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Sample records for antti ainamo janne

  1. The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator

    PubMed Central

    Bakolitsa, Constantina; Bateman, Alex; Jin, Kevin K.; McMullan, Daniel; Krishna, S. Sri; Miller, Mitchell D.; Abdubek, Polat; Acosta, Claire; Astakhova, Tamara; Axelrod, Herbert L.; Burra, Prasad; Carlton, Dennis; Chiu, Hsiu-Ju; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Elias, Ylva; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Grzechnik, Slawomir K.; Han, Gye Won; Jaroszewski, Lukasz; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Kumar, Abhinav; Marciano, David; Morse, Andrew T.; Murphy, Kevin D.; Nigoghossian, Edward; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry; Trame, Christine B.; Trout, Christina V.; van den Bedem, Henry; Weekes, Dana; White, Aprilfawn; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott; Wilson, Ian A.

    2010-01-01

    The crystal structure of Jann_2411 from Jannaschia sp. strain CCS1, a member of the Pfam PF07336 family classified as a domain of unknown function (DUF1470), was solved to a resolution of 1.45 Å by multiple-wavelength anomalous dispersion (MAD). This protein is the first structural representative of the DUF1470 Pfam family. Structural analysis revealed a two-domain organization, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc finger that is likely to be involved in DNA binding. Analysis of the Jann_2411 protein and the broader ABATE-domain family suggests a role as stress-induced transcriptional regulators. PMID:20944211

  2. Moynier Receives 2013 Hisashi Kuno Award: Response

    NASA Astrophysics Data System (ADS)

    Moynier, Frédéric

    2014-09-01

    I would like to thank the Volcanology, Geochemistry, and Petrology section for awarding me this prize and all the people who were involved in my nomination and wrote the letters. When Catherine McCammon phoned me to let me know that I was awarded the Kuno Award, I was very surprised at first, and then I felt very honored and lucky. I have been very lucky to have Francis Albarède and Janne Blichert-Toft as Ph.D. advisors. Without their mentoring, I would not be standing here today. Completing my Ph.D. in this dynamic laboratory was an incredible experience, and I was very fortunate to meet many people who became mentors, collaborators, and friends, among whom I will cite Arnaud Agranier, Pierre Beck, and Toshi Fujii.

  3. Influence of oral health on mucositis in patients undergoing hematopoietic progenitor cell transplantation (HPCT)

    PubMed Central

    Oñate-Sánchez, Ricardo E.; Cabrerizo-Merino, María C.; de Arriba de la Fuente, Felipe; Heras Fernando, Inmaculada; Vicente García, Vicente

    2012-01-01

    Aims: To establish whether or not the state of patient oral health can influence the occurrence and/or severity of oral mucositis during hematopoietic progenitor cell transplantation (HPCT). Materials and Methods: The study included 72 patients awaiting HPCT. Prior to transplantation, clinical exploration and radiology were carried out and oral photographs were taken. This evaluated the extent of caries present, the number of missing teeth and the number of dental fillings in each patient; CAO (Caries and Obturations Index) DMFS (Decayed, Missing, and Filled Surfaces) and Restoration Indices were calculated. Gingival pathology was also examined by means of the Ainamo and Bay Gingival Bleeding Index. O’Leary’s Plaque Index was used to evaluate the level of patient oral hygiene. This data was analyzed to see if it exercised any influence on the mucositis grade suffered during HPCT. Results: 96,87% of patients suffered some degree of mucositis during their treatment by the Transplant Unit. The grade of mucositis was seen to be influenced by the number of missing teeth (ANOVA p<0.016) and by the DMFS Index (ANOVA p< 0.038). Although this was not one of the aims of this study, patient age and the administration of colony-stimulating factors were also seen to influence these clinical manifestations. Conclusions: The state of prior oral health can influence decisively the mucositis suffered during transplantation. Key words: Hematopoietic progenitor cell transplantation, mucositis, state of oral health. PMID:22157660

  4. Evaluation of antiplaque and antigingivitis effect of herbal mouthwash in treatment of plaque induced gingivitis: A randomized, clinical trial

    PubMed Central

    Aspalli, Shivanand; Shetty, V. Sudhir; Devarathnamma, M. V.; Nagappa, G.; Archana, D.; Parab, Prachi

    2014-01-01

    Background: Ayurvedic drugs have been used since ancient times to treat diseases including periodontal diseases. Oral rinses made from ayurvedic medicines are used in periodontal therapy to control bleeding and reduce inflammation. The aim of this clinical study is to verify the efficacy of herbal mouthwash containing Pilu, Bibhitaka, Nagavalli, Gandhapura taila, Ela, Peppermint satva, and Yavani satva on reduction of plaque and gingivitis. Materials and Methods: A total of 100 volunteers with clinical signs of mild to moderate gingivitis were selected and assigned to Group A (only scaling done) and Group B (scaling along with the use of herbal mouthwash). After recording the clinical parameters, the patients were instructed to use herbal mouthwash 15 ml for 30 s twice daily after food in Group B and oral hygiene instructions were given to all patients. Plaque and gingivitis assessment were carried out using the plaque index (Silness nd Loe, 1964), Gingival index (Loe And Silness, 1963), Gingival bleeding index (Ainamo and Bay, 1975) at baseline and at 21 days of the herbal mouthwash use. Statistically analysis was carried out using the student's t-test for normally distributed data and Wilcoxson test or Mann-Whitney U-test for skewed data. Results: Our results showed that herbal mouthwash was effective in treatment of plaque induced gingivitis in Group B when compared with the Group A. Conclusion: Herbal mouthwash is effective in treatment of plaque induced gingivitis and can be effectively used as an adjunct to mechanical therapy with lesser side-effects. PMID:24744544

  5. [Epidemiologic studies of oral mucosa changes occurring in children, adolescents, and adults 13-24 years of age in Warsaw].

    PubMed

    Górska, R

    1997-01-01

    The aim of the study was the analysis of RAS occurrence in the population and a comparison to other oral mucosa lesions as well as an analysis of the influence of various factors on RAS occurrence: age, social status of the subject's, parents' education, CPITN index. In the school year 1994/95 a questionnaire concerning the frequency of RAS was distributed to children and adolescents (13-18y) from two Warsaw schools and a group of soldiers of the Polish Army serving in Warsaw. Additionally, all study participants were checked towards RAS by the use of the clinical methods according to WHO methodological guidelines. The periodontal state was measured with the CPITN index described by Ainamo. The following diseases were identified: RAS, leukoplakia, lichen planus, herpes simplex and tongue lesions. The most common declared diseases of oral mucosa was RAS, which usually occurred to patients of age below 18. Clinically the most often observed diseases were oral leukoplakia in soldiers' group and RAS in both students' groups. RAS occurs more often in students, whose parents have higher education compared with persons whose parents have primary education. Parental history of disease (cases of RAS among family members) predisposes to occurrence of RAS. Stress and exhaustion are the supporting factors of RAS incidence. Furthermore, clinical periodontal status and treatment needs may also cause the increase of RAS incidence. PMID:9411506

  6. Efficacy of chlorhexidine and green tea mouthwashes in the management of dental plaque-induced gingivitis: A comparative clinical study

    PubMed Central

    Priya, B. Meena; Anitha, V.; Shanmugam, M.; Ashwath, B.; Sylva, Suganthi D.; Vigneshwari, S. K.

    2015-01-01

    Background: The intake of green tea has been increased recently due to its medicinal values. The antibacterial and antioxidant properties of green tea were found to be beneficial in the treatment of gingival and periodontal diseases. The aim of this comparative study was to compare the efficacy of the mouthwash containing green tea and chlorhexidine in the management of dental plaque-induced gingivitis. Materials and Methods: Thirty patients who participated in the study were divided randomly into two groups, each group of 15 patients was prescribed with either chlorhexidine or green tea mouthwash. Turesky modification of Quigley-Hein plaque index, Löe and Silness gingival index, Ainamo and Bay bleeding index, tooth stain, and tongue stain (TS) were recorded at baseline, 15 days, and 1 month. The subjects were asked to report any discomfort or alteration in taste. Results: There was a significant decrease in plaque index, gingival index, and bleeding index in both the groups. However, green tea mouthwash resulted in a statistically significant decrease in bleeding index compared to chlorhexidine group. There was no significant difference in tooth stain and TS in both the groups. Conclusion: The green tea-containing mouthwash is equally effective in reducing the gingival inflammation and plaque to chlorhexidine. PMID:26681856

  7. Changeability of Oral Cavity Environment

    PubMed Central

    Surdacka, Anna; Strzyka³a, Krystyna; Rydzewska, Anna

    2007-01-01

    Objectives In dentistry, the results of in vivo studies on drugs, dental fillings or prostheses are routinely evaluated based on selected oral cavity environment parameters at specific time points. Such evaluation may be confounded by ongoing changes in the oral cavity environment induced by diet, drug use, stress and other factors. The study aimed to confirm oral cavity environment changeability. Methods 24 healthy individuals aged 20–30 had their oral cavity environment prepared by having professional hygiene procedures performed and caries lesions filled. Baseline examination and the examination two years afterwards, evaluated clinical and laboratory parameters of oral cavity environment. Caries incidence was determined based on DMFT and DMFS values, oral cavity hygiene on Plaque Index (acc. Silness & Loe) and Hygiene Index (acc. O’Leary), and the gingival status on Gingival Index (acc. Loe & Silness) and Gingival Bleeding Index (acc. Ainamo & Bay). Saliva osmolarity, pH and concentrations of Ca2+, Pi, Na+, Cl−, total protein, albumins, F− and Sr2+ were determined. Results The results confirmed ongoing changeability of the oral cavity environment. After 2 years of the study reduction in oral cavity hygiene parameters PLI and HI (P<0.1), and gingival indices as well as lower saliva concentration of Ca2+ (P<.001), Pi (P<.06), K+ (P<.04), Sr2+ (P<.03), Na+ (P<.1), against the baseline values, were observed. Total protein and albumin saliva concentrations were also significantly lower. Conclusion Physiological oral cavity environment is subject to constant, individually different, changes which should be considered when analysing studies that employ oral cavity environment parameters. PMID:19212491

  8. How to select study designs and parameters to investigate the effect of mouthrinses? Part II: comparisons between the parameters used.

    PubMed

    Lorenz, K; Bruhn, G; Heumann, C; Hoffmann, T; Netuschil, L

    2009-12-01

    A variety of parameters is available to assess the efficacy of oral antiseptics. Most study protocols select the parameters according to the specific study goal or according to preferences of the researchers. Beside general recommendations for home-use studies, no recommendations exist for other study types. Therefore, pre-selected parameters should be compared within several study designs and the most suitable parameters should be recommended for further application. The following parameters were selected before study start: plaque indices (PlI, Silness & Loe 1964, M-QHI, Turesky et al. 1970), plaque area (PlA), bacterial vitality (BV, Netuschil et al. 1989), gingivitis indices (GI, Loe 1967; M-GI, Lobene et al. 1986; BOP, Ainamo & Bay 1975), gingival crevicular fluid, colony forming units, and the discoloration index (DI, Brecx et al. 1993). The parameters were applied in four study designs: eight-hour substantivity studies, four-day plaque re-growth studies, 21-day experimental gingivitis studies, and six-month home-use studies. Pearson correlation coefficients were computed. The highest correlations were found between PlI and M-QHI and between GI and M-GI (p<0.01) in all corresponding studies and treatment groups. Few middle correlations existed between BOP and the other gingival indices. Neither GI nor M-GI correlated with GCF nor did BV with plaque indices. Inconsistent correlations were obtained between PlA and plaque indices and between PlI and GI. It is concluded, that primary parameters for these designs should be one plaque index and/or one gingivitis index to monitor plaque and gingivitis. The other parameters did not yield additional information about the study outcome. PMID:20400799

  9. [The clinical and microbiological evaluation of the efficacy of oral irrigation on the periodontal tissues of patients wearing fixed orthodontic appliances].

    PubMed

    Di Murro, C; Paolantonio, M; Petti, S; Tomassini, E; Festa, F; Grippaudo, C; Sbolgi, S

    1992-11-01

    The aim of the present study has been the evaluation of the effectiveness of oral irrigation with or without toothbrushing and dental flossing, in individuals treated with fixed orthodontic appliances, on controlling the development of dental plaque and, hence, of gingivitis. Eight individuals with a good general and oral status have been chosen. Before the experimental period, they received instructions about oral hygiene with toothbrushing and dental flossing and then they have been monitored to verify they were doing well. At the time T0, the upper tooth have been banded, three Periodontal Indexes (Plaque Index according to Silness and Loe, Modified Gingival Index according to Lobene and Gingival Bleeding Index according to Ainamo and Bay) registered and subgingival plaque samples from the premolars' gingival sulcus collected in order to point out the total anaerobes bacterial counts, the rates of motile bacteria, spirochetes, Gram positive and Gram negative cocci and bacteria, by means of optical and dark field microscopy and of cultural methods. For their oral hygiene, the patients had to use, in the right side toothbrush and dental floss (Control 1), in the left side the oral irrigator alone (Test 1). One month later (time T1), the lower teeth have been banded, too. In the right side the patients had to use toothbrush and dental floss (Control 2), while in the left one they used the same devices as Control 2 plus the oral irrigator (Test 2). At the time T1 Periodontal Indexes and Microbiological analyses have been extended to all the four quadrants.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1294872

  10. Analysis of differential splicing suggests different modes of short-term splicing regulation

    PubMed Central

    Topa, Hande; Honkela, Antti

    2016-01-01

    Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal physiological functions but also linked to the development of diseases such as cancer. We analyse differential expression and splicing using RNA-sequencing time series in three different settings: overall gene expression levels, absolute transcript expression levels and relative transcript expression levels. Results: Using estrogen receptor α signaling response as a model system, our Gaussian process-based test identifies genes with differential splicing and/or differentially expressed transcripts. We discover genes with consistent changes in alternative splicing independent of changes in absolute expression and genes where some transcripts change whereas others stay constant in absolute level. The results suggest classes of genes with different modes of alternative splicing regulation during the experiment. Availability and Implementation: R and Matlab codes implementing the method are available at https://github.com/PROBIC/diffsplicing. An interactive browser for viewing all model fits is available at http://users.ics.aalto.fi/hande/splicingGP/ Contact: hande.topa@helsinki.fi or antti.honkela@helsinki.fi Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307611

  11. Exploration and retrieval of whole-metagenome sequencing samples

    PubMed Central

    Seth, Sohan; Välimäki, Niko; Kaski, Samuel; Honkela, Antti

    2014-01-01

    Motivation: Over the recent years, the field of whole-metagenome shotgun sequencing has witnessed significant growth owing to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster and with better coverage than before. This technical advancement has initiated the trend of sequencing multiple samples in different conditions or environments to explore the similarities and dissimilarities of the microbial communities. Examples include the human microbiome project and various studies of the human intestinal tract. With the availability of ever larger databases of such measurements, finding samples similar to a given query sample is becoming a central operation. Results: In this article, we develop a content-based exploration and retrieval method for whole-metagenome sequencing samples. We apply a distributed string mining framework to efficiently extract all informative sequence k-mers from a pool of metagenomic samples and use them to measure the dissimilarity between two samples. We evaluate the performance of the proposed approach on two human gut metagenome datasets as well as human microbiome project metagenomic samples. We observe significant enrichment for diseased gut samples in results of queries with another diseased sample and high accuracy in discriminating between different body sites even though the method is unsupervised. Availability and implementation: A software implementation of the DSM framework is available at https://github.com/HIITMetagenomics/dsm-framework. Contact: sohan.seth@hiit.fi or antti.honkela@hiit.fi Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24845653

  12. Influence of internal structure of Coronal Mass Ejections (CMEs) on their propagation in WSA-ENLIL cone modeling

    NASA Astrophysics Data System (ADS)

    Garcia-Burgos, A.; Pulkkinen, A.; Taktakishvili, A.; Odstrcil, D.

    2012-12-01

    Community Coordinated Modeling Center Team Axel A. García Burgos Embry Riddle Aeronautical University (ERAU) Intern at NASA Goddard Space Flight Center Antti Pulkkinen, Ph.D. Catholic University of America (CUA) NASA Goddard Space Flight Center Aleksandre Taktakishvili, Ph.D. University of Maryland, Baltimore County (UMBC) NASA Goddard Space Flight Center Dusan Odstrcil, Ph.D. George Mason University (GUM) NASA Goddard Space Flight Center We studied the influence of internal structure of Coronal Mass Ejections (CMEs) on their propagation in the heliosphere using WSA-ENLIL Cone Modeling. The Integrated Space Weather Analysis System and Stereo Analysis Tool at NASA/GSFC Community Coordinated Modeling Center Team were used to derive CMEs parameters: velocity, latitude, longitude, and opening angle of the cone. We studied earthward CMEs events, running five simulations for each event using different cavity parameters for the CMEs internal structure. The relationship between the cavity size and CMEs propagation time and Kp index for these events was studied. As expected, when the velocities of CMEs are higher than the ambient wind velocity, CMEs with smaller cavity propagate faster than the same size CMEs with larger cavity (lighter CMEs). Quite naturally the opposite behavior is observed when the velocities of CMEs are less than the solar wind speed. By searching for optimal way of including cavity in CME simulations this research is very important for improving capability to forecast space weather

  13. Understanding the Significance of Mutations in Tumor Suppressor Genes Identified Using Next-Generation Sequencing: A Case Report

    PubMed Central

    Sorscher, Steven

    2016-01-01

    Next-generation sequencing (NGS) of tumors has been heralded as a promising tool to identify ‘actionable’ abnormalities susceptible to therapies targeting these mutated genes. Inhibiting the oncoprotein expressed from a single dominant mutated gene (oncogene) forms the basis for the success of most of the targeted gene therapies approved in the last several years. The well over 20 FDA-approved kinase inhibitors for cancer treatment are examples [Janne et al.: Nat Rev Drug Discov 2009;8: 709–723]. These and other similar agents in development might prove effective therapies for tumors originating from tissues other than those for which these drugs are currently approved. Finding such mutations in tumors of patients through NGS is being aggressively pursued by patients and their oncologists. For identified mutated tumor suppressor genes (TSG) the challenge is really the opposite. Rather than inhibiting the action of an oncoprotein, targeting would involve restoring the activity of the wild-type (WT) TSG function [Knudson: Proc Natl Acad Sci USA 1971;249: 912–915]. Here, a case is reported that illustrates the implications of a mutated TSG (BRIP1) identified by NGS as potentially actionable. In such cases, measuring allelic mutation frequency potentially allows for the identification of tumors where the loss of heterozygosity of a TSG exists. Without substantial loss of expression of the WT TSG product, it would seem very unlikely that ‘replacing’ a WT TSG product that is not a lost product would be a useful therapy. PMID:27462233

  14. [Maintenance care for dental implant].

    PubMed

    Kamoi, K

    1989-10-01

    with patient himself. Ultimate concept of implantology have supported common concordance with periodontal therapy. 2) Patients consent and co-operation the right of informed consent, agreement to treatment by the patient has been gaining increased importance to implantology. Even the patient has consent, they must co-operate the process of dental implant with co-therapist (Fig. 2). 3) The clinical examination of clinical parameters in dental implants. (1) Plaque Index (Silness & Loe 1964) and Plaque Control Record (0 Leary 1978) (Table 5). (2) Gingival inflammation (Fig. 3). Ordinarlly, Gingival Bleeding Index (GBI Ainamo & Bay 1975) and Papilla Bleeding Index (Saxer & Jühlemann 1975) are used. (3) The depth of peri-implant sulcus with the plastic probe. (NDU style) (Fig. 4).(ABSTRACT TRUNCATED AT 400 WORDS) PMID:2489287

  15. Effectiveness of three different types of electric toothbrushes compared with a manual technique in orthodontic patients.

    PubMed

    Heintze, S D; Jost-Brinkmann, P G; Loundos, J

    1996-12-01

    Patients undergoing orthodontic treatment with fixed appliances are at risk of developing carious white spot lesions and gingival inflammation because of the challenge of oral hygiene. The purpose of this study was to evaluate under home conditions the effectiveness of three different types of electric toothbrushes during active appliance therapy: Interplak (Bausch & Lomb, Berlin, Germany), Rota-dent (Rota-dent, Kusnacht, Switzerland), and Braun Oral-B Plaque Remover (Braun/Oral-B, Kronberg, Germany). A manual technique, which included normal toothbrush, interdental brush, and dental floss, served as reference. The study was structured as a single-blind "Latin square design" study. Thirty-eight orthodontic patients were randomly allocated to groups who, within the test period, alternately used the toothbrushes. Before getting a new toothbrush that was to be used for a period of 4 weeks, each patient received video and written instructions. For another 4 weeks, the patient returned to the usual oral hygiene procedures before receiving the next new toothbrush. Oral hygiene was evaluated at the start of a new test period and after 2 and 4 weeks. Clinical scores included a modified O'Leary Plaque Index and Ainamo Gingival Bleeding Index. Wilcoxon rank testing for aggregated surfaces revealed statistically significantly lower plaque scores for Rota-dent than for the manual technique (p < 0.01). For all other toothbrushes, no differences were found in comparison to the manual technique. For Plaque Indices of specific sites, statistical analysis revealed all electric toothbrushes to be equal to the manual technique. No differences in Gingival Bleeding Indices were found after 4 weeks with either toothbrush. Patients with poor oral hygiene who used Rota-dent and Braun Oral-B Plaque Remover OD5 had statistically significantly lower plaque scores compared with the manual technique (p < 0.01; p < 0.05); for patients with good oral hygiene, these differences were neutralized

  16. Gaussian process test for high-throughput sequencing time series: application to experimental evolution

    PubMed Central

    Topa, Hande; Jónás, Ágnes; Kofler, Robert; Kosiol, Carolin; Honkela, Antti

    2015-01-01

    Motivation: Recent advances in high-throughput sequencing (HTS) have made it possible to monitor genomes in great detail. New experiments not only use HTS to measure genomic features at one time point but also monitor them changing over time with the aim of identifying significant changes in their abundance. In population genetics, for example, allele frequencies are monitored over time to detect significant frequency changes that indicate selection pressures. Previous attempts at analyzing data from HTS experiments have been limited as they could not simultaneously include data at intermediate time points, replicate experiments and sources of uncertainty specific to HTS such as sequencing depth. Results: We present the beta-binomial Gaussian process model for ranking features with significant non-random variation in abundance over time. The features are assumed to represent proportions, such as proportion of an alternative allele in a population. We use the beta-binomial model to capture the uncertainty arising from finite sequencing depth and combine it with a Gaussian process model over the time series. In simulations that mimic the features of experimental evolution data, the proposed method clearly outperforms classical testing in average precision of finding selected alleles. We also present simulations exploring different experimental design choices and results on real data from Drosophila experimental evolution experiment in temperature adaptation. Availability and implementation: R software implementing the test is available at https://github.com/handetopa/BBGP. Contact: hande.topa@aalto.fi, agnes.jonas@vetmeduni.ac.at, carolin.kosiol@vetmeduni.ac.at, antti.honkela@hiit.fi Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25614471

  17. PREFACE: 7th EEIGM International Conference on Advanced Materials Research

    NASA Astrophysics Data System (ADS)

    Joffe, Roberts

    2013-12-01

    The 7th EEIGM Conference on Advanced Materials Research (AMR 2013) was held at Luleå University of Technology on the 21-22 March 2013 in Luleå, SWEDEN. This conference is intended as a meeting place for researchers involved in the EEIGM programme, in the 'Erasmus Mundus' Advanced Materials Science and Engineering Master programme (AMASE) and the 'Erasmus Mundus' Doctoral Programme in Materials Science and Engineering (DocMASE). This is great opportunity to present their on-going research in the various fields of Materials Science and Engineering, exchange ideas, strengthen co-operation as well as establish new contacts. More than 60 participants representing six countries attended the meeting, in total 26 oral talks and 19 posters were presented during two days. This issue of IOP Conference Series: Materials Science and Engineering presents a selection of articles from EEIGM-7 conference. Following tradition from previous EEIGM conferences, it represents the interdisciplinary nature of Materials Science and Engineering. The papers presented in this issue deal not only with basic research but also with applied problems of materials science. The presented topics include theoretical and experimental investigations on polymer composite materials (synthetic and bio-based), metallic materials and ceramics, as well as nano-materials of different kind. Special thanks should be directed to the senior staff of Division of Materials Science at LTU who agreed to review submitted papers and thus ensured high scientific level of content of this collection of papers. The following colleagues participated in the review process: Professor Lennart Walström, Professor Roberts Joffe, Professor Janis Varna, Associate Professor Marta-Lena Antti, Dr Esa Vuorinen, Professor Aji Mathew, Professor Alexander Soldatov, Dr Andrejs Purpurs, Dr Yvonne Aitomäki, Dr Robert Pederson. Roberts Joffe October 2013, Luleå Conference photograph EEIGM7 conference participants, 22 March 2013 The PDF

  18. The Role of Multiple Shocks in the Production of GeV Gamma-ray Flaring in the Blazar 1156+295

    NASA Astrophysics Data System (ADS)

    Aller, Margo F.; Hughes, Philip A.; Aller, Hugh D.; Hovatta, Talvikki; Jorstad, Svetlana G.; Marscher, Alan P.; Ramakrishnan, Venkatessh

    2014-06-01

    As part of work to identify jet conditions during GeV flaring detected by the Fermi-LAT, we have carried out radiative transfer modeling of a pair of centimeter-band, total and polarized flux outbursts in the FSRQ 1156+295 from the UMRAO data archive. The modeling incorporates propagating shocks and uses the observed spectral evolution between 14.5 and 4.8 GHz as constraints. The two outbursts are nearly identical in amplitude, spectrum and duration. However, the centimeter-band outburst peaking in 2010.75 is temporally associated with a series of GeV flares extending over nearly 300 days with peak photon flux exceeding 10^{-6} photons/cm^2/s, while the centimeter-band outburst which commenced in early August 2008 is temporally associated with a well-defined gamma-ray quiescent state. Our analysis reveals that the shocks in the parsec-scale jet during the two events have a similar sense (forward), orientation (transverse) and compression, but in the case of the orphan radio-band flare only 2 shocks were required to reproduce the light curves, while in the event with a paired gamma-ray flare, 4 shocks were required. VLBA imaging of the inner jet at 43 GHz identifies a single jet component during the orphan flare and complex structure in the later event. This suggests that differences in shock structure, and associated shock interactions, play a role in the production of gamma-ray flares. This work was supported in part by Fermi GI grants NNX11AO13G, and NNX13AP18G (U. Michigan) and NNX11AQ03G (Boston U.). T. H. was supported in part by a grant from the Jenny and Antti Wihuri foundation and by the Academy of Finland project number 267324.

  19. Expression of the Escherichia coli K5 capsular antigen: immunoelectron microscopic and biochemical studies with recombinant E. coli.

    PubMed Central

    Kröncke, K D; Boulnois, G; Roberts, I; Bitter-Suermann, D; Golecki, J R; Jann, B; Jann, K

    1990-01-01

    The capsular K5 polysaccharide, a representative of group II capsular antigens of Escherichia coli, has been cloned previously, and three gene regions responsible for polymerization and surface expression have been defined (I. S. Roberts, R. Mountford, R. Hodge, K. B. Jann, and G. J. Boulnois, J. Bacteriol. 170:1305-1310, 1988). In this report, we describe the immunoelectron microscopic analysis of recombinant bacteria expressing the K5 antigen and of mutants defective in either region 1 or region 3 gene functions, as well as the biochemical analysis of the K5 capsular polysaccharide. Whereas the K5 clone expressed the K5 polysaccharide as a well-developed capsule in about 25% of its population, no capsule was observed in whole mount preparations and ultrathin sections of the expression mutants. Immunogold labeling of sections from the region 3 mutant revealed the capsular K5 polysaccharide in the cytoplasm. With the region 1 mutant, the capsular polysaccharide appeared associated with the cell membrane, and, unlike the region 3 mutant polysaccharide, the capsular polysaccharide could be detected in the periplasm after plasmolysis of the bacteria. Polysaccharides were isolated from the homogenized mutants with cetyltrimethylammonium bromide. The polysaccharide from the region 1 mutant had the same size as that isolated from the capsule of the original K5 clone, and both polysaccharides were substituted with phosphatidic acid. The polysaccharide from the region 3 mutant was smaller and was not substituted with phosphatidic acid. These results prompt us to postulate that gene region 3 products are involved in the translocation of the capsular polysaccharide across the cytoplasmic membrane and that region 1 directs the transport of the lipid-substituted capsular polysaccharide through the periplasm and across the outer membrane. Images FIG. 1 FIG. 2 FIG. 3 FIG. 4 FIG. 6 PMID:2404935

  20. PREFACE: Progress in Nonequilibrium Green's Functions V (PNGF V)

    NASA Astrophysics Data System (ADS)

    van Leeuwen, Robert; Tuovinen, Riku; Bonitz, Michael

    2013-03-01

    , for assistance. We further thank professor Antti-Pekka Jauho for invaluable help and advice during the organization of the conference. The editors of the present conference proceedings acknowledge the authors for their excellent papers and all the referees for participating in a thorough peer-reviewing of the manuscripts. Finally, it is our pleasure to announce that the sixth conference 'Progress in Nonequilibrium Green's Functions' (PNGF6) will be held in August 2015 at the University of Lund, Sweden. Riku Tuovinen and Robert van Leeuwen University of Jyväskylä Michael Bonitz University of Kiel February 2013

  1. Purification and visualization of lipopolysaccharide from Gram-negative bacteria by hot aqueous-phenol extraction.

    PubMed

    Davis, Michael R; Goldberg, Joanna B

    2012-01-01

    can lead to poor quality LPS that is not well resolved by any of the aforementioned methods. For these reasons, we believe that the following protocol, adapted from Westpahl and Jann(10), is ideal for LPS extraction. PMID:22688346

  2. FOREWORD: The 9th International Colloquium on Atomic Spectra and Oscillator Strengths for Astrophysical and Laboratory Plasmas (ASOS 9)

    NASA Astrophysics Data System (ADS)

    Wahlgren, Glenn M.; Wiese, Wolfgang L.; Beiersdorfer, Peter

    2008-07-01

    For the first time since its inaugural meeting in Lund in 1983, the triennial international conference on Atomic Spectroscopy and Oscillator Strengths for Astrophysical and Laboratory Plasmas (ASOS) returned to Lund, Sweden. Lund has been a home to atomic spectroscopy since the time of Janne Rydberg, and included the pioneering work in laboratory and solar spectroscopy of Bengt Edlén, who presented the initial ASOS talk in 1983. The ninth ASOS was hosted by the Lund Observatory and the Physics Department of Lund University during from 8 to 10 August 2007 and was attended by nearly 100 registrants. An encouraging sign for the field was the number of young researchers in attendance. This volume contains the submitted contributions from the poster presentations of the conference, and represents approximately forty percent of the presented posters. A complementary volume of Physica Scripta provides the written transactions of the ASOS9 invited presentations. With these two volumes the character of ASOS9 is more fully evident, and they serve as a review of the state of atomic spectroscopy for spectrum analysis and the determination of oscillator strengths and their applications. The goal of ASOS is to be a forum for atomic spectroscopy where both the providers and users of atomic data, which includes wavelengths, energy levels, lifetimes, oscillator strengths, and line shape parameters, can meet to discuss recent advances in experimental and theoretical techniques and their application to understanding the physical processes that are responsible for producing observed spectra. The applications mainly originate from the fields of astrophysics and plasma physics, the latter including fusion energy and lighting research. As a part of ASOS9 we were honored to celebrate the retirement of Professor Sveneric Johansson. At a special session on the spectroscopy of iron, which was conducted in his honor, he presented his insights into the Fe II term system and his most recent

  3. PREFACE: Atomic Spectra and Oscillator Strengths (ASOS9) Atomic Spectra and Oscillator Strengths (ASOS9)

    NASA Astrophysics Data System (ADS)

    Wahlgren, Glenn M.; Wiese, Wolfgang L.; Beiersdorfer, Peter

    2009-05-01

    For the first time since its inaugural meeting in Lund in 1983, the triennial international conference on Atomic Spectroscopy and Oscillator Strengths for Astrophysical and Laboratory Plasmas (ASOS) returned to Lund, Sweden. Lund has been a home to atomic spectroscopy since the time of Janne Rydberg, and included the pioneering work in laboratory and solar spectroscopy by Bengt Edlén, who presented the initial ASOS talk in 1983. The ninth ASOS was hosted by the Lund Observatory and Physics Department of Lund University, 7-10 August 2007, and was attended by 99 registrants. An encouraging sign for the field was the number of young researchers in attendance. This volume of Physica Scripta contains contributions from the invited presentations of the conference. For the first time, papers from the ASOS9 poster presentations have been made feely available online in a complementary volume of Journal of Physics: Conference Series. With these two volumes the character of ASOS9 is more evident, and together they serve as a review of the state of atomic spectroscopy for spectrum analysis and the determination of oscillator strengths and their applications. The goal of ASOS is to be a forum for atomic spectroscopy, where both the providers and the users of atomic data, which includes wavelengths, energy levels, lifetimes, oscillator strengths and line shape parameters, can meet to discuss recent advances in experimental and theoretical techniques and their application to understanding the physical processes that are responsible for producing observed spectra. The applications mainly originate from the fields of astrophysics and plasma physics, which includes fusion energy and lighting research. The oral presentations, all but one of which are presented in this volume, provided an extensive synopsis of techniques currently in use and those that are being planned. New to ASOS9 was the extent to which techniques such as cold, trapped atoms and molecules and frequency combs are

  4. From ASCAT to Sentinel-1: Soil Moisture Monitoring using European C-Band Radars

    NASA Astrophysics Data System (ADS)

    Wagner, Wolfgang; Bauer-Marschallinger, Bernhard; Hochstöger, Simon

    2016-04-01

    backscatter observation, the same physical processes and geophysical variables (e.g. vegetation optical depth, surface roughness, soil volume scattering, etc.) need to be considered. The difference lies mainly in the scaling, i.e. how prominently the different variables influence the C-band data at the different spatial (25 km versus 20 m) and temporal (daily versus 3-30 days repeat coverage) scales. Therefore, while the general properties of soil moisture retrievals schemes used for ASCAT and Sentinel-1 can be the same, the details of the algorithm and parameterization will be different. This presentation will review similarities and differences of soil moisture retrieval approaches used for ASCAT and Sentinel-1, with a focus on the change detection method developed by TU Wien. Some first comparisons of ASCAT and Sentinel-1 soil moisture data over Europe will also be shown. REFERENCES Entekhabi, D., Njoku, E.G., O'Neill, P.E., Kellog, K.H., Crow, W.T., Edelstein, W.N., Entin, J.K., Goodman, S.D., Jackson, T.J., Johnson, J., Kimball, J., Piepmeier, J.R., Koster, R., Martin, N., McDonald, K.C., Moghaddam, M., Moran, S., Reichle, R., Shi, J.C., Spencer, M.W., Thurman, S.W., Tsang, L., & Van Zyl, J. (2010). The Soil Moisture Active Passive (SMAP) mission. Proceedings of the IEEE, 98, 704-716 Hornacek, M., Wagner, W., Sabel, D., Truong, H.L., Snoeij, P., Hahmann, T., Diedrich, E., & Doubkova, M. (2012). Potential for High Resolution Systematic Global Surface Soil Moisture Retrieval via Change Detection Using Sentinel-1. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 5, 1303-1311 Wagner, W., Hahn, S., Kidd, R., Melzer, T., Bartalis, Z., Hasenauer, S., Figa-Saldana, J., De Rosnay, P., Jann, A., Schneider, S., Komma, J., Kubu, G., Brugger, K., Aubrecht, C., Züger, C., Gangkofer, U., Kienberger, S., Brocca, L., Wang, Y., Blöschl, G., Eitzinger, J., Steinnocher, K., Zeil, P., & Rubel, F. (2013). The ASCAT soil moisture product: A review of its

  5. From ASCAT to Sentinel-1: Soil Moisture Monitoring using European C-Band Radars

    NASA Astrophysics Data System (ADS)

    Wagner, Wolfgang; Bauer-Marschallinger, Bernhard; Hochstöger, Simon

    2016-04-01

    backscatter observation, the same physical processes and geophysical variables (e.g. vegetation optical depth, surface roughness, soil volume scattering, etc.) need to be considered. The difference lies mainly in the scaling, i.e. how prominently the different variables influence the C-band data at the different spatial (25 km versus 20 m) and temporal (daily versus 3-30 days repeat coverage) scales. Therefore, while the general properties of soil moisture retrievals schemes used for ASCAT and Sentinel-1 can be the same, the details of the algorithm and parameterization will be different. This presentation will review similarities and differences of soil moisture retrieval approaches used for ASCAT and Sentinel-1, with a focus on the change detection method developed by TU Wien. Some first comparisons of ASCAT and Sentinel-1 soil moisture data over Europe will also be shown. REFERENCES Entekhabi, D., Njoku, E.G., O'Neill, P.E., Kellog, K.H., Crow, W.T., Edelstein, W.N., Entin, J.K., Goodman, S.D., Jackson, T.J., Johnson, J., Kimball, J., Piepmeier, J.R., Koster, R., Martin, N., McDonald, K.C., Moghaddam, M., Moran, S., Reichle, R., Shi, J.C., Spencer, M.W., Thurman, S.W., Tsang, L., & Van Zyl, J. (2010). The Soil Moisture Active Passive (SMAP) mission. Proceedings of the IEEE, 98, 704-716 Hornacek, M., Wagner, W., Sabel, D., Truong, H.L., Snoeij, P., Hahmann, T., Diedrich, E., & Doubkova, M. (2012). Potential for High Resolution Systematic Global Surface Soil Moisture Retrieval via Change Detection Using Sentinel-1. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 5, 1303-1311 Wagner, W., Hahn, S., Kidd, R., Melzer, T., Bartalis, Z., Hasenauer, S., Figa-Saldana, J., De Rosnay, P., Jann, A., Schneider, S., Komma, J., Kubu, G., Brugger, K., Aubrecht, C., Züger, C., Gangkofer, U., Kienberger, S., Brocca, L., Wang, Y., Blöschl, G., Eitzinger, J., Steinnocher, K., Zeil, P., & Rubel, F. (2013). The ASCAT soil moisture product: A review of its

  6. FOREWORD: The 70th birthday of Professor Stig Stenholm The 70th birthday of Professor Stig Stenholm

    NASA Astrophysics Data System (ADS)

    Suominen, Kalle-Antti

    2010-09-01

    information [7] and in Stockholm he had, again, very successful postdocs such as Ulf Leonhardt. Finally, in 2005, Stig Stenholm retired, although he is still active, writing papers, taking part in conferences and making research visits. We honoured his 70th birthday at the CEWQO2009 conference, and hope that the future provides us with further opportunities for such events. Looking at the obituary of Dirk ter Haar, I see that his style with students reminds me of Stig's approach. In my opinion, Stig expects independence and initiative from a student, giving perhaps a broad topic in which the student is expected to find his or her own way, whilst working perhaps with a postdoc. Juha Javanainen has talked about the 'sink or swim' style (not referring to Stig, though). There is a famous series of children's books about Moomin trolls by Tove Jansson (another Swedish-speaking Finn like Stig). In one of them, the Moomin find in early spring a small flower in a patch of land uncovered by snow, pushing its way up. One of them wants to cover it against frost during the night, but another says 'Don't, it'll fare better later if it has some difficulties at first'. At CEWQO2009 Stig gave the full list of his finished PhD students: Rainer Salomaa (1973), Temba Dlodlo (1980), Juha Javanainen (1980), Markus Lindberg (1985), Matti Kaivola (1985), Birger Ståhlberg (1985), Kalle-Antti Suominen (1992), Mackillo Kira (1995), Päivi Törmä (1996), Asta Paloviita (1997), Patrik Öhberg (1998), Martti Havukainen (1999), Erika Andersson (2000), Pawel Piwnicki (2001), Åsa Larson (2001), Markku Jääskeläinen (2003), and Jonas Larson (2005). One should also mention Erkki Kyrölä, who eventually graduated at Rochester and Olli Serimaa, who never graduated but published some important early-stage laser cooling work. As a final note I must mention a passion that Stig and I share, namely books. I have nearly 400 professional physics and mathematics books, but I am certain that the size of Stig

  7. PREFACE: CEWQO Topical Issue CEWQO Topical Issue

    NASA Astrophysics Data System (ADS)

    Bozic, Mirjana; Man'ko, Margarita

    2009-09-01

    Kalle-Antti Suominen (http://www.congress.utu.fi/cewqo2009). The conference site is the new ICT building at chaired by Professor Kalle-Antti Suominen (http://www.congress.utu.fi/cewqo2009, www.congress.utu.fi/cewqo2009). The conference site was the new ICT building at the University of Turku campus area and the Viking Line ferry boat. Turku is the central city of historical Finland established on the mouth of the river Aura in the 13th century. It is the birthplace of Finnish academic life, since the Academy of Turku was established there in 1640. In 2011, Turku will be one of the cultural capitals of Europe. The city has a strong maritime tradition and is shielded from the Baltic sea by a large and beautiful archipelago. The 17th Central European Workshop on Quantum Optics will be held in 2010 in St Andrews, UK. It will be chaired by Professors Ulf Leonhardt and Natalia Korolkova from the School of Physics and Astronomy, University of St Andrews. St Andrews is home to the first university of Scotland, the third-oldest in the English-speaking world, and is the home of golf. It remains a charming, eccentric seaside town that is sufficiently secluded - the ideal place for a stimulating and thought-provoking conference.