goal of our work is to simulate, trough the multiscale modeling approach, the damage accumulation in {alpha}-Fe under conditions relevant to a IFE Reactor. We discuss how the pulse frequency, 1 Hz, 10 Hz, and the dose rate of 10{_} and 10{_}dpa/s affect the damage production and accumulation. Results of the damage that this demanding environment can produce on a protected first structural exposed to 150 keV average recoil ion will be presented. A further comparison it has been made with the damage produced by a continuous irradiation at similar average dose.

  19. Micromechanics-Based Damage Analysis of Fracture in Ti5553 Alloy with Application to Bolted Sectors

    NASA Astrophysics Data System (ADS)

    Bettaieb, Mohamed Ben; Van Hoof, Thibaut; Minnebo, Hans; Pardoen, Thomas; Dufour, Philippe; Jacques, Pascal J.; Habraken, Anne Marie

    2015-03-01

    A physics-based, uncoupled damage model is calibrated using cylindrical notched round tensile specimens made of Ti5553 and Ti-6Al-4V alloys. The fracture strain of Ti5553 is lower than for Ti-6Al-4V in the full range of stress triaxiality. This lower ductility originates from a higher volume fraction of damage sites. By proper heat treatment, the fracture strain of Ti5553 increases by almost a factor of two, as a result of a larger damage nucleation stress. This result proves the potential for further optimization of the damage resistance of the Ti5553 alloy. The damage model is combined with an elastoviscoplastic law in order to predict failure in a wide range of loading conditions. In particular, a specific application involving bolted sectors is addressed in order to determine the potential of replacing the Ti-6Al-4V by the Ti5553 alloy.

  20. Wavelet Analysis of Acceleration Response of Beam Under the Moving Mass for Damage Assessment

    NASA Astrophysics Data System (ADS)

    Vaidya, Tanuja; Chatterjee, Animesh

    2016-04-01

    In the present study, acceleration response of cracked beam is analyzed by using the wavelet transform to detect the crack presence, its location and also to predict the crack severity. The equation of motion of beam under the moving mass is solved by using the fourth order Runge-Kutta method. A code is written by expanding the equation for first three vibration modes. Acceleration signal of the damaged beam under the moving mass contains the discontinuity at the crack location. This discontinuity contained in the acceleration signal is sufficiently visible but it is very small for some signals. Therefore, the acceleration signals are transformed using the wavelet analysis. A wavelet coefficient peak occurs at the location of discontinuity, so that we can identify the crack presence and its location. From the value of wavelet coefficient peak, we can also predict the crack effect with respect to the change in velocity of moving mass and change in crack depth. The main advantage of this method is that the wavelet coefficient peak is sufficiently higher even for the higher velocities and small size crack.

  1. Multifractal analysis of two-dimensional images for damage assessment of reinforced concrete structures

    NASA Astrophysics Data System (ADS)

    Ebrahimkhanlou, Arvin; Farhidzadeh, Alireza; Salamone, Salvatore

    2015-03-01

    The most common assessment technique for reinforced concrete shear walls (RCSW) is Visual Inspection (VI). The current practice suffers from subjective and labor intensive nature as it highly relies on judgment and expertise of the inspectors. In post-earthquake events where urgent and objective decisions are crucial, failure of the conventional VI could be catastrophic. Conventional VI is mainly based on width of residual cracks. Given that cracks could close partially (e.g., due to weight of the structure, behavior of adjacent elastic members, earthquake displacement spectrum, etc.), methods based on crack width may lead to underestimating the state of damage and eventually an erroneous decision. This paper proposes a novel method to circumvent the aforementioned limitations by utilizing the information hidden in crack patterns. Crack patterns from images of the surface cracks on RCSW are extracted automatically, and Multifractal Analysis (MFA) are applied on them. Images were taken from two large scale low aspect ratio RCSW under quasi-static cyclic loading, and MFA showed clear correlation with tri-linear shear controlled behavior of walls which was observed in their backbone curves.

  2. A Computational Methodology to Support Reimbursement Requests Analysis Concerning Electrical Damages

    NASA Astrophysics Data System (ADS)

    Almeida Junior, Afonso Bernardino; Gondim, Isaque Nogueira; Rezende, Paulo Henrique Oliveira; Oliveira, José Carlos

    2015-12-01

    In light of the growing number of reimbursement requests processed from consumers for electrical damage to equipment, supposedly caused through the manifestation of anomalies on the power grid, there comes the need for reliable means for providing a decision on the issues highlighted herein. Through the recognition that in the current context, the procedures used are based on reviews, information and records of occurrences in the field, there has been significant inadequacy and fragility in the issuing of conclusive advice or opinions. In particular, the search for mechanisms grounded in classical principles and accepted in electrical engineering presents itself as an important challenge on which to base the decision making process in full awareness of its incumbent science and technology. Therefore, with the aim of meeting these assumptions, the study in question excels in its presentation of the principles that guided the software analysis, which intend above all else to correlate cause and effect. The elaborated strategy involves modelling stages as well as studies aimed at: distribution supply reproduction; characterization of the distribution network to the complainant consumer; representation of the diverse electro-electronic appliances and lastly, a proposal for correlating the disturbances impacting on equipment with their dielectric and thermal supportability requirements. For the purpose of illustrating the software process, an actual case study coupled with a loss and claim scenario is presented.

  3. Proteomic and genomic analysis reveals novel Campylobacter jejuni outer membrane proteins and potential heterogeneity.

    PubMed

    Watson, Eleanor; Sherry, Aileen; Inglis, Neil F; Lainson, Alex; Jyothi, Dushyanth; Yaga, Raja; Manson, Erin; Imrie, Lisa; Everest, Paul; Smith, David G E

    2014-09-01

    Gram-negative bacterial outer membrane proteins play important roles in the interaction of bacteria with their environment including nutrient acquisition, adhesion and invasion, and antibiotic resistance. In this study we identified 47 proteins within the Sarkosyl-insoluble fraction of Campylobacter jejuni 81-176, using LC-ESI-MS/MS. Comparative analysis of outer membrane protein sequences was visualised to reveal protein distribution within a panel of Campylobacter spp., identifying several C. jejuni-specific proteins. Smith-Waterman analyses of C. jejuni homologues revealed high sequence conservation amongst a number of hypothetical proteins, sequence heterogeneity of other proteins and several proteins which are absent in a proportion of strains.

  4. An Analysis Methodology to Predict Damage Propagation in Notched Composite Fuselage Structures

    NASA Technical Reports Server (NTRS)

    Bergan, A.; Davila, C.; Leone, F.; Awerbuch, J.; Tan, T.-M.

    2015-01-01

    A new methodology is proposed for predicting damage propagation in notched composite skin-stiffened structures. The proposed approach considers the interaction of damage propagation in the skin with delamination of the stiffener in order to assess the damage containment behavior of the structure. The damage propagating from a notch within a thin fiber-reinforced polymer skin is idealized as a through-the-thickness cohesive crack. The cohesive law for the through-the-thickness crack is characterized using a compact tension test. The approach was applied to a full-scale pultruded rod stitched efficient unitized structure (PRSEUS) concept fuselage panel that was tested recently. The stitched skin/stringer interfaces, a key feature of the PRSEUS concept, were modeled to assess the effectiveness of the stitching at containing damage propagation. Comparison between the predicted and observed damage extension shows acceptable agreement throughout loading. These results indicate that the model can represent accurately the complex interactions between a through-the-thickness crack in the skin and delamination between the skin and stringer. The model is used to demonstrate that the skin-stiffener interface toughness is critical to damage containment capability

  5. Wavelet coefficient analysis for the quantitative determination of damage in tendons and cables

    NASA Astrophysics Data System (ADS)

    Rizzo, Piervincenzo; Lanza di Scalea, Francesco

    2005-05-01

    Wires, bars, multi-wire strands made of steel or composite materials are widely used in civil infrastructures as tensioning members in cable-stayed bridges, suspension bridges and prestressed concrete. The health monitoring of these components is a long-standing challenge in the NDE community. In the last few years, the authors have been conducting a study on the application of ultrasonic guided waves for the structural health monitoring of bars and multi-wire strands. This paper presents an application of a signal processing technique based on the Discrete Wavelet Transform (DWT) for the detection and the quantification of damage (in the form of small notches) in loaded seven-wire steel strands. The DWT is applied to ultrasonic signals generated and detected via magnetostrictive transducers. The detection and the quantification of damage in the strands are accomplished by constructing and computing a damage index based on the variance and the root mean square of the wavelet coefficient vector of the ultrasonic damage signatures. It is shown that the logarithmic value of the damage index is linearly dependent on the damage size. In the last portion of the paper an eight-dimensional damage index is constructed and it is fed to an artificial neural network that classifies the size and the location of the notch.

  6. Acoustic emission-based sensor analysis and damage classification for structural health monitoring of composite structures

    NASA Astrophysics Data System (ADS)

    Uprety, Bibhisha

    Within the aerospace industry the need to detect and locate impact events, even when no visible damage is present, is important both from the maintenance and design perspectives. This research focused on the use of Acoustic Emission (AE) based sensing technologies to identify impact events and characterize damage modes in composite structures for structural health monitoring. Six commercially available piezoelectric AE sensors were evaluated for use with impact location estimation algorithms under development at the University of Utah. Both active and passive testing were performed to estimate the time of arrival and plate wave mode velocities for impact location estimation. Four sensors were recommended for further comparative investigations. Furthermore, instrumented low-velocity impact experiments were conducted on quasi-isotropic carbon/epoxy composite laminates to initiate specific types of damage: matrix cracking, delamination and fiber breakage. AE signal responses were collected during impacting and the test panels were ultrasonically C-scanned after impact to identify the internal damage corresponding to the AE signals. Matrix cracking and delamination damage produced using more compliant test panels and larger diameter impactor were characterized by lower frequency signals while fiber breakage produced higher frequency responses. The results obtained suggest that selected characteristics of sensor response signals can be used both to determine whether damage is produced during impacting and to characterize the types of damage produced in an impacted composite structure.

  7. Impact damage detection in smart composites using nonlinear acoustics—cointegration analysis for removal of undesired load effect

    NASA Astrophysics Data System (ADS)

    Dao, Phong B.; Klepka, Andrzej; Pieczonka, Łukasz; Aymerich, Francesco; Staszewski, Wieslaw J.

    2017-03-01

    The paper presents a reliable methodology—based on nonlinear acoustics—for impact damage detection in composite materials. The nonlinear vibro-acoustic wave modulation technique is used to detect damage. The problem of operational variability of the method with respect to the selection of frequency and amplitude of low-frequency (LF) modal excitation is investigated. This problem is addressed using the concept of stationarity of time series of vibro-acoustic data. Cointegration analysis is employed to compensate for the effect of variable operational conditions associated with LF modal (or vibration) excitation in nonlinear vibro-acoustic wave modulations. Analysis of stationary statistical characteristics of vibro-acoustic responses—after cointegration analysis—are used for damage detection. The proposed method is validated using vibro-acoustic data from laminated composite plates and composite sandwich panels. The results demonstrate that the proposed approach can effectively compensate for the effect of LF modal excitation on nonlinear vibro-acoustic wave modulations and detect the damage more accurately and robustly than the existing nonlinear acoustics based on the analysis of modulation sidebands.

  8. UMAT Implementation of Coupled, Multilevel, Structural Deformation and Damage Analysis of General Hereditary Materials

    NASA Technical Reports Server (NTRS)

    Arnold, S. M.; Saleeb, A. F.; Wilt, T. E.; Trowbridge, D.

    2000-01-01

    Extensive research efforts have been made over the years on the phenomenological representations of constitutive material behavior in the inelastic analysis and life assessment of structures composed of advanced monolithic and composite (CMC, MMC, and PMC) materials. Recently, emphasis has been placed on concurrently addressing three important and related areas of constitutive and degradation modeling; i.e. (i) mathematical formulation, (ii) algorithmic developments for the updating (integrating) of external (e.g. stress) and internal state variable, as well as (iii) parameter estimation for the characterization of the specific model. This concurrent perspective has resulted in; i) the formulation of a fully-associative viscoelastoplastic model (GVIPS), (ii) development of an efficient implicit integration and it's associative, symmetric, consistent tangent stiffness matrix algorithm for integration of the underlying rate flow/evolutionary equations, and iii) a robust, stand-alone, Constitutive Material Parameter Estimator (COMPARE) for automatically characterizing the various time-dependent, nonlinear, material models. Furthermore, to provide a robust multi-scale framework for the deformation and life analysis of structures composed of composite materials, NASA Glenn has aggressively pursued the development of a sufficiently general, accurate, and efficient micromechanics approach known as the generalized method of cells (GMC). This work has resulted in the development of MAC/GMC, a stand-alone micromechanics analysis tool that can easily and accurately design/analyze multiphase (composite) materials subjected to complex histories. MAC/GMC admits generalized, physically based, deformation and damage models for each constituent and provides "closed-form" expressions for the macroscopic composite response in terms of the properties, size, shape, distribution, and response of the individual constituents or phases that comprise the material. Consequently, MAC/GMC can

  9. Fatigue and Damage Tolerance Analysis of a Hybrid Composite Tapered Flexbeam

    NASA Technical Reports Server (NTRS)

    Murri, Gretchen B.; Schaff, Jeffrey R.; Dobyns, Al

    2001-01-01

    The behavior of nonlinear tapered composite flexbeams under combined axial tension and cyclic bending loading was studied using coupon test specimens and finite element (FE) analyses. The flexbeams used a hybrid material system of graphite/epoxy and glass/epoxy and had internal dropped plies, dropped in an overlapping stepwise pattern. Two material configurations, differing only in the use of glass or graphite plies in the continuous plies near the midplane, were studied. Test specimens were cut from a full-size helicopter tail-rotor flexbeam and were tested in a hydraulic load frame under combined constant axialtension load and transverse cyclic bending loads. The first determination damage observed in the specimens occurred at the area around the tip of the outermost ply-drop group in the tapered region of the flexbeam, near the thick end. Delaminations grew slowly and stably, toward the thick end of the flexbeam, at the interfaces above and below the dropped-ply region. A 2D finite element model of the flexbeam was developed. The model was analyzed using a geometrically non-linear analysis with both the ANSYS and ABAQUS FE codes. The global responses of each analysis agreed well with the test results. The ANSYS model was used to calculate strain energy release rates (G) for delaminations initiating at two different ply-ending locations. The results showed that delaminations were more inclined to grow at the locations where they were observed in the test specimens. Both ANSYS and ABAQUS were used to calculate G values associated with delamination initiating at the observed location but growing in different interfaces, either above or below the ply-ending group toward the thick end, or toward the thin end from the tip of the resin pocket. The different analysis codes generated the same trends and comparable peak values, within 5-11 % for each delamination path. Both codes showed that delamination toward the thick region was largely mode II, and toward the thin

  10. Non-ionic surfactant concentration profiles in undamaged and damaged hair fibres determined by scanning ion beam nuclear reaction analysis

    NASA Astrophysics Data System (ADS)

    Jenneson, P. M.; Clough, A. S.; Keddie, J. L.; Lu, J. R.; Meredith, P.

    1997-12-01

    Nuclear Reaction Analysis (NRA) was used with a scanning MeV 3He ion microbeam to determine the extent of permeation and segregation of a deuterated non-ionic surfactant (dC 12E 5) into virgin (undamaged) and alkalinic perm damaged hair fibres. 2-D concentration maps show an accumulation of deuterated surfactant in the cortex and medulla of both the virgin and damaged hair. By normalising to the matrix carbon, surfactant levels in the damaged hair were found to be three times higher than in the undamaged hair. This is the first reported direct spatial evidence of the penetration of surfactant into the centre of hair fibres. Furthermore it is the first application of NRA to this type of complex biological matrix.

  11. Probabilistic Fatigue Damage Prognosis Using a Surrogate Model Trained Via 3D Finite Element Analysis

    NASA Technical Reports Server (NTRS)

    Leser, Patrick E.; Hochhalter, Jacob D.; Newman, John A.; Leser, William P.; Warner, James E.; Wawrzynek, Paul A.; Yuan, Fuh-Gwo

    2015-01-01

    Utilizing inverse uncertainty quantification techniques, structural health monitoring can be integrated with damage progression models to form probabilistic predictions of a structure's remaining useful life. However, damage evolution in realistic structures is physically complex. Accurately representing this behavior requires high-fidelity models which are typically computationally prohibitive. In the present work, a high-fidelity finite element model is represented by a surrogate model, reducing computation times. The new approach is used with damage diagnosis data to form a probabilistic prediction of remaining useful life for a test specimen under mixed-mode conditions.

  12. Meta-Analysis of Gene Expression Profiles in Acute Promyelocytic Leukemia Reveals Involved Pathways

    PubMed Central

    Jalili, Mahdi; Salehzadeh-Yazdi, Ali; Mohammadi, Saeed; Yaghmaie, Marjan; Ghavamzadeh, Ardeshir; Alimoghaddam, Kamran

    2017-01-01

    Background: Acute promyelocytic leukemia (APL) is a unique subtype of acute leukemia. APL is a curable disease; however, drug resistance, early mortality, disease relapse and treatment-related complications remain challenges in APL patient management. One issue underlying these challenges is that the molecular mechanisms of the disease are not sufficiently understood. Materials and Methods: In this study, we performed a meta-analysis of gene expression profiles derived from microarray experiments and explored the background of disease by functional and pathway analysis. Results: Our analysis revealed a gene signature with 406 genes that are up or down-regulated in APL. The pathway analysis determined that MAPK pathway and its involved elements such as JUN gene and AP-1 play important roles in APL pathogenesis along with insulin-like growth factor–binding protein-7. Conclusion: The results of this meta-analysis could be useful for developing more effective therapy strategies and new targets for diagnosis and drugs. PMID:28286608

  13. Analysis and Characterization of Damage Utilizing an Orthotropic Generalized Composite Material Model Suitable for Use in Impact Problems

    NASA Technical Reports Server (NTRS)

    Goldberg, Robert K.; Carney, Kelly S.; DuBois, Paul; Hoffarth, Canio; Rajan, Subramaniam; Blankenhorn, Gunther

    2016-01-01

    The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased usage in the aerospace and automotive communities. In order to address a series of issues identified by the aerospace community as being desirable to include in a next generation composite impact model, an orthotropic, macroscopic constitutive model incorporating both plasticity and damage suitable for implementation within the commercial LS-DYNA computer code is being developed. The plasticity model is based on extending the Tsai-Wu composite failure model into a strain hardening-based orthotropic plasticity model with a non-associative flow rule. The evolution of the yield surface is determined based on tabulated stress-strain curves in the various normal and shear directions and is tracked using the effective plastic strain. To compute the evolution of damage, a strain equivalent semi-coupled formulation is used in which a load in one direction results in a stiffness reduction in multiple material coordinate directions. A detailed analysis is carried out to ensure that the strain equivalence assumption is appropriate for the derived plasticity and damage formulations that are employed in the current model. Procedures to develop the appropriate input curves for the damage model are presented and the process required to develop an appropriate characterization test matrix is discussed

  14. Analysis and Characterization of Damage Utilizing an Orthotropic Generalized Composite Material Model Suitable for Use in Impact Problems

    NASA Technical Reports Server (NTRS)

    Goldberg, Robert K.; Carney, Kelly S.; DuBois, Paul; Hoffarth, Canio; Rajan, Subramaniam; Blankenhorn, Gunther

    2016-01-01

    The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased usage in the aerospace and automotive communities. In order to address a series of issues identified by the aerospace community as being desirable to include in a next generation composite impact model, an orthotropic, macroscopic constitutive model incorporating both plasticity and damage suitable for implementation within the commercial LS-DYNA computer code is being developed. The plasticity model is based on extending the Tsai-Wu composite failure model into a strain hardening-based orthotropic plasticity model with a non-associative flow rule. The evolution of the yield surface is determined based on tabulated stress-strain curves in the various normal and shear directions and is tracked using the effective plastic strain. To compute the evolution of damage, a strain equivalent semi-coupled formulation is used in which a load in one direction results in a stiffness reduction in multiple material coordinate directions. A detailed analysis is carried out to ensure that the strain equivalence assumption is appropriate for the derived plasticity and damage formulations that are employed in the current model. Procedures to develop the appropriate input curves for the damage model are presented and the process required to develop an appropriate characterization test matrix is discussed.

  15. Failure Analysis of a Sheet Metal Blanking Process Based on Damage Coupling Model

    NASA Astrophysics Data System (ADS)

    Wen, Y.; Chen, Z. H.; Zang, Y.

    2013-11-01

    In this paper, a blanking process of sheet metal is studied by the methods of numerical simulation and experimental observation. The effects of varying technological parameters related to the quality of products are investigated. An elastoplastic constitutive equation accounting for isotropic ductile damage is implemented into the finite element code ABAQUS with a user-defined material subroutine UMAT. The simulations of the damage evolution and ductile fracture in a sheet metal blanking process have been carried out by the FEM. In order to guarantee computation accuracy and avoid numerical divergence during large plastic deformation, a specified remeshing technique is successively applied when severe element distortion occurs. In the simulation, the evolutions of damage at different stage of the blanking process have been evaluated and the distributions of damage obtained from simulation are in proper agreement with the experimental results.

  16. Measurements and analysis of surface damage on oil-impregnated insulation paper caused by partial discharge

    NASA Astrophysics Data System (ADS)

    Yan, Jiaming; Liao, Ruijin; Yang, Lijun; Zhu, Mengzhao

    2011-05-01

    Surface topography, surface roughness, and surface conductivity of oil-impregnated insulation paper were studied during the damage process caused by partial discharge within the cavity of the paper. Products generated on the surface during this process were studied, as well. According to phase-resolved partial discharge patterns, the damage process can be divided into five stages. At each of the stages, surface conditions of insulation were analyzed by optical microscopy, scanning electron microscopy, atomic force microscopy and high-resistance meter. 'Ablating', 'peeling', 'cracking in silk', 'pitting' and 'electrical treeing' appear on insulation surfaces one after another during the five stages of the damage process, along with sequential generation of droplets and crystalline solids. Surface roughness initially decreases, then increases. Finally, surface conductivity exhibits a general increasing trend, before it eventually stabilizes. However, its growth rate varies in different stages of damage.

  17. Analysis of primary damage in silicon carbide under fusion and fission neutron spectra

    NASA Astrophysics Data System (ADS)

    Guo, Daxi; Zang, Hang; Zhang, Peng; Xi, Jianqi; Li, Tao; Ma, Li; He, Chaohui

    2014-12-01

    Irradiation parameters on primary damage states of SiC are evaluated and compared for the first wall of ITER under deuterium-deuterium (DD) and deuterium-tritium (DT) operation, the high temperature gas-cooled reactor (HTGR) and high flux isotope reactor (HFIR). With the same neutron fluence, the studied fusion spectra produce more damage and much higher gas production than the fission spectra. Due to comparable gas production and similar weighted primary recoil spectra, HFIR is considered suitable to simulate the neutron irradiation in an HTGR. In contrast to the significant differences between the weighted primary recoil spectra of the fission and the fusion spectra, the weighted secondary recoil spectra of HFIR and HTGR match those of DD and DT, indicating that displacement cascades by the fission and the fusion irradiation are similar when the damage distribution among damaged regions by secondary recoils is taken into account.

  18. Finite Element Analysis of Damage in Fibrous Composites Using a Micromechanical Model

    DTIC Science & Technology

    1993-12-01

    polymer matrix composite laminate with a center hole in order to study the progression of damage and final failure during tensile loading. The comparisons between the present predictions and the experimental results for the previous examples are very

  19. The characteristic analysis of spectral image for cabbage leaves damaged by diamondback moth pests

    NASA Astrophysics Data System (ADS)

    Lin, Li-bo; Li, Hong-ning; Cao, Peng-fei; Qin, Feng; Yang, Shu-ming; Feng, Jie

    2015-02-01

    Cabbage growth and health diagnosis are important parts for cabbage fine planting, spectral imaging technology with the advantages of obtaining spectrum and space information of the target at the same time, which has become a research hotspot at home and abroad. The experiment measures the reflection spectrum at different stages using liquid crystal tunable filter (LCTF) and monochromatic CMOS camera composed of spectral imaging system for cabbage leaves damaged by diamondback moth pests, and analyzes its feature bands and the change of spectral parameters. The study shows that the feature bands of cabbage leaves damaged by diamondback moth pests have a tendency to blue light direction, the red edge towards blue shift, and red valley raising in spectral characteristic parameters, which have a good indication in diagnosing the extent of cabbage damaged by pests. Therefore, it has a unique advantage of monitoring the cabbage leaves damaged by diamondback moth pests by combinating feature bands and spectral characteristic parameters in spectral imaging technology.

  20. Physical limits of semiconductor laser operation: A time-resolved analysis of catastrophic optical damage

    SciTech Connect

    Ziegler, Mathias; Hempel, Martin; Tomm, Jens W.; Elsaesser, Thomas; Larsen, Henning E.; Andersen, Peter E.; Clausen, Soennik; Elliott, Stella N.

    2010-07-12

    The early stages of catastrophic optical damage (COD) in 808 nm emitting diode lasers are mapped by simultaneously monitoring the optical emission with a 1 ns time resolution and deriving the device temperature from thermal images. COD occurs in highly localized damage regions on a 30 to 400 ns time scale which is determined by the accumulation of excess energy absorbed from the optical output. We identify regimes in which COD is avoided by the proper choice of operation parameters.

  1. Numerical analysis of dynamic thermoviscoelastic contact with damage of a rod

    NASA Astrophysics Data System (ADS)

    Andrews, K. T.; Fernandez, J. R.; Shillor, M.

    2005-12-01

    We describe and analyse a model for a problem of thermoviscoelastic dynamic contact which allows for the general evolution of the material damage. The effects on the mechanical properties of the material due to crack expansion are described by a damage field, which measures the decrease in the load-bearing capacity of the material. The damage process is assumed to be reversible and the microcracks which develop as a result of tension or compression may grow or disappear. The geometric setting is that of a 1D rod which may contact a deformable obstacle. The contact is modelled by the normal compliance condition and the stress-strain constitutive equation is of Kelvin-Voigt type. The model consists of a coupled system of energy-elasticity equations together with a non-linear parabolic inclusion for the damage field. The existence of a local weak solution is established using penalization, a finite element algorithm for the solution is constructed and analysed and the results of numerical simulations based on this algorithm are presented. The simulations illustrate how the size of the normal compliance coefficients, the damage rate coefficients and the applied force affect the character of the evolution of the damage. In particular, cycles of bonding and debonding can occur.

  2. Failure Analysis of Warm Stamping of Magnesium Alloy Sheet Based on an Anisotropic Damage Model

    NASA Astrophysics Data System (ADS)

    Zhao, P. J.; Chen, Z. H.; Dong, C. F.

    2014-11-01

    Based on the frame work of continuum damage mechanics, a research work of anisotropic damage evolution in warm stamping process of magnesium alloy sheets has been carried out by means of a combined experimental-numerical method. The aim was to predict formability of warm stamping of AZ31 Mg alloy sheets by taking the thermal and damage effects into account. In the presented work, a temperature-dependent anisotropic yield function suitable for cold rolling sheet metals together with an anisotropic damage model was implemented into the a VUMAT subroutine for ABAQUS/EXPLICIT. The evolution of internal damage in the form of void growth and coalescence in AZ31 Mg alloy sheet was observed by means of scanning electron microscopy (SEM). Moreover, a coupled thermo-mechanical simulation of the stamping process was performed using the implemented code at different temperatures. The parameters employed in the simulation were determined by the standard tensile tests and algebraic manipulation. The overall anisotropic damage process from crack initiation to final propagation in local area of blank was simulated. Numerical results show that the prediction of the site of crack initiation and the orientation of crack propagation are consistent with the data observed in warm stamping experiments.

  3. Dynamic transcriptional signature and cell fate analysis reveals plasticity of individual neural plate border cells.

    PubMed

    Roellig, Daniela; Tan-Cabugao, Johanna; Esaian, Sevan; Bronner, Marianne E

    2017-03-29

    The 'neural plate border' of vertebrate embryos contains precursors of neural crest and placode cells, both defining vertebrate characteristics. How these lineages segregate from neural and epidermal fates has been a matter of debate. We address this by performing a fine-scale quantitative temporal analysis of transcription factor expression in the neural plate border of chick embryos. The results reveal significant overlap of transcription factors characteristic of multiple lineages in individual border cells from gastrula through neurula stages. Cell fate analysis using a Sox2 (neural) enhancer reveals that cells that are initially Sox2+ cells can contribute not only to neural tube but also to neural crest and epidermis. Moreover, modulating levels of Sox2 or Pax7 alters the apportionment of neural tube versus neural crest fates. Our results resolve a long-standing question and suggest that many individual border cells maintain ability to contribute to multiple ectodermal lineages until or beyond neural tube closure.

  4. Progressive Damage Analysis of Laminated Composite (PDALC) (A Computational Model Implemented in the NASA COMET Finite Element Code). 2.0

    NASA Technical Reports Server (NTRS)

    Coats, Timothy W.; Harris, Charles E.; Lo, David C.; Allen, David H.

    1998-01-01

    A method for analysis of progressive failure in the Computational Structural Mechanics Testbed is presented in this report. The relationship employed in this analysis describes the matrix crack damage and fiber fracture via kinematics-based volume-averaged damage variables. Damage accumulation during monotonic and cyclic loads is predicted by damage evolution laws for tensile load conditions. The implementation of this damage model required the development of two testbed processors. While this report concentrates on the theory and usage of these processors, a complete listing of all testbed processors and inputs that are required for this analysis are included. Sample calculations for laminates subjected to monotonic and cyclic loads were performed to illustrate the damage accumulation, stress redistribution, and changes to the global response that occurs during the loading history. Residual strength predictions made with this information compared favorably with experimental measurements.

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

    PubMed Central

    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

  6. Comparative Proteomic Analysis Reveals the Effects of Exogenous Calcium against Acid Rain Stress in Liquidambar formosana Hance Leaves.

    PubMed

    Hu, Wen-Jun; Wu, Qian; Liu, Xiang; Shen, Zhi-Jun; Chen, Juan; Liu, Ting-Wu; Chen, Juan; Zhu, Chun-Quan; Wu, Fei-Hua; Chen, Lin; Wei, Jia; Qiu, Xiao-Yun; Shen, Guo-Xin; Zheng, Hai-Lei

    2016-01-04

    Acid rain (AR) impacts forest health by leaching calcium (Ca) away from soils and plants. Ca is an essential element and participates in various plant physiological responses. In the present study, the protective role of exogenous Ca in alleviating AR stress in Liquidambar formosana Hance at the physiological and proteomic levels was examined. Our results showed that low Ca condition resulted in the chlorophyll content and photosynthesis decreasing significantly in L. formosana leaves; however, these effects could be reversed by high Ca supplementation. Further proteomic analyses successfully identified 81 differentially expressed proteins in AR-treated L. formosana under different Ca levels. In particular, some of the proteins are involved in primary metabolism, photosynthesis, energy production, antioxidant defense, transcription, and translation. Moreover, quantitative real time polymerase chain reaction (qRT-PCR) results indicated that low Ca significantly increased the expression level of the investigated Ca-related genes, which can be reversed by high Ca supplementation under AR stress. Further, Western blotting analysis revealed that exogenous Ca supply reduced AR damage by elevating the expression of proteins involved in the Calvin cycle, reactive oxygen species (ROS) scavenging system. These findings allowed us to better understand how woody plants respond to AR stress at various Ca levels and the protective role of exogenous Ca against AR stress in forest tree species.

  7. Principal Component Analysis Reveals Age-Related and Muscle-Type-Related Differences in Protein Carbonyl Profiles of Muscle Mitochondria

    PubMed Central

    Feng, Juan; Navratil, Marian; Thompson, LaDora V.; Arriaga, Edgar A.

    2011-01-01

    Carbonyl-modified proteins are considered markers of oxidative damage caused by oxidative stress, aging, and disease. Here we use a previously developed capillary electrophoretic method for detecting femtomole (10−15 mole) carbonyl levels in mitochondrial proteins that are size separated and profiled. For protein labeling, carbonyls were tagged with Alexa 488 hydrazine and amine groups in proteins with 3-(2-furoyl)quinoline-2-carboxaldehyde. Total mitochondrial protein carbonyl levels were statistically higher in fast- than in slow-twitch muscle of young Fischer 344 rats, and statistically higher in old than in young slow-twitch muscle. Even when some statistical comparisons of the total protein carbonyl levels would not reveal differences, principal component analysis (PCA) classified the carbonyl profiles into four distinct sample groups of different age and muscle types. In addition, PCA was used to predict that most age-related or muscle-type-related changes in carbonyl levels occur in proteins with a molecular weight between 9.8 and 11.7 kD. PMID:19126840

  8. Finite Element Analysis on the Impact-Induced Damage of Composite Fan Blades Subjected to a Bird Strike

    NASA Astrophysics Data System (ADS)

    Nishikawa, Masaaki; Hemmi, Kei; Park, Sangchul; Nadabe, Takeaki; Takeda, Nobuo

    Carbon fiber-reinforced composites have been recently applied for engine fan blades, because of their high specific strength. In the design of the fan blade, the bird-strike impact is one of the greatest concerns, since impact-induced damage can lead to the engine stall. This study presented a numerical method to analyze the bird-strike impact as a soft-body impact on cantilevered composite panel. Especially, we coupled a stabilized dynamic contact analysis, which enables predicting impact force on the panel appropriately, with laminate damage analysis to predict the impact-induced progressive damage in the composite. This method was verified through the comparison with the experimental results. With the numerical method, we investigated the effect of impact condition, blade thickness and shape on the impact-induced damage in composite fan blade subjected to a bird strike. An intermediate blade thickness and a large blade curvature help improving the bird-striking impact resistance of the composite.

  9. Analysis of Deformation Damage and Fracture of 7050 Aluminum Alloy During Double Shear Based on Experiment and Simulation

    NASA Astrophysics Data System (ADS)

    Chen, Han; Li, Fuguo; Cao, Jun; Li, Jinghui; Wang, Qianru; Li, Weina

    2017-02-01

    Based on the finite element simulation and experimental analysis, this paper mainly studies the deformation damage and fracture of 7050-H112 aluminum alloy during double shear based on the elastic strain energy density. The analyses of deformation damage and fracture for ends-free and ends-constrained specimens in complex stress and strain states have been carried out. The different stress and strain states which are characterized by stress triaxiality and strain Lode parameter have important effects on damage and fracture according to the simulation and experimental results. The final fracture is mainly caused by tensile stress both for specimens with ends free and ends constraint. Meanwhile, the shear planes are mainly in a state of shear strain when fracture occurs according to the analysis of stress triaxiality and strain Lode parameter. Three characteristic areas (radiation area, fiber area and shear lips) are observed from fracture morphology and account for different proportions on fracture surface for ends-free and ends-constrained specimens. The simulated results on the damage evolution and fracture from finite element method (FEM) are in good agreement with the experimental ones. Besides, there are competitive relations between ductile fracture and brittle fracture during the process of fracture in this paper.

  10. Vibration-based damage detection in an aircraft wing scaled model using principal component analysis and pattern recognition

    NASA Astrophysics Data System (ADS)

    Trendafilova, I.; Cartmell, M. P.; Ostachowicz, W.

    2008-06-01

    This study deals with vibration-based fault detection in structures and suggests a viable methodology based on principal component analysis (PCA) and a simple pattern recognition (PR) method. The frequency response functions (FRFs) of the healthy and the damaged structure are used as initial data. A PR procedure based on the nearest neighbour principle is applied to recognise between the categories of the damaged and the healthy wing data. A modified PCA method is suggested here, which not only reduces the dimensionality of the FRFs but in addition makes the PCA transformed data from the two categories more differentiable. It is applied to selected frequency bands of FRFs which permits the reduction of the PCA transformed FRFs to two new variables, which are used as damage features. In this study, the methodology is developed and demonstrated using the vibration response of a scaled aircraft wing simulated by a finite element (FE) model. The suggested damage detection methodology is based purely on the analysis of the vibration response of the structure. This makes it quite generic and permits its potential development and application for measured vibration data from real aircraft wings as well as for other real and complex structures.

  11. Analysis of Deformation Damage and Fracture of 7050 Aluminum Alloy During Double Shear Based on Experiment and Simulation

    NASA Astrophysics Data System (ADS)

    Chen, Han; Li, Fuguo; Cao, Jun; Li, Jinghui; Wang, Qianru; Li, Weina

    2017-03-01

    Based on the finite element simulation and experimental analysis, this paper mainly studies the deformation damage and fracture of 7050-H112 aluminum alloy during double shear based on the elastic strain energy density. The analyses of deformation damage and fracture for ends-free and ends-constrained specimens in complex stress and strain states have been carried out. The different stress and strain states which are characterized by stress triaxiality and strain Lode parameter have important effects on damage and fracture according to the simulation and experimental results. The final fracture is mainly caused by tensile stress both for specimens with ends free and ends constraint. Meanwhile, the shear planes are mainly in a state of shear strain when fracture occurs according to the analysis of stress triaxiality and strain Lode parameter. Three characteristic areas (radiation area, fiber area and shear lips) are observed from fracture morphology and account for different proportions on fracture surface for ends-free and ends-constrained specimens. The simulated results on the damage evolution and fracture from finite element method (FEM) are in good agreement with the experimental ones. Besides, there are competitive relations between ductile fracture and brittle fracture during the process of fracture in this paper.

  12. Application of ion-beam analysis techniques to the study of irradiationn damage in zirconium alloys

    SciTech Connect

    Howe, L.M.; Phillips, D.; Zou, H.; Forster, J.; Siegele, R.; Davies, J.A.; Motta, A.T.; Faldowski, J.A.; Okamoto, P.R.

    1995-12-01

    Ion-beam-analysis techniques are being used to provide an understanding of the nature of collision cascades, irradiation-induced phase changes, lattice location of solute atoms and defect-solute atom interactions in various zirconium alloys. In zirconium intermetallic compounds, such as Zr{sub 3}Fe, Zr{sub 2}Fe, ZrFe{sub 2}, Zr{sub 3}(Fe{sub x},Ni{sub 1-x}) and (Zr,M){sub 3}Fe, electron and ion irradiations have been used to obtain detailed information on the crystalline-to-amorphous transformation occurring during the irradiation. Transmission-electron-microscopy (TEM) observations have provided information on the nature of the damage produced in individual cascades, the critical dose required for amorphization, and the critical temperature for amorphization. In a study on the electron-energy dependence of amorphization in Zr{sub 3}Fe, Zr{sub 2},Fe and ZrCr{sub 2}, in situ high-voltage-electron-microscope investigations were combined with high-energy forward-elastic-recoil measurements to yield information on the threshold displacement energies for Zr and Fe or Cr in these lattices, as well as the role of secondary displacements of lattice atoms by recoil impurities (C,O) at low electron energies. In Zr implanted with {sup 56}Fe ions and subsequently bombarded with {sup 40}Ar ions at 723 K, subsequent secondary-ion-mass-spectrometry (SIMS) analyses were used to monitor the effect of irradiation on the migration of Fe in the Zr lattice. In addition, ion-channeling investigations have been used to determine the lattice sites of solute atoms in Zr as well as the details of the interaction between the solute atoms and the irradiation-produced defects.

  13. Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.

    PubMed

    Wen, Dingqiao; Yu, Yun; Hahn, Matthew W; Nakhleh, Luay

    2016-06-01

    The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.

  14. Proteomics Analysis of Ovarian Cancer Cell Lines and Tissues Reveals Drug Resistance-associated Proteins

    PubMed Central

    CRUZ*, ISA N.; COLEY*, HELEN M.; KRAMER, HOLGER B.; MADHURI, THUMULURU KAVITAH; SAFUWAN, NUR A.M.; ANGELINO, ANA RITA; YANG, MIN

    2016-01-01

    Background: Carboplatin and paclitaxel form the cornerstone of chemotherapy for epithelial ovarian cancer, however, drug resistance to these agents continues to present challenges. Despite extensive research, the mechanisms underlying this resistance remain unclear. Materials and Methods: A 2D-gel proteomics method was used to analyze protein expression levels of three human ovarian cancer cell lines and five biopsy samples. Representative proteins identified were validated via western immunoblotting. Ingenuity pathway analysis revealed metabolomic pathway changes. Results: A total of 189 proteins were identified with restricted criteria. Combined treatment targeting the proteasome-ubiquitin pathway resulted in re-sensitisation of drug-resistant cells. In addition, examination of five surgical biopsies of ovarian tissues revealed α-enolase (ENOA), elongation factor Tu, mitochondrial (EFTU), glyceraldehyde-3-phosphate dehydrogenase (G3P), stress-70 protein, mitochondrial (GRP75), apolipoprotein A-1 (APOA1), peroxiredoxin (PRDX2) and annexin A (ANXA) as candidate biomarkers of drug-resistant disease. Conclusion: Proteomics combined with pathway analysis provided information for an effective combined treatment approach overcoming drug resistance. Analysis of cell lines and tissues revealed potential prognostic biomarkers for ovarian cancer. *These Authors contributed equally to this study. PMID:28031236

  15. Meta-analysis of genetic and environmental Parkinson's disease models reveals a common role of mitochondrial protection pathways.

    PubMed

    Soreq, Lilach; Ben-Shaul, Yoram; Israel, Zvi; Bergman, Hagai; Soreq, Hermona

    2012-03-01

    Both genetic and environmental factors trigger risks of and protection from Parkinson's disease, the second most common neurodegenerative syndrome, but possible inter-relationships between these risk and protection processes were not yet explored. By examining gene expression changes in the brains of mice under multiple treatments that increase or attenuate PD symptoms we detected underlying disease and protection-associated genes and pathways. In search for potential links between these different genes and pathways, we conducted meta-analysis on 131 brain region transcriptomes from mice over-expressing native or mutated α-synuclein (SNCA) with or without the protective HSP70 chaperone, or exposed to the dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), with or without the protective acetylcholinesterase (AChE-R) variant. All these models showed shared risk-inducible and protection-suppressible transcript modifications. Self-organized map (SOM) classification revealed risk- and protection-associated alterations in nuclear and mitochondrial metal ion-regulated transcripts, respectively; Gene Ontology based analysis validated these pathways. To complement this approach, and identify potential outcome damages, we further searched for shared functional enrichments in the lists of genes detected in young SNCA mutant or in old SNCA mutants and MPTP-exposed mice. This post-hoc functional analysis identified early-onset changes in Parkinsonian, immune and alternative splicing pathways which shifted into late-onset or exposure-associated NFkB-mediated neuro-inflammation. Our study suggests metal ions-mediated cross-talk between nuclear and mitochondrial pathways by both environmental and genetic risk and protective factors involved in Parkinson's disease, which eventually culminates in neuro-inflammation. Together, these findings offer new insights and novel targets for therapeutic interference with the gene-environment interactions underlying

  16. Debris Flow Damage Incurred to Buildings: An In-Situ Back Analysis

    NASA Astrophysics Data System (ADS)

    Jalayer, Fatemeh; Aronica, Giuseppe T.; Recupero, Antonino; Carozza, Stefano; Manfredi, Gaetano

    2016-04-01

    The flash-flood debris event of the October 1st 2009 in the area of Messina, Sicily, Italy has led to loss of life and significant damage to the constructed environment. Focusing the attention on an eighteenth masonry building (damaged and upgraded after the Messina-Reggio Calabria Earthquake of 1906) located in the village of Scaletta Zanclea, we have strived to reconstruct analytically the damages incurred to this building due to the debris flow event of 2009. In order to re-construct the damages incurred to the building due to the flash flood/debris flow event, hydrostatic and hydrodynamic force envelopes, calculated via a 2D hydrodynamic finite element model specifically designed for debris flow spatial propagation, have been applied to the building in question (assuming perfect coherence between static and dynamic maxima). The hydrograph for the solid discharge is then estimated by scaling up the liquid volume to the estimated debris volume. The hydrodynamic model used for the debris flow propagation proved to be well suited for these specific applications. The debris flow diffusion is simulated by solving the differential equations for a single-phase 2D flow employing triangular mesh elements, taking into account also the channeling of the flow through the building. The damage to the building is modeled, based on the maximum hydraulic actions caused by the debris flow, using 2D finite shell elements, modeling the boundary conditions provided by the openings, floor slab, orthogonal wall panels and the foundation. The finite element approach showed its capability in describing the complex geometries of the urban environments as the distributed nature of the 2D code allows to derive a reliable spatial distribution of debris flow actions. The reconstruction of the event and the damages to the case-study building confirms the location of the damages induced by the event.

  17. Scaring as a tool to alleviate crop damage by geese: Revealing differences between farmers' perceptions and the scale of the problem.

    PubMed

    Simonsen, Caroline E; Tombre, Ingunn M; Madsen, Jesper

    2017-03-01

    Expanding populations of farmland foraging geese are causing escalating conflict with agriculture. We used questionnaires to investigate farmers´ perceptions in mid-Norway of spring staging geese and the extent to which they attempt to reduce pasture damage by goose scaring. We predicted farmers' scaring effort (a measure of dissatisfaction) to increase on fields closer to goose roosting sites where goose grazing intensity was highest (measured by dropping counts). Results showed no such relationship, suggesting that farmers' perception of goose use was not linked to actual goose use, but influenced by sociological factors and individual opinion. These results confirm the need to distribute subsidies/compensation to affected farmers based upon quantifiable measures of goose use rather than complaint levels. To avoid further conflict escalation, it is equally important that managers are aware of farmers´ perceptions and their causes, to effectively target communication about policies and measures to mitigate goose-agriculture problems.

  18. Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA.

    PubMed

    Redrejo-Rodríguez, Modesto; Vigouroux, Armelle; Mursalimov, Aibek; Grin, Inga; Alili, Doria; Koshenov, Zhanat; Akishev, Zhiger; Maksimenko, Andrei; Bissenbaev, Amangeldy K; Matkarimov, Bakhyt T; Saparbaev, Murat; Ishchenko, Alexander A; Moréra, Solange

    2016-01-01

    Oxidatively damaged DNA bases are substrates for two overlapping repair pathways: DNA glycosylase-initiated base excision repair (BER) and apurinic/apyrimidinic (AP) endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, an AP endonuclease cleaves DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases, whereas in the NIR pathway, the same AP endonuclease incises DNA 5' to an oxidized base. The majority of characterized AP endonucleases possess classic BER activities, and approximately a half of them can also have a NIR activity. At present, the molecular mechanism underlying DNA substrate specificity of AP endonucleases remains unclear mainly due to the absence of a published structure of the enzyme in complex with a damaged base. To identify critical residues involved in the NIR function, we performed biochemical and structural characterization of Bacillus subtilis AP endonuclease ExoA and compared its crystal structure with the structures of other AP endonucleases: Escherichia coli exonuclease III (Xth), human APE1, and archaeal Mth212. We found conserved amino acid residues in the NIR-specific enzymes APE1, Mth212, and ExoA. Four of these positions were studied by means of point mutations in APE1: we applied substitution with the corresponding residue found in NIR-deficient E. coli Xth (Y128H, N174Q, G231S, and T268D). The APE1-T268D mutant showed a drastically decreased NIR activity and an inverted Mg(2+) dependence of the AP site cleavage activity, which is in line with the presence of an aspartic residue at the equivalent position among other known NIR-deficient AP endonucleases. Taken together, these data show that NIR is an evolutionarily conserved function in the Xth family of AP endonucleases.

  19. Two damaging hydrogeological events in Calabria, September 2000 and November 2015. Comparative analysis of causes and effects

    NASA Astrophysics Data System (ADS)

    Petrucci, Olga; Caloiero, Tommaso; Aurora Pasqua, Angela

    2016-04-01

    Each year, especially during winter season, some episode of intense rain affects Calabria, the southernmost Italian peninsular region, triggering flash floods and mass movements that cause damage and fatalities. This work presents a comparative analysis between two events that affected the southeast sector of the region, in 2000 and 2014, respectively. The event occurred between 9th and 10th of September 2000 is known in Italy as Soverato event, after the name of the municipality where it reached the highest damage severity. In the Soverato area, more than 200 mm of rain that fell in 24 hours caused a disastrous flood that swept away a campsite at about 4 a.m., killing 13 people and hurting 45. Besides, the rain affected a larger area, causing damage in 89 (out of 409) municipalities of the region. Flooding was the most common process, which damaged housing and trading. Landslide mostly affected the road network, housing and cultivations. The most recent event affected the same regional sector between 30th October and 2nd November 2015. The daily rain recorded at some of the rain gauges of the area almost reached 400 mm. Out of the 409 municipalities of Calabria, 109 suffered damage. The most frequent types of processes were both flash floods and landslides. The most heavily damaged element was the road network: the representative picture of the event is a railway bridge destroyed by the river flow. Housing was damaged too, and 486 people were temporarily evacuated from home. The event also caused a victim killed by a flood. The event-centred study approach aims to highlight differences and similarities in both the causes and the effects of the two events that occurred at a temporal distance of 14 years. The comparative analysis focus on three main aspects: the intensity of triggering rain, the modifications of urbanised areas, and the evolution of emergency management. The comparative analysis of rain is made by comparing the return period of both daily and

  20. Experimental and Numerical Analysis of Damage in Woven GFRP Composites Under Large-deflection Bending

    NASA Astrophysics Data System (ADS)

    Ullah, Himayat; Harland, Andy R.; Silberschmidt, Vadim V.

    2012-10-01

    Textile-reinforced composites such as glass fibre-reinforced polymer (GFRP) used in sports products can be exposed to different in-service conditions such as large bending deformation and multiple impacts. Such loading conditions cause high local stresses and strains, which result in multiple modes of damage and fracture in composite laminates due to their inherent heterogeneity and non-trivial microstructure. In this paper, various damage modes in GFRP laminates are studied using experimental material characterisation, non-destructive micro-structural damage evaluation and numerical simulations. Experimental tests are carried out to characterise the behaviour of these materials under large-deflection bending. To obtain in-plane shear properties of laminates, tensile tests are performed using a full-field strain-measurement digital image correlation technique. X-ray micro computed tomography (Micro CT) is used to investigate internal material damage modes - delamination and cracking. Two-dimensional finite element (FE) models are implemented in the commercial code Abaqus to study the deformation behaviour and damage in GFRP. In these models, multiple layers of bilinear cohesive-zone elements are employed to study the onset and progression of inter-ply delamination and intra-ply fabric fracture of composite laminate, based on the X-ray Micro CT study. The developed numerical models are capable to simulate these features with their mechanisms as well as subsequent mode coupling observed in tests and Micro CT scanning. The obtained results of simulations are in agreement with experimental data.

  1. Analysis of DNA damage using the comet assay in infants fed cow's milk.

    PubMed

    Dündaröz, Ruşen; Ulucan, Hakan; Aydin, Halil Ibrahim; Güngör, Tayfun; Baltaci, Volkan; Denli, Metin; Sanisoğlu, Yavuz

    2003-01-01

    It has been hypothesized that non-human milk feeding may increase the risk for cancer or for a specific cancer or group of cancers as well as the risk for diseases such as type-1 diabetes mellitus and Crohn's disease. Regarding DNA damage leading to cancer development in the absence of human milk protection, a comparison between infants fed human milk and cow's milk has been performed. Each group consisted of 35 infants, whose ages ranged from 9 to 12 months. The level of DNA damage in the peripheral blood lymphocytes of infants has been studied by the comet assay. A significant increase has been found in the number of limited DNA-damaged (p < 0.001) and extensive DNA-damaged (p < 0.001) cells of infants fed cow's milk. To our knowledge, this is the first study using the comet assay on infants not breast-fed. Supporting our previous SCE study, these results suggest that there is some level of DNA damage in the lymphocytes of infants not breast-fed and this may lead to malignancy in childhood or later in life.

  2. Multiscale Modeling and Analysis of an Ultra-Precision Damage Free Machining Method

    NASA Astrophysics Data System (ADS)

    Guan, Chaoliang; Peng, Wenqiang

    2016-06-01

    Under the condition of high laser flux, laser induced damage of optical element does not occur is the key to success of laser fusion ignition system. US government survey showed that the processing defects caused the laser induced damage threshold (LIDT) to decrease is one of the three major challenges. Cracks and scratches caused by brittle and plastic removal machining are fatal flaws. Using hydrodynamic effect polishing method can obtain damage free surface on quartz glass. The material removal mechanism of this typical ultra-precision machining process was modeled in multiscale. In atomic scale, chemical modeling illustrated the weakening and breaking of chemical bond energy. In particle scale, micro contact modeling given the elastic remove mode boundary of materials. In slurry scale, hydrodynamic flow modeling showed the dynamic pressure and shear stress distribution which are relations with machining effect. Experiment was conducted on a numerically controlled system, and one quartz glass optical component was polished in the elastic mode. Results show that the damages are removed away layer by layer as the removal depth increases due to the high damage free machining ability of the HEP. And the LIDT of sample was greatly improved.

  3. Analytical and numerical analysis of frictional damage in quasi brittle materials

    NASA Astrophysics Data System (ADS)

    Zhu, Q. Z.; Zhao, L. Y.; Shao, J. F.

    2016-07-01

    Frictional sliding and crack growth are two main dissipation processes in quasi brittle materials. The frictional sliding along closed cracks is the origin of macroscopic plastic deformation while the crack growth induces a material damage. The main difficulty of modeling is to consider the inherent coupling between these two processes. Various models and associated numerical algorithms have been proposed. But there are so far no analytical solutions even for simple loading paths for the validation of such algorithms. In this paper, we first present a micro-mechanical model taking into account the damage-friction coupling for a large class of quasi brittle materials. The model is formulated by combining a linear homogenization procedure with the Mori-Tanaka scheme and the irreversible thermodynamics framework. As an original contribution, a series of analytical solutions of stress-strain relations are developed for various loading paths. Based on the micro-mechanical model, two numerical integration algorithms are exploited. The first one involves a coupled friction/damage correction scheme, which is consistent with the coupling nature of the constitutive model. The second one contains a friction/damage decoupling scheme with two consecutive steps: the friction correction followed by the damage correction. With the analytical solutions as reference results, the two algorithms are assessed through a series of numerical tests. It is found that the decoupling correction scheme is efficient to guarantee a systematic numerical convergence.

  4. Metagenomic analysis reveals presence of Treponema denticola in a tissue biopsy of the Iceman.

    PubMed

    Maixner, Frank; Thomma, Anton; Cipollini, Giovanna; Widder, Stefanie; Rattei, Thomas; Zink, Albert

    2014-01-01

    Ancient hominoid genome studies can be regarded by definition as metagenomic analyses since they represent a mixture of both hominoid and microbial sequences in an environment. Here, we report the molecular detection of the oral spirochete Treponema denticola in ancient human tissue biopsies of the Iceman, a 5,300-year-old Copper Age natural ice mummy. Initially, the metagenomic data of the Iceman's genomic survey was screened for bacterial ribosomal RNA (rRNA) specific reads. Through ranking the reads by abundance a relatively high number of rRNA reads most similar to T. denticola was detected. Mapping of the metagenome sequences against the T. denticola genome revealed additional reads most similar to this opportunistic pathogen. The DNA damage pattern of specifically mapped reads suggests an ancient origin of these sequences. The haematogenous spread of bacteria of the oral microbiome often reported in the recent literature could already explain the presence of metagenomic reads specific for T. denticola in the Iceman's bone biopsy. We extended, however, our survey to an Iceman gingival tissue sample and a mouth swab sample and could thereby detect T. denticola and Porphyrimonas gingivalis, another important member of the human commensal oral microflora. Taken together, this study clearly underlines the opportunity to detect disease-associated microorganisms when applying metagenomics-enabled approaches on datasets of ancient human remains.

  5. Analysis and Support Initiative for Structural Technology (ASIST) Delivery Order 0016: USAF Damage Tolerant Design Handbook: Guidelines For the Analysis and Design of Damage Tolerant Aircraft Structures

    DTIC Science & Technology

    2002-11-01

    229-4417 email: berens@udri.udayton.edu DARWIN Design Assessment of Reliability WIth INspection ( DARWIN ) is a risk analysis program for...calculating the probability of failure in turbine engine disks. With a graphical user interface for problem setup and output, DARWIN integrates finite...Analysis of Cracks Handbook (Tada, et al., 1973), • Compendium of Stress Intensity Factors (Rooke & Cartwright , 1976), • Stress Intensity Factors

  6. New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis.

    PubMed

    Pérez-Amador, M A; Lidder, P; Johnson, M A; Landgraf, J; Wisman, E; Green, P J

    2001-12-01

    In this study, DNA microarray analysis was used to expand our understanding of the dst1 mutant of Arabidopsis. The dst (downstream) mutants were isolated originally as specifically increasing the steady state level and the half-life of DST-containing transcripts. As such, txhey offer a unique opportunity to study rapid sequence-specific mRNA decay pathways in eukaryotes. These mutants show a threefold to fourfold increase in mRNA abundance for two transgenes and an endogenous gene, all containing DST elements, when examined by RNA gel blot analysis; however, they show no visible aberrant phenotype. Here, we use DNA microarrays to identify genes with altered expression levels in dst1 compared with the parental plants. In addition to verifying the increase in the transgene mRNA levels, which were used to isolate these mutants, we were able to identify new genes with altered mRNA abundance in dst1. RNA gel blot analysis confirmed the microarray data for all genes tested and also was used to catalog the first molecular differences in gene expression between the dst1 and dst2 mutants. These differences revealed previously unknown molecular phenotypes for the dst mutants that will be helpful in future analyses. Cluster analysis of genes altered in dst1 revealed new coexpression patterns that prompt new hypotheses regarding the nature of the dst1 mutation and a possible role of the DST-mediated mRNA decay pathway in plants.

  7. Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells

    PubMed Central

    Liu, Bing; Gao, Yankun; Ruan, Hai-Bin; Chen, Yue

    2016-01-01

    Proline hydroxylation is a critical cellular mechanism regulating oxygen-response pathways in tumor initiation and progression. Yet, its substrate diversity and functions remain largely unknown. Here, we report a system-wide analysis to characterize proline hydroxylation substrates in cancer cells using an immunoaffinity-purification assisted proteomics strategy. We identified 562 sites from 272 proteins in HeLa cells. Bioinformatic analysis revealed that proline hydroxylation substrates are significantly enriched with mRNA processing and stress-response cellular pathways with canonical and diverse flanking sequence motifs. Structural analysis indicates a significant enrichment of proline hydroxylation participating in the secondary structure of substrate proteins. Our study identified and validated Brd4, a key transcription factor, as a novel proline hydroxylation substrate. Functional analysis showed that the inhibition of proline hydroxylation pathway significantly reduced the proline hydroxylation abundance on Brd4 and affected Brd4-mediated transcriptional activity as well as cell proliferation in AML leukemia cells. Taken together, our study identified a broad regulatory role of proline hydroxylation in cellular oxygen-sensing pathways and revealed potentially new targets that dynamically respond to hypoxia microenvironment in tumor cells. PMID:27764789

  8. mBAND Analysis of Early and Late Damages in the Chromosome of Human Lymphocytes after Exposures to Gamma Rays and Fe Ions

    NASA Technical Reports Server (NTRS)

    Sunagawa, Mayumi; Zhang, Ye; Yeshitla, Samrawit; Kadhim, Munira; Wilson, Bobby; Wu, Honglu

    2013-01-01

    Stable type chromosome aberrations that survive multiple generations of cell division include translocation and inversions. An efficient method to detect an inversion is multi-color banding fluorescent in situ hybridization (mBAND) which allows identification of both inter- and intrachromosome aberrations simultaneously. Post irradiation, chromosome aberrations may also arise after multiple cell divisions as a result of genomic instability. To investigate the stable or late-arising chromosome aberrations induced after radiation exposure, we exposed human lymphocytes to gamma rays and Fe ions ex vivo, and cultured the cells for multiple generations. Chromosome aberrations were analyzed in cells collected at first mitosis and at several time intervals during the culture period post irradiation. With gamma irradiation, about half of the damages observed at first mitosis remained after 7 day- and 14 day- culture, suggesting the transmissibility of damages to the surviving progeny. At the doses that produced similar frequencies of gamma-induced chromosome aberrations as observed at first mitosis, a significantly lower yield of aberrations remained at the same population doublings after Fe ion exposure. At these equitoxic doses, more complex type aberrations were observed for Fe ions, indicating that Fe ion-induced initial chromosome damages are more severe and may lead to cell death. Detailed analysis of breaks participating in total chromosome exchanges within the first cell cycle post irradiation revealed a common hotspot located in the 3p21 region, which is a known fragile site corresponding to the band 6 in the mBand analysis. The breakpoint distribution in chromosomes collected at 7 days, but not at 14 days, post irradiation appeared similar to the distribution in cells collected within the first cell cycle post irradiation. The breakpoint distribution for human lymphocytes after radiation exposure was different from the previously published distribution for human

  9. Analysis of liver damage from radon, X-ray, or alcohol treatments in mice using a self-organizing map

    PubMed Central

    Kanzaki, Norie; Kataoka, Takahiro; Etani, Reo; Sasaoka, Kaori; Kanagawa, Akihiro; Yamaoka, Kiyonori

    2017-01-01

    In our previous studies, we found that low-dose radiation inhibits oxidative stress–induced diseases due to increased antioxidants. Although these effects of low-dose radiation were demonstrated, further research was needed to clarify the effects. However, the analysis of oxidative stress is challenging, especially that of low levels of oxidative stress, because antioxidative substances are intricately involved. Thus, we proposed an approach for analysing oxidative liver damage via use of a self-organizing map (SOM)—a novel and comprehensive technique for evaluating hepatic and antioxidative function. Mice were treated with radon inhalation, irradiated with X-rays, or subjected to intraperitoneal injection of alcohol. We evaluated the oxidative damage levels in the liver from the SOM results for hepatic function and antioxidative substances. The results showed that the effects of low-dose irradiation (radon inhalation at a concentration of up to 2000 Bq/m3, or X-irradiation at a dose of up to 2.0 Gy) were comparable with the effect of alcohol administration at 0.5 g/kg bodyweight. Analysis using the SOM to discriminate small changes was made possible by its ability to ‘learn’ to adapt to unexpected changes. Moreover, when using a spherical SOM, the method comprehensively examined liver damage by radon, X-ray, and alcohol. We found that the types of liver damage caused by radon, X-rays, and alcohol have different characteristics. Therefore, our approaches would be useful as a method for evaluating oxidative liver damage caused by radon, X-rays and alcohol. PMID:27614200

  10. Single-cell analysis challenges the connection between autophagy and senescence induced by DNA damage.

    PubMed

    Filippi-Chiela, Eduardo Cremonese; Bueno e Silva, Mardja Manssur; Thomé, Marcos Paulo; Lenz, Guido

    2015-01-01

    Autophagy and senescence have been described as central features of cell biology, but the interplay between these mechanisms remains obscure. Using a therapeutically relevant model of DNA damage-induced senescence in human glioma cells, we demonstrated that acute treatment with temozolomide induces DNA damage, a transitory activation of PRKAA/AMPK-ULK1 and MAPK14/p38 and the sustained inhibition of AKT-MTOR. This produced a transient induction of autophagy, which was followed by senescence. However, at the single cell level, this coordinated transition was not observed, and autophagy and senescence were triggered in a very heterogeneous manner. Indeed, at a population level, autophagy was highly negatively correlated with senescence markers, while in single cells this correlation did not exist. The inhibition of autophagy triggered apoptosis and decreased senescence, while its activation increased temozolomide-induced senescence, showing that DNA damage-induced autophagy acts by suppressing apoptosis.

  11. Quantifying Traces of Tool Use: A Novel Morphometric Analysis of Damage Patterns on Percussive Tools

    PubMed Central

    Caruana, Matthew V.; Carvalho, Susana; Braun, David R.; Presnyakova, Darya; Haslam, Michael; Archer, Will; Bobe, Rene; Harris, John W. K.

    2014-01-01

    Percussive technology continues to play an increasingly important role in understanding the evolution of tool use. Comparing the archaeological record with extractive foraging behaviors in nonhuman primates has focused on percussive implements as a key to investigating the origins of lithic technology. Despite this, archaeological approaches towards percussive tools have been obscured by a lack of standardized methodologies. Central to this issue have been the use of qualitative, non-diagnostic techniques to identify percussive tools from archaeological contexts. Here we describe a new morphometric method for distinguishing anthropogenically-generated damage patterns on percussive tools from naturally damaged river cobbles. We employ a geomatic approach through the use of three-dimensional scanning and geographical information systems software to statistically quantify the identification process in percussive technology research. This will strengthen current technological analyses of percussive tools in archaeological frameworks and open new avenues for translating behavioral inferences of early hominins from percussive damage patterns. PMID:25415303

  12. An analysis of pump cavitation damage. [Space Shuttle main engine high pressure oxidizer turbopump

    NASA Technical Reports Server (NTRS)

    Brophy, M. C.; Stinebring, D. R.; Billet, M. L.

    1985-01-01

    The cavitation assessment for the space shuttle main engine high pressure oxidizer turbopump is documented. A model of the flow through the pump was developed. Initially, a computational procedure was used to analyze the flow through the inlet casing including the prediction of wakes downstream of the casing vanes. From these flow calculations, cavitation patterns on the inducer blades were approximated and the damage rate estimated. The model correlates the heavy damage on the housing and over the inducer with unsteady blade surface cavitation. The unsteady blade surface cavitation is due to the large incidence changes caused by the wakes of the upstream vanes. Very high cavitation damage rates are associated with this type of cavitation. Design recommendations for reducing the unsteady cavitation include removing the set of vanes closest to the inducer and modifying the remaining vanes.

  13. Implementation and Validation of the Viscoelastic Continuum Damage Theory for Asphalt Mixture and Pavement Analysis in Brazil

    NASA Astrophysics Data System (ADS)

    Nascimento, Luis Alberto Herrmann do

    This dissertation presents the implementation and validation of the viscoelastic continuum damage (VECD) model for asphalt mixture and pavement analysis in Brazil. It proposes a simulated damage-to-fatigue cracked area transfer function for the layered viscoelastic continuum damage (LVECD) program framework and defines the model framework's fatigue cracking prediction error for asphalt pavement reliability-based design solutions in Brazil. The research is divided into three main steps: (i) implementation of the simplified viscoelastic continuum damage (S-VECD) model in Brazil (Petrobras) for asphalt mixture characterization, (ii) validation of the LVECD model approach for pavement analysis based on field performance observations, and defining a local simulated damage-to-cracked area transfer function for the Fundao Project's pavement test sections in Rio de Janeiro, RJ, and (iii) validation of the Fundao project local transfer function to be used throughout Brazil for asphalt pavement fatigue cracking predictions, based on field performance observations of the National MEPDG Project's pavement test sections, thereby validating the proposed framework's prediction capability. For the first step, the S-VECD test protocol, which uses controlled-on-specimen strain mode-of-loading, was successfully implemented at the Petrobras and used to characterize Brazilian asphalt mixtures that are composed of a wide range of asphalt binders. This research verified that the S-VECD model coupled with the GR failure criterion is accurate for fatigue life predictions of Brazilian asphalt mixtures, even when very different asphalt binders are used. Also, the applicability of the load amplitude sweep (LAS) test for the fatigue characterization of the asphalt binders was checked, and the effects of different asphalt binders on the fatigue damage properties of the asphalt mixtures was investigated. The LAS test results, modeled according to VECD theory, presented a strong correlation with

  14. Experimental and numerical analysis of the high-speed deformation and erosion damage of the titanium alloy VT-6

    NASA Astrophysics Data System (ADS)

    Petrov, Yu. V.; Bragov, A. M.; Kazarinov, N. A.; Evstifeev, A. D.

    2017-01-01

    The temporal characteristics of the dynamic fracture of the titanium alloy VT-6 have been investigated under high-speed loading conditions. A relationship has been established between the process of dynamic tension of the specimen according to the Kolsky method and the surface erosion damage. A numerical analysis of the experimental data has been carried out. The method of erosion loading has been further developed as a tool for the dynamic testing of strength properties of materials.

  15. Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data

    PubMed Central

    Geraets, James A.; Dykeman, Eric C.; Stockley, Peter G.; Ranson, Neil A.; Twarock, Reidun

    2015-01-01

    Cryo-electron microscopy permits 3-D structures of viral pathogens to be determined in remarkable detail. In particular, the protein containers encapsulating viral genomes have been determined to high resolution using symmetry averaging techniques that exploit the icosahedral architecture seen in many viruses. By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection. Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization of viral genomes in proximity to the capsid in such viruses. The method uses geometric constraints on genome organization, formulated based on knowledge of icosahedrally-averaged reconstructions and the roles of the RNA-capsid protein contacts, to analyse cryo-electron tomographic data. We apply this method to the low-resolution tomographic data of a model virus and infer the unique asymmetric organization of its genome in contact with the protein shell of the capsid. This opens unprecedented opportunities to analyse viral genomes, revealing conserved structural features and mechanisms that can be targeted in antiviral drug design. PMID:25793998

  16. Local coexistence of VO2 phases revealed by deep data analysis

    SciTech Connect

    Strelcov, Evgheni; Ievlev, Anton; Tselev, Alexander; Kolmakov, Andrei; Kalinin, Sergei V.

    2016-07-07

    We report a synergistic approach of micro-Raman spectroscopic mapping and deep data analysis to study the distribution of crystallographic phases and ferroelastic domains in a defected Al-doped VO2 microcrystal. Bayesian linear unmixing revealed an uneven distribution of the T phase, which is stabilized by the surface defects and uneven local doping that went undetectable by other classical analysis techniques such as PCA and SIMPLISMA. This work demonstrates the impact of information recovery via statistical analysis and full mapping in spectroscopic studies of vanadium dioxide systems, which is commonly substituted by averaging or single point-probing approaches, both of which suffer from information misinterpretation due to low resolving power.

  17. Local coexistence of VO2 phases revealed by deep data analysis

    PubMed Central

    Strelcov, Evgheni; Ievlev, Anton; Belianinov, Alex; Tselev, Alexander; Kolmakov, Andrei; Kalinin, Sergei V.

    2016-01-01

    We report a synergistic approach of micro-Raman spectroscopic mapping and deep data analysis to study the distribution of crystallographic phases and ferroelastic domains in a defected Al-doped VO2 microcrystal. Bayesian linear unmixing revealed an uneven distribution of the T phase, which is stabilized by the surface defects and uneven local doping that went undetectable by other classical analysis techniques such as PCA and SIMPLISMA. This work demonstrates the impact of information recovery via statistical analysis and full mapping in spectroscopic studies of vanadium dioxide systems, which is commonly substituted by averaging or single point-probing approaches, both of which suffer from information misinterpretation due to low resolving power. PMID:27384473

  18. Local coexistence of VO2 phases revealed by deep data analysis

    DOE PAGES

    Strelcov, Evgheni; Ievlev, Anton; Tselev, Alexander; ...

    2016-07-07

    We report a synergistic approach of micro-Raman spectroscopic mapping and deep data analysis to study the distribution of crystallographic phases and ferroelastic domains in a defected Al-doped VO2 microcrystal. Bayesian linear unmixing revealed an uneven distribution of the T phase, which is stabilized by the surface defects and uneven local doping that went undetectable by other classical analysis techniques such as PCA and SIMPLISMA. This work demonstrates the impact of information recovery via statistical analysis and full mapping in spectroscopic studies of vanadium dioxide systems, which is commonly substituted by averaging or single point-probing approaches, both of which suffer frommore » information misinterpretation due to low resolving power.« less

  19. Heating process and damage threshold analysis of Au film coated on Cu substrate for femtosecond laser

    NASA Astrophysics Data System (ADS)

    Wang, Tingfeng; Guo, Jin; Shao, Junfeng; Sun, Tao; Chen, Anmin; Liu, Hang; Ding, Dajun

    2012-07-01

    The heating processes of a two-layer film assembly of Au padded with Cu irradiated by femtosecond laser pulse are studied using a two-temperature model. It is found that the chosen substantially influence the energy transport, and consequently the temperature variation, and thermal equilibrium time. At the same laser fluence, the different thickness of gold film leads to a change of gold surface temperature. By choosing the thickness of the gold layer in the two-layer film assemblies, the damage threshold of the gold film can be maximized. The results can be used to optimize the damage threshold of gold coating optical components.

  20. Non-destructive estimation of fatigue damage for steel by Barkhausen noise analysis

    SciTech Connect

    Tomita, Yasumitsu; Hashimoto, Kiyoshi; Osawa, Naoki; Inai, Hirohisa

    1993-12-31

    A magnetic Barkhausen noise signals are detected when magnetized domain walls move discontinuously in a ferromagnetic material. This non-uniform motion is sensitive to the microstructures of material which vary continuously with the increase of applied loading cycles. In this paper, the process of fatigue damage accumulation subjected to constant cyclic loading are explored by measuring the Barkhausen noise signal with the progress of loading cycles. The experimental results show the possibility to detect the progress of fatigue damage using the peak Barkhausen noise signal.

  1. Identification of Fracture Toughness for Discrete Damage Mechanics Analysis of Glass-Epoxy Laminates

    NASA Astrophysics Data System (ADS)

    Barbero, E. J.; Cosso, F. A.; Martinez, X.

    2014-08-01

    A methodology for determination of the intralaminar fracture toughness is presented, based on fitting discrete damage mechanics (DDM) model predictions to available experimental data. DDM is constitutive model that, when incorporated into commercial finite element software via user material subroutines, is able to predict intralaminar transverse and shear damage initiation and evolution in terms of the fracture toughness of the composite. The applicability of the DDM model is studied by comparison to available experimental data for Glass-Epoxy laminates. Sensitivity of the DDM model to h- and p-refinement is studied. Also, the effect of in-situ correction of strength is highlighted.

  2. A comprehensive analysis of earthquake damage patterns using high dimensional model representation feature selection

    NASA Astrophysics Data System (ADS)

    Taşkin Kaya, Gülşen

    2013-10-01

    Recently, earthquake damage assessment using satellite images has been a very popular ongoing research direction. Especially with the availability of very high resolution (VHR) satellite images, a quite detailed damage map based on building scale has been produced, and various studies have also been conducted in the literature. As the spatial resolution of satellite images increases, distinguishability of damage patterns becomes more cruel especially in case of using only the spectral information during classification. In order to overcome this difficulty, textural information needs to be involved to the classification to improve the visual quality and reliability of damage map. There are many kinds of textural information which can be derived from VHR satellite images depending on the algorithm used. However, extraction of textural information and evaluation of them have been generally a time consuming process especially for the large areas affected from the earthquake due to the size of VHR image. Therefore, in order to provide a quick damage map, the most useful features describing damage patterns needs to be known in advance as well as the redundant features. In this study, a very high resolution satellite image after Iran, Bam earthquake was used to identify the earthquake damage. Not only the spectral information, textural information was also used during the classification. For textural information, second order Haralick features were extracted from the panchromatic image for the area of interest using gray level co-occurrence matrix with different size of windows and directions. In addition to using spatial features in classification, the most useful features representing the damage characteristic were selected with a novel feature selection method based on high dimensional model representation (HDMR) giving sensitivity of each feature during classification. The method called HDMR was recently proposed as an efficient tool to capture the input

  3. High-Throughput Sequencing Reveals Circulating miRNAs as Potential Biomarkers of Kidney Damage in Patients with Systemic Lupus Erythematosus

    PubMed Central

    Pacheco-Lugo, Lisandro; Lorenzi, Hernan; Díaz-Olmos, Yirys; Almendrales, Lisneth; Rico, Edwin; Navarro, Roberto; España-Puccini, Pierine; Iglesias, Antonio; Egea, Eduardo; Aroca, Gustavo

    2016-01-01

    Renal involvement is one of the most severe manifestations of systemic lupus erythematosus (SLE). Renal biopsy is the gold standard when it comes to knowing whether a patient has lupus nephritis, and the degree of renal disease present. However, the biopsy has various complications, bleeding being the most common. Therefore, the development of alternative, non-invasive diagnostic tests for kidney disease in patients with SLE is a priority. Micro RNAs (miRNAs) are differentially expressed in various tissues, and changes in their expression have been associated with several pathological processes. The aim of this study was to identify changes in the abundance of miRNAs in plasma samples from patients with lupus nephritis that could potentially allow the diagnosis of renal damage in SLE patients. This is an observational case-control cross-sectional study, in which we characterized the differential abundance profiles of miRNAs among patients with different degrees of lupus compared with SLE patients without renal involvement and healthy control individuals. We found 89 miRNAs with changes in their abundance between lupus nephritis patients and healthy controls, and 17 miRNAs that showed significant variations between SLE patients with or without renal involvement. Validation for qPCR of a group of miRNAs on additional samples from lupus patients with or without nephritis, and from healthy individuals, showed that five miRNAs presented an average detection sensitivity of 97%, a specificity of 70.3%, a positive predictive value of 82.5%, a negative predictive value of 96% and a diagnosis efficiency of 87.9%. These results strongly suggest that miR-221-5p, miR-380-3p, miR-556-5p, miR-758-3p and miR-3074-3p are potential diagnostic biomarkers of lupus nephritis in patients with SLE. The observed differential pattern of miRNA abundance may have functional implications in the pathophysiology of SLE renal damage. PMID:27835701

  4. High-Throughput Sequencing Reveals Circulating miRNAs as Potential Biomarkers of Kidney Damage in Patients with Systemic Lupus Erythematosus.

    PubMed

    Navarro-Quiroz, Elkin; Pacheco-Lugo, Lisandro; Lorenzi, Hernan; Díaz-Olmos, Yirys; Almendrales, Lisneth; Rico, Edwin; Navarro, Roberto; España-Puccini, Pierine; Iglesias, Antonio; Egea, Eduardo; Aroca, Gustavo

    2016-01-01

    Renal involvement is one of the most severe manifestations of systemic lupus erythematosus (SLE). Renal biopsy is the gold standard when it comes to knowing whether a patient has lupus nephritis, and the degree of renal disease present. However, the biopsy has various complications, bleeding being the most common. Therefore, the development of alternative, non-invasive diagnostic tests for kidney disease in patients with SLE is a priority. Micro RNAs (miRNAs) are differentially expressed in various tissues, and changes in their expression have been associated with several pathological processes. The aim of this study was to identify changes in the abundance of miRNAs in plasma samples from patients with lupus nephritis that could potentially allow the diagnosis of renal damage in SLE patients. This is an observational case-control cross-sectional study, in which we characterized the differential abundance profiles of miRNAs among patients with different degrees of lupus compared with SLE patients without renal involvement and healthy control individuals. We found 89 miRNAs with changes in their abundance between lupus nephritis patients and healthy controls, and 17 miRNAs that showed significant variations between SLE patients with or without renal involvement. Validation for qPCR of a group of miRNAs on additional samples from lupus patients with or without nephritis, and from healthy individuals, showed that five miRNAs presented an average detection sensitivity of 97%, a specificity of 70.3%, a positive predictive value of 82.5%, a negative predictive value of 96% and a diagnosis efficiency of 87.9%. These results strongly suggest that miR-221-5p, miR-380-3p, miR-556-5p, miR-758-3p and miR-3074-3p are potential diagnostic biomarkers of lupus nephritis in patients with SLE. The observed differential pattern of miRNA abundance may have functional implications in the pathophysiology of SLE renal damage.

  5. An Integrated Approach for Analysis of the DNA Damage Response in Mammalian Cells: NUCLEOTIDE EXCISION REPAIR, DNA DAMAGE CHECKPOINT, AND APOPTOSIS.

    PubMed

    Choi, Jun-Hyuk; Kim, So-Young; Kim, Sook-Kyung; Kemp, Michael G; Sancar, Aziz

    2015-11-27

    DNA damage by UV and UV-mimetic agents elicits a set of inter-related responses in mammalian cells, including DNA repair, DNA damage checkpoints, and apoptosis. Conventionally, these responses are analyzed separately using different methodologies. Here we describe a unified approach that is capable of quantifying all three responses in parallel using lysates from the same population of cells. We show that a highly sensitive in vivo excision repair assay is capable of detecting nucleotide excision repair of a wide spectrum of DNA lesions (UV damage, chemical carcinogens, and chemotherapeutic drugs) within minutes of damage induction. This method therefore allows for a real-time measure of nucleotide excision repair activity that can be monitored in conjunction with other components of the DNA damage response, including DNA damage checkpoint and apoptotic signaling. This approach therefore provides a convenient and reliable platform for simultaneously examining multiple aspects of the DNA damage response in a single population of cells that can be applied for a diverse array of carcinogenic and chemotherapeutic agents.

  6. Dispersion analysis of Lamb waves and damage detection for aluminum structures using ridge in the time-scale domain

    NASA Astrophysics Data System (ADS)

    Li, Fucai; Meng, Guang; Ye, Lin; Lu, Ye; Kageyama, Kazuro

    2009-09-01

    In this paper, the dispersion of Lamb waves in aluminum structures was systematically analyzed to differentiate the mode of each package in Lamb wave signals and localize damage. Piezoelectric transducers were bonded on the surfaces of aluminum structures, functioning as actuator and sensor to excite and acquire Lamb waves, respectively. Wavelet transform was applied to the acquired Lamb wave signals, in which the optimal mother wavelet was selected using the concept of Shannon entropy to obtain the most accurate location of each wave package. The ridge and contour of the Lamb wave signals in the time-scale domain were obtained to distinguish the mode of each wave package and pinpoint these packages for estimating the actual group velocities of dispersion curves and localizing damage. The proposed approach could help search the actual dispersion curves in the excitation frequency band by using only one Lamb wave signal. Ridges in the time-scale domain and the actual group velocities were further used to identify damage in the structures. Results demonstrate that the proposed approaches were effective in dispersion analysis, wave mode differentiation and damage localization.

  7. Full-Scale Test and Analysis Results of a PRSEUS Fuselage Panel to Assess Damage Containment Features

    NASA Technical Reports Server (NTRS)

    Bergan, Andrew; Bakuckas, John G., Jr.; Lovejoy, Andrew; Jegley, Dawn; Linton, Kim; Neal, Bert; Korkosz, Gregory; Awerbuch, Jonathan; Tan, Tein-Min

    2012-01-01

    Integrally stitched composite technology is an area that shows promise in enhancing the structural integrity of aircraft and aerospace structures. The most recent generation of this technology is the Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) concept. The goal of the PRSEUS concept relevant to this test is to provide damage containment capability for composite structures while reducing overall structural weight. The National Aeronautics and Space Administration (NASA), the Federal Aviation Administration (FAA), and The Boeing Company have partnered in an effort to assess the damage containment features of a full-scale curved PRSEUS panel using the FAA Full-Scale Aircraft Structural Test Evaluation and Research (FASTER) facility. A single PRSEUS test panel was subjected to axial tension, internal pressure, and combined axial tension and internal pressure loads. The test results showed excellent performance of the PRSEUS concept. No growth of Barely Visible Impact Damage (BVID) was observed after ultimate loads were applied. With a two-bay notch severing the central stringer, damage was contained within the two-bay region well above the required limit load conditions. Catastrophic failure was well above the ultimate load level. Information describing the test panel and procedure has been previously presented, so this paper focuses on the experimental procedure, test results, nondestructive inspection results, and preliminary test and analysis correlation.

  8. Gene Expression of Mesothelioma in Vinylidene Chloride-Exposed F344/N Rats Reveals Immune Dysfunction, Tissue Damage, and Inflammation Pathways

    PubMed Central

    Blackshear, Pamela E.; Pandiri, Arun R.; Nagai, Hiroaki; Bhusari, Sachin; Hong, Lily; Ton, Thai-Vu T.; Clayton, Natasha P.; Wyde, Michael; Shockley, Keith R.; Peddada, Shyamal D.; Gerrish, Kevin E.; Sills, Robert C.; Hoenerhoff, Mark J.

    2014-01-01

    A majority (~80%) of human malignant mesotheliomas are asbestos-related. However, non-asbestos risk factors (radiation, chemicals, genetic factors) account for up to 30% of cases. A recent two-year National Toxicology Program carcinogenicity bioassay showed that male F344/N rats exposed to the industrial toxicant vinylidene chloride (VDC) resulted in a marked increase in malignant mesothelioma. Global gene expression profiles of these tumors were compared to spontaneous mesotheliomas and the F344/N rat mesothelial cell line (Fred-PE) in order to characterize the molecular features and chemical-specific profiles of mesothelioma in VDC-exposed rats. As expected, mesotheliomas from control and vinylidene chloride-exposed rats shared pathways associated with tumorigenesis, including cellular and tissue development, organismal injury, embryonic development, inflammatory response, cell cycle regulation, and cellular growth and proliferation, while mesotheliomas from vinylidene chloride-exposed rats alone showed overrepresentation of pathways associated with pro-inflammatory pathways and immune dysfunction such as the NF-kB signaling pathway, IL-8 and IL-12 signaling, interleukin responses, Fc receptor signaling, and NK and DC signaling, as well as overrepresentation of DNA damage and repair. These data suggest that a chronic, proinflammatory environment associated with VDC exposure may exacerbate disturbances in oncogene, growth factor and cell cycle regulation, resulting in an increased incidence of mesothelioma. PMID:24958746

  9. Analysis of the Contribution of Charge Transport in Iodine-125 induced DNA Damage

    PubMed Central

    Ndlebe, Thabisile; Panyutin, Igor; Neumann, Ronald

    2009-01-01

    Auger electron emitters, like iodine-125, are the radionuclides of choice for gene-targeted radiotherapy. The highly localized damage they induced in DNA is produced by three mechanisms: direct damage by the emitted Auger electrons, indirect damage by diffusible free radicals produced by Auger electrons travelling in water, and charge neutralization of the residual, highly positively charged, tellurium daughter atom by stripping electrons from covalent bonds of neighboring residues. The purpose of our work was to determine whether these mechanisms proceed through an intermediate energy transfer step along DNA. It was proposed that this intermediate step proceeds through the charge transport mechanism in DNA. Conventional charge transport has been described as either a hopping mechanism initiated by charge injection into DNA and propagated by charge migration along the DNA, or a tunneling mechanism in which charge moves directly from a donor to an acceptor within DNA. Well-known barriers for the hopping mechanism were used to probe the role of charge transport in 125I induced DNA damage. We studied their effect on the distribution of DNA breaks produced by the decay of iodine-125 in samples frozen at −80°C. We found that these barriers had no measurable effect on the iodine-125 breaks distribution. PMID:20041764

  10. Bayesian reliability analysis in connection with the evaluation of multiple-site damage

    NASA Astrophysics Data System (ADS)

    Itagaki, Hiroshi; Asada, H.; Ito, S.

    A rivet splice model for analyzing multiple-site damage is presented. The effectiveness of the periodic inspection of multiple-site fatigue cracks along a rivet joint is discussed. The relative frequency distribution of visible crack length and joint posterior probability density are described.

  11. Analysis of the Damage Mechanism Related to CO2 Laser Cochleostomy on Guinea Pig Cochlea

    PubMed Central

    Liu, Xiang; Qian, Xiao-qing; Ma, Rui

    2016-01-01

    Different types of lasers have been used in inner ear surgery. Therefore, it is of the utmost importance to avoid damage to the inner ear (e.g., hyperthermia and acoustic effects) caused by the use of such lasers. The aim of this study was to use a high powered fibre-enabled CO2 laser (10 W, 606 J/cm2) to perform cochleostomies on guinea pig cochlea and to investigate the possible laser-induced damage mechanisms. The temperature changes in the round window membrane, auditory evoked brainstem response, and morphological of the hair cells were measured and recorded before and after laser application. All of the outcomes differed in comparison with the control group. A rise in temperature and subsequent increased hearing loss were observed in animals that underwent surgery with a 10 W CO2 laser. These findings correlated with increased injury to the cochlear ultrastructure and a higher positive expression of E-cadherin and β-catenin in the damaged organ of Corti. We assume that enhanced cell-cell adhesion and the activated β-catenin-related canonical Wnt-signalling pathway may play a role in the protection of the cochlea to prevent further damage. PMID:28070426

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

    PubMed Central

    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

  13. Analysis of hydrocarbon-contaminated groundwater metagenomes as revealed by high-throughput sequencing.

    PubMed

    Abbai, Nathlee S; Pillay, Balakrishna

    2013-07-01

    The tendency for chlorinated aliphatics and aromatic hydrocarbons to accumulate in environments such as groundwater and sediments poses a serious environmental threat. In this study, the metabolic capacity of hydrocarbon (aromatics and chlorinated aliphatics)-contaminated groundwater in the KwaZulu-Natal province of South Africa has been elucidated for the first time by analysis of pyrosequencing data. The taxonomic data revealed that the metagenomes were dominated by the phylum Proteobacteria (mainly Betaproteobacteria). In addition, Flavobacteriales, Sphingobacteria, Burkholderiales, and Rhodocyclales were the predominant orders present in the individual metagenomes. These orders included microorganisms (Flavobacteria, Dechloromonas aromatica RCB, and Azoarcus) involved in the degradation of aromatic compounds and various other hydrocarbons that were present in the groundwater. Although the metabolic reconstruction of the metagenome represented composite cell networks, the information obtained was sufficient to address questions regarding the metabolic potential of the microbial communities and to correlate the data to the contamination profile of the groundwater. Genes involved in the degradation of benzene and benzoate, heavy metal-resistance mechanisms appeared to provide a survival strategy used by the microbial communities. Analysis of the pyrosequencing-derived data revealed that the metagenomes represent complex microbial communities that have adapted to the geochemical conditions of the groundwater as evidenced by the presence of key enzymes/genes conferring resistance to specific contaminants. Thus, pyrosequencing analysis of the metagenomes provided insights into the microbial activities in hydrocarbon-contaminated habitats.

  14. The relationship between periodic dinucleotides and the nucleosomal DNA deformation revealed by normal mode analysis

    NASA Astrophysics Data System (ADS)

    Wang, Debby D.; Yan, Hong

    2011-12-01

    Nucleosomes, which contain DNA and proteins, are the basic unit of eukaryotic chromatins. Polymers such as DNA and proteins are dynamic, and their conformational changes can lead to functional changes. Periodic dinucleotide patterns exist in nucleosomal DNA chains and play an important role in the nucleosome structure. In this paper, we use normal mode analysis to detect significant structural deformations of nucleosomal DNA and investigate the relationship between periodic dinucleotides and DNA motions. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing that they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently.

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

    PubMed Central

    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

  16. Incontinence-associated skin damage in nursing home residents: a secondary analysis of a prospective, multicenter study.

    PubMed

    Zimmaro Bliss, Donna; Zehrer, Cindy; Savik, Kay; Thayer, Debra; Smith, Graham

    2006-12-01

    More than half of the nursing home population is incontinent of urine or feces, presenting challenges to perineal skin health. To determine the occurrence and severity of skin damage in nursing home residents with incontinence, a secondary analysis of data collected from a multisite, open-label, quasi-experimental study of cost and efficacy of four regimens for preventing incontinence-associated dermatitis in nursing home residents was performed. Sixteen randomly selected nursing homes from across the US were included in the study. Participating nursing home residents were incontinent of urine and/or feces and free of skin damage. Of the 1,918 persons screened, 51% (n = 981) qualified for prospective surveillance. Perineal skin was assessed over a 6-week period; frequency, type, and severity of skin damage were observed. Skin damage developed after a median of 13 (range 6 to 42) days in 45 out of 981 residents (4.6%), of which 3.4% was determined to be incontinence-associated dermatitis. Some residents (14 out of 45, 31%) had incontinence-associated dermatitis of other skin damage in more than one area. This study is one of the first to report the characteristics of incontinence-associated dermatitis in a large sample of nursing home residents. The sample size and random selection of nursing homes impart generalizability to the findings. Incontinence-associated dermatitis is a risk in nursing home residents, especially those with fecal incontinence. These findings suggest that the rate and severity of incontinence-associated dermatitis are low with close monitoring and use of a defined skin care regimen that includes a pH-balanced cleanser and moisture barrier.

  17. LC-MS/MS Analysis and Comparison of Oxidative Damages on Peptides Induced by Pathogen Reduction Technologies for Platelets

    NASA Astrophysics Data System (ADS)

    Prudent, Michel; Sonego, Giona; Abonnenc, Mélanie; Tissot, Jean-Daniel; Lion, Niels

    2014-04-01

    Pathogen reduction technologies (PRT) are photochemical processes that use a combination of photosensitizers and UV-light to inactivate pathogens in platelet concentrates (PCs), a blood-derived product used to prevent hemorrhage. However, different studies have questioned the impact of PRT on platelet function and transfusion efficacy, and several proteomic analyses revealed possible oxidative damages to proteins. The present work focused on the oxidative damages produced by the two main PRT on peptides. Model peptides containing residues prone to oxidation (tyrosine, histidine, tryptophane, and cysteine) were irradiated with a combination of amotosalen/UVA (Intercept process) or riboflavin/UVB (Mirasol-like process). Modifications were identified and quantified by liquid chromatography coupled to tandem mass spectrometry. Cysteine-containing peptides formed disulfide bridges (R-SS-R, -2 Da; favored following amotosalen/UVA), sulfenic and sulfonic acids (R-SOH, +16 Da, R-SO3H, +48 Da, favored following riboflavin/UVB) upon treatment and the other amino acids exhibited different oxidations revealed by mass shifts from +4 to +34 Da involving different mechanisms; no photoadducts were detected. These amino acids were not equally affected by the PRT and the combination riboflavin/UVB generated more oxidation than amotosalen/UVA. This work identifies the different types and sites of peptide oxidations under the photochemical treatments and demonstrates that the two PRT may behave differently. The potential impact on proteins and platelet functions may thus be PRT-dependent.

  18. Chromosome-specific segmentation revealed by structural analysis of individually isolated chromosomes.

    PubMed

    Kitada, Kunio; Taima, Akira; Ogasawara, Kiyomoto; Metsugi, Shouichi; Aikawa, Satoko

    2011-04-01

    Analysis of structural rearrangements at the individual chromosomal level is still technologically challenging. Here we optimized a chromosome isolation method using fluorescent marker-assisted laser-capture and laser-beam microdissection and applied it to structural analysis of two aberrant chromosomes found in a lung cancer cell line. A high-density array-comparative genomic hybridization (array-CGH) analysis of DNA samples prepared from each of the chromosomes revealed that these two chromosomes contained 296 and 263 segments, respectively, ranging from 1.5 kb to 784.3 kb in size, derived from different portions of chromosome 8. Among these segments, 242 were common in both aberrant chromosomes, but 75 were found to be chromosome-specific. Sequences of 263 junction sites connecting the ends of segments were determined using a PCR/Sanger-sequencing procedure. Overlapping microhomologies were found at 169 junction sites. Junction partners came from various portions of chromosome 8 and no biased pattern in the positional distribution of junction partners was detected. These structural characteristics suggested the occurrence of random fragmentation of the entire chromosome 8 followed by random rejoining of these fragments. Based on that, we proposed a model to explain how these aberrant chromosomes are formed. Through these structural analyses, it was demonstrated that the optimized chromosome isolation method described here can provide high-quality chromosomal DNA for high resolution array-CGH analysis and probably for massively parallel sequencing analysis.

  19. Genetic analysis of an allergic rhinitis cohort reveals an intercellular epistasis between FAM134B and CD39

    PubMed Central

    2014-01-01

    Background Extracellular ATP is a pro-inflammatory molecule released by damaged cells. Regulatory T cells (Treg) can suppress inflammation by hydrolysing this molecule via ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1), also termed as CD39. Multiple studies have reported differences in CD39+ Treg percentages in diseases such as multiple sclerosis, Hepatitis B and HIV-1. In addition, CD39 polymorphisms have been implicated in immune-phenotypes such as susceptibility to inflammatory bowel disease and AIDS progression. However none of the studies published so far has linked disease-associated variants with differences in CD39 Treg surface expression. This study aims at identifying variants affecting CD39 expression on Treg and at evaluating their association with allergic rhinitis, a disease characterized by a strong Treg involvement. Methods Cohorts consisting of individuals of different ethnicities were employed to identify any association of CD39 variants to surface expression. Significant variant(s) were tested for disease association in a published GWAS cohort by one-locus and two-locus genetic analyses based on logistic models. Further functional characterization was performed using existing microarray data and quantitative RT-PCR on sorted cells. Results Our study shows that rs7071836, a promoter SNP in the CD39 gene region, affects the cell surface expression on Treg cells but not on other CD39+ leukocyte subsets. Epistasis analysis revealed that, in conjunction with a SNP upstream of the FAM134B gene (rs257174), it increased the risk of allergic rhinitis (P = 1.98 × 10-6). As a promoter SNP, rs257174 controlled the expression of the gene in monocytes but, notably, not in Treg cells. Whole blood transcriptome data of three large cohorts indicated an inverse relation in the expression of the two proteins. While this observation was in line with the epistasis data, it also implied that a functional link must exist. Exposure of monocytes to

  20. Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines

    PubMed Central

    Campbell-Sills, Hugo; El Khoury, Mariette; Favier, Marion; Romano, Andrea; Biasioli, Franco; Spano, Giuseppe; Sherman, David J.; Bouchez, Olivier; Coton, Emmanuel; Coton, Monika; Okada, Sanae; Tanaka, Naoto; Dols-Lafargue, Marguerite; Lucas, Patrick M.

    2015-01-01

    Oenococcus oeni is a lactic acid bacteria species encountered particularly in wine, where it achieves the malolactic fermentation. Molecular typing methods have previously revealed that the species is made of several genetic groups of strains, some being specific to certain types of wines, ciders or regions. Here, we describe 36 recently released O. oeni genomes and the phylogenomic analysis of these 36 plus 14 previously reported genomes. We also report three genome sequences of the sister species Oenococcus kitaharae that were used for phylogenomic reconstructions. Phylogenomic and population structure analyses performed revealed that the 50 O. oeni genomes delineate two major groups of 12 and 37 strains, respectively, named A and B, plus a putative group C, consisting of a single strain. A study on the orthologs and single nucleotide polymorphism contents of the genetic groups revealed that the domestication of some strains to products such as cider, wine, or champagne, is reflected at the genetic level. While group A strains proved to be predominant in wine and to form subgroups adapted to specific types of wine such as champagne, group B strains were found in wine and cider. The strain from putative group C was isolated from cider and genetically closer to group B strains. The results suggest that ancestral O. oeni strains were adapted to low-ethanol containing environments such as overripe fruits, and that they were domesticated to cider and wine, with group A strains being naturally selected in a process of further domestication to specific wines such as champagne. PMID:25977455

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

    PubMed

    Vannini, Candida; Bracale, Marcella; Crinelli, Rita; Marconi, Valerio; Campomenosi, Paola; Marsoni, Milena; Scoccianti, Valeria

    2014-01-01

    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.

  2. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis

    NASA Astrophysics Data System (ADS)

    Kaminski, Naftali; Allard, John D.; Pittet, Jean F.; Zuo, Fengrong; Griffiths, Mark J. D.; Morris, David; Huang, Xiaozhu; Sheppard, Dean; Heller, Renu A.

    2000-02-01

    The molecular mechanisms of pulmonary fibrosis are poorly understood. We have used oligonucleotide arrays to analyze the gene expression programs that underlie pulmonary fibrosis in response to bleomycin, a drug that causes lung inflammation and fibrosis, in two strains of susceptible mice (129 and C57BL/6). We then compared the gene expression patterns in these mice with 129 mice carrying a null mutation in the epithelial-restricted integrin 6 subunit (6/-), which develop inflammation but are protected from pulmonary fibrosis. Cluster analysis identified two distinct groups of genes involved in the inflammatory and fibrotic responses. Analysis of gene expression at multiple time points after bleomycin administration revealed sequential induction of subsets of genes that characterize each response. The availability of this comprehensive data set should accelerate the development of more effective strategies for intervention at the various stages in the development of fibrotic diseases of the lungs and other organs.

  3. Analysis of miRNA market trends reveals hotspots of research activity.

    PubMed

    Oosta, Gary; Razvi, Enal

    2012-04-01

    We have conducted an analysis of the miRNA research marketplace by evaluating the publication trends in the field. In this article, we present the results of our analysis which reveals that hotspots exist in terms of research activities in the miRNA space--these hotspots illustrate the areas in the miRNA research space where specific miRNAs have been extensively studied, and other areas that represent new territory. We frame these data into the context of areas of opportunity for miRNA content harvest versus segments of opportunity for the development of research tools. Also presented in this article are the primary market data from online surveys we have performed with researchers involved in miRNA research around the world. Taken together, these data frame the current state of the miRNA marketplace and provide niches of opportunity for new entrants into this space.

  4. Reprint: A multivariate data analysis approach towards vibration analysis and vibration-based damage assessment: Application for delamination detection in a composite beam

    NASA Astrophysics Data System (ADS)

    Garcia, David; Trendafilova, Irina

    2015-03-01

    This paper introduces a novel methodology for structural vibration analysis and vibration-based monitoring which utilises a special type of Principal Components Analysis (PCA), known as Singular Spectrum Analysis (SSA). In this study the methodology is introduced and demonstrated for the purposes of damage assessment in structures using their free decay response. The method's damage assessment properties are first demonstrated on a numerical example for a two-degree-of-freedom (2-DoF) spring-mass and damper system with nonlinear stiffness. The method is then applied to an experimental case study of a composite laminate beam. The method is based on the decomposition of the frequency domain structural variation response using new variables, the Principal Components (PCs). Only a certain number of the new variables are used to approximate the original vibration signal with very good accuracy. The presented results demonstrate the potential of the method for vibration based signal reconstruction and damage diagnosis. The healthy and the different damaged scenarios are clearly distinguishable in the new space of only two reconstructed components where a strong clustering effect is observed.

  5. A multivariate data analysis approach towards vibration analysis and vibration-based damage assessment:. Application for delamination detection in a composite beam

    NASA Astrophysics Data System (ADS)

    García, David; Trendafilova, Irina

    2014-12-01

    This paper introduces a novel methodology for structural vibration analysis and vibration-based monitoring which utilises a special type of Principal Components Analysis (PCA), known as Singular Spectrum Analysis (SSA). In this study the methodology is introduced and demonstrated for the purposes of damage assessment in structures using their free decay response. The method's damage assessment properties are first demonstrated on a numerical example for a two degree-of-freedom (2DoF) spring-mass and damper system with nonlinear stiffness. The method is then applied to an experimental case study of a composite laminate beam. The method is based on the decomposition of the frequency domain structural variation response using new variables, the Principal Components (PCs). Only a certain number of new variables are used to approximate the original vibration signal with very good accuracy. The presented results demonstrate the potential of the method for vibration based signal reconstruction and damage diagnosis. The healthy and the different damaged scenarios are clearly distinguishable in the new space of only two reconstructed components where a strong clustering effect is observed.

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

    PubMed

    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.

  7. Damage of the bacterial cell envelope by antimicrobial peptides gramicidin S and PGLa as revealed by transmission and scanning electron microscopy.

    PubMed

    Hartmann, Mareike; Berditsch, Marina; Hawecker, Jacques; Ardakani, Mohammad Fotouhi; Gerthsen, Dagmar; Ulrich, Anne S

    2010-08-01

    Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used to examine the ultrastructural changes in bacteria induced by antimicrobial peptides (AMPs). Both the beta-stranded gramicidin S and the alpha-helical peptidyl-glycylleucine-carboxyamide (PGLa) are cationic amphiphilic AMPs known to interact with bacterial membranes. One representative Gram-negative strain, Escherichia coli ATCC 25922, and one representative Gram-positive strain, Staphylococcus aureus ATCC 25923, were exposed to the AMPs at sub-MICs and supra-MICs in salt-free medium. SEM revealed a shortening and swelling of the E. coli cells, and multiple blisters and bubbles formed on their surface. The S. aureus cells seemed to burst upon AMP exposure, showing open holes and deep craters in their envelope. TEM revealed the formation of intracellular membranous structures in both strains, which is attributed to a lateral expansion of the lipid membrane upon peptide insertion. Also, some morphological alterations in the DNA region were detected for S. aureus. After E. coli was incubated with AMPs in medium with low ionic strength, the cells appeared highly turgid compared to untreated controls. This observation suggests that the AMPs enhance osmosis through the inner membrane, before they eventually cause excessive leakage of the cellular contents. The adverse effect on the osmoregulatory capacity of the bacteria is attributed to the membrane-permeabilizing action of the amphiphilic peptides, even at low (sub-MIC) AMP concentrations. Altogether, the results demonstrate that both TEM and SEM, as well as appropriate sample preparation protocols, are needed to obtain detailed mechanistic insights into peptide function.

  8. Effects of creep damage, shot peening, and case hardening on magnetic Barkhausen noise analysis

    SciTech Connect

    Sipahi, L.B. Iowa State Univ., Ames, IA . Inst. for Physical Research and Technology)

    1994-11-01

    The micromagnetic emissions, commonly known as Barkhausen noise, are very sensitive to variations in the microstructure and sub-surface stress states of magnetic materials. Steel pipelines at power plants often have creep damage due to microstructural changes in their service life. Early detection of this damage will prevent costly failures. There is also an increasing demand to characterize the sub-surface stress states in structural materials such as high strength materials used in landing gear components in the aerospace industry. Shot peening is used to improve the fatigue strength of these components by the introduction of residual compressive stresses to the surface. Because the magnitude of Barkhausen noise varies with the magnitude of compressive stress, these noise measurements can be used for in-situ evaluation of the effectiveness of the shot peening process. Furthermore, surface modification such as case hardened magnetic samples can be easily observed using micromagnetic Barkhausen noise (MBE) to determine further modification needs.

  9. Pulsed-field gel electrophoresis analysis of multicellular DNA double-strand break damage and repair.

    PubMed

    Joshi, Nina; Grant, Stephen G

    2014-01-01

    This assay quantifies the extent of double-strand break (DSB) DNA damage in cell populations embedded in agarose and analyzed for migratory DNA using pulsed-field gel electrophoresis with ethidium bromide staining. The assay can measure preexisting damage as well as induction of DSB by chemical (e.g., bleomycin), physical (e.g., X-irradiation), or biological (e.g., restriction enzymes) agents. By incubating the cells under physiological conditions prior to processing, the cells can be allowed to repair DSB, primarily via the process of nonhomologous end joining. The amount of repair, corresponding to the repair capacity of the treated cells, is then quantified by determining the ratio of the fractions of activity released in the lanes in comparison to the total amount of DNA fragmentation following determination of an optimal exposure for maximum initial fragmentation. Repair kinetics can also be analyzed through a time-course regimen.

  10. Muscle Tissue Damage Induced by the Venom of Bothrops asper: Identification of Early and Late Pathological Events through Proteomic Analysis

    PubMed Central

    Herrera, Cristina; Macêdo, Jéssica Kele A.; Feoli, Andrés; Escalante, Teresa; Rucavado, Alexandra; Gutiérrez, José María; Fox, Jay W.

    2016-01-01

    The time-course of the pathological effects induced by the venom of the snake Bothrops asper in muscle tissue was investigated by a combination of histology, proteomic analysis of exudates collected in the vicinity of damaged muscle, and immunodetection of extracellular matrix proteins in exudates. Proteomic assay of exudates has become an excellent new methodological tool to detect key biomarkers of tissue alterations for a more integrative perspective of snake venom-induced pathology. The time-course analysis of the intracellular proteins showed an early presence of cytosolic and mitochondrial proteins in exudates, while cytoskeletal proteins increased later on. This underscores the rapid cytotoxic effect of venom, especially in muscle fibers, due to the action of myotoxic phospholipases A2, followed by the action of proteinases in the cytoskeleton of damaged muscle fibers. Similarly, the early presence of basement membrane (BM) and other extracellular matrix (ECM) proteins in exudates reflects the rapid microvascular damage and hemorrhage induced by snake venom metalloproteinases. The presence of fragments of type IV collagen and perlecan one hour after envenoming suggests that hydrolysis of these mechanically/structurally-relevant BM components plays a key role in the genesis of hemorrhage. On the other hand, the increment of some ECM proteins in the exudate at later time intervals is likely a consequence of the action of endogenous matrix metalloproteinases (MMPs) or of de novo synthesis of ECM proteins during tissue remodeling as part of the inflammatory reaction. Our results offer relevant insights for a more integrative and systematic understanding of the time-course dynamics of muscle tissue damage induced by B. asper venom and possibly other viperid venoms. PMID:27035343

  11. Dynamic transcriptional signature and cell fate analysis reveals plasticity of individual neural plate border cells

    PubMed Central

    Roellig, Daniela; Tan-Cabugao, Johanna; Esaian, Sevan; Bronner, Marianne E

    2017-01-01

    The ‘neural plate border’ of vertebrate embryos contains precursors of neural crest and placode cells, both defining vertebrate characteristics. How these lineages segregate from neural and epidermal fates has been a matter of debate. We address this by performing a fine-scale quantitative temporal analysis of transcription factor expression in the neural plate border of chick embryos. The results reveal significant overlap of transcription factors characteristic of multiple lineages in individual border cells from gastrula through neurula stages. Cell fate analysis using a Sox2 (neural) enhancer reveals that cells that are initially Sox2+ cells can contribute not only to neural tube but also to neural crest and epidermis. Moreover, modulating levels of Sox2 or Pax7 alters the apportionment of neural tube versus neural crest fates. Our results resolve a long-standing question and suggest that many individual border cells maintain ability to contribute to multiple ectodermal lineages until or beyond neural tube closure. DOI: http://dx.doi.org/10.7554/eLife.21620.001 PMID:28355135

  12. Molecular analysis of Drosophila eyes absent mutants reveals features of the conserved Eya domain.

    PubMed Central

    Bui, Q T; Zimmerman, J E; Liu, H; Bonini, N M

    2000-01-01

    The eyes absent (eya) gene is critical to eye formation in Drosophila; upon loss of eya function, eye progenitor cells die by programmed cell death. Moreover, ectopic eya expression directs eye formation, and eya functionally synergizes in vivo and physically interacts in vitro with two other genes of eye development, sine oculis and dachshund. The Eya protein sequence, while highly conserved to vertebrates, is novel. To define amino acids critical to the function of the Eya protein, we have sequenced eya alleles. These mutations have revealed that loss of the entire Eya Domain is null for eya activity, but that alleles with truncations within the Eya Domain display partial function. We then extended the molecular genetic analysis to interactions within the Eya Domain. This analysis has revealed regions of special importance to interaction with Sine Oculis or Dachshund. Select eya missense mutations within the Eya Domain diminished the interactions with Sine Oculis or Dachshund. Taken together, these data suggest that the conserved Eya Domain is critical for eya activity and may have functional subregions within it. PMID:10835393

  13. Phenotypic Analysis Reveals that the 2010 Haiti Cholera Epidemic Is Linked to a Hypervirulent Strain

    PubMed Central

    Jones, Christopher J.; Wong, Jennifer; Queen, Jessica; Agarwal, Shivani; Yildiz, Fitnat H.

    2016-01-01

    Vibrio cholerae O1 El Tor strains have been responsible for pandemic cholera since 1961. These strains have evolved over time, spreading globally in three separate waves. Wave 3 is caused by altered El Tor (AET) variant strains, which include the strain with the signature ctxB7 allele that was introduced in 2010 into Haiti, where it caused a devastating epidemic. In this study, we used phenotypic analysis to compare an early isolate from the Haiti epidemic to wave 1 El Tor isolates commonly used for research. It is demonstrated that the Haiti isolate has increased production of cholera toxin (CT) and hemolysin, increased motility, and a reduced ability to form biofilms. This strain also outcompetes common wave 1 El Tor isolates for colonization of infant mice, indicating that it has increased virulence. Monitoring of CT production and motility in additional wave 3 isolates revealed that this phenotypic variation likely evolved over time rather than in a single genetic event. Analysis of available whole-genome sequences and phylogenetic analyses suggested that increased virulence arose from positive selection for mutations found in known and putative regulatory genes, including hns and vieA, diguanylate cyclase genes, and genes belonging to the lysR and gntR regulatory families. Overall, the studies presented here revealed that V. cholerae virulence potential can evolve and that the currently prevalent wave 3 AET strains are both phenotypically distinct from and more virulent than many El Tor isolates. PMID:27297393

  14. Phenotypic Analysis Reveals that the 2010 Haiti Cholera Epidemic Is Linked to a Hypervirulent Strain.

    PubMed

    Satchell, Karla J F; Jones, Christopher J; Wong, Jennifer; Queen, Jessica; Agarwal, Shivani; Yildiz, Fitnat H

    2016-09-01

    Vibrio cholerae O1 El Tor strains have been responsible for pandemic cholera since 1961. These strains have evolved over time, spreading globally in three separate waves. Wave 3 is caused by altered El Tor (AET) variant strains, which include the strain with the signature ctxB7 allele that was introduced in 2010 into Haiti, where it caused a devastating epidemic. In this study, we used phenotypic analysis to compare an early isolate from the Haiti epidemic to wave 1 El Tor isolates commonly used for research. It is demonstrated that the Haiti isolate has increased production of cholera toxin (CT) and hemolysin, increased motility, and a reduced ability to form biofilms. This strain also outcompetes common wave 1 El Tor isolates for colonization of infant mice, indicating that it has increased virulence. Monitoring of CT production and motility in additional wave 3 isolates revealed that this phenotypic variation likely evolved over time rather than in a single genetic event. Analysis of available whole-genome sequences and phylogenetic analyses suggested that increased virulence arose from positive selection for mutations found in known and putative regulatory genes, including hns and vieA, diguanylate cyclase genes, and genes belonging to the lysR and gntR regulatory families. Overall, the studies presented here revealed that V. cholerae virulence potential can evolve and that the currently prevalent wave 3 AET strains are both phenotypically distinct from and more virulent than many El Tor isolates.

  15. Transcriptome Analysis Reveals Silver Nanoparticle-Decorated Quercetin Antibacterial Molecular Mechanism.

    PubMed

    Sun, Dongdong; Zhang, Weiwei; Mou, Zhipeng; Chen, Ying; Guo, Feng; Yang, Endong; Wang, Weiyun

    2017-03-22

    Facile and simple method is developed to synthesize silver-nanoparticle-decorated quercetin nanoparticles (QA NPs). Modification suggests that synergistic quercetin (Qe) improves the antibacterial effect of silver nanoparticles (Ag NPs). Characterization experiment indicates that QA NPs have a diameter of approximately 10 nm. QA NPs show highly effective antibacterial activities against drug-resistant Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). We explore antibacterial mechanisms using S. aureus and E. coli treated with QA NPs. Through morphological changes in E. coli and S. aureus, mechanisms are examined for bacterial damage caused by particulate matter from local dissociation of silver ion and Qe from QA NPs trapped inside membranes. Moreover, we note that gene expression profiling methods, such as RNA sequencing, can be used to predict discover mechanisms of toxicity of QA NPs. Gene ontology (GO) assay analyses demonstrate the molecular mechanism of the antibacterial effect of QA NPs. Regarding cellular component ontology, "cell wall organization or biogenesis" (GO: 0071554) and "cell wall macromolecule metabolic process" (GO: 0044036) are the most represented categories. The present study reports that transcriptome analysis of the mechanism offers novel insights into the molecular mechanism of antibacterial assays.

  16. Transcriptome Analysis of Hamelia patens (Rubiaceae) Anthers Reveals Candidate Genes for Tapetum and Pollen Wall Development

    PubMed Central

    Yue, Lin; Twell, David; Kuang, Yanfeng; Liao, Jingping; Zhou, Xianqiang

    2017-01-01

    Studies of the anther transcriptome on non-model plants without a known genome are surprisingly scarce. RNA-Seq and digital gene expression (DGE) profiling provides a comprehensive approach to identify candidate genes contributing to developmental processes in non-model species. Here we built a transcriptome library of developing anthers of Hamelia patens and analyzed DGE profiles from each stage to identify genes that regulate tapetum and pollen development. In total 7,720 putative differentially expressed genes across four anther stages were identified. The number of putative stage-specific genes was: 776 at microspore mother cell stage, 807 at tetrad stage, 322 at uninucleate microspore stage, and the highest number (1,864) at bicellular pollen stage. GO enrichment analysis revealed 243 differentially expressed and 108 stage-specific genes that are potentially related to tapetum development, sporopollenin synthesis, and pollen wall. The number of expressed genes, their function and expression profiles were all significantly correlated with anther developmental processes. Overall comparisons of anther and pollen transcriptomes with those of rice and Arabidopsis together with the expression profiles of homologs of known anther-expressed genes, revealed conserved patterns and also divergence. The divergence may reflect taxon-specific differences in gene expression, the use RNA-seq as a more sensitive methodology, variation in tissue composition and sampling strategies. Given the lack of genomic sequence, this study succeeded in assigning putative identity to a significant proportion of anther-expressed genes and genes relevant to tapetum and pollen development in H. patens. The anther transcriptome revealed a molecular distinction between developmental stages, serving as a resource to unravel the functions of genes involved in anther development in H. patens and informing the analysis of other members of the Rubiaceae. PMID:28119704

  17. LED-Induced fluorescence and image analysis to detect stink bug damage in cotton bolls

    PubMed Central

    2013-01-01

    Background Stink bugs represent a major agricultural pest complex attacking more than 200 wild and cultivated plants, including cotton in the southeastern US. Stink bug feeding on developing cotton bolls will cause boll abortion or lint staining and thus reduced yield and lint value. Current methods for stink bug detection involve manual harvesting and cracking open of a sizable number of immature cotton bolls for visual inspection. This process is cumbersome, time consuming, and requires a moderate level of experience to obtain accurate estimates. To improve detection of stink bug feeding, we present here a method based on fluorescent imaging and subsequent image analyses to determine the likelihood of stink bug damage in cotton bolls. Results Damage to different structures of cotton bolls including lint and carpal wall can be observed under blue LED-induced fluorescence. Generally speaking, damaged regions fluoresce green, whereas non-damaged regions with chlorophyll fluoresce red. However, similar fluorescence emission is also observable on cotton bolls that have not been fed upon by stink bugs. Criteria based on fluorescent intensity and the size of the fluorescent spot allow to differentiate between true positives (fluorescent regions associated with stink bug feeding) and false positives (fluorescent regions due to other causes). We found a detection rates with two combined criteria of 87% for true-positive marks and of 8% for false-positive marks. Conclusions The imaging technique presented herein gives rise to a possible detection apparatus where a cotton boll is imaged in the field and images processed by software. The unique fluorescent signature left by stink bugs can be used to determine with high probability if a cotton boll has been punctured by a stink bug. We believe this technique, when integrated in a suitable device, could be used for more accurate detection in the field and allow for more optimized application of pest control. PMID:23421982

  18. Re-examination of cumulative fatigue damage analysis: An engineering perspective

    NASA Technical Reports Server (NTRS)

    Manson, S. S.; Halford, G. R.

    1986-01-01

    A method which has evolved in our laboratories for the past 20 yr is re-examined with the intent of improving its accuracy and simplicity of application to engineering problems. Several modifications are introduced both to the analytical formulation of the Damage Curve Approach, and to the procedure for modifying this approach to achieve a Double Linear Damage Rule formulation which immensely simplifies the calculation. Improvements are also introduced in the treatment of mean stress for determining fatigue life of the individual events that enter into a complex loading history. While the procedure is completely consistent with the results of numerous two level tests that have been conducted on many materials, it is still necessary to verify applicability to complex loading histories. Caution is expressed that certain phenomena can also influence the applicability - for example, unusual deformation and fracture modes inherent in complex loading - especially if stresses are multiaxial. Residual stresses at crack tips, and metallurgical factors are also important in creating departures from the cumulative damage theories; examples of departures are provided.

  19. DPA damage analysis for 14-MeV neutrons on PFC materials

    NASA Astrophysics Data System (ADS)

    Kim, Dong-woo; Lee, Bo-young; Ko, Seung-kook; Kim, Hee-soo; Noh, Seung-jung

    2015-06-01

    The dpa (displacement per atom) damage for 14-MeV neutron in a pfc materials was simulated using MCNPX/SPECTER code. The dpa values in the main components of the structural material SS316L, Fe, Cr and Ni, were calculated to analyze the effect of nuclear damage. According to the neutron wall load for ITER design base, a neutron flux of 3.5 × 1013 neutrons/cm2·sec was applied. The simulated dpa values were found to be as 3.0 dpa/fpy for Fe, 2.9 dpa/fpy for Cr and 3.1 dpa/fpy for Ni. For practical experiments, the simulated dpa values due to the irradiation damage of 17-MeV protons were found to be as 0.67 dpa at the peak and 0.05 at the surface for SS316L using by SRIM code at the same fluence. For the 17-MeV proton irradiation, the Bragg peak appears at a 0.64-mm depth. Also, SS316L specimens irradiated by a 17-MeV proton beam with a fluence of 1016 protons/cm2 were analyzed by using transmission electron microscopy.

  20. Analysis of progressive damage in thin circular laminates due to static-equivalent impact loads

    NASA Technical Reports Server (NTRS)

    Shivakumar, K. N.; Elber, W.; Illg, W.

    1983-01-01

    Clamped circular graphite/epoxy plates (25.4, 38.1, and 50.8 mm radii) with an 8-ply quasi-isotropic layup were analyzed for static-equivalent impact loads using the minimum-total-potential-energy method and the von Karman strain-displacement equations. A step-by-step incremental transverse displacement procedure was used to calculate plate load and ply stresses. The ply failure region was calculated using the Tsai-Wu criterion. The corresponding failure modes (splitting and fiber failure) were determined using the maximum stress criteria. The first-failure mode was splitting and initiated first in the bottom ply. The splitting-failure thresholds were relatively low and tended to be lower for larger plates than for small plates. The splitting-damage region in each ply was elongated in its fiber direction; the bottom ply had the largest damage region. The calculated damage region for the 25.4-mm-radius plate agreed with limited static test results from the literature.

  1. Clinical and pathological analysis of renal damage in elderly patients with type 2 diabetes mellitus.

    PubMed

    Yan, Shuang-Tong; Liu, Jun-Yan; Tian, Hui; Li, Chun-Lin; Li, Jian; Shao, Ying-Hong; Shi, Huai-Yin; Liu, Yu; Gong, Yan-Ping; Fang, Fu-Sheng; Sun, Ban-Ruo

    2016-08-01

    The aim of this study was to investigate the causes and influential factors of renal damage in elderly patients with type 2 diabetes mellitus (T2DM). Clinical data and pathological findings at autopsy of 161 elderly T2DM patients died between October 1994 and August 2011 were retrospectively reviewed. The mean age of these patients was 80.8 ± 8.3 years (range 60-105 years). The incidences of diabetic nephropathy (DN), non-diabetic renal diseases (NDRD), and DN complicated with NDRD were 31.1, 62.7, and 16.2 %, respectively. In patients with NDRD, the incidence of hypertensive renal damage (HRD) was 54.7 %. In the factors causing renal damage, DN and NDRD accounted for 1/3 and 2/3, respectively. HRD accounted for the largest proportion of NDRD. Blood pressure control may provide additional benefits for elderly T2DM patients by preventing and delaying the occurrence and development of renal disease.

  2. Quantitative Analysis of Clustered DNA Damages Induced by Silicon Beams of Different Kinetic Energy

    SciTech Connect

    Keszenman D. J.; Keszenman, D.J.; Bennett, P.V.; Sutherland, B.M.; Wilson, P.F.

    2013-05-14

    Humans may b exposed to highly energetic charged particle radiation as a result of medical treatments, occupational activitie or accidental events. In recent years, our increasing presence and burgeoning interest in space exploration beyond low Earth orbit has led to a large increase in the research of the biological effects ofcharged particle radiation typical of that encountered in the space radiation environment. The study of the effects of these types of radiation qualities in terms ofDNA damage induction and repair is fundamental to understand mechanisms both underlying their greater biological effectiveness as we)) as the short and long term risks of health effects such as carcinogenesis, degen rative diseases and premature aging. Charged particle radiation induces a variety of DNA alterations, notably bistranded clustered damages, defined as two or more closely-opposed strand break , oxidized bases or abasic sites within a few helical turns. The induction of such highly complex DNA damage enhances the probability of incorrect or incomplete repair and thus constitutes greater potential for genomic instability, cell death and transformation.

  3. Damage assessment of a two-span RC slab using wavelet analysis

    NASA Astrophysics Data System (ADS)

    Zhu, X. Q.; Hao, H.

    2007-04-01

    A two-span RC slab that measures 6400mm×800mm×100mm with 3000mm spans and 200mm overhang on each end was tested to failure in the laboratory. UB sections were used as supports. The slab was designed according to the moment redistribution method with 11 N6 bars at 75mm centres for both positive and negative reinforcement. The slab was incrementally loaded at the middle of each span to different load levels to create crack damage using four-point loading. Twelve loading stages were performed with increasing maximum load level. Two load cells are used to record the static loads on left and right spans. The crack locations and lengths were monitored in addition to the displacement measurements. Four displacement transducers are located at two sides of the middle of each span to measure the deflection under the static load. Three sets of accelerometers with nine of them in each set are evenly distributed along the slab to measure the dynamic responses. The measured responses from the RC slab in different cracked damage states are analyzed using the wavelet transform (WT). The damping ratios and instantaneous frequency are extracted. The results show that the damping ratio and instantaneous frequency changes could be two good indicators of damage in the reinforced concrete structure.

  4. Gene expression analysis of endometrium reveals progesterone resistance and candidate susceptibility genes in women with endometriosis.

    PubMed

    Burney, Richard O; Talbi, Said; Hamilton, Amy E; Vo, Kim Chi; Nyegaard, Mette; Nezhat, Camran R; Lessey, Bruce A; Giudice, Linda C

    2007-08-01

    The identification of molecular differences in the endometrium of women with endometriosis is an important step toward understanding the pathogenesis of this condition and toward developing novel strategies for the treatment of associated infertility and pain. In this study, we conducted global gene expression analysis of endometrium from women with and without moderate/severe stage endometriosis and compared the gene expression signatures across various phases of the menstrual cycle. The transcriptome analysis revealed molecular dysregulation of the proliferative-to-secretory transition in endometrium of women with endometriosis. Paralleled gene expression analysis of endometrial specimens obtained during the early secretory phase demonstrated a signature of enhanced cellular survival and persistent expression of genes involved in DNA synthesis and cellular mitosis in the setting of endometriosis. Comparative gene expression analysis of progesterone-regulated genes in secretory phase endometrium confirmed the observation of attenuated progesterone response. Additionally, interesting candidate susceptibility genes were identified that may be associated with this disorder, including FOXO1A, MIG6, and CYP26A1. Collectively these findings provide a framework for further investigations on causality and mechanisms underlying attenuated progesterone response in endometrium of women with endometriosis.

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

    PubMed Central

    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

  6. Multilocus sequence analysis reveals high genetic diversity in clinical isolates of Burkholderia cepacia complex from India.

    PubMed

    Gautam, Vikas; Patil, Prashant P; Kumar, Sunil; Midha, Samriti; Kaur, Mandeep; Kaur, Satinder; Singh, Meenu; Mali, Swapna; Shastri, Jayanthi; Arora, Anita; Ray, Pallab; Patil, Prabhu B

    2016-10-21

    Burkholderia cepacia complex (Bcc) is a complex group of bacteria causing opportunistic infections in immunocompromised and cystic fibrosis (CF) patients. Herein, we report multilocus sequence typing and analysis of the 57 clinical isolates of Bcc collected over the period of seven years (2005-2012) from several hospitals across India. A total of 21 sequence types (ST) including two STs from cystic fibrosis patient's isolates and twelve novel STs were identified in the population reflecting the extent of genetic diversity. Multilocus sequence analysis revealed two lineages in population, a major lineage belonging to B. cenocepacia and a minor lineage belonging to B. cepacia. Split-decomposition analysis suggests absence of interspecies recombination and intraspecies recombination contributed in generating genotypic diversity amongst isolates. Further linkage disequilibrium analysis indicates that recombination takes place at a low frequency, which is not sufficient to break down the clonal relationship. This knowledge of the genetic structure of Bcc population from a rapidly developing country will be invaluable in the epidemiology, surveillance and understanding global diversity of this group of a pathogen.

  7. Multilocus sequence analysis reveals high genetic diversity in clinical isolates of Burkholderia cepacia complex from India

    PubMed Central

    Gautam, Vikas; Patil, Prashant P.; Kumar, Sunil; Midha, Samriti; Kaur, Mandeep; Kaur, Satinder; Singh, Meenu; Mali, Swapna; Shastri, Jayanthi; Arora, Anita; Ray, Pallab; Patil, Prabhu B.

    2016-01-01

    Burkholderia cepacia complex (Bcc) is a complex group of bacteria causing opportunistic infections in immunocompromised and cystic fibrosis (CF) patients. Herein, we report multilocus sequence typing and analysis of the 57 clinical isolates of Bcc collected over the period of seven years (2005–2012) from several hospitals across India. A total of 21 sequence types (ST) including two STs from cystic fibrosis patient’s isolates and twelve novel STs were identified in the population reflecting the extent of genetic diversity. Multilocus sequence analysis revealed two lineages in population, a major lineage belonging to B. cenocepacia and a minor lineage belonging to B. cepacia. Split-decomposition analysis suggests absence of interspecies recombination and intraspecies recombination contributed in generating genotypic diversity amongst isolates. Further linkage disequilibrium analysis indicates that recombination takes place at a low frequency, which is not sufficient to break down the clonal relationship. This knowledge of the genetic structure of Bcc population from a rapidly developing country will be invaluable in the epidemiology, surveillance and understanding global diversity of this group of a pathogen. PMID:27767197

  8. Cerebral Degeneration in Amyotrophic Lateral Sclerosis Revealed by 3-Dimensional Texture Analysis

    PubMed Central

    Maani, Rouzbeh; Yang, Yee-Hong; Emery, Derek; Kalra, Sanjay

    2016-01-01

    Introduction: Routine MR images do not consistently reveal pathological changes in the brain in ALS. Texture analysis, a method to quantitate voxel intensities and their patterns and interrelationships, can detect changes in images not apparent to the naked eye. Our objective was to evaluate cerebral degeneration in ALS using 3-dimensional texture analysis of MR images of the brain. Methods: In a case-control design, voxel-based texture analysis was performed on T1-weighted MR images of 20 healthy subjects and 19 patients with ALS. Four texture features, namely, autocorrelation, sum of squares variance, sum average, and sum variance were computed. Texture features were compared between the groups by statistical parametric mapping and correlated with clinical measures of disability and upper motor neuron dysfunction. Results: Texture features were different in ALS in motor regions including the precentral gyrus and corticospinal tracts. To a lesser extent, changes were also found in the thalamus, cingulate gyrus, and temporal lobe. Texture features in the precentral gyrus correlated with disease duration, and in the corticospinal tract they correlated with finger tapping speed. Conclusions: Changes in MR image textures are present in motor and non-motor regions in ALS and correlate with clinical features. Whole brain texture analysis has potential in providing biomarkers of cerebral degeneration in ALS. PMID:27064416

  9. Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity.

    PubMed

    Wei, Feifei; Ito, Kengo; Sakata, Kenji; Date, Yasuhiro; Kikuchi, Jun

    2015-03-03

    Extracting useful information from high dimensionality and large data sets is a major challenge for data-driven approaches. The present study was aimed at developing novel integrated analytical strategies for comprehensively characterizing seaweed similarities based on chemical diversity. The chemical compositions of 107 seaweed and 2 seagrass samples were analyzed using multiple techniques, including Fourier transform infrared (FT-IR) and solid- and solution-state nuclear magnetic resonance (NMR) spectroscopy, thermogravimetry-differential thermal analysis (TG-DTA), inductively coupled plasma-optical emission spectrometry (ICP-OES), CHNS/O total elemental analysis, and isotope ratio mass spectrometry (IR-MS). The spectral data were preprocessed using non-negative matrix factorization (NMF) and NMF combined with multivariate curve resolution-alternating least-squares (MCR-ALS) methods in order to separate individual component information from the overlapping and/or broad spectral peaks. Integrated analysis of the preprocessed chemical data demonstrated distinct discrimination of differential seaweed species. Further network analysis revealed a close correlation between the heavy metal elements and characteristic components of brown algae, such as cellulose, alginic acid, and sulfated mucopolysaccharides, providing a componential basis for its metal-sorbing potential. These results suggest that this integrated analytical strategy is useful for extracting and identifying the chemical characteristics of diverse seaweeds based on large chemical data sets, particularly complicated overlapping spectral data.

  10. Eigenproperties of suspension bridges with damage

    NASA Astrophysics Data System (ADS)

    Materazzi, Annibale Luigi; Ubertini, Filippo

    2011-12-01

    The vertical vibration of suspension bridges with a damage in the main cables is studied using a continuum formulation. Starting from a model for damaged suspended cables recently proposed in the literature, an improved expression for the dynamic increment of cable tension is derived. The nonlinear equation of motion of the damaged bridge is obtained by extending this model to include the stiffening girder. The linear undamped modal eigenproperties are then extracted, in closed-form, from the linearized equation of motion, thus generalizing to the presence of an arbitrary damage the expressions known from the literature for undamaged suspension bridges. The linear dynamics of the damaged bridge reveals to be completely described by means of the same two non-dimensional parameters that govern the linear dynamics of undamaged bridges and which account for the mechanical characteristics of both the main cable and the girder, with the addition of three non-dimensional parameters characterizing damage intensity, position and extent. After presenting the mathematical formulation, a parametric analysis is conducted with the purpose of investigating the sensitivity of natural frequencies and mode shapes to damage, which, in fact, is a crucial point concerning damage detection applications using inverse methods. All through the paper, systematic comparisons with finite element simulations are presented for the purpose of model validation.

  11. Crack propagation analysis of surface enhanced titanium alloys with fretting induced damage

    NASA Astrophysics Data System (ADS)

    Garcia, Daniel Benjamin

    2005-11-01

    The objectives of this research project were to analyze, characterize, and predict the influences that surface treatments have on crack propagation in the presence of fretting fatigue damage. The titanium alloys, Ti-6Al-4V and Ti-17, were implemented for this research, and the surface enhancement methods consisted of shot peening and laser shock peening. The approach was to incorporate methods of contact mechanics, fractography, and fracture mechanics so that the influence of surface enhancements on fretting fatigue could be better understood. The specimens were obtained from prior fretting fatigue experiments that consisted of dog-bones and contact pads with both surface enhanced and bare conditions. The dog-bone specimens had fretting fatigue damage, which is a combination of a cyclic bulk load and the fretting induced damage. These specimens were incorporated in life prediction analyses in which a procedure for calculating fretting fatigue life by correlating nucleation and propagation through a non-arbitrary crack initiation criterion was introduced. The life prediction results show that the fretting fatigue life can be determined with knowledge of the fretting stress field and nature of the fretting cracks. The results also show that surface enhancements do not stop fretting fatigue cracks from forming, do slow the propagation and increase the fretting fatigue life. The contact pads had what is known as 'pure fretting' damage, which consists of the damage from the contact stresses but no cyclic bulk load. The contact pads are the basis for the development of the C-specimen experiment. The contact pads were machined into C-specimens that help measure the threshold stress intensity factor. The objective of the C-specimen experiment is to increase the cyclically applied load of the specimen through step testing until a fatigue crack propagates from the existing fretting induced crack. The testing technique provides for the threshold stress intensity factor to be

  12. An Acoustic Emission and Acousto-Ultrasonic Analysis of Impact Damaged Composite Pressure Vessels

    NASA Technical Reports Server (NTRS)

    Walker, James L.; Workman, Gary L.; Workman, Gary L.

    1996-01-01

    The research presented herein summarizes the development of acoustic emission (AE) and acousto-ultrasonic (AU) techniques for the nondestructive evaluation of filament wound composite pressure vessels. Vessels fabricated from both graphite and kevlar fibers with an epoxy matrix were examined prior to hydroburst using AU and during hydroburst using AE. A dead weight drop apparatus featuring both blunt and sharp impactor tips was utilized to produce a single known energy 'damage' level in each of the vessels so that the degree to which the effects of impact damage could be measured. The damage levels ranged from barely visible to obvious fiber breakage and delamination. Independent neural network burst pressure prediction models were developed from a sample of each fiber/resin material system. Here, the cumulative AE amplitude distribution data collected from low level proof test (25% of the expected burst for undamaged vessels) were used to measure the effects of the impact on the residual burst pressure of the vessels. The results of the AE/neural network model for the inert propellant filled graphite/epoxy vessels 'IM7/3501-6, IM7/977-2 and IM7/8553-45' demonstrated that burst pressures can be predicted from low level AE proof test data, yielding an average error of 5.0%. The trained network for the IM7/977-2 class vessels was also able to predict the expected burst pressure of taller vessels (three times longer hoop region length) constructed of the same material and using the same manufacturing technique, with an average error of 4.9%. To a lesser extent, the burst pressure prediction models could also measure the effects of impact damage to the kevlar/epoxy 'Kevlar 49/ DPL862' vessels. Here though, due to the higher attenuation of the material, an insufficient amount of AE amplitude information was collected to generate robust network models. Although, the worst case trial errors were less than 6%, when additional blind predictions were attempted, errors as

  13. Whole population cell analysis of a landmark-rich mammalian epithelium reveals multiple elongation mechanisms

    PubMed Central

    Economou, Andrew D.; Brock, Lara J.; Cobourne, Martyn T.; Green, Jeremy B. A.

    2013-01-01

    Tissue elongation is a fundamental component of developing and regenerating systems. Although localised proliferation is an important mechanism for tissue elongation, potentially important contributions of other elongation mechanisms, specifically cell shape change, orientated cell division and cell rearrangement, are rarely considered or quantified, particularly in mammalian systems. Their quantification, together with proliferation, provides a rigorous framework for the analysis of elongation. The mammalian palatal epithelium is a landmark-rich tissue, marked by regularly spaced ridges (rugae), making it an excellent model in which to analyse the contributions of cellular processes to directional tissue growth. We captured confocal stacks of entire fixed mouse palate epithelia throughout the mid-gestation growth period, labelled with membrane, nuclear and cell proliferation markers and segmented all cells (up to ∼20,000 per palate), allowing the quantification of cell shape and proliferation. Using the rugae as landmarks, these measures revealed that the so-called growth zone is a region of proliferation that is intermittently elevated at ruga initiation. The distribution of oriented cell division suggests that it is not a driver of tissue elongation, whereas cell shape analysis revealed that both elongation of cells leaving the growth zone and apico-basal cell rearrangements do contribute significantly to directional growth. Quantitative comparison of elongation processes indicated that proliferation contributes most to elongation at the growth zone, but cell shape change and rearrangement contribute as much as 40% of total elongation. We have demonstrated the utility of an approach to analysing the cellular mechanisms underlying tissue elongation in mammalian tissues. It should be broadly applied to higher-resolution analysis of links between genotypes and malformation phenotypes. PMID:24173805

  14. Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos.

    PubMed

    Wen, Jing; Zeng, Yanwu; Fang, Zhuoqing; Gu, Junjie; Ge, Laixiang; Tang, Fan; Qu, Zepeng; Hu, Jing; Cui, Yaru; Zhang, Kunshan; Wang, Junbang; Li, Siguang; Sun, Yi; Jin, Ying

    2017-03-15

    The mammalian post-implantation embryo has been extensively investigated at the tissue level. However, to unravel the molecular basis for the cell-fate plasticity and determination, it is essential to study the characteristics of individual cells. Especially, the individual definitive endoderm (DE) cells have not been characterized in vivo. Here, we report gene expression patterns in single cells freshly isolated from mouse embryos on days 5.5 and 6.5. Initial transcriptome data from 124 single cells yielded signature genes for the epiblast, visceral endoderm, and extra-embryonic ectoderm and revealed a unique distribution pattern of fibroblast growth factor (Fgf) ligands and receptors. Further analysis indicated that early-stage epiblast cells do not segregate into lineages of the major germ layers. Instead, some cells began to diverge from epiblast cells, displaying molecular features of the pre-mesendoderm by expressing higher levels of mesendoderm markers and lower levels of Sox3 transcripts. Analysis of single-cell high-throughput quantitative RT-PCR data from 441 cells identified a late stage of the day 6.5 embryo in which mesoderm and DE cells emerge, with many of them coexpressing Oct4 and Gata6. Analysis of single-cell RNA-seq data from 112 cells of the late-stage day 6.5 embryos revealed differentially expressed signaling genes and networks of transcription factors that might underlie the segregation of the mesoderm and DE lineages. Moreover, we discovered a subpopulation of mesoderm cells that possess molecular features of the extraembryonic mesoderm. This study provides fundamental insight into the molecular basis for lineage segregation in post-implantation mouse embryos.

  15. Sub-Nyquist signal-reconstruction-free operational modal analysis and damage detection in the presence of noise

    NASA Astrophysics Data System (ADS)

    Gkoktsi, Kyriaki; Giaralis, Agathoklis; TauSiesakul, Bamrung

    2016-04-01

    Motivated by a need to reduce energy consumption in wireless sensors for vibration-based structural health monitoring (SHM) associated with data acquisition and transmission, this paper puts forth a novel approach for undertaking operational modal analysis (OMA) and damage localization relying on compressed vibrations measurements sampled at rates well below the Nyquist rate. Specifically, non-uniform deterministic sub-Nyquist multi-coset sampling of response acceleration signals in white noise excited linear structures is considered in conjunction with a power spectrum blind sampling/estimation technique which retrieves/samples the power spectral density matrix from arrays of sensors directly from the sub-Nyquist measurements (i.e., in the compressed domain) without signal reconstruction in the time-domain and without posing any signal sparsity conditions. The frequency domain decomposition algorithm is then applied to the power spectral density matrix to extract natural frequencies and mode shapes as a standard OMA step. Further, the modal strain energy index (MSEI) is considered for damage localization based on the mode shapes extracted directly from the compressed measurements. The effectiveness and accuracy of the proposed approach is numerically assessed by considering simulated vibration data pertaining to a white-noise excited simply supported beam in healthy and in 3 damaged states, contaminated with Gaussian white noise. Good accuracy is achieved in estimating mode shapes (quantified in terms of the modal assurance criterion) and natural frequencies from an array of 15 multi-coset devices sampling at a 70% slower than the Nyquist frequency rate for SNRs as low as 10db. Damage localization of equal level/quality is also achieved by the MSEI applied to mode shapes derived from noisy sub-Nyquist (70% compression) and Nyquist measurements for all damaged states considered. Overall, the furnished numerical results demonstrate that the herein considered sub

  16. Workshop: Improving the Assessment and Valuation of Climate Change Impacts for Policy and Regulatory Analysis: Research on Climate Change Impacts and Associated Economic Damages (part 2)

    EPA Pesticide Factsheets

    This is a workshop titled Improving the Assessment and Valuation of Climate Change Impacts for Policy and Regulatory Analysis: Research on Climate Change Impacts and Associated Economic Damages (part 2)

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

    PubMed

    Damaraju, E; Allen, E A; Belger, A; Ford, J M; McEwen, S; Mathalon, D H; Mueller, B A; Pearlson, G D; Potkin, S G; Preda, A; Turner, J A; Vaidya, J G; van Erp, T G; Calhoun, V D

    2014-01-01

    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. Group

  18. An analysis of the expression of cyclophilin C reveals tissue restriction and an intriguing pattern in the mouse kidney.

    PubMed Central

    Friedman, J.; Weissman, I.; Friedman, J.; Alpert, S.

    1994-01-01

    Cyclophilin C (cyp C) is a cyclosporin A (CsA) binding protein originally isolated from a mouse bone marrow stromal cell line. We have compared the expression patterns of the mammalian cyclophilins A, B, and C in mouse tissues using in situ hybridization. These studies reveal that cyp C is expressed in a restricted subset of tissues including mouse ovary, testis, bone marrow, and kidney. Within the kidney, cyp C is highly expressed in a narrow zone in the outer medulla. Using monoclonal antibodies reactive against cyp C, we find that the kidney cells expressing cyp C correspond to the S3 segment of the nephron. The S3 segment has been shown to sustain histopathological damage from high dosages of CsA, raising the possibility that cyp C may be involved in mediating this damage. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 PMID:8203464

  19. Deformation analysis through the SBAS-DInSAR technique and geotechnical methods for structural damage assessment

    NASA Astrophysics Data System (ADS)

    Bonano, M.; Arangio, S.; Calò, F.; Di Mauro, M.; Manunta, M.; Marsella, M.; Sansosti, E.; Sonnessa, A.; Tagliafierro, V.; Lanari, R.

    2012-04-01

    Monitoring of displacements affecting single buildings or human-made infrastructures is of key importance for their diagnostic and damage assessment. The evaluation of the structural damage in urban areas is a critical problem related to the complexity of soil-structure interaction. Indeed, the structural damage is influenced by several factors, such as the uniformity of the settlements, the variability on the soil property, the type of foundations, the rigidity and type of the considered structure, as well as the rate at which the settlements occur. Concerning this latter issue, settlements occurring very slowly over periods of decades or more may be tolerable by masonry or reinforced concrete structures; on the other hand, the same settlements related to a few months or a few years would result in severe structural damage. In this context, remote sensing techniques allow non-invasive and non-destructive deformation analyses over large areas by properly exploiting a large number of space-borne radar data. Within this framework, Differential SAR Interferometry (DInSAR) has emerged as a valuable microwave methodology to detect and monitor ground displacements, with centimeter to millimeter accuracy, by exploiting the phase difference (interferogram) between two SAR images relevant to the same area. Recent developments of advanced DInSAR techniques are aimed at investigating not only single event deformation phenomena, but also the temporal evolution of the detected displacements through the generation of deformation time-series. These approaches benefit of the availability of huge archives of SAR data, including the ones acquired over the last 20 years by the Synthetic Aperture Radar (SAR) sensors on-board the ERS-1/2 and ENVISAT satellites of the European Space Agency (ESA). Among these advanced DInSAR approaches, we focus on the Small BAseline Subset (SBAS) algorithm (Berardino et al., 2002) that implements an easy combination of DInSAR data pairs characterized by

  20. Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for BMD Variation.

    PubMed

    Zhang, Ji-Gang; Tan, Li-Jun; Xu, Chao; He, Hao; Tian, Qing; Zhou, Yu; Qiu, Chuan; Chen, Xiang-Ding; Deng, Hong-Wen

    2015-01-01

    Integration of multiple profiling data and construction of functional gene networks may provide additional insights into the molecular mechanisms of complex diseases. Osteoporosis is a worldwide public health problem, but the complex gene-gene interactions, post-transcriptional modifications and regulation of functional networks are still unclear. To gain a comprehensive understanding of osteoporosis etiology, transcriptome gene expression microarray, epigenomic miRNA microarray and methylome sequencing were performed simultaneously in 5 high hip BMD (Bone Mineral Density) subjects and 5 low hip BMD subjects. SPIA (Signaling Pathway Impact Analysis) and PCST (Prize Collecting Steiner Tree) algorithm were used to perform pathway-enrichment analysis and construct the interaction networks. Through integrating the transcriptomic and epigenomic data, firstly we identified 3 genes (FAM50A, ZNF473 and TMEM55B) and one miRNA (hsa-mir-4291) which showed the consistent association evidence from both gene expression and methylation data; secondly in network analysis we identified an interaction network module with 12 genes and 11 miRNAs including AKT1, STAT3, STAT5A, FLT3, hsa-mir-141 and hsa-mir-34a which have been associated with BMD in previous studies. This module revealed the crosstalk among miRNAs, mRNAs and DNA methylation and showed four potential regulatory patterns of gene expression to influence the BMD status. In conclusion, the integration of multiple layers of omics can yield in-depth results than analysis of individual omics data respectively. Integrative analysis from transcriptomics and epigenomic data improves our ability to identify causal genetic factors, and more importantly uncover functional regulation pattern of multi-omics for osteoporosis etiology.

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

    PubMed

    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.

  2. Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma.

    PubMed

    Azevedo, Hátylas; Moreira-Filho, Carlos Alberto

    2015-11-19

    Biological networks display high robustness against random failures but are vulnerable to targeted attacks on central nodes. Thus, network topology analysis represents a powerful tool for investigating network susceptibility against targeted node removal. Here, we built protein interaction networks associated with chemoresistance to temozolomide, an alkylating agent used in glioma therapy, and analyzed their modular structure and robustness against intentional attack. These networks showed functional modules related to DNA repair, immunity, apoptosis, cell stress, proliferation and migration. Subsequently, network vulnerability was assessed by means of centrality-based attacks based on the removal of node fractions in descending orders of degree, betweenness, or the product of degree and betweenness. This analysis revealed that removing nodes with high degree and high betweenness was more effective in altering networks' robustness parameters, suggesting that their corresponding proteins may be particularly relevant to target temozolomide resistance. In silico data was used for validation and confirmed that central nodes are more relevant for altering proliferation rates in temozolomide-resistant glioma cell lines and for predicting survival in glioma patients. Altogether, these results demonstrate how the analysis of network vulnerability to topological attack facilitates target prioritization for overcoming cancer chemoresistance.

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

    PubMed Central

    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. PMID:27588023

  4. Comprehensive profiling of lysine acetylproteome analysis reveals diverse functions of lysine acetylation in common wheat

    PubMed Central

    Zhang, Yumei; Song, Limin; Liang, Wenxing; Mu, Ping; Wang, Shu; Lin, Qi

    2016-01-01

    Lysine acetylation of proteins, a dynamic and reversible post-translational modification, plays a critical regulatory role in both eukaryotes and prokaryotes. Several researches have been carried out on acetylproteome in plants. However, until now, there have been no data on common wheat, the major cereal crop in the world. In this study, we performed a global acetylproteome analysis of common wheat variety (Triticum aestivum L.), Chinese Spring. In total, 416 lysine modification sites were identified on 277 proteins, which are involved in a wide variety of biological processes. Consistent with previous studies, a large proportion of the acetylated proteins are involved in metabolic process. Interestingly, according to the functional enrichment analysis, 26 acetylated proteins are involved in photosynthesis and Calvin cycle, suggesting an important role of lysine acetylation in these processes. Moreover, protein interaction network analysis reveals that diverse interactions are modulated by protein acetylation. These data represent the first report of acetylome in common wheat and serve as an important resource for exploring the physiological role of lysine acetylation in this organism and likely in all plants. PMID:26875666

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

    NASA Astrophysics Data System (ADS)

    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.

  6. Molecular genetic analysis of Drosophila eyes absent mutants reveals an eye enhancer element.

    PubMed Central

    Zimmerman, J E; Bui, Q T; Liu, H; Bonini, N M

    2000-01-01

    The eyes absent (eya) gene is critical for normal eye development in Drosophila and is highly conserved to vertebrates. To define regions of the gene critical for eye function, we have defined the mutations in the four viable eya alleles. Two of these mutations are eye specific and undergo transvection with other mutations in the gene. These were found to be deletion mutations that remove regulatory sequence critical for eye cell expression of the gene. Two other viable alleles cause a reduced eye phenotype and affect the function of the gene in additional tissues, such as the ocelli. These mutations were found to be insertion mutations of different transposable elements within the 5' UTR of the transcript. Detailed analysis of one of these revealed that the transposable element has become subject to regulation by eye enhancer sequences of the eya gene, disrupting normal expression of EYA in the eye. More extended analysis of the deletion region in the eye-specific alleles indicated that the deleted region defines an enhancer that activates gene expression in eye progenitor cells. This enhancer is responsive to ectopic expression of the eyeless gene. This analysis has defined a critical regulatory region required for proper eye expression of the eya gene. PMID:10628984

  7. Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200.

    PubMed

    Zhang, Sheng-Da; Santini, Claire-Lise; Zhang, Wei-Jia; Barbe, Valérie; Mangenot, Sophie; Guyomar, Charlotte; Garel, Marc; Chen, Hai-Tao; Li, Xue-Gong; Yin, Qun-Jian; Zhao, Yuan; Armengaud, Jean; Gaillard, Jean-Charles; Martini, Séverine; Pradel, Nathalie; Vidaud, Claude; Alberto, François; Médigue, Claudine; Tamburini, Christian; Wu, Long-Fei

    2016-05-01

    Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantial eco-physiological diversity including free-living, symbiotic and piezophilic life styles. Genomic characteristics underlying this variability across species are poorly understood. Here we carried out genomic and physiological analysis of Photobacterium phosphoreum strain ANT-2200, the first deep-sea luminous bacterium of which the genome has been sequenced. Using optical mapping we updated the genomic data and reassembled it into two chromosomes and a large plasmid. Genomic analysis revealed a versatile energy metabolic potential and physiological analysis confirmed its growth capacity by deriving energy from fermentation of glucose or maltose, by respiration with formate as electron donor and trimethlyamine N-oxide (TMAO), nitrate or fumarate as electron acceptors, or by chemo-organo-heterotrophic growth in rich media. Despite that it was isolated at a site with saturated dissolved oxygen, the ANT-2200 strain possesses four gene clusters coding for typical anaerobic enzymes, the TMAO reductases. Elevated hydrostatic pressure enhances the TMAO reductase activity, mainly due to the increase of isoenzyme TorA1. The high copy number of the TMAO reductase isoenzymes and pressure-enhanced activity might imply a strategy developed by bacteria to adapt to deep-sea habitats where the instant TMAO availability may increase with depth.

  8. Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma

    NASA Astrophysics Data System (ADS)

    Azevedo, Hátylas; Moreira-Filho, Carlos Alberto

    2015-11-01

    Biological networks display high robustness against random failures but are vulnerable to targeted attacks on central nodes. Thus, network topology analysis represents a powerful tool for investigating network susceptibility against targeted node removal. Here, we built protein interaction networks associated with chemoresistance to temozolomide, an alkylating agent used in glioma therapy, and analyzed their modular structure and robustness against intentional attack. These networks showed functional modules related to DNA repair, immunity, apoptosis, cell stress, proliferation and migration. Subsequently, network vulnerability was assessed by means of centrality-based attacks based on the removal of node fractions in descending orders of degree, betweenness, or the product of degree and betweenness. This analysis revealed that removing nodes with high degree and high betweenness was more effective in altering networks’ robustness parameters, suggesting that their corresponding proteins may be particularly relevant to target temozolomide resistance. In silico data was used for validation and confirmed that central nodes are more relevant for altering proliferation rates in temozolomide-resistant glioma cell lines and for predicting survival in glioma patients. Altogether, these results demonstrate how the analysis of network vulnerability to topological attack facilitates target prioritization for overcoming cancer chemoresistance.

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

    PubMed

    Li, Yue; Zhang, Zhaolei

    2014-11-18

    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.

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

    PubMed

    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.

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

    PubMed Central

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

    2017-01-01

    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 × 105 to 1 × 106 cells/mm3. 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. PMID:28255161

  12. Microarray analysis reveals altered circulating microRNA expression in mice infected with Coxsackievirus B3

    PubMed Central

    Sun, Chaoyu; Tong, Lei; Zhao, Wenran; Wang, Yan; Meng, Yuan; Lin, Lexun; Liu, Bingchen; Zhai, Yujia; Zhong, Zhaohua; Li, Xueqi

    2016-01-01

    Coxsackievirus B3 (CVB3) is a common causative agent in the development of inflammatory cardiomyopathy. However, whether the expression of peripheral blood microRNAs (miRNAs) is altered in this process is unknown. The present study investigated changes to miRNA expression in the peripheral blood of CVB3-infected mice. Utilizing miRNA microarray technology, differential miRNA expression was examined between normal and CVB3-infected mice. The present results suggest that specific miRNAs were differentially expressed in the peripheral blood of mice infected with CVB3, varying with infection duration. Using miRNA microarray analysis, a total of 96 and 89 differentially expressed miRNAs were identified in the peripheral blood of mice infected with CVB3 for 3 and 6 days, respectively. Quantitative polymerase chain reaction was used to validate differentially expressed miRNAs, revealing a consistency of these results with the miRNA microarray analysis results. The biological functions of the differentially expressed miRNAs were then predicted by bioinformatics analysis. The potential biological roles of differentially expressed miRNAs included hypertrophic cardiomyopathy, dilated cardiomyopathy and arrh