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Sample records for previously observed sequence

  1. An evaluation of Comparative Genome Sequencing (CGS by comparing two previously-sequenced bacterial genomes

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    Herring Christopher D

    2007-08-01

    Full Text Available Abstract Background With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected. Results In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence. Conclusion CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.

  2. Clinical observation of phacoemulsification in patients with previous trabeculectomy

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    Li Li

    2013-09-01

    Full Text Available AIM: To observe the clinical effect of transparent corneal incision phacoemulsification in cataract patients who had undergone different kinds of glaucoma filtration surgeries.METHODS: Totally 43 cases(50 eyes, in which 23 patients with primary angle-closure glaucoma(group A, 26 eyesand 20 patients with primary open angle glaucoma(group B, 24 eyes, all had undergone glaucoma filtration surgery for more than 6 months. Visual acuity, intraocular pressure, slit lamp, gonioscope, corneal endothelial cell counts, etc., were done before surgery.And transparent corneal incision phacoemulsification combined with artificial lens implantation operation were preformed, postoperative follow-up of 3 to 12 months, visual acuity, intraocular pressure, corneal endothelial cell counts and vision field, etc. were observed and recorded.RESULTS: The visual acuity of 50 eyes(100%increased with different degree postoperatively, 41 eyes(82%with postoperative visual acuity ≥0.3; average preoperative intraocular pressure: group A 18.08±5.08mmHg(1mmHg=0.133kpa, group B 14.48±3.52mmHg; Postoperative follow-up average intraocular pressure: group A 13.65±3.51mmHg, group B 14.28±3.41 mmHg, intraocular pressure changed significantly pre and post-operation in group A(PP>0.05; Postoperative intraocular pressure of 1 eye in group A and 3 eyes in group B rose within three days post-operation, the intraocular pressure fluctuated between 21-33mmHg, with drug therapy and drug withdral when intraocular pressure epistrophy; Intraocular pressure was stable in the follow-up process.Corneal endothelial cell density: pre-operation group A was 2 293.57±352.24(cells/mm2, group B 2 658.14±458.69(cells/mm2, post- operation group A 2 175.95±379.16(cells/mm2, group B 2 442.97±477.30(cells/mm2, cell loss rate: 5.13% in group A, and 8.10% in group B. Postoperative visual acuity was related to vision field damage in patients, the more visual field damage, the longer the duration

  3. Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples

    DEFF Research Database (Denmark)

    Wikman, Friedrik; Lu, Ming-Lan; Andersen, Thomas Thykjær

    2000-01-01

    sensitivity, from 0.92 to 0.84, leading to a much better concordance (92%) with results obtained by traditional sequencing. The chip method detected as little as 1% mutated DNA. Conclusions: Microarray-based sequencing is a novel option to assess TP53 mutations, representing a fast and inexpensive method...

  4. Phylogenetic relationships of seven previously unclassified viruses within the family Rhabdoviridae using partial nucleoprotein gene sequences.

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    Kuzmin, I V; Hughes, G J; Rupprecht, C E

    2006-08-01

    Partial nucleoprotein (N) gene sequences of the rhabdoviruses Obodhiang (OBOV), Kotonkon (KOTV), Rochambeau (RBUV), Kern canyon (KCV), Mount Elgon bat (MEBV), Kolongo (KOLV) and Sandjimba (SJAV) were generated and their phylogenetic positions within the family Rhabdoviridae were determined. Both OBOV and KOTV were placed within the genus Ephemerovirus. RBUV was joined to the same cluster, but more distantly. MEBV and KCV were grouped into a monophyletic cluster (putative genus) with Oita virus (OITAV). These three viruses, originating from different regions of the world, were all isolated from insectivorous bats and may be specific for these mammals. African avian viruses KOLV and SJAV were joined to each other and formed another clade at the genus level. Further, they were grouped with the recently characterized rhabdovirus Tupaia virus (TRV). Although the genetic distance was great, the grouping was supported by consistent bootstrap values. This observation suggests that viruses of this group may be distributed widely in the Old World. Non-synonymous/synonymous substitution ratio estimations (dN/dS) using a partial N gene fragment (241 codons) for the three rhabdovirus genera revealed contrasting patterns of evolution, where dN/dS values follow the pattern Ephemerovirus > Vesiculovirus > Lyssavirus. The magnitude of this ratio corresponds well with the number of negatively selected codons. The accumulation of dS appears evenly distributed along the gene fragment for all three genera. These estimations demonstrated clearly that lyssaviruses are subjected to the strongest constraints against amino acid substitutions, probably related to their particular niche and unique pathobiology.

  5. Technical Note: A novel leaf sequencing optimization algorithm which considers previous underdose and overdose events for MLC tracking radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Wisotzky, Eric, E-mail: eric.wisotzky@charite.de, E-mail: eric.wisotzky@ipk.fraunhofer.de; O’Brien, Ricky; Keall, Paul J., E-mail: paul.keall@sydney.edu.au [Radiation Physics Laboratory, Sydney Medical School, University of Sydney, Sydney, NSW 2006 (Australia)

    2016-01-15

    Purpose: Multileaf collimator (MLC) tracking radiotherapy is complex as the beam pattern needs to be modified due to the planned intensity modulation as well as the real-time target motion. The target motion cannot be planned; therefore, the modified beam pattern differs from the original plan and the MLC sequence needs to be recomputed online. Current MLC tracking algorithms use a greedy heuristic in that they optimize for a given time, but ignore past errors. To overcome this problem, the authors have developed and improved an algorithm that minimizes large underdose and overdose regions. Additionally, previous underdose and overdose events are taken into account to avoid regions with high quantity of dose events. Methods: The authors improved the existing MLC motion control algorithm by introducing a cumulative underdose/overdose map. This map represents the actual projection of the planned tumor shape and logs occurring dose events at each specific regions. These events have an impact on the dose cost calculation and reduce recurrence of dose events at each region. The authors studied the improvement of the new temporal optimization algorithm in terms of the L1-norm minimization of the sum of overdose and underdose compared to not accounting for previous dose events. For evaluation, the authors simulated the delivery of 5 conformal and 14 intensity-modulated radiotherapy (IMRT)-plans with 7 3D patient measured tumor motion traces. Results: Simulations with conformal shapes showed an improvement of L1-norm up to 8.5% after 100 MLC modification steps. Experiments showed comparable improvements with the same type of treatment plans. Conclusions: A novel leaf sequencing optimization algorithm which considers previous dose events for MLC tracking radiotherapy has been developed and investigated. Reductions in underdose/overdose are observed for conformal and IMRT delivery.

  6. Influence of Previous Knowledge, Language Skills and Domain-specific Interest on Observation Competency

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    Kohlhauf, Lucia; Rutke, Ulrike; Neuhaus, Birgit

    2011-10-01

    Many epoch-making biological discoveries (e.g. Darwinian Theory) were based upon observations. Nevertheless, observation is often regarded as `just looking' rather than a basic scientific skill. As observation is one of the main research methods in biological sciences, it must be considered as an independent research method and systematic practice of this method is necessary. Because observation skills form the basis of further scientific methods (e.g. experiments or comparisons) and children from the age of 4 years are able to independently generate questions and hypotheses, it seems possible to foster observation competency at a preschool level. To be able to provide development-adequate individual fostering of this competency, it is first necessary to assess each child's competency. Therefore, drawing on the recent literature, we developed in this study a competency model that was empirically evaluated within learners ( N = 110) from different age groups, from kindergarten to university. In addition, we collected data on language skills, domain-specific interest and previous knowledge to analyse coherence between these skills and observation competency. The study showed as expected that previous knowledge had a high impact on observation competency, whereas the influence of domain-specific interest was nonexistent. Language skills were shown to have a weak influence. By utilising the empirically validated model consisting of three dimensions (`Describing', `Scientific reasoning' and `Interpreting') and three skill levels, it was possible to assess each child's competency level and to develop and evaluate guided play activities to individually foster a child's observation competency.

  7. Hereditary spastic paraplegia in Greece: characterisation of a previously unexplored population using next-generation sequencing.

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    Lynch, David S; Koutsis, Georgios; Tucci, Arianna; Panas, Marios; Baklou, Markella; Breza, Marianthi; Karadima, Georgia; Houlden, Henry

    2016-06-01

    Hereditary Spastic Paraplegia (HSP) is a syndrome characterised by lower limb spasticity, occurring alone or in association with other neurological manifestations, such as cognitive impairment, seizures, ataxia or neuropathy. HSP occurs worldwide, with different populations having different frequencies of causative genes. The Greek population has not yet been characterised. The purpose of this study was to describe the clinical presentation and molecular epidemiology of the largest cohort of HSP in Greece, comprising 54 patients from 40 families. We used a targeted next-generation sequencing (NGS) approach to genetically assess a proband from each family. We made a genetic diagnosis in >50% of cases and identified 11 novel variants. Variants in SPAST and KIF5A were the most common causes of autosomal dominant HSP, whereas SPG11 and CYP7B1 were the most common cause of autosomal recessive HSP. We identified a novel variant in SPG11, which led to disease with later onset and may be unique to the Greek population and report the first nonsense mutation in KIF5A. Interestingly, the frequency of HSP mutations in the Greek population, which is relatively isolated, was very similar to other European populations. We confirm that NGS approaches are an efficient diagnostic tool and should be employed early in the assessment of HSP patients.

  8. Low temperature magneto-morphological characterisation of coronene and the resolution of previously observed unexplained phenomena

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    Potticary, Jason; Boston, Rebecca; Vella-Zarb, Liana; Few, Alex; Bell, Christopher; Hall, Simon R.

    2016-12-01

    The polyaromatic hydrocarbon coronene has been the molecule of choice for understanding the physical properties of graphene for over a decade. The modelling of the latter by the former was considered to be valid, as since it was first synthesised in 1932, the physical behaviour of coronene has been determined extremely accurately. We recently discovered however, an unforeseen polymorph of coronene, which exists as an enantiotrope with the previously observed crystal structure. Using low-temperature magnetisation and crystallographic measurements, we show here for the first time that the electronic and magnetic properties of coronene depend directly on the temperature at which it is observed, with hysteretic behaviour exhibited between 300 K and 100 K. Furthermore we determine that this behaviour is a direct result of the appearance and disappearance of the newly-discovered polymorph during thermal cycling. Our results not only highlight the need for theoretical models of graphene to take into account this anomalous behaviour at low temperatures, but also explain puzzling experimental observations of coronene dating back over 40 years.

  9. RECONCILING THE OBSERVED STAR-FORMING SEQUENCE WITH THE OBSERVED STELLAR MASS FUNCTION

    International Nuclear Information System (INIS)

    Leja, Joel; Van Dokkum, Pieter G.; Franx, Marijn; Whitaker, Katherine E.

    2015-01-01

    We examine the connection between the observed star-forming sequence (SFR ∝ M α ) and the observed evolution of the stellar mass function in the range 0.2 < z < 2.5. We find that the star-forming sequence cannot have a slope α ≲ 0.9 at all masses and redshifts because this would result in a much higher number density at 10 < log (M/M ☉ ) < 11 by z = 1 than is observed. We show that a transition in the slope of the star-forming sequence, such that α = 1 at log (M/M ☉ ) < 10.5 and α = 0.7-0.13z (Whitaker et al.) at log (M/M ☉ ) > 10.5, greatly improves agreement with the evolution of the stellar mass function. We then derive a star-forming sequence that reproduces the evolution of the mass function by design. This star-forming sequence is also well described by a broken power law, with a shallow slope at high masses and a steep slope at low masses. At z = 2, it is offset by ∼0.3 dex from the observed star-forming sequence, consistent with the mild disagreement between the cosmic star formation rate (SFR) and recent observations of the growth of the stellar mass density. It is unclear whether this problem stems from errors in stellar mass estimates, errors in SFRs, or other effects. We show that a mass-dependent slope is also seen in other self-consistent models of galaxy evolution, including semianalytical, hydrodynamical, and abundance-matching models. As part of the analysis, we demonstrate that neither mergers nor hidden low-mass quiescent galaxies are likely to reconcile the evolution of the mass function and the star-forming sequence. These results are supported by observations from Whitaker et al

  10. Observation sequences and onboard data processing of Planet-C

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    Suzuki, M.; Imamura, T.; Nakamura, M.; Ishi, N.; Ueno, M.; Hihara, H.; Abe, T.; Yamada, T.

    Planet-C or VCO Venus Climate Orbiter will carry 5 cameras IR1 IR 1micrometer camera IR2 IR 2micrometer camera UVI UV Imager LIR Long-IR camera and LAC Lightning and Airglow Camera in the UV-IR region to investigate atmospheric dynamics of Venus During 30 hr orbiting designed to quasi-synchronize to the super rotation of the Venus atmosphere 3 groups of scientific observations will be carried out i image acquisition of 4 cameras IR1 IR2 UVI LIR 20 min in 2 hrs ii LAC operation only when VCO is within Venus shadow and iii radio occultation These observation sequences will define the scientific outputs of VCO program but the sequences must be compromised with command telemetry downlink and thermal power conditions For maximizing science data downlink it must be well compressed and the compression efficiency and image quality have the significant scientific importance in the VCO program Images of 4 cameras IR1 2 and UVI 1Kx1K and LIR 240x240 will be compressed using JPEG2000 J2K standard J2K is selected because of a no block noise b efficiency c both reversible and irreversible d patent loyalty free and e already implemented as academic commercial software ICs and ASIC logic designs Data compression efficiencies of J2K are about 0 3 reversible and 0 1 sim 0 01 irreversible The DE Digital Electronics unit which controls 4 cameras and handles onboard data processing compression is under concept design stage It is concluded that the J2K data compression logics circuits using space

  11. Observations in the Sequence of UMo Monolithic Miniplates Preparation

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    Lopez, Marisol; Gonzalez, Alfredo; Taboada, Horacio [Gerencia Ciclo del Combustible Nuclear, CAC, Comision Nacional de Energia Atomica, Av. Gral. Paz 1499, B1650KNA (Argentina)

    2011-07-01

    According with the works that the National Atomic Energy Commission of Argentina (CNEA) has being deploying in the frame of the reactor core conversion from HEU to LEU fuel, specially working with UMo monolithic core with Zyrcalloy based cladding concept, we put in sequence and give explanation to the observations recorded during our fabrication development tests. To that aim we performed several tests with different parameters conditions and we list all the observations and the possible causes of presence of undesirable phases, shapes or errors appeared during the fabrication tests of those miniplates. The binding techniques of materials employed in our fabrication include the process in solid state without fusion, but that requires pressure or temperature. The principal method employed in this work is a union process of continues rolling at temperature which is called co-rolling in order to produce a union of the surfaces in touch where it can be observed a new structure, and dog bone presence depending on the fabrication conditions. (author)

  12. Draft Genome Sequence of Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome and Previous d-Lactic Acidosis and Encephalopathy.

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    Domann, Eugen; Fischer, Florence; Glowatzki, Fabian; Fritzenwanker, Moritz; Hain, Torsten; Zechel-Gran, Silke; Giffhorn-Katz, Susanne; Neubauer, Bernd A

    2016-07-28

    d-Lactic acidosis with associated encephalopathy caused by overgrowth of intestinal lactic acid bacteria is a rarely diagnosed neurological complication of patients with short bowel syndrome. Here, we report the draft genome sequence of Lactobacillus delbrueckii strain #22 isolated from a patient with short bowel syndrome and previous d-lactic acidosis/encephalopathy. Copyright © 2016 Domann et al.

  13. Chronic Chagas disease: PCR-xenodiagnosis without previous microscopic observation is a useful tool to detect viable Trypanosoma cruzi

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    Miguel Saavedra

    2013-01-01

    Full Text Available We evaluate the elimination of the microscopic stage of conventional xenodiagnosis (XD to optimize the parasitological diagnosis of Trypanosoma cruzi in chronic Chagas disease. To this purpose we applied under informed consent two XD cages to 150 Chilean chronic chagasic patients. The fecal samples (FS of the triatomines at 30, 60 and 90 days post feeding were divided into two parts: in one a microscopic search for mobile trypomastigote and/or epimastigote forms was performed. In the other part, DNA extraction-purification for PCR directed to the conserved region of kDNA minicircles of trypanosomes (PCR-XD, without previous microscopic observation was done. An XD was considered positive when at least one mobile T. cruzi parasite in any one of three periods of incubation was observed, whereas PCR-XD was considered positive when the 330 bp band specific for T. cruzi was detected. 25 of 26 cases with positive conventional XD were PCR-XD positive (concordance 96.2%, whereas 85 of 124 cases with negative conventional XD were positive by PCR-XD (68.5%. Human chromosome 12 detected by Real-time PCR used as exogenous internal control of PCR-XD reaction allowed to discounting of PCR inhibition and false negative in 40 cases with negative PCR-XD. Conclusion: PCR-XD performed without previous microscopic observation is a useful tool for detection of viable parasites with higher efficiency then conventional XD.

  14. Chronic Chagas disease: PCR-xenodiagnosis without previous microscopic observation is a useful tool to detect viable Trypanosoma cruzi.

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    Saavedra, Miguel; Zulantay, Inés; Apt, Werner; Martínez, Gabriela; Rojas, Antonio; Rodríguez, Jorge

    2013-01-01

    We evaluate the elimination of the microscopic stage of conventional xenodiagnosis (XD) to optimize the parasitological diagnosis of Trypanosoma cruzi in chronic Chagas disease. To this purpose we applied under informed consent two XD cages to 150 Chilean chronic chagasic patients. The fecal samples (FS) of the triatomines at 30, 60 and 90 days post feeding were divided into two parts: in one a microscopic search for mobile trypomastigote and/or epimastigote forms was performed. In the other part, DNA extraction-purification for PCR directed to the conserved region of kDNA minicircles of trypanosomes (PCR-XD), without previous microscopic observation was done. An XD was considered positive when at least one mobile T. cruzi parasite in any one of three periods of incubation was observed, whereas PCR-XD was considered positive when the 330 bp band specific for T. cruzi was detected. 25 of 26 cases with positive conventional XD were PCR-XD positive (concordance 96.2%), whereas 85 of 124 cases with negative conventional XD were positive by PCR-XD (68.5%). Human chromosome 12 detected by Real-time PCR used as exogenous internal control of PCR-XD reaction allowed to discounting of PCR inhibition and false negative in 40 cases with negative PCR-XD. PCR-XD performed without previous microscopic observation is a useful tool for detection of viable parasites with higher efficiency then conventional XD.

  15. De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences.

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    Josephine A Reinhardt

    Full Text Available How non-coding DNA gives rise to new protein-coding genes (de novo genes is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs, while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

  16. Temporal sequence in observational studies to establish causality

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    Luis Carlos Silva Ayçaguer, PhD

    2014-05-01

    Full Text Available The article includes a brief summary on the scope of the notions of causality and risk and considers some operational difficulties that arise when dealing with problems associated with them. It underscores the vital importance of timing and its link with the most commonly used observational research designs that address causal relationships. The article describes in detail the need to record the order in which the relevant events occur and how to consider this in the analysis. A detailed example of errors that are usually incurred in and their effect is provided.

  17. Temporal patterns of fire sequences observed in Canton of Ticino (southern Switzerland

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    L. Telesca

    2010-04-01

    Full Text Available Temporal dynamical analysis in fire sequences recorded from 1969 to 2008 in Canton Ticino (Switzerland was carried out by using the Allan Factor statistics. The obtained results show the presence of daily periodicities, superimposed to two time-scaling regimes. The daily cycle vanishes for sequences of higher altitude fires, for which a single scaling behaviour is observed.

  18. Enactment versus observation: item-specific and relational processing in goal-directed action sequences (and lists of single actions.

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    Janette Schult

    Full Text Available What are the memory-related consequences of learning actions (such as "apply the patch" by enactment during study, as compared to action observation? Theories converge in postulating that enactment encoding increases item-specific processing, but not the processing of relational information. Typically, in the laboratory enactment encoding is studied for lists of unrelated single actions in which one action execution has no overarching purpose or relation with other actions. In contrast, real-life actions are usually carried out with the intention to achieve such a purpose. When actions are embedded in action sequences, relational information provides efficient retrieval cues. We contrasted memory for single actions with memory for action sequences in three experiments. We found more reliance on relational processing for action-sequences than single actions. To what degree can this relational information be used after enactment versus after the observation of an actor? We found indicators of superior relational processing after observation than enactment in ordered pair recall (Experiment 1A and in emerging subjective organization of repeated recall protocols (recall runs 2-3, Experiment 2. An indicator of superior item-specific processing after enactment compared to observation was recognition (Experiment 1B, Experiment 2. Similar net recall suggests that observation can be as good a learning strategy as enactment. We discuss possible reasons why these findings only partly converge with previous research and theorizing.

  19. Comparison of nucleotide sequences of recent and previous lineages of peste-des-petits-ruminants viruses of sheep and goats in Nigeria

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    Samuel Mantip

    2016-08-01

    Full Text Available Peste-des-petits-ruminants virus (PPRV is a highly contagious, fatal and economically important viral disease of small ruminants that is still endemic and militates against the production of sheep and goats in endemic areas of the world. The aim of this study was to describe the viral strains within the country. This was carried out by collecting tissue and swab samples from sheep and goats in various agro-ecological zones of Nigeria. The phylogeny of archived PPRV strains or isolates and those circulating and causing recent outbreaks was determined by sequencing of the nucleoprotein (N-gene. Twenty tissue and swab samples from apparently healthy and sick sheep and goats were collected randomly from 18 states, namely 3 states in each of the 6 agro-ecological zones visited. A total of 360 samples were collected. A total of 35 samples of 360 (9.7% tested positive by reverse transcriptase–polymerase chain reaction, of which 25 were from oculo-nasal swabs and 10 were from tissue samples. Neighbour-joining phylogenetic analysis using Phylogenetic Analysis Using Parsimony (PAUP identified four different lineages, that is, lineages I, II, III and IV. Interestingly, the Nigerian strains described in this study grouped in two separate major lineages, that is, lineages II and IV. Strains from Sokoto, Oyo, Plateau and Ondo states grouped according to the historical distribution of PPRV together with the Nigerian 75/1 strain of lineage II, while other strains from Sokoto, Oyo, Plateau, Akwa-Ibom, Adamawa, Kaduna, Lagos, Bauchi, Niger and Kano states grouped together with the East African and Asian strains of lineage IV. This finding confirms that both lineage II and IV strains of PPRV are circulating in Nigeria. Previously, only strains of lineage II were found to be present in the country.

  20. Observational learning of new movement sequences is reflected in fronto-parietal coherence.

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    Jurjen van der Helden

    Full Text Available Mankind is unique in her ability for observational learning, i.e. the transmission of acquired knowledge and behavioral repertoire through observation of others' actions. In the present study we used electrophysiological measures to investigate brain mechanisms of observational learning. Analysis investigated the possible functional coupling between occipital (alpha and motor (mu rhythms operating in the 10 Hz frequency range for translating "seeing" into "doing". Subjects observed movement sequences consisting of six consecutive left or right hand button presses directed at one of two target-buttons for subsequent imitation. Each movement sequence was presented four times, intervened by short pause intervals for sequence rehearsal. During a control task subjects observed the same movement sequences without a requirement for subsequent reproduction. Although both alpha and mu rhythms desynchronized during the imitation task relative to the control task, modulations in alpha and mu power were found to be largely independent from each other over time, arguing against a functional coupling of alpha and mu generators during observational learning. This independence was furthermore reflected in the absence of coherence between occipital and motor electrodes overlaying alpha and mu generators. Instead, coherence analysis revealed a pair of symmetric fronto-parietal networks, one over the left and one over the right hemisphere, reflecting stronger coherence during observation of movements than during pauses. Individual differences in fronto-parietal coherence were furthermore found to predict imitation accuracy. The properties of these networks, i.e. their fronto-parietal distribution, their ipsilateral organization and their sensitivity to the observation of movements, match closely with the known properties of the mirror neuron system (MNS as studied in the macaque brain. These results indicate a functional dissociation between higher order areas for

  1. The Lower Main Sequence of Stars in the Solar Neighborhood: Model Predictions Versus Observation

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    Bartašiūtė S.

    2012-09-01

    Full Text Available We have used the Simbad database and VizieR catalogue access tools to construct the observational color-absolute magnitude diagrams of nearby K-M dwarfs with precise Hipparcos parallaxes (σπ/π ≤ 0:05. Particular attention has been paid to removing unresolved double/multiple stars and variables. In addition to archival data, we have made use of nearly 2000 new radial-velocity measurements of K-M dwarfs to identify spectroscopic binary candidates. The main sequences, cleaned from unresolved binaries, variable stars, and old population stars which can also widen the sequence due to their presumably lower metallicity, were compared to available solar-metallicity models. Significant offsets of most of the model main-sequence lines are seen with respect to observational data, especially for the lower-mass stars. Only the location and slope of the Victoria-Regina and, partly, BaSTI isochrones match the data quite well.

  2. Oscillation mode linewidths of main-sequence and subgiant stars observed by Kepler

    DEFF Research Database (Denmark)

    Appourchaux, T.; Benomar, O.; Gruberbauer, M.

    2012-01-01

    Solar-like oscillations have been observed by {{\\it Kepler}} and CoRoT in several solar-type stars. We study the variations of stellar p-mode linewidth as a function of effective temperature. Time series of 9 months of Kepler data have been used. The power spectra of 42 cool main-sequence stars a...

  3. Observing complex action sequences: The role of the fronto-parietal mirror neuron system.

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    Molnar-Szakacs, Istvan; Kaplan, Jonas; Greenfield, Patricia M; Iacoboni, Marco

    2006-11-15

    A fronto-parietal mirror neuron network in the human brain supports the ability to represent and understand observed actions allowing us to successfully interact with others and our environment. Using functional magnetic resonance imaging (fMRI), we wanted to investigate the response of this network in adults during observation of hierarchically organized action sequences of varying complexity that emerge at different developmental stages. We hypothesized that fronto-parietal systems may play a role in coding the hierarchical structure of object-directed actions. The observation of all action sequences recruited a common bilateral network including the fronto-parietal mirror neuron system and occipito-temporal visual motion areas. Activity in mirror neuron areas varied according to the motoric complexity of the observed actions, but not according to the developmental sequence of action structures, possibly due to the fact that our subjects were all adults. These results suggest that the mirror neuron system provides a fairly accurate simulation process of observed actions, mimicking internally the level of motoric complexity. We also discuss the results in terms of the links between mirror neurons, language development and evolution.

  4. Effects of cloning and root-tip size on observations of fungal ITS sequences from Picea glauca roots

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    Daniel L. Lindner; Mark T. Banik

    2009-01-01

    To better understand the effects of cloning on observations of fungal ITS sequences from Picea glauca (white spruce) roots two techniques were compared: (i) direct sequencing of fungal ITS regions from individual root tips without cloning and (ii) cloning and sequencing of fungal ITS regions from individual root tips. Effect of root tip size was...

  5. Lung MRI at 1.5 and 3 Tesla: observer preference study and lesion contrast using five different pulse sequences.

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    Fink, Christian; Puderbach, Michael; Biederer, Juergen; Fabel, Michael; Dietrich, Olaf; Kauczor, Hans-Ulrich; Reiser, Maximilian F; Schönberg, Stefan O

    2007-06-01

    To compare the image quality and lesion contrast of lung MRI using 5 different pulse sequences at 1.5 T and 3 T. Lung MRI was performed at 1.5 T and 3 T using 5 pulse sequences which have been previously proposed for lung MRI: 3D volumetric interpolated breath-hold examination (VIBE), true fast imaging with steady-state precession (TrueFISP), half-Fourier single-shot turbo spin-echo (HASTE), short tau inversion recovery (STIR), T2-weighted turbo spin-echo (TSE). In addition to 4 healthy volunteers, 5 porcine lungs were examined in a dedicated chest phantom. Lung pathology (nodules and infiltrates) was simulated in the phantom by intrapulmonary and intrabronchial injections of agarose. CT was performed in the phantom for correlation. Image quality of the sequences was ranked in a side-by-side comparison by 3 blinded radiologists regarding the delineation of pulmonary and mediastinal anatomy, conspicuity of pulmonary nodules and infiltrates, and presence of artifacts. The contrast of nodules and infiltrates (CNODULES and CINFILTRATES) defined by the ratio of the signal intensities of the lesion and adjacent normal lung parenchyma was determined. There were no relevant differences regarding the preference for the individual sequences between both field strengths. TSE was the preferred sequence for the visualization of the mediastinum at both field strengths. For the visualization of lung parenchyma the observers preferred TrueFISP in volunteers and TSE in the phantom studies. At both field strengths VIBE achieved the best rating for the depiction of nodules, whereas HASTE was rated best for the delineation of infiltrates. TrueFISP had the fewest artifacts in volunteers, whereas STIR showed the fewest artifacts in the phantom. For all but the TrueFISP sequence the lesion contrast increased from 1.5 T to 3 T. At both field strengths VIBE showed the highest CNODULES (6.6 and 7.1) and HASTE the highest CINFILTRATES (6.1 and 6.3). The imaging characteristics of different

  6. Rotational motions from the 2016, Central Italy seismic sequence, as observed by an underground ring laser gyroscope

    Science.gov (United States)

    Simonelli, A.; Igel, H.; Wassermann, J.; Belfi, J.; Di Virgilio, A.; Beverini, N.; De Luca, G.; Saccorotti, G.

    2018-05-01

    We present the analysis of rotational and translational ground motions from earthquakes recorded during October/November, 2016, in association with the Central Italy seismic-sequence. We use co-located measurements of the vertical ground rotation rate from a large ring laser gyroscope (RLG), and the three components of ground velocity from a broadband seismometer. Both instruments are positioned in a deep underground environment, within the Gran Sasso National Laboratories (LNGS) of the Istituto Nazionale di Fisica Nucleare (INFN). We collected dozens of events spanning the 3.5-5.9 Magnitude range, and epicentral distances between 30 km and 70 km. This data set constitutes an unprecedented observation of the vertical rotational motions associated with an intense seismic sequence at local distance. Under the plane wave approximation we process the data set in order to get an experimental estimation of the events back azimuth. Peak values of rotation rate (PRR) and horizontal acceleration (PGA) are markedly correlated, according to a scaling constant which is consistent with previous measurements from different earthquake sequences. We used a prediction model in use for Italy to calculate the expected PGA at the recording site, obtaining consequently predictions for PRR. Within the modeling uncertainties, predicted rotations are consistent with the observed ones, suggesting the possibility of establishing specific attenuation models for ground rotations, like the scaling of peak velocity and peak acceleration in empirical ground-motion prediction relationships. In a second step, after identifying the direction of the incoming wave-field, we extract phase velocity data using the spectral ratio of the translational and rotational components.. This analysis is performed over time windows associated with the P-coda, S-coda and Lg phase. Results are consistent with independent estimates of shear-wave velocities in the shallow crust of the Central Apennines.

  7. Genome sequence analysis of five Canadian isolates of strawberry mottle virus reveals extensive intra-species diversity and a longer RNA2 with increased coding capacity compared to a previously characterized European isolate.

    Science.gov (United States)

    Bhagwat, Basdeo; Dickison, Virginia; Ding, Xinlun; Walker, Melanie; Bernardy, Michael; Bouthillier, Michel; Creelman, Alexa; DeYoung, Robyn; Li, Yinzi; Nie, Xianzhou; Wang, Aiming; Xiang, Yu; Sanfaçon, Hélène

    2016-06-01

    In this study, we report the genome sequence of five isolates of strawberry mottle virus (family Secoviridae, order Picornavirales) from strawberry field samples with decline symptoms collected in Eastern Canada. The Canadian isolates differed from the previously characterized European isolate 1134 in that they had a longer RNA2, resulting in a 239-amino-acid extension of the C-terminal region of the polyprotein. Sequence analysis suggests that reassortment and recombination occurred among the isolates. Phylogenetic analysis revealed that the Canadian isolates are diverse, grouping in two separate branches along with isolates from Europe and the Americas.

  8. Multilocus sequence typing of Pseudomonas syringae sensu lato confirms previously described genomospecies and permits rapid identification of P. syringae pv. coriandricola and P. syringae pv. apii causing bacterial leaf spot on parsley.

    Science.gov (United States)

    Bull, Carolee T; Clarke, Christopher R; Cai, Rongman; Vinatzer, Boris A; Jardini, Teresa M; Koike, Steven T

    2011-07-01

    Since 2002, severe leaf spotting on parsley (Petroselinum crispum) has occurred in Monterey County, CA. Either of two different pathovars of Pseudomonas syringae sensu lato were isolated from diseased leaves from eight distinct outbreaks and once from the same outbreak. Fragment analysis of DNA amplified between repetitive sequence polymerase chain reaction; 16S rDNA sequence analysis; and biochemical, physiological, and host range tests identified the pathogens as Pseudomonas syringae pv. apii and P. syringae pv. coriandricola. Koch's postulates were completed for the isolates from parsley, and host range tests with parsley isolates and pathotype strains demonstrated that P. syringae pv. apii and P. syringae pv. coriandricola cause leaf spot diseases on parsley, celery, and coriander or cilantro. In a multilocus sequence typing (MLST) approach, four housekeeping gene fragments were sequenced from 10 strains isolated from parsley and 56 pathotype strains of P. syringae. Allele sequences were uploaded to the Plant-Associated Microbes Database and a phylogenetic tree was built based on concatenated sequences. Tree topology directly corresponded to P. syringae genomospecies and P. syringae pv. apii was allocated appropriately to genomospecies 3. This is the first demonstration that MLST can accurately allocate new pathogens directly to P. syringae sensu lato genomospecies. According to MLST, P. syringae pv. coriandricola is a member of genomospecies 9, P. cannabina. In a blind test, both P. syringae pv. coriandricola and P. syringae pv. apii isolates from parsley were correctly identified to pathovar. In both cases, MLST described diversity within each pathovar that was previously unknown.

  9. Effect of donepezil in patients with Alzheimer's disease previously untreated or treated with memantine or nootropic agents in Germany: an observational study.

    Science.gov (United States)

    Klinger, Tatjana; Ibach, Bernd; Schoenknecht, Peter; Kamleiter, Martin; Silver, Gabrielle; Schroeder, Johannes; Mielke, Ruediger

    2005-05-01

    This open-label, prospective, observational, Post-Marketing Surveillance (PMS) study assessed the efficacy and safety of donepezil in patients who had been switched from therapies currently used in Germany to treat Alzheimer's disease (AD), such as memantine and nootropics, due to insufficient efficacy or poor tolerability. A treatment-naive population was included as a comparator. Patients with AD were treated with donepezil and observed for a period of approximately 3 months. A cognitive assessment was made using the Mini-Mental State Examination (MMSE). Quality of life (QoL) was assessed by the investigators who answered the question 'How did therapy with donepezil influence the QoL of the patient and/or his family over the observation period?' and was graded using three ratings: improved/unchanged/worsened. Adverse events (AEs) were also monitored. A total of 913 patients entered the study (mean +/- SD MMSE score 18.03 +/- 5.34). Efficacy assessments were analyzed for three groups: an overall group of patients who had received any form of prior AD drug therapy (N+ group; n = 709); a subgroup of patients from the N+ group who had received prior memantine therapy only (M+ group; n = 111) and patients who were drug treatment naive (N- group; n = 204). In the evaluable population donepezil improved MMSE scores by 2.21 +/- 3.47 points on average, with similar improvements observed in all three groups. QoL was judged to be improved in at least 70% of patients, again with similar results obtained for all three groups. Donepezil was well tolerated, with 85 of 913 (9.3%) patients reporting AEs. The most common AEs were those typically seen with cholinergic therapies (i.e., diarrhoea, vomiting and nausea). In this observational PMS study, donepezil was shown to be efficacious and well tolerated in patients who were being insufficiently treated with memantine or nootropic therapy. The magnitude of response was similar to that observed in patients who were previously

  10. Plantar pressure in diabetic peripheral neuropathy patients with active foot ulceration, previous ulceration and no history of ulceration: a meta-analysis of observational studies.

    Science.gov (United States)

    Fernando, Malindu Eranga; Crowther, Robert George; Pappas, Elise; Lazzarini, Peter Anthony; Cunningham, Margaret; Sangla, Kunwarjit Singh; Buttner, Petra; Golledge, Jonathan

    2014-01-01

    Elevated dynamic plantar pressures are a consistent finding in diabetes patients with peripheral neuropathy with implications for plantar foot ulceration. This meta-analysis aimed to compare the plantar pressures of diabetes patients that had peripheral neuropathy and those with neuropathy with active or previous foot ulcers. Published articles were identified from Medline via OVID, CINAHL, SCOPUS, INFORMIT, Cochrane Central EMBASE via OVID and Web of Science via ISI Web of Knowledge bibliographic databases. Observational studies reporting barefoot dynamic plantar pressure in adults with diabetic peripheral neuropathy, where at least one group had a history of plantar foot ulcers were included. Interventional studies, shod plantar pressure studies and studies not published in English were excluded. Overall mean peak plantar pressure (MPP) and pressure time integral (PTI) were primary outcomes. The six secondary outcomes were MPP and PTI at the rear foot, mid foot and fore foot. The protocol of the meta-analysis was published with PROPSERO, (registration number CRD42013004310). Eight observational studies were included. Overall MPP and PTI were greater in diabetic peripheral neuropathy patients with foot ulceration compared to those without ulceration (standardised mean difference 0.551, 95% CI 0.290-0.811, pdiabetic peripheral neuropathy with a history of foot ulceration compared to those with diabetic neuropathy without a history of ulceration. More homogenous data is needed to confirm these findings.

  11. Four Forensic Entomology Case Studies: Records and Behavioral Observations on Seldom Reported Cadaver Fauna With Notes on Relevant Previous Occurrences and Ecology.

    Science.gov (United States)

    Lindgren, Natalie K; Sisson, Melissa S; Archambeault, Alan D; Rahlwes, Brent C; Willett, James R; Bucheli, Sibyl R

    2015-03-01

    A yearlong survey of insect taxa associated with human decomposition was conducted at the Southeast Texas Applied Forensic Science (STAFS) facility located in the Center for Biological Field Studies of Sam Houston State University in Huntsville, TX. During this study, four insect-cadaver interactions were observed that represent previously poorly documented yet forensically significant interactions: Syrphidae maggots colonized a corpse in an aquatic situation; Psychodidae adults mated and oviposited on an algal film that was present on a corpse that had been recently removed from water; several Panorpidae were the first insects to feed upon a freshly placed corpse in the autumn; and a noctuid caterpillar was found chewing and ingesting dried human skin. Baseline knowledge of insect-cadaver interactions is the foundation of forensic entomology, and unique observations have the potential to expand our understanding of decomposition ecology. © The Author 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags.

    Science.gov (United States)

    Matsumoto, Toshimi; Okumura, Naohiko; Uenishi, Hirohide; Hayashi, Takeshi; Hamasima, Noriyuki; Awata, Takashi

    2012-01-01

    We have collected more than 190000 porcine expressed sequence tags (ESTs) from full-length complementary DNA (cDNA) libraries and identified more than 2800 single nucleotide polymorphisms (SNPs). In this study, we tentatively chose 222 SNPs observed in assembled ESTs to study pigs of different breeds; 104 were selected by comparing the cDNA sequences of a Meishan pig and samples of three-way cross pigs (Landrace, Large White, and Duroc: LWD), and 118 were selected from LWD samples. To evaluate the genetic variation between the chosen SNPs from pig breeds, we determined the genotypes for 192 pig samples (11 pig groups) from our DNA reference panel with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Of the 222 reference SNPs, 186 were successfully genotyped. A neighbor-joining tree showed that the pig groups were classified into two large clusters, namely, Euro-American and East Asian pig populations. F-statistics and the analysis of molecular variance of Euro-American pig groups revealed that approximately 25% of the genetic variations occurred because of intergroup differences. As the F(IS) values were less than the F(ST) values(,) the clustering, based on the Bayesian inference, implied that there was strong genetic differentiation among pig groups and less divergence within the groups in our samples. © 2011 The Authors. Animal Science Journal © 2011 Japanese Society of Animal Science.

  13. The Evolution of the Observed Hubble Sequence over the past 6Gyr

    Science.gov (United States)

    Delgado-Serrano, R.; Hammer, F.; Yang, Y. B.; Puech, M.; Flores, H.; Rodrigues, M.

    2011-10-01

    During the past years we have confronted serious problems of methodology concerning the morphological and kinematic classification of distant galaxies. This has forced us to create a new simple and effective morphological classification methodology, in order to guarantee a morpho-kinematic correlation, make the reproducibility easier and restrict the classification subjectivity. Giving the characteristic of our morphological classification, we have thus been able to apply the same methodology, using equivalent observations, to representative samples of local and distant galaxies. It has allowed us to derive, for the first time, the distant Hubble sequence (~6 Gyr ago), and determine a morphological evolution of galaxies over the past 6 Gyr. Our results strongly suggest that more than half of the present-day spirals had peculiar morphologies, 6 Gyr ago.

  14. A Macro-Observation Scheme for Abnormal Event Detection in Daily-Life Video Sequences

    Directory of Open Access Journals (Sweden)

    Chiu Wei-Yao

    2010-01-01

    Full Text Available Abstract We propose a macro-observation scheme for abnormal event detection in daily life. The proposed macro-observation representation records the time-space energy of motions of all moving objects in a scene without segmenting individual object parts. The energy history of each pixel in the scene is instantly updated with exponential weights without explicitly specifying the duration of each activity. Since possible activities in daily life are numerous and distinct from each other and not all abnormal events can be foreseen, images from a video sequence that spans sufficient repetition of normal day-to-day activities are first randomly sampled. A constrained clustering model is proposed to partition the sampled images into groups. The new observed event that has distinct distance from any of the cluster centroids is then classified as an anomaly. The proposed method has been evaluated in daily work of a laboratory and BEHAVE benchmark dataset. The experimental results reveal that it can well detect abnormal events such as burglary and fighting as long as they last for a sufficient duration of time. The proposed method can be used as a support system for the scene that requires full time monitoring personnel.

  15. Observations of energetic helium ions in the Earth's radiation belts during a sequence of geomagnetic storms

    International Nuclear Information System (INIS)

    Spjeldvik, W.N.; Fritz, T.A.

    1981-01-01

    Every year a significant number of magnetic storms disturb the earth's magnetosphere and the trapped particle populations. In this paper, we present observations of energetic (MeV) helium ions made with Explorer 45 during a sequence of magnetic storms during June through December of 1972. The first of these storms started on June 17 and had a Dst index excursion to approx.190 gamma, and the MeV helium ions were perturbed primarily beyond 3 earth radii in the equatorial radiation belts with a typical flux increase of an order of magnitude at L = 4. The second storm period took place during August and was associated with very major solar flare activity. Although the Dst extremum was at best 35 gamma less than the June storm, this period can be characterized as irregular (or multi-storm) with strong compression of the magnetosphere and very large (order of magnitude) MeV helium ion flux enhancements down to Lapprox.2. Following this injection the trapped helium ion fluxes showed positive spectral slope with the peak beyond 3.15 MeV at L = 2.5; and at the lowest observable L shells (Lapprox.2--3) little flux decay (tau>100 days) was seen during the rest of the year. Any effects of two subsequent major magnetic storms in September and November were essentially undetectable in the prolonged after-effect of the August solar flare associated MeV helium ion injection. The helium ion radial profile of the phase space density showed a significant negative slope during this period, and we infer that radial diffusion constitutes a significant loss of helium ions on L shells above Lapprox. =4 during the aftermath of the August 1972 magnetic storm

  16. Low back pain in military recruits in relation to social background and previous low back pain. A cross-sectional and prospective observational survey

    DEFF Research Database (Denmark)

    Hestbæk, Lise; Larsen, K.; Weidich, F.

    2005-01-01

    back pain in the development of low back pain in military recruits. METHODS: During a three-month period, Danish military recruits with different social backgrounds live and work under the same conditions. Thus, there is an opportunity to investigate the influence of social background......BACKGROUND: Traditionally, studies on the etiology of low back pain have been carried out in adult populations. However, since low back pain often appears early in life, more research on young populations is needed. This study focuses on the importance of social background factors and previous low...... on the development of low back pain, when persons are removed from their usual environment and submitted to a number of new stressors. In addition, the importance of the recruits' previous low back pain history in relation to low back pain during military service was studied. This was done by means of questionnaires...

  17. Variations of the ISM conditions accross the Main Sequence of star forming galaxies: observations and simulations.

    Science.gov (United States)

    Martinez Galarza, Juan R.; Smith, Howard Alan; Lanz, Lauranne; Hayward, Christopher C.; Zezas, Andreas; Hung, Chao-Ling; Rosenthal, Lee; Weiner, Aaron

    2015-01-01

    A significant amount of evidence has been gathered that leads to the existence of a main sequence (MS) of star formation in galaxies. This MS is expressed in terms of a correlation between the SFR and the stellar mass of the form SFR ∝ M* and spans a few orders of magnitude in both quantities. Several ideas have been suggested to explain fundamental properties of the MS, such as its slope, its dispersion, and its evolution with redshift, but no consensus has been reached regarding its true nature, and whether the membership or not of particular galaxies to this MS underlies the existence of two different modes of star formation. In order to advance in the understanding of the MS, here we use a statistically robust Bayesian SED analysis method (CHIBURST) to consistently analyze the star-forming properties of a set of hydro-dynamical simulations of mergers, as well as observations of real mergers, both local and at intermediate redshift. We find a remarkable, very tight correlation between the specific star formation rate (sSFR) of galaxies, and the typical ISM conditions near their inernal star-forming regions, parametrized via a novel quantity: the compactness parameter (C). The evolution of mergers along this correlation explains the spread of the MS, and implies that the physical conditions of the ISM smoothly evolve between on-MS (secular) conditions and off-MS (coalescence/starburst) conditions. Furthermore, we show that the slope of the correlation can be interpreted in terms of the efficiency in the conversion of gas into stars, and that this efficiency remains unchanged along and across the MS. Finally, we discuss differences in the normalization of the correlation as a function of merger mass and redshift, and conclude that these differences imply the existence of two different modes of star formation, unrelated to the smooth evolution across the MS: a disk-like, low pressure mode and a compact nuclear-starburst mode.

  18. Low back pain in military recruits in relation to social background and previous low back pain. A cross-sectional and prospective observational survey

    Directory of Open Access Journals (Sweden)

    Weidick Flemming

    2005-05-01

    Full Text Available Abstract Background Traditionally, studies on the etiology of low back pain have been carried out in adult populations. However, since low back pain often appears early in life, more research on young populations is needed. This study focuses on the importance of social background factors and previous low back pain in the development of low back pain in military recruits. Methods During a three-month period, Danish military recruits with different social backgrounds live and work under the same conditions. Thus, there is an opportunity to investigate the influence of social background on the development of low back pain, when persons are removed from their usual environment and submitted to a number of new stressors. In addition, the importance of the recruits' previous low back pain history in relation to low back pain during military service was studied. This was done by means of questionnaires to 1,711 recruits before and after this three-month period. Results Sedentary occupation was negatively associated with long-lasting low back pain (>30 days during the past year at baseline with an odds ratios of 0.55 (95% CI: 0.33–0.90. This effect vanished during service. Having parents with higher education increased the risk of low back pain during service (OR: 1.9;1.2–3.0, for the highest educated group, but not of the consequences (leg pain and exemption from duty, whereas high IQ decreased the risk of these consequences (odds ratios as low as 0.2;0.1–0.8 for exemption from duty in the group with highest IQ. Long-lasting low back pain prior to service increased the risk of long-lasting low back pain (OR: 4.8;2.1–10.8, leg pain (OR: 3.3;1.3–8.3 and exemption from duty during service (OR: 5.9;2.4–14.8. Conclusion Sedentary occupation is negatively associated with low back pain at baseline. This protective effect disappears, when the person becomes physically active. For predicting trouble related to the low back during service, the

  19. Detailed observations of California foreshock sequences: Implications for the earthquake initiation process

    Science.gov (United States)

    Dodge, D.A.; Beroza, G.C.; Ellsworth, W.L.

    1996-01-01

    We find that foreshocks provide clear evidence for an extended nucleation process before some earthquakes. In this study, we examine in detail the evolution of six California foreshock sequences, the 1986 Mount Lewis (ML, = 5.5), the 1986 Chalfant (ML = 6.4), the. 1986 Stone Canyon (ML = 4.7), the 1990 Upland (ML = 5.2), the 1992 Joshua Tree (MW= 6.1), and the 1992 Landers (MW = 7.3) sequence. Typically, uncertainties in hypocentral parameters are too large to establish the geometry of foreshock sequences and hence to understand their evolution. However, the similarity of location and focal mechanisms for the events in these sequences leads to similar foreshock waveforms that we cross correlate to obtain extremely accurate relative locations. We use these results to identify small-scale fault zone structures that could influence nucleation and to determine the stress evolution leading up to the mainshock. In general, these foreshock sequences are not compatible with a cascading failure nucleation model in which the foreshocks all occur on a single fault plane and trigger the mainshock by static stress transfer. Instead, the foreshocks seem to concentrate near structural discontinuities in the fault and may themselves be a product of an aseismic nucleation process. Fault zone heterogeneity may also be important in controlling the number of foreshocks, i.e., the stronger the heterogeneity, the greater the number of foreshocks. The size of the nucleation region, as measured by the extent of the foreshock sequence, appears to scale with mainshock moment in the same manner as determined independently by measurements of the seismic nucleation phase. We also find evidence for slip localization as predicted by some models of earthquake nucleation. Copyright 1996 by the American Geophysical Union.

  20. Shared decision making observed in clinical practice: visual displays of communication sequence and patterns.

    Science.gov (United States)

    Elwyn, G; Edwards, A; Wensing, M; Hibbs, R; Wilkinson, C; Grol, R

    2001-05-01

    The aim of the study was to examine the communication strategies of general practitioners attempting to involve patients in treatment or management decisions. This empirical data was then compared with theoretical 'competences' derived for 'shared decision making'. The subjects were four general practitioners, who taped conducted consultations with the specific intent of involving patients in the decision-making process. The consultations were transcribed, coded into skill categorizations and presented as visual display using a specifically devised sequential banding The empirical data from these purposively selected consultation from clinicians who are experienced in shared decision making did not match suggested theoretical frameworks. The views of patients about treatment possibilities and their preferred role in decision making were not explored. The interactions were initiated by a problem-defining phase, statements of 'equipoise' consistently appeared and the portrayal of option information was often intermingled with opportunities to allow patients to question and reflect. A decision-making stage occurred consistently after approximately 80% of the total consultation duration and arrangements were consistently made for follow-up and review. Eight of the 10 consultations took more than 11 min - these specific consultations were characterized by significant proportions of time provided for information exchange and patient interaction. The results demonstrate that some theoretical competences are not distinguishable in practice and other stages, not previously described, such as the 'portrayal of equipoise', are observed. The suggested ideal of a shared decision-making interaction will either require more time than currently allocated, or alternative strategies to enable information exchange outside the consultation.

  1. Fall Detection for Elderly from Partially Observed Depth-Map Video Sequences Based on View-Invariant Human Activity Representation

    Directory of Open Access Journals (Sweden)

    Rami Alazrai

    2017-03-01

    Full Text Available This paper presents a new approach for fall detection from partially-observed depth-map video sequences. The proposed approach utilizes the 3D skeletal joint positions obtained from the Microsoft Kinect sensor to build a view-invariant descriptor for human activity representation, called the motion-pose geometric descriptor (MPGD. Furthermore, we have developed a histogram-based representation (HBR based on the MPGD to construct a length-independent representation of the observed video subsequences. Using the constructed HBR, we formulate the fall detection problem as a posterior-maximization problem in which the posteriori probability for each observed video subsequence is estimated using a multi-class SVM (support vector machine classifier. Then, we combine the computed posteriori probabilities from all of the observed subsequences to obtain an overall class posteriori probability of the entire partially-observed depth-map video sequence. To evaluate the performance of the proposed approach, we have utilized the Kinect sensor to record a dataset of depth-map video sequences that simulates four fall-related activities of elderly people, including: walking, sitting, falling form standing and falling from sitting. Then, using the collected dataset, we have developed three evaluation scenarios based on the number of unobserved video subsequences in the testing videos, including: fully-observed video sequence scenario, single unobserved video subsequence of random lengths scenarios and two unobserved video subsequences of random lengths scenarios. Experimental results show that the proposed approach achieved an average recognition accuracy of 93 . 6 % , 77 . 6 % and 65 . 1 % , in recognizing the activities during the first, second and third evaluation scenario, respectively. These results demonstrate the feasibility of the proposed approach to detect falls from partially-observed videos.

  2. An Observational Study of Children's Involvement in Informed Consent for Exome Sequencing Research.

    Science.gov (United States)

    Miller, Victoria A; Werner-Lin, Allison; Walser, Sarah A; Biswas, Sawona; Bernhardt, Barbara A

    2017-02-01

    The goal of this study was to examine children's involvement in consent sessions for exome sequencing research and associations of involvement with provider and parent communication. Participants included 44 children (8-17 years) from five cohorts who were offered participation in an exome sequencing study. The consent sessions were audiotaped, transcribed, and coded. Providers attempted to facilitate the child's involvement in the majority (73%) of sessions, and most (75%) children also verbally participated. Provider facilitation was strongly associated with likelihood of child participation. These findings underscore that strategies such as asking for children's opinions and soliciting their questions show respect for children and may increase the likelihood that they are engaged and involved in decisions about research participation.

  3. Observational Learning of New Movement Sequences Is Reflected in Fronto-Parietal Coherence

    NARCIS (Netherlands)

    Helden, J. van der; Schie, H.T. van; Rombouts, C.

    2010-01-01

    Mankind is unique in her ability for observational learning, i.e. the transmission of acquired knowledge and behavioral repertoire through observation of others' actions. In the present study we used electrophysiological measures to investigate brain mechanisms of observational learning. Analysis

  4. Observational learning of new movement sequences is reflected in fronto-parietal coherence

    NARCIS (Netherlands)

    van der Helden, J.; van Schie, Hein T.; Rombouts, Christiaan

    2010-01-01

    Mankind is unique in her ability for observational learning, i.e. the transmission of acquired knowledge and behavioral repertoire through observation of others' actions. In the present study we used electrophysiological measures to investigate brain mechanisms of observational learning. Analysis

  5. Observation of Multiple Volume Reflection of Ultrarelativistic Protons by a Sequence of Several Bent Silicon Crystals

    CERN Document Server

    Scandale, Walter; Baricordi, S; Dalpiaz, P; Fiorini, M; Guidi, V; Mazzolari, A; Della Mea, G; Milan, R; Ambrosi, G; Zuccon, P; Bertucci, B; Bürger, W; Duranti, M; Cavoto, G; Santacesaria, R; Valente, P; Luci, C; Iacoangeli, F; Vallazza, E; Afonin, A G; Chesnokov, Yu A; Kotov, V I; Maisheev, V A; Yazynin, I A; Kovalenko, A D; Taratin, A M; Denisov, A S; Gavrikov, Y A; Ivanov, Yu M; Lapina, L P; Malyarenko, L G; Skorogobogatov, V V; Suvorov, V M; Vavilov, S A; Bolognini, D; Hasan, S; Mozzanica, A; Prest, M

    2009-01-01

    The interactions of 400 GeV protons with different sequences of bent silicon crystals have been investigated at the H8 beam line of the CERN Super Proton Synchrotron. The multiple volume reflection of the proton beam has been studied in detail on a five-crystal reflector measuring an angular beam deflection =52.96±0.14 µrad. The efficiency was found larger than 80% for an angular acceptance at the reflector entrance of 70 µrad, with a maximal efficiency value of =0.90±0.01±0.03.

  6. Spatio-temporal Hotelling observer for signal detection from image sequences.

    Science.gov (United States)

    Caucci, Luca; Barrett, Harrison H; Rodriguez, Jeffrey J

    2009-06-22

    Detection of signals in noisy images is necessary in many applications, including astronomy and medical imaging. The optimal linear observer for performing a detection task, called the Hotelling observer in the medical literature, can be regarded as a generalization of the familiar prewhitening matched filter. Performance on the detection task is limited by randomness in the image data, which stems from randomness in the object, randomness in the imaging system, and randomness in the detector outputs due to photon and readout noise, and the Hotelling observer accounts for all of these effects in an optimal way. If multiple temporal frames of images are acquired, the resulting data set is a spatio-temporal random process, and the Hotelling observer becomes a spatio-temporal linear operator. This paper discusses the theory of the spatio-temporal Hotelling observer and estimation of the required spatio-temporal covariance matrices. It also presents a parallel implementation of the observer on a cluster of Sony PLAYSTATION 3 gaming consoles. As an example, we consider the use of the spatio-temporal Hotelling observer for exoplanet detection.

  7. THE EVOLVED MAIN-SEQUENCE CHANNEL: HST AND LBT OBSERVATIONS OF CSS 120422:111127+571239

    Energy Technology Data Exchange (ETDEWEB)

    Kennedy, M.; Callanan, P. [Department of Physics, University College Cork, Cork (Ireland); Garnavich, P.; Littlefield, C. [Department of Physics, University of Notre Dame, Notre Dame, IN 46556 (United States); Szkody, P. [Department of Astronomy, University of Washington, Seattle, WA (United States); Pogge, R. [Department of Astronomy, The Ohio State University, 140 W. 18th Avenue, Columbus, OH 43202 (United States)

    2015-12-20

    The “evolved main-sequence (EMS)” channel is thought to contribute significantly to the population of AM CVn-type systems in the Galaxy, and also to the number of cataclysmic variables (CVs) detected below the period minimum for hydrogen rich systems. CSS 120422:J111127+571239 was discovered by the Catalina Sky Survey in 2012 April. Its period was found to be 56 minutes, well below the minimum, and the optical spectrum is clearly depleted in hydrogen relative to helium, but still has two orders of magnitude more hydrogen than AM CVn stars. Doppler tomography of the Hα line hinted at a spiral structure existing in the disk. Here we present spectroscopy of CSS 120422:J111127+571239 using the Cosmic Origins Spectrograph FUV instrument on the Hubble Space Telescope and using the MODS spectrograph on the Large Binocular Telescope. The UV spectrum shows Si iv, N v, and He ii, but no detectable C iv. The anomalous nitrogen/carbon ratio is seen in a small number of other CVs and confirms a unique binary evolution. We also present and compare the optical spectrum of V418 Ser and advocate that it is also an EMS system.

  8. Oscillation mode frequencies of 61 main-sequence and subgiant stars observed by Kepler

    DEFF Research Database (Denmark)

    Appourchaux, T.; Chaplin, W. J.; García, R. A.

    2012-01-01

    Solar-like oscillations have been observed by Kepler and CoRoT in several solar-type stars, thereby providing a way to probe the stars using asteroseismology Aims. We provide the mode frequencies of the oscillations of various stars required to perform a comparison with those obtained from stella...

  9. Radio-emission of pre-main sequence stars of the Rho Ophiuchi cloud: observations and interpretation

    International Nuclear Information System (INIS)

    Andre, P.

    1987-11-01

    Observations of the radio continuum emission of a young star population have been made at VLA on the whole molecular cloud Rho Ophiuchi, one of the closest site of star formation. A dozen of stellar sources have been detected. Radio emission of some identified objects seems to have a magnetic nature and be produced by gyrosynchrotron mechanism. In particular, one of the sources shows a radio radiation circularly polarized; two other stars have a radiation strongly variable probably due to magnetic eruptions more important than those detected in X radiation. More generally, radio observations select probably a specific population of young stars characterized by magnetic field presence extended on several stellar radii and by absence of dense circumstellar environment. Spatial distribution of these objects suggest, they are younger than most of the pre-main sequence stars [fr

  10. Variability in prostate and seminal vesicle delineations defined on magnetic resonance images, a multi-observer, -center and -sequence study

    DEFF Research Database (Denmark)

    Nyholm, Tufve; Jonsson, Joakim; Söderström, Karin

    2013-01-01

    and approximately equal for the prostate and seminal vesicles. Large differences in variability were observed for individual patients, and also for individual imaging sequences used at the different centers. There was however no indication of decreased variability with higher field strength. CONCLUSION: The overall......BACKGROUND: The use of magnetic resonance (MR) imaging as a part of preparation for radiotherapy is increasing. For delineation of the prostate several publications have shown decreased delineation variability using MR compared to computed tomography (CT). The purpose of the present work....... Two physicians from each center delineated the prostate and the seminal vesicles on each of the 25 image sets. The variability between the delineations was analyzed with respect to overall, intra- and inter-physician variability, and dependence between variability and origin of the MR images, i...

  11. Laparoscopy After Previous Laparotomy

    Directory of Open Access Journals (Sweden)

    Zulfo Godinjak

    2006-11-01

    Full Text Available Following the abdominal surgery, extensive adhesions often occur and they can cause difficulties during laparoscopic operations. However, previous laparotomy is not considered to be a contraindication for laparoscopy. The aim of this study is to present that an insertion of Veres needle in the region of umbilicus is a safe method for creating a pneumoperitoneum for laparoscopic operations after previous laparotomy. In the last three years, we have performed 144 laparoscopic operations in patients that previously underwent one or two laparotomies. Pathology of digestive system, genital organs, Cesarean Section or abdominal war injuries were the most common causes of previouslaparotomy. During those operations or during entering into abdominal cavity we have not experienced any complications, while in 7 patients we performed conversion to laparotomy following the diagnostic laparoscopy. In all patients an insertion of Veres needle and trocar insertion in the umbilical region was performed, namely a technique of closed laparoscopy. Not even in one patient adhesions in the region of umbilicus were found, and no abdominal organs were injured.

  12. Rotational motions from the 2016, Central Italy seismic sequence, as observed by an underground ring laser gyroscope

    Science.gov (United States)

    Simonelli, Andreino; Belfi, Jacopo; Beverini, Nicolò; Di Virgilio, Angela; Maccioni, Enrico; De Luca, Gaetano; Saccorotti, Gilberto; Wassermann, Joachim; Igel, Heiner

    2017-04-01

    We present analyses of rotational and translational ground motions from earthquakes recorded during October-November, 2016, in association with the Central Italy seismic-sequence. We use co-located measurements of the vertical ground rotation rate from a large ring laser gyroscope (RLG), and the three components of ground velocity from a broadband seismometer. Both instruments are positioned in a deep underground environment, within the Gran Sasso National Laboratories (LNGS) of the Istituto Nazionale di Fisica Nucleare (INFN). We collected dozen of events spanning the 3.5-5.9 Magnitude range, and epicentral distances between 40 km and 80 km. This data set constitutes an unprecedented observation of the vertical rotational motions associated with an intense seismic sequence at local distance. In theory - assuming plane wave propagation - the ratio between the vertical rotation rate and the transverse acceleration permits, in a single station approach, the estimation of apparent phase velocity in the case of SH arrivals or real phase velocity in the case of Love surface waves. This is a standard approach for the analysis of earthquakes at teleseismic distances, and the results reported by the literature are compatible with the expected phase velocities from the PREM model. Here we extend the application of the same approach to local events, thus exploring higher frequency ranges and larger rotation rate amplitudes. We use a novel approach to joint rotation/acceleration analysis based on the continuous wavelet transform (CWT). Wavelet coherence (WTC) is used as a filter for identifying those regions of the time-period plane where the rotation rate and transverse acceleration signals exhibit significant coherence. This allows retrieving estimates of phase velocities over the period range spanned by correlated arrivals. Coherency among ground rotation and translation is also observed throughout the coda of the P-wave arrival, an observation which is interpreted in

  13. Strong motions observed by K-NET and KiK-net during the 2016 Kumamoto earthquake sequence

    Science.gov (United States)

    Suzuki, Wataru; Aoi, Shin; Kunugi, Takashi; Kubo, Hisahiko; Morikawa, Nobuyuki; Nakamura, Hiromitsu; Kimura, Takeshi; Fujiwara, Hiroyuki

    2017-01-01

    The nationwide strong-motion seismograph network of K-NET and KiK-net in Japan successfully recorded the strong ground motions of the 2016 Kumamoto earthquake sequence, which show the several notable characteristics. For the first large earthquake with a JMA magnitude of 6.5 (21:26, April 14, 2016, JST), the large strong motions are concentrated near the epicenter and the strong-motion attenuations are well predicted by the empirical relation for crustal earthquakes with a moment magnitude of 6.1. For the largest earthquake of the sequence with a JMA magnitude of 7.3 (01:25, April 16, 2016, JST), the large peak ground accelerations and velocities extend from the epicentral area to the northeast direction. The attenuation feature of peak ground accelerations generally follows the empirical relation, whereas that for velocities deviates from the empirical relation for stations with the epicentral distance of greater than 200 km, which can be attributed to the large Love wave having a dominant period around 10 s. The large accelerations were observed at stations even in Oita region, more than 70 km northeast from the epicenter. They are attributed to the local induced earthquake in Oita region, whose moment magnitude is estimated to be 5.5 by matching the amplitudes of the corresponding phases with the empirical attenuation relation. The real-time strong-motion observation has a potential for contributing to the mitigation of the ongoing earthquake disasters. We test a methodology to forecast the regions to be exposed to the large shaking in real time, which has been developed based on the fact that the neighboring stations are already shaken, for the largest event of the Kumamoto earthquakes, and demonstrate that it is simple but effective to quickly make warning. We also shows that the interpolation of the strong motions in real time is feasible, which will be utilized for the real-time forecast of ground motions based on the observed shakings.[Figure not available

  14. SPITZER OBSERVATIONS OF PASSIVE AND STAR-FORMING EARLY-TYPE GALAXIES: AN INFRARED COLOR-COLOR SEQUENCE

    International Nuclear Information System (INIS)

    Temi, Pasquale; Brighenti, Fabrizio; Mathews, William G.

    2009-01-01

    We describe the infrared properties of a large sample of early-type galaxies, comparing data from the Spitzer archive with Ks-band emission from the Two Micron All Sky Survey. While most representations of this data result in correlations with large scatter, we find a remarkably tight relation among colors formed by ratios of luminosities in Spitzer-Multiband Imaging Photometer bands (24, 70, and 160 μm) and the Ks band. Remarkably, this correlation among E and S0 galaxies follows that of nearby normal galaxies of all morphological types. In particular, the tight infrared color-color correlation for S0 galaxies alone follows that of the entire Hubble sequence of normal galaxies, roughly in order of galaxy type from ellipticals to spirals to irregulars. The specific star formation rate (SFR) of S0 galaxies estimated from the 24 μm luminosity increases with decreasing K-band luminosity (or stellar mass) from essentially zero, as with most massive ellipticals, to rates typical of irregular galaxies. Moreover, the luminosities of the many infrared-luminous S0 galaxies can significantly exceed those of the most luminous (presumably post-merger) E galaxies. SFRs in the most infrared-luminous S0 galaxies approach 1-10 solar masses per year. Consistently, with this picture we find that while most early-type galaxies populate an infrared red sequence, about 24% of the objects (mostly S0s) are in an infrared blue cloud together with late-type galaxies. For those early-type galaxies also observed at radio frequencies, we find that the far-infrared luminosities correlate with the mass of neutral and molecular hydrogen, but the scatter is large. This scatter suggests that the star formation may be intermittent or that similar S0 galaxies with cold gaseous disks of nearly equal mass can have varying radial column density distributions that alter the local and global SFRs.

  15. Seismic sequences and swarms in the Latium-Abruzzo-Molise Apennines (central Italy): New observations and analysis from a dense monitoring of the recent activity

    Science.gov (United States)

    Frepoli, A.; Cimini, G. B.; De Gori, P.; De Luca, G.; Marchetti, A.; Monna, S.; Montuori, C.; Pagliuca, N. M.

    2017-08-01

    We present a detailed analysis of the seismic activity in the central Apennines based on a high quality seismogram data set collected from two temporary and three permanent networks. This integrated network recorded, between January 2009 and December 2013, a total of 7011 local earthquakes (6270 selected for this study), with local magnitudes ML ranging from 0.4 to 4.7. Hypocentres were located by using a reference 1D crustal velocity model determined with a genetic algorithm. The majority of the hypocenters are located beneath the axis of the Apenninic belt, while the rest are found along the peri-Tyrrhenian margin. Hypocentral depth distribution extends to a depth of 31 km with a pronounced peak between 8 and 12 km. Both low-to-moderate magnitude seismic sequences and diffuse swarm-like seismicity was observed. There were two major seismic swarms and a seismic sequence, which included the Marsica-Sora ML 4.7 main shock. A total of 468 fault plane solutions were derived from P-wave polarities. This new data set more than quadruples the number of focal mechanisms that was previously available for regional stress field analysis in the study region. The majority of the fault plane solutions in the central Apennines show predominantly normal fault movements, with T-axis trends oriented NE-SW. Focal mechanisms calculated in this study confirm that this area is in extension. For the seismic swarms-sequence in the Marsica-Sora area we also derived the azimuth and plunge of the principal stress axes by inverting fault plane solutions. We find a few right-lateral strike-slip focal mechanisms that possibly identify the prolongation of the strike-slip kinematics in the Gargano-Apulia foreland to the west, and mark the passage to the NW-SE striking normal faults of the inner Apenninic belt. The seismicity and stress distribution we observe might be consistent with a fragmented tectonic scenario in which faults with small dimensions release seismic energy in a diffused way.

  16. Previously unknown species of Aspergillus.

    Science.gov (United States)

    Gautier, M; Normand, A-C; Ranque, S

    2016-08-01

    The use of multi-locus DNA sequence analysis has led to the description of previously unknown 'cryptic' Aspergillus species, whereas classical morphology-based identification of Aspergillus remains limited to the section or species-complex level. The current literature highlights two main features concerning these 'cryptic' Aspergillus species. First, the prevalence of such species in clinical samples is relatively high compared with emergent filamentous fungal taxa such as Mucorales, Scedosporium or Fusarium. Second, it is clearly important to identify these species in the clinical laboratory because of the high frequency of antifungal drug-resistant isolates of such Aspergillus species. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been shown to enable the identification of filamentous fungi with an accuracy similar to that of DNA sequence-based methods. As MALDI-TOF MS is well suited to the routine clinical laboratory workflow, it facilitates the identification of these 'cryptic' Aspergillus species at the routine mycology bench. The rapid establishment of enhanced filamentous fungi identification facilities will lead to a better understanding of the epidemiology and clinical importance of these emerging Aspergillus species. Based on routine MALDI-TOF MS-based identification results, we provide original insights into the key interpretation issues of a positive Aspergillus culture from a clinical sample. Which ubiquitous species that are frequently isolated from air samples are rarely involved in human invasive disease? Can both the species and the type of biological sample indicate Aspergillus carriage, colonization or infection in a patient? Highly accurate routine filamentous fungi identification is central to enhance the understanding of these previously unknown Aspergillus species, with a vital impact on further improved patient care. Copyright © 2016 European Society of Clinical Microbiology and

  17. The influence of selection on the evolutionary distance estimated from the base changes observed between homologous nucleotide sequences.

    Science.gov (United States)

    Otsuka, J; Kawai, Y; Sugaya, N

    2001-11-21

    In most studies of molecular evolution, the nucleotide base at a site is assumed to change with the apparent rate under functional constraint, and the comparison of base changes between homologous genes is thought to yield the evolutionary distance corresponding to the site-average change rate multiplied by the divergence time. However, this view is not sufficiently successful in estimating the divergence time of species, but mostly results in the construction of tree topology without a time-scale. In the present paper, this problem is investigated theoretically by considering that observed base changes are the results of comparing the survivals through selection of mutated bases. In the case of weak selection, the time course of base changes due to mutation and selection can be obtained analytically, leading to a theoretical equation showing how the selection has influence on the evolutionary distance estimated from the enumeration of base changes. This result provides a new method for estimating the divergence time more accurately from the observed base changes by evaluating both the strength of selection and the mutation rate. The validity of this method is verified by analysing the base changes observed at the third codon positions of amino acid residues with four-fold codon degeneracy in the protein genes of mammalian mitochondria; i.e. the ratios of estimated divergence times are fairly well consistent with a series of fossil records of mammals. Throughout this analysis, it is also suggested that the mutation rates in mitochondrial genomes are almost the same in different lineages of mammals and that the lineage-specific base-change rates indicated previously are due to the selection probably arising from the preference of transfer RNAs to codons.

  18. Columnar modelling of nucleation burst evolution in the convective boundary layer – first results from a feasibility study Part IV: A compilation of previous observations for valuation of simulation results from a columnar modelling study

    Directory of Open Access Journals (Sweden)

    O. Hellmuth

    2006-01-01

    Full Text Available In the preceding Papers I, II and III a revised columnar high-order modelling approach to model gas-aerosol-turbulence interactions in the convective boundary layer (CBL was proposed, and simulation results of two synthetic nucleation scenarios (binary vs. ternary on new particle formation (NPF in the anthropogenically influenced CBL were presented and discussed. The purpose of the present finishing Paper IV is twofold: Firstly, an attempt is made to compile previous observational findings on NPF bursts in the CBL, obtained from a number of field experiments. Secondly, the scenario simulations discussed in Paper III will be evaluated with respect to the role of CBL turbulence in NPF burst evolution. It was demonstrated, that completely different nucleation mechanisms can lead to the occurrence of NPF bursts in the surface layer, but the corresponding evolution patterns strongly differ with respect to the origin, amplitude and phase of the NPF burst as well as with respect to the time-height evolution of turbulent vertical fluxes and double correlation terms of physicochemical and aerosoldynamical variables. The large differences between the binary and ternary case scenario indicate, that ammonia (NH3 can not be considered as a time-independent tuning parameter in nucleation modelling. Its contribution to the evolution of the NPF burst pattern is much more complicated and reflects the influence of CBL turbulence as well as the strong non-linearity of the ternary nucleation rate. The impact of water (H2O vapour on the nucleation rate is quite varying depending on the considered nucleation mechanism. According to the classical theory of binary nucleation involving H2O and sulphuric acid (H2SO4, H2O vapour favours NPF, according to the classical theory of ternary nuncleation involving H2O, H2SO4 and NH3 and according to organic nucleation via chemical reactions involving stabilised Criegee intermediates (SCIs, H2O vapour disfavours nucleation, and

  19. Assessment of Cultivar Distinctness in Alfalfa: A Comparison of Genotyping-by-Sequencing, Simple-Sequence Repeat Marker, and Morphophysiological Observations

    Directory of Open Access Journals (Sweden)

    Paolo Annicchiarico

    2016-07-01

    Full Text Available Cultivar registration agencies typically require morphophysiological trait-based distinctness of candidate cultivars. This requirement is difficult to achieve for cultivars of major perennial forages because of their genetic structure and ever-increasing number of registered material, leading to possible rejection of agronomically valuable cultivars. This study aimed to explore the value of molecular markers applied to replicated bulked plants (three bulks of 100 independent plants each per cultivar to assess alfalfa ( L. subsp. cultivar distinctness. We compared genotyping-by-sequencing information based on 2902 polymorphic single-nucleotide polymorphism (SNP markers (>30 reads per DNA sample with morphophysiological information based on 11 traits and with simple-sequence repeat (SSR marker information from 41 polymorphic markers for their ability to distinguish 11 alfalfa landraces representative of the germplasm from northern Italy. Three molecular criteria, one based on cultivar differences for individual SSR bands and two based on overall SNP marker variation assessed either by statistically significant cultivar differences on principal component axes or discriminant analysis, distinctly outperformed the morphophysiological criterion. Combining the morphophysiological criterion with either molecular marker method increased discrimination among cultivars, since morphophysiological diversity was unrelated to SSR marker-based diversity ( = 0.04 and poorly related to SNP marker-based diversity ( = 0.23, < 0.15. The criterion based on statistically significant SNP allele frequency differences was less discriminating than morphophysiological variation. Marker-based distinctness, which can be assessed at low cost and without interactions with testing conditions, could validly substitute for (or complement morphophysiological distinctness in alfalfa cultivar registration schemes. It also has interest in sui generis registration systems aimed at

  20. Previous exposure in a high-risk area for travellers' diarrhoea within the past year is associated with a significant protective effect for travellers' diarrhoea: a prospective observational cohort study in travellers to South Asia.

    Science.gov (United States)

    Kuenzli, Esther; Juergensen, David; Kling, Kerstin; Jaeger, Veronika K; DeCrom, Susan; Steffen, Robert; Widmer, Andreas F; Battegay, Manuel; Hatz, Christoph; Neumayr, Andreas

    2017-09-01

    Travellers' diarrhoea is the most common health problem in travellers. Depending on the region visited, up to 40% of travellers develop diarrhoea during a 2-week trip. The aim of this study was to assess risk factors for TD among travellers to the Indian subcontinent. An observational prospective multicentre cohort study investigated travellers to the Indian subcontinent. Participants completed questionnaires assessing the incidence of travellers' diarrhoea and identifying potential risk factors. Covariates were assessed univariately, followed by a multivariate regression. Two-hundred and twenty-six travellers were enrolled into the study, 178 filled in both pre- and post-travel questionnaires. Overall, the attack rate of travellers' diarrhoea was 38.2%. Travel destination is a key risk factor for the occurrence of TD. Travelling to India or Nepal vs Bhutan is associated with an increased risk for TD (OR 6.68 and 6.62, respectively). A length of stay of more than 3 weeks compared to less than 2 weeks is also associated with a significantly increased risk (OR 5.45). Having stayed in a high-risk area for travellers' diarrhoea within the past year before the current trip is associated with a significantly decreased risk (OR 0.19). No association was found between consumption of high risk food (i.e. tap water, ice cream, raw meat and hamburgers) and travellers' diarrhoea. Travellers' diarrhoea is a frequent problem in travellers to the Indian subcontinent. Previous exposure in a high-risk area for travellers' diarrhoea within the past year appears to have a significant protective effect. Furthermore, an association between the occurrence of travellers' diarrhoea and travel destination and length of stay, respectively, was observed. Consumption of risk food did not confer a TD risk in our study. © International Society of Travel Medicine, 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  1. NOESY-WaterControl: a new NOESY sequence for the observation of under-water protein resonances

    Energy Technology Data Exchange (ETDEWEB)

    Torres, Allan M.; Zheng, Gang, E-mail: g.zheng@westernsydney.edu.au; Price, William S. [Western Sydney University, Nanoscale Organisation and Dynamics Group, School of Science and Health (Australia)

    2017-03-15

    Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω{sub 2}). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω{sub 2}. The 2D NOESY maps obtained using the new sequence thus provide more information than the maps obtained with conventional water suppression, thereby lessening the number of experiments needed to complete resonance assignments of biomolecules. The 2D NOESY-WaterControl map of BPTI showed strong bound water and exchangeable proton signals in ω{sub 1} but these signals were absent in ω{sub 2}, indicating the possibility of using the new sequence to discriminate bound water and exchangeable proton resonances from non-labile proton resonances with similar chemical shifts to water.

  2. NOESY-WaterControl: a new NOESY sequence for the observation of under-water protein resonances

    International Nuclear Information System (INIS)

    Torres, Allan M.; Zheng, Gang; Price, William S.

    2017-01-01

    Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω 2 ). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω 2 . The 2D NOESY maps obtained using the new sequence thus provide more information than the maps obtained with conventional water suppression, thereby lessening the number of experiments needed to complete resonance assignments of biomolecules. The 2D NOESY-WaterControl map of BPTI showed strong bound water and exchangeable proton signals in ω 1 but these signals were absent in ω 2 , indicating the possibility of using the new sequence to discriminate bound water and exchangeable proton resonances from non-labile proton resonances with similar chemical shifts to water.

  3. Taphonomic expressions of sedimentary hiatuses: field observations on bioclastic concentrations and sequence anatomy in low, moderate and high subsidence settings

    Science.gov (United States)

    Kidwell, S. M.

    1993-07-01

    Field studies of post-Palaeozoic siliciclastic records reveal a strong concordance between different types of bioclastic concentrations and discontinuity surfaces within third-order sequences (≈ 1 My duration), supporting the use of taphonomic criteria in establishing the relative magnitudes of sedimentary hiatuses. Comparison of records across a spectrum of subsidence rates, however (from ≤ 10 m to > 1 km/My), shows that, along with appreciable changes in sequence anatomy, the nature of surface-mantling bioclastic concentrations also changes. The most significant surfaces (second- and third-order sequence boundaries, surfaces or intervals of maximum transgression, transgressive surfaces) tend to be either bare or mantled with taphonomically complex hiatal and lag concentrations. These were more consistently encountered in low subsidence than in moderate subsidence records. In high subsidence records, major surfaces were more often mantled by composite or event concentrations, if they were bioclastic at all. In all subsidence settings, comparatively minor surfaces (parasequence boundaries, bed set boundaries and bedding planes) were bare or mantled with relatively simple event and composite concentrations. Although all fossil assemblages are biased taphonomically to some degree, relative degrees of bias should almost certainly vary among discontinuities as a general rule, suggesting specific adjustments in sampling strategies for evolutionary studies.

  4. Observation of a sequence of wetting transitions in the binary water+ethylene glycol monobutyl ether mixture

    Science.gov (United States)

    Wu, Chih-Kang; Chen, Li-Jen

    2005-08-01

    A homemade pendant drop/bubble tensiometer was assembled and applied to perform the surface-interfacial tension measurements for the binary water+ethylene glycol monobutyl ether (C4E1) mixture over the temperature range from 50to128°C at 10bar. The symbol CiEj is the abbreviation of a nonionic polyoxyethylene alcohol CiH2i+1(OCH2CH2)jOH. The wetting behavior of the C4E1-rich phase at the interface separating the gas and the aqueous phases was systematically examined according to the wetting coefficient calculated from the experimental results of surface/interfacial tensions. It was found that the C4E1-rich phase exhibits a sequence of wetting transitions, nonwetting→partial wetting→complete wetting, at the gas-water interface in the water+C4E1 system along with increasing the temperature, consistent with the conjecture of Kahlweit and Busse [J. Chem. Phys. 91, 1339 (1989)]. In addition, the relationship of the mutual solubility and the interfacial tension of the interface separating the C4E1-rich phase and the aqueous phase is discussed.

  5. Time-resolved echo-shared parallel MRA of the lung: observer preference study of image quality in comparison with non-echo-shared sequences

    International Nuclear Information System (INIS)

    Fink, C.; Puderbach, M.; Zaporozhan, J.; Plathow, C.; Kauczor, H.-U.; Ley, S.

    2005-01-01

    The aim of this study was to evaluate the image quality of time-resolved echo-shared parallel MRA of the lung. The pulmonary vasculature of nine patients (seven females, two males; median age: 44 years) with pulmonary disease was examined using a time-resolved MRA sequence combining echo sharing with parallel imaging (time-resolved echo-shared angiography technique, or TREAT). The sharpness of the vessel borders, conspicuousness of peripheral lung vessels, artifact level, and overall image quality of TREAT was assessed independently by four readers in a side-by-side comparison with non-echo-shared time-resolved parallel MRA data (pMRA) previously acquired in the same patients. Furthermore, the SNR of pulmonary arteries (PA) and veins (PV) achieved with both pulse sequences was compared. The mean voxel size of TREAT MRA was decreased by 24% compared with the non-echo-shared MRA. Regarding the sharpness of the vessel borders, conspicuousness of peripheral lung vessels, and overall image quality the TREAT sequence was rated superior in 75-76% of all cases. If the TREAT images were preferred over the pMRA images, the advantage was rated as major in 61-71% of all cases. The level of artifacts was not increased with the TREAT sequence. The mean interobserver agreement for all categories ranged between fair (artifact level) and good (overall image quality). The maximum SNR of TREAT did not differ from non-echo-shared parallel MRA (PA: TREAT: 273±45; pMRA: 280±71; PV: TREAT: 273±33; pMRA: 258±62). TREAT achieves a higher spatial resolution than non-echo-shared parallel MRA which is also perceived as an improved image quality. (orig.)

  6. Characteristic interpersonal behavior in dependent and avoidant personality disorder can be observed within very short interaction sequences.

    Science.gov (United States)

    Leising, Daniel; Sporberg, Doreen; Rehbein, Diana

    2006-08-01

    We present a behavior observation study of interpersonal behavior in 96 female subjects, who had been screened for the presence of dependent, avoidant, narcissistic and histrionic personality disorder features. Each subject took part in three short role-plays, taken from assertiveness training. Afterwards, both the subject and her role-play partner judged, how assertive the subject had been. Although observation time was very short, dependent and avoidant subjects could be easily identified from their overly submissive behavior in the role-plays. Histrionic and narcissistic subjects did not show distinctive interpersonal behavior. Contrary to a common belief, higher scores on some personality disorder (PD) scales were positively related to cross-situational variability of behavior. Results are discussed with regard to their implications for clinical diagnostics, therapy and the methodology of personality disorder research in general.

  7. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. FuzzyStatProb: An R Package for the Estimation of Fuzzy Stationary Probabilities from a Sequence of Observations of an Unknown Markov Chain

    Directory of Open Access Journals (Sweden)

    Pablo J. Villacorta

    2016-07-01

    Full Text Available Markov chains are well-established probabilistic models of a wide variety of real systems that evolve along time. Countless examples of applications of Markov chains that successfully capture the probabilistic nature of real problems include areas as diverse as biology, medicine, social science, and engineering. One interesting feature which characterizes certain kinds of Markov chains is their stationary distribution, which stands for the global fraction of time the system spends in each state. The computation of the stationary distribution requires precise knowledge of the transition probabilities. When the only information available is a sequence of observations drawn from the system, such probabilities have to be estimated. Here we review an existing method to estimate fuzzy transition probabilities from observations and, with them, obtain the fuzzy stationary distribution of the resulting fuzzy Markov chain. The method also works when the user directly provides fuzzy transition probabilities. We provide an implementation in the R environment that is the first available to the community and serves as a proof of concept. We demonstrate the usefulness of our proposal with computational experiments on a toy problem, namely a time-homogeneous Markov chain that guides the randomized movement of an autonomous robot that patrols a small area.

  9. Strong-motion observations of the M 7.8 Gorkha, Nepal, earthquake sequence and development of the N-shake strong-motion network

    Science.gov (United States)

    Dixit, Amod; Ringler, Adam; Sumy, Danielle F.; Cochran, Elizabeth S.; Hough, Susan E.; Martin, Stacey; Gibbons, Steven; Luetgert, James H.; Galetzka, John; Shrestha, Surya; Rajaure, Sudhir; McNamara, Daniel E.

    2015-01-01

    We present and describe strong-motion data observations from the 2015 M 7.8 Gorkha, Nepal, earthquake sequence collected using existing and new Quake-Catcher Network (QCN) and U.S. Geological Survey NetQuakes sensors located in the Kathmandu Valley. A comparison of QCN data with waveforms recorded by a conventional strong-motion (NetQuakes) instrument validates the QCN data. We present preliminary analysis of spectral accelerations, and peak ground acceleration and velocity for earthquakes up to M 7.3 from the QCN stations, as well as preliminary analysis of the mainshock recording from the NetQuakes station. We show that mainshock peak accelerations were lower than expected and conclude the Kathmandu Valley experienced a pervasively nonlinear response during the mainshock. Phase picks from the QCN and NetQuakes data are also used to improve aftershock locations. This study confirms the utility of QCN instruments to contribute to ground-motion investigations and aftershock response in regions where conventional instrumentation and open-access seismic data are limited. Initial pilot installations of QCN instruments in 2014 are now being expanded to create the Nepal–Shaking Hazard Assessment for Kathmandu and its Environment (N-SHAKE) network.

  10. Epigenetic Loss of MLH1 Expression in Normal Human Hematopoietic Stem Cell Clones is Defined by the Promoter CpG Methylation Pattern Observed by High-Throughput Methylation Specific Sequencing.

    Science.gov (United States)

    Kenyon, Jonathan; Nickel-Meester, Gabrielle; Qing, Yulan; Santos-Guasch, Gabriela; Drake, Ellen; PingfuFu; Sun, Shuying; Bai, Xiaodong; Wald, David; Arts, Eric; Gerson, Stanton L

    Normal human hematopoietic stem and progenitor cells (HPC) lose expression of MLH1 , an important mismatch repair (MMR) pathway gene, with age. Loss of MMR leads to replication dependent mutational events and microsatellite instability observed in secondary acute myelogenous leukemia and other hematologic malignancies. Epigenetic CpG methylation upstream of the MLH1 promoter is a contributing factor to acquired loss of MLH1 expression in tumors of the epithelia and proximal mucosa. Using single molecule high-throughput bisulfite sequencing we have characterized the CpG methylation landscape from -938 to -337 bp upstream of the MLH1 transcriptional start site (position +0), from 30 hematopoietic colony forming cell clones (CFC) either expressing or not expressing MLH1 . We identify a correlation between MLH1 promoter methylation and loss of MLH1 expression. Additionally, using the CpG site methylation frequencies obtained in this study we were able to generate a classification algorithm capable of sorting the expressing and non-expressing CFC. Thus, as has been previously described for many tumor cell types, we report for the first time a correlation between the loss of MLH1 expression and increased MLH1 promoter methylation in CFC derived from CD34 + selected hematopoietic stem and progenitor cells.

  11. THE EVOLUTION OF DUSTY STAR FORMATION IN GALAXY CLUSTERS TO z = 1: SPITZER INFRARED OBSERVATIONS OF THE FIRST RED-SEQUENCE CLUSTER SURVEY

    International Nuclear Information System (INIS)

    Webb, T. M. A.; O'Donnell, D.; Coppin, Kristen; Faloon, Ashley; Geach, James E.; Noble, Allison; Yee, H. K. C.; Gilbank, David; Ellingson, Erica; Gladders, Mike; Muzzin, Adam; Wilson, Gillian; Yan, Renbin

    2013-01-01

    We present the results of an infrared (IR) study of high-redshift galaxy clusters with the MIPS camera on board the Spitzer Space Telescope. We have assembled a sample of 42 clusters from the Red-Sequence Cluster Survey-1 over the redshift range 0.3 14-15 M ☉ . We statistically measure the number of IR-luminous galaxies in clusters above a fixed inferred IR luminosity of 2 × 10 11 M ☉ , assuming a star forming galaxy template, per unit cluster mass and find it increases to higher redshift. Fitting a simple power-law we measure evolution of (1 + z) 5.1±1.9 over the range 0.3 cluster ). The evolution is similar, with ΣSFR/M cluster ∼ (1 + z) 5.4±1.9 . We show that this can be accounted for by the evolution of the IR-bright field population over the same redshift range; that is, the evolution can be attributed entirely to the change in the in-falling field galaxy population. We show that the ΣSFR/M cluster (binned over all redshift) decreases with increasing cluster mass with a slope (ΣSFR/M cluster ∼M cluster -1.5±0.4 ) consistent with the dependence of the stellar-to-total mass per unit cluster mass seen locally. The inferred star formation seen here could produce ∼5%-10% of the total stellar mass in massive clusters at z = 0, but we cannot constrain the descendant population, nor how rapidly the star-formation must shut-down once the galaxies have entered the cluster environment. Finally, we show a clear decrease in the number of IR-bright galaxies per unit optical galaxy in the cluster cores, confirming star formation continues to avoid the highest density regions of the universe at z ∼ 0.75 (the average redshift of the high-redshift clusters). While several previous studies appear to show enhanced star formation in high-redshift clusters relative to the field we note that these papers have not accounted for the overall increase in galaxy or dark matter density at the location of clusters. Once this is done, clusters at z ∼ 0.75 have the same

  12. THE EVOLUTION OF DUSTY STAR FORMATION IN GALAXY CLUSTERS TO z = 1: SPITZER INFRARED OBSERVATIONS OF THE FIRST RED-SEQUENCE CLUSTER SURVEY

    Energy Technology Data Exchange (ETDEWEB)

    Webb, T. M. A.; O' Donnell, D.; Coppin, Kristen; Faloon, Ashley; Geach, James E.; Noble, Allison [McGill University, 3600 rue University, Montreal, QC, H3A 2T8 (Canada); Yee, H. K. C. [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George St., Toronto, ON, M5S 3H4 (Canada); Gilbank, David [South African Astronomical Observatory, P.O. Box 9, Observatory, 7935 (South Africa); Ellingson, Erica [Department of Astrophysical and Planetary Sciences, University of Colorado at Boulder, Boulder, CO 80309 (United States); Gladders, Mike [Department of Astronomy and Astrophysics, University of Chicago, 5640 S. Ellis Ave., Chicago, IL 60637 (United States); Muzzin, Adam [Leiden Observatory, University of Leiden, Niels Bohrweg 2, NL-2333 CA, Leiden (Netherlands); Wilson, Gillian [Department of Physics and Astronomy, University of California at Riverside, 900 University Avenue, Riverside, CA 92521 (United States); Yan, Renbin [Center for Cosmology and Particle Physics, Department of Physics, New York University, 4 Washington Place, New York, NY 10003 (United States)

    2013-10-01

    We present the results of an infrared (IR) study of high-redshift galaxy clusters with the MIPS camera on board the Spitzer Space Telescope. We have assembled a sample of 42 clusters from the Red-Sequence Cluster Survey-1 over the redshift range 0.3 < z < 1.0 and spanning an approximate range in mass of 10{sup 14-15} M {sub ☉}. We statistically measure the number of IR-luminous galaxies in clusters above a fixed inferred IR luminosity of 2 × 10{sup 11} M {sub ☉}, assuming a star forming galaxy template, per unit cluster mass and find it increases to higher redshift. Fitting a simple power-law we measure evolution of (1 + z){sup 5.1±1.9} over the range 0.3 < z < 1.0. These results are tied to the adoption of a single star forming galaxy template; the presence of active galactic nuclei, and an evolution in their relative contribution to the mid-IR galaxy emission, will alter the overall number counts per cluster and their rate of evolution. Under the star formation assumption we infer the approximate total star formation rate per unit cluster mass (ΣSFR/M {sub cluster}). The evolution is similar, with ΣSFR/M {sub cluster} ∼ (1 + z){sup 5.4±1.9}. We show that this can be accounted for by the evolution of the IR-bright field population over the same redshift range; that is, the evolution can be attributed entirely to the change in the in-falling field galaxy population. We show that the ΣSFR/M {sub cluster} (binned over all redshift) decreases with increasing cluster mass with a slope (ΣSFR/M{sub cluster}∼M{sub cluster}{sup -1.5±0.4}) consistent with the dependence of the stellar-to-total mass per unit cluster mass seen locally. The inferred star formation seen here could produce ∼5%-10% of the total stellar mass in massive clusters at z = 0, but we cannot constrain the descendant population, nor how rapidly the star-formation must shut-down once the galaxies have entered the cluster environment. Finally, we show a clear decrease in the number of IR

  13. Grateloupia tenuis Wang et Luan sp. nov. (Halymeniaceae, Rhodophyta: A New Species from South China Sea Based on Morphological Observation and rbcL Gene Sequences Analysis

    Directory of Open Access Journals (Sweden)

    Ling Yu

    2013-01-01

    Full Text Available Grateloupia tenuis Wang et Luan sp. nov. is a new species described from Lingshui, Hainan Province, South China Sea. Based on the external form and internal structure, combined with rbcL gene sequence analysis, Grateloupia tenuis is distinct from other Grateloupia species as follows: (1 thalli is slippery and cartilaginous in texture; possess fewer branches, relatively slight main axes, and two or three dichotomous branches; (2 cortex is 5-6 layers; medulla is solid when young, but hollow in old branches; reproductive structures are dispersed in main axes of thalli and lower portions of branchlets; exhibits Grateloupia-type auxiliary cell ampullae; (3 the four studied G. tenuis sequences were positioned in a large Grateloupia clade of Halymeniaceae, which included sister group generitype G. filicina with 68 bp differences; G. tenuis was determined to be a sister taxon to the G. catenata, G. ramosissima, G. orientalis, and G. filiformis subclade. The pairwise distances between G. tenuis and these species were 39 to 50 bp. The sequences of G. tenuis differed by 81–108 bp from the sequences of other samples in Grateloupia; there are 114–133 bp changes between G. tenuis and other genera of Halymeniaceae. In final analysis, we considered Grateloupia tenuis Wang et Luan sp. nov. to be a new species of genus Grateloupia.

  14. Grateloupia tenuis Wang et Luan sp. nov. (Halymeniaceae, Rhodophyta): a new species from South China Sea based on morphological observation and rbcL gene sequences analysis.

    Science.gov (United States)

    Yu, Ling; Wang, Hongwei; Luan, Rixiao

    2013-01-01

    Grateloupia tenuis Wang et Luan sp. nov. is a new species described from Lingshui, Hainan Province, South China Sea. Based on the external form and internal structure, combined with rbcL gene sequence analysis, Grateloupia tenuis is distinct from other Grateloupia species as follows: (1) thalli is slippery and cartilaginous in texture; possess fewer branches, relatively slight main axes, and two or three dichotomous branches; (2) cortex is 5-6 layers; medulla is solid when young, but hollow in old branches; reproductive structures are dispersed in main axes of thalli and lower portions of branchlets; exhibits Grateloupia-type auxiliary cell ampullae; (3) the four studied G. tenuis sequences were positioned in a large Grateloupia clade of Halymeniaceae, which included sister group generitype G. filicina with 68 bp differences; G. tenuis was determined to be a sister taxon to the G. catenata, G. ramosissima, G. orientalis, and G. filiformis subclade. The pairwise distances between G. tenuis and these species were 39 to 50 bp. The sequences of G. tenuis differed by 81-108 bp from the sequences of other samples in Grateloupia; there are 114-133 bp changes between G. tenuis and other genera of Halymeniaceae. In final analysis, we considered Grateloupia tenuis Wang et Luan sp. nov. to be a new species of genus Grateloupia.

  15. Grateloupia tenuis Wang et Luan sp. nov. (Halymeniaceae, Rhodophyta): A New Species from South China Sea Based on Morphological Observation and rbcL Gene Sequences Analysis

    Science.gov (United States)

    Wang, Hongwei; Luan, Rixiao

    2013-01-01

    Grateloupia tenuis Wang et Luan sp. nov. is a new species described from Lingshui, Hainan Province, South China Sea. Based on the external form and internal structure, combined with rbcL gene sequence analysis, Grateloupia tenuis is distinct from other Grateloupia species as follows: (1) thalli is slippery and cartilaginous in texture; possess fewer branches, relatively slight main axes, and two or three dichotomous branches; (2) cortex is 5-6 layers; medulla is solid when young, but hollow in old branches; reproductive structures are dispersed in main axes of thalli and lower portions of branchlets; exhibits Grateloupia-type auxiliary cell ampullae; (3) the four studied G. tenuis sequences were positioned in a large Grateloupia clade of Halymeniaceae, which included sister group generitype G. filicina with 68 bp differences; G. tenuis was determined to be a sister taxon to the G. catenata, G. ramosissima, G. orientalis, and G. filiformis subclade. The pairwise distances between G. tenuis and these species were 39 to 50 bp. The sequences of G. tenuis differed by 81–108 bp from the sequences of other samples in Grateloupia; there are 114–133 bp changes between G. tenuis and other genera of Halymeniaceae. In final analysis, we considered Grateloupia tenuis Wang et Luan sp. nov. to be a new species of genus Grateloupia. PMID:24455703

  16. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  17. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  18. Stenostomum cf. leucops (Platyhelminthes in Thailand: a surface observation using scanning electron microscopy and phylogenetic analysis based on 18S ribosomal DNA sequences

    Directory of Open Access Journals (Sweden)

    Arin Ngamniyom

    2016-02-01

    Full Text Available The genus Stenostomum contains small turbellaria that are widely distributed in freshwater environments worldwide. However, there are only rare reports or studies of this genus from Thailand. Therefore, the objective of this study was to report S. cf. leucops in Thailand collected from Pathum Thani Province. The worm morphology and surface topography using scanning electron microscopy were determined. Moreover, the phylogenetic tree of S. cf. leucops was analysed with 17 flatworms based on the 18S ribosomal DNA sequences. The phylogenetic relationship shared a common ancestry of Catenulida species, and S. cf. leucops displayed a monophyletic pattern within Stenostomum spp. The results of the morphological and molecular data are discussed. These results may increase the knowledge of freshwater microturbellarians in Thailand.

  19. Observation of the energy transfer sequence in an organic host–guest system of a luminescent polymer and a phosphorescent molecule

    Energy Technology Data Exchange (ETDEWEB)

    Basel, Tek; Sun, Dali; Gautam, Bhoj; Valy Vardeny, Z., E-mail: val@physics.utah.edu

    2014-11-15

    We used steady state optical spectroscopies such as photoluminescence and photoinduced absorption (PA), and magnetic-field PA (MPA) for studying the energy transfer dynamics in films and organic light emitting diodes (OLED) based on host–guest blends with different guest concentrations of the fluorescent polymer poly-[2-methoxy, 5-(2′-ethyl-hexyloxy)phenylene vinylene] (MEHPPV-host), and phosphorescent molecule PtII-tetraphenyltetrabenzoporphyrin [Pt(tpbp); guest]. We show that the energy transfer process between the excited states of the host polymer and guest molecule takes a ‘ping-pong’ type sequence, because the lowest guest triplet exciton energy, E{sub T}(guest), lies higher than that of the host, E{sub T}(host). Upon photon excitation the photogenerated singlet excitons in the host polymer chains first undergo a Förster resonant energy transfer process to the guest singlet manifold, which subsequently reaches E{sub T}(guest) by intersystem crossing. Because E{sub T}(guest)>E{sub T}(host) there is a subsequent Dexter type energy transfer from E{sub T}(guest) to E{sub T}(host). This energy transfer sequence has profound influence on the photoluminescence and electroluminescence emission spectra in both films and OLED devices based on the MEHPPV-Pt(tpbp) system. - Highlights: • We studied electroluminescence of OLEDs based on host–guest blends. • The emission efficiency decreases with the guest concentration. • We found a dominant Dexter energy transfer from the triplet(guest) to triplet(host). • Energy transfer occurs from the host to guest and back to the host again.

  20. Observation of the energy transfer sequence in an organic host–guest system of a luminescent polymer and a phosphorescent molecule

    International Nuclear Information System (INIS)

    Basel, Tek; Sun, Dali; Gautam, Bhoj; Valy Vardeny, Z.

    2014-01-01

    We used steady state optical spectroscopies such as photoluminescence and photoinduced absorption (PA), and magnetic-field PA (MPA) for studying the energy transfer dynamics in films and organic light emitting diodes (OLED) based on host–guest blends with different guest concentrations of the fluorescent polymer poly-[2-methoxy, 5-(2′-ethyl-hexyloxy)phenylene vinylene] (MEHPPV-host), and phosphorescent molecule PtII-tetraphenyltetrabenzoporphyrin [Pt(tpbp); guest]. We show that the energy transfer process between the excited states of the host polymer and guest molecule takes a ‘ping-pong’ type sequence, because the lowest guest triplet exciton energy, E T (guest), lies higher than that of the host, E T (host). Upon photon excitation the photogenerated singlet excitons in the host polymer chains first undergo a Förster resonant energy transfer process to the guest singlet manifold, which subsequently reaches E T (guest) by intersystem crossing. Because E T (guest)>E T (host) there is a subsequent Dexter type energy transfer from E T (guest) to E T (host). This energy transfer sequence has profound influence on the photoluminescence and electroluminescence emission spectra in both films and OLED devices based on the MEHPPV-Pt(tpbp) system. - Highlights: • We studied electroluminescence of OLEDs based on host–guest blends. • The emission efficiency decreases with the guest concentration. • We found a dominant Dexter energy transfer from the triplet(guest) to triplet(host). • Energy transfer occurs from the host to guest and back to the host again

  1. Sequence-Stratigraphic Analysis of the Regional Observation Monitoring Program (ROMP) 29A Test Corehole and Its Relation to Carbonate Porosity and Regional Transmissivity in the Floridan Aquifer System, Highlands County, Florida

    Science.gov (United States)

    Ward, W. C.; Cunningham, K.J.; Renken, R.A.; Wacker, M.A.; Carlson, J.I.

    2003-01-01

    An analysis was made to describe and interpret the lithology of a part of the Upper Floridan aquifer penetrated by the Regional Observation Monitoring Program (ROMP) 29A test corehole in Highlands County, Florida. This information was integrated into a one-dimensional hydrostratigraphic model that delineates candidate flow zones and confining units in the context of sequence stratigraphy. Results from this test corehole will serve as a starting point to build a robust three-dimensional sequence-stratigraphic framework of the Floridan aquifer system. The ROMP 29A test corehole penetrated the Avon Park Formation, Ocala Limestone, Suwannee Limestone, and Hawthorn Group of middle Eocene to Pliocene age. The part of the Avon Park Formation penetrated in the ROMP 29A test corehole contains two composite depositional sequences. A transgressive systems tract and a highstand systems tract were interpreted for the upper composite sequence; however, only a highstand systems tract was interpreted for the lower composite sequence of the deeper Avon Park stratigraphic section. The composite depositional sequences are composed of at least five high-frequency depositional sequences. These sequences contain high-frequency cycle sets that are an amalgamation of vertically stacked high-frequency cycles. Three types of high-frequency cycles have been identified in the Avon Park Formation: peritidal, shallow subtidal, and deeper subtidal high-frequency cycles. The vertical distribution of carbonate-rock diffuse flow zones within the Avon Park Formation is heterogeneous. Porous vuggy intervals are less than 10 feet, and most are much thinner. The volumetric arrangement of the diffuse flow zones shows that most occur in the highstand systems tract of the lower composite sequence of the Avon Park Formation as compared to the upper composite sequence, which contains both a backstepping transgressive systems tract and a prograding highstand systems tract. Although the porous and permeable

  2. Sequence analysis reveals how G protein-coupled receptors transduce the signal to the G protein.

    NARCIS (Netherlands)

    Oliveira, L.; Paiva, P.B.; Paiva, A.C.; Vriend, G.

    2003-01-01

    Sequence entropy-variability plots based on alignments of very large numbers of sequences-can indicate the location in proteins of the main active site and modulator sites. In the previous article in this issue, we applied this observation to a series of well-studied proteins and concluded that it

  3. Underestimation of Severity of Previous Whiplash Injuries

    Science.gov (United States)

    Naqui, SZH; Lovell, SJ; Lovell, ME

    2008-01-01

    INTRODUCTION We noted a report that more significant symptoms may be expressed after second whiplash injuries by a suggested cumulative effect, including degeneration. We wondered if patients were underestimating the severity of their earlier injury. PATIENTS AND METHODS We studied recent medicolegal reports, to assess subjects with a second whiplash injury. They had been asked whether their earlier injury was worse, the same or lesser in severity. RESULTS From the study cohort, 101 patients (87%) felt that they had fully recovered from their first injury and 15 (13%) had not. Seventy-six subjects considered their first injury of lesser severity, 24 worse and 16 the same. Of the 24 that felt the violence of their first accident was worse, only 8 had worse symptoms, and 16 felt their symptoms were mainly the same or less than their symptoms from their second injury. Statistical analysis of the data revealed that the proportion of those claiming a difference who said the previous injury was lesser was 76% (95% CI 66–84%). The observed proportion with a lesser injury was considerably higher than the 50% anticipated. CONCLUSIONS We feel that subjects may underestimate the severity of an earlier injury and associated symptoms. Reasons for this may include secondary gain rather than any proposed cumulative effect. PMID:18201501

  4. [Electronic cigarettes - effects on health. Previous reports].

    Science.gov (United States)

    Napierała, Marta; Kulza, Maksymilian; Wachowiak, Anna; Jabłecka, Katarzyna; Florek, Ewa

    2014-01-01

    Currently very popular in the market of tobacco products have gained electronic cigarettes (ang. E-cigarettes). These products are considered to be potentially less harmful in compared to traditional tobacco products. However, current reports indicate that the statements of the producers regarding to the composition of the e- liquids not always are sufficient, and consumers often do not have reliable information on the quality of the product used by them. This paper contain a review of previous reports on the composition of e-cigarettes and their impact on health. Most of the observed health effects was related to symptoms of the respiratory tract, mouth, throat, neurological complications and sensory organs. Particularly hazardous effects of the e-cigarettes were: pneumonia, congestive heart failure, confusion, convulsions, hypotension, aspiration pneumonia, face second-degree burns, blindness, chest pain and rapid heartbeat. In the literature there is no information relating to passive exposure by the aerosols released during e-cigarette smoking. Furthermore, the information regarding to the use of these products in the long term are not also available.

  5. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  6. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  7. Novel primer specific false terminations during DNA sequencing reactions: danger of inaccuracy of mutation analysis in molecular diagnostics

    Science.gov (United States)

    Anwar, R; Booth, A; Churchill, A J; Markham, A F

    1996-01-01

    The determination of nucleotide sequence is fundamental to the identification and molecular analysis of genes. Direct sequencing of PCR products is now becoming a commonplace procedure for haplotype analysis, and for defining mutations and polymorphism within genes, particularly for diagnostic purposes. A previously unrecognised phenomenon, primer related variability, observed in sequence data generated using Taq cycle sequencing and T7 Sequenase sequencing, is reported. This suggests that caution is necessary when interpreting DNA sequence data. This is particularly important in situations where treatment may be dependent on the accuracy of the molecular diagnosis. Images PMID:16696096

  8. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  9. Preoperative screening: value of previous tests.

    Science.gov (United States)

    Macpherson, D S; Snow, R; Lofgren, R P

    1990-12-15

    To determine the frequency of tests done in the year before elective surgery that might substitute for preoperative screening tests and to determine the frequency of test results that change from a normal value to a value likely to alter perioperative management. Retrospective cohort analysis of computerized laboratory data (complete blood count, sodium, potassium, and creatinine levels, prothrombin time, and partial thromboplastin time). Urban tertiary care Veterans Affairs Hospital. Consecutive sample of 1109 patients who had elective surgery in 1988. At admission, 7549 preoperative tests were done, 47% of which duplicated tests performed in the previous year. Of 3096 previous results that were normal as defined by hospital reference range and done closest to the time of but before admission (median interval, 2 months), 13 (0.4%; 95% CI, 0.2% to 0.7%), repeat values were outside a range considered acceptable for surgery. Most of the abnormalities were predictable from the patient's history, and most were not noted in the medical record. Of 461 previous tests that were abnormal, 78 (17%; CI, 13% to 20%) repeat values at admission were outside a range considered acceptable for surgery (P less than 0.001, frequency of clinically important abnormalities of patients with normal previous results with those with abnormal previous results). Physicians evaluating patients preoperatively could safely substitute the previous test results analyzed in this study for preoperative screening tests if the previous tests are normal and no obvious indication for retesting is present.

  10. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  11. Automatic electromagnetic valve for previous vacuum

    International Nuclear Information System (INIS)

    Granados, C. E.; Martin, F.

    1959-01-01

    A valve which permits the maintenance of an installation vacuum when electric current fails is described. It also lets the air in the previous vacuum bomb to prevent the oil ascending in the vacuum tubes. (Author)

  12. Molecular characterization of previously elusive badnaviruses associated with symptomatic cacao in the New World.

    Science.gov (United States)

    Chingandu, Nomatter; Zia-Ur-Rehman, Muhammad; Sreenivasan, Thyail N; Surujdeo-Maharaj, Surendra; Umaharan, Pathmanathan; Gutierrez, Osman A; Brown, Judith K

    2017-05-01

    Suspected virus-like symptoms were observed in cacao plants in Trinidad during 1943, and the viruses associated with these symptoms were designated as strains A and B of cacao Trinidad virus (CTV). However, viral etiology has not been demonstrated for either phenotype. Total DNA was isolated from symptomatic cacao leaves exhibiting the CTV A and B phenotypes and subjected to Illumina HiSeq and Sanger DNA sequencing. Based on de novo assembly, two apparently full-length badnavirus genomes of 7,533 and 7,454 nucleotides (nt) were associated with CTV strain A and B, respectively. The Trinidad badnaviral genomes contained four open reading frames, three of which are characteristic of other known badnaviruses, and a fourth that is present in only some badnaviruses. Both badnaviral genomes harbored hallmark caulimovirus-like features, including a tRNA Met priming site, a TATA box, and a polyadenylation-like signal. Pairwise comparisons of the RT-RNase H region indicated that the Trinidad isolates share 57-71% nt sequence identity with other known badnaviruses. Based on the system for badnavirus species demarcation in which viruses with less than 80% nt sequence identity in the RT-RNase gene are considered members of separate species, these isolates represent two previously unidentified badnaviruses, herein named cacao mild mosaic virus and cacao yellow vein banding virus, making them the first cacao-infecting badnaviruses identified thus far in the Western Hemisphere.

  13. 77 FR 70176 - Previous Participation Certification

    Science.gov (United States)

    2012-11-23

    ... participants' previous participation in government programs and ensure that the past record is acceptable prior... information is designed to be 100 percent automated and digital submission of all data and certifications is... government programs and ensure that the past record is acceptable prior to granting approval to participate...

  14. On the Tengiz petroleum deposit previous study

    International Nuclear Information System (INIS)

    Nysangaliev, A.N.; Kuspangaliev, T.K.

    1997-01-01

    Tengiz petroleum deposit previous study is described. Some consideration about structure of productive formation, specific characteristic properties of petroleum-bearing collectors are presented. Recommendation on their detail study and using of experience on exploration and development of petroleum deposit which have analogy on most important geological and industrial parameters are given. (author)

  15. Subsequent pregnancy outcome after previous foetal death

    NARCIS (Netherlands)

    Nijkamp, J. W.; Korteweg, F. J.; Holm, J. P.; Timmer, A.; Erwich, J. J. H. M.; van Pampus, M. G.

    Objective: A history of foetal death is a risk factor for complications and foetal death in subsequent pregnancies as most previous risk factors remain present and an underlying cause of death may recur. The purpose of this study was to evaluate subsequent pregnancy outcome after foetal death and to

  16. A previous hamstring injury affects kicking mechanics in soccer players.

    Science.gov (United States)

    Navandar, Archit; Veiga, Santiago; Torres, Gonzalo; Chorro, David; Navarro, Enrique

    2018-01-10

    Although the kicking skill is influenced by limb dominance and sex, how a previous hamstring injury affects kicking has not been studied in detail. Thus, the objective of this study was to evaluate the effect of sex and limb dominance on kicking in limbs with and without a previous hamstring injury. 45 professional players (males: n=19, previously injured players=4, age=21.16 ± 2.00 years; females: n=19, previously injured players=10, age=22.15 ± 4.50 years) performed 5 kicks each with their preferred and non-preferred limb at a target 7m away, which were recorded with a three-dimensional motion capture system. Kinematic and kinetic variables were extracted for the backswing, leg cocking, leg acceleration and follow through phases. A shorter backswing (20.20 ± 3.49% vs 25.64 ± 4.57%), and differences in knee flexion angle (58 ± 10o vs 72 ± 14o) and hip flexion velocity (8 ± 0rad/s vs 10 ± 2rad/s) were observed in previously injured, non-preferred limb kicks for females. A lower peak hip linear velocity (3.50 ± 0.84m/s vs 4.10 ± 0.45m/s) was observed in previously injured, preferred limb kicks of females. These differences occurred in the backswing and leg-cocking phases where the hamstring muscles were the most active. A variation in the functioning of the hamstring muscles and that of the gluteus maximus and iliopsoas in the case of a previous injury could account for the differences observed in the kicking pattern. Therefore, the effects of a previous hamstring injury must be considered while designing rehabilitation programs to re-educate kicking movement.

  17. Investigation of previously derived Hyades, Coma, and M67 reddenings

    International Nuclear Information System (INIS)

    Taylor, B.J.

    1980-01-01

    New Hyades polarimetry and field star photometry have been obtained to check the Hyades reddening, which was found to be nonzero in a previous paper. The new Hyades polarimetry implies essentially zero reddening; this is also true of polarimetry published by Behr (which was incorrectly interpreted in the previous paper). Four photometric techniques which are presumed to be insensitive to blanketing are used to compare the Hyades to nearby field stars; these four techniques also yield essentially zero reddening. When all of these results are combined with others which the author has previously published and a simultaneous solution for the Hyades, Coma, and M67 reddenings is made, the results are E (B-V) =3 +- 2 (sigma) mmag, -1 +- 3 (sigma) mmag, and 46 +- 6 (sigma) mmag, respectively. No support for a nonzero Hyades reddening is offered by the new results. When the newly obtained reddenings for the Hyades, Coma, and M67 are compared with results from techniques given by Crawford and by users of the David Dunlap Observatory photometric system, no differences between the new and other reddenings are found which are larger than about 2 sigma. The author had previously found that the M67 main-sequence stars have about the same blanketing as that of Coma and less blanketing than the Hyades; this conclusion is essentially unchanged by the revised reddenings

  18. Subsequent childbirth after a previous traumatic birth.

    Science.gov (United States)

    Beck, Cheryl Tatano; Watson, Sue

    2010-01-01

    Nine percent of new mothers in the United States who participated in the Listening to Mothers II Postpartum Survey screened positive for meeting the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria for posttraumatic stress disorder after childbirth. Women who have had a traumatic birth experience report fewer subsequent children and a longer length of time before their second baby. Childbirth-related posttraumatic stress disorder impacts couples' physical relationship, communication, conflict, emotions, and bonding with their children. The purpose of this study was to describe the meaning of women's experiences of a subsequent childbirth after a previous traumatic birth. Phenomenology was the research design used. An international sample of 35 women participated in this Internet study. Women were asked, "Please describe in as much detail as you can remember your subsequent pregnancy, labor, and delivery following your previous traumatic birth." Colaizzi's phenomenological data analysis approach was used to analyze the stories of the 35 women. Data analysis yielded four themes: (a) riding the turbulent wave of panic during pregnancy; (b) strategizing: attempts to reclaim their body and complete the journey to motherhood; (c) bringing reverence to the birthing process and empowering women; and (d) still elusive: the longed-for healing birth experience. Subsequent childbirth after a previous birth trauma has the potential to either heal or retraumatize women. During pregnancy, women need permission and encouragement to grieve their prior traumatic births to help remove the burden of their invisible pain.

  19. Rapid fish stock depletion in previously unexploited seamounts: the ...

    African Journals Online (AJOL)

    Rapid fish stock depletion in previously unexploited seamounts: the case of Beryx splendens from the Sierra Leone Rise (Gulf of Guinea) ... A spectral analysis and red-noise spectra procedure (REDFIT) algorithm was used to identify the red-noise spectrum from the gaps in the observed time-series of catch per unit effort by ...

  20. Statistical properties and fractals of nucleotide clusters in DNA sequences

    International Nuclear Information System (INIS)

    Sun Tingting; Zhang Linxi; Chen Jin; Jiang Zhouting

    2004-01-01

    Statistical properties of nucleotide clusters in DNA sequences and their fractals are investigated in this paper. The average size of nucleotide clusters in non-coding sequence is larger than that in coding sequence. We investigate the cluster-size distribution P(S) for human chromosomes 21 and 22, and the results are different from previous works. The cluster-size distribution P(S 1 +S 2 ) with the total size of sequential Pu-cluster and Py-cluster S 1 +S 2 is studied. We observe that P(S 1 +S 2 ) follows an exponential decay both in coding and non-coding sequences. However, we get different results for human chromosomes 21 and 22. The probability distribution P(S 1 ,S 2 ) of nucleotide clusters with the size of sequential Pu-cluster and Py-cluster S 1 and S 2 respectively, is also examined. In the meantime, some of the linear correlations are obtained in the double logarithmic plots of the fluctuation F(l) versus nucleotide cluster distance l along the DNA chain. The power spectrums of nucleotide clusters are also discussed, and it is concluded that the curves are flat and hardly changed and the 1/3 frequency is neither observed in coding sequence nor in non-coding sequence. These investigations can provide some insights into the nucleotide clusters of DNA sequences

  1. DOE Research and Development Accomplishments Previous Highlights

    Science.gov (United States)

    through his Nobel Lecture in 1961, about unraveling the secrets of photosynthesis -- the process by which . March 10, 2015 Twenty years ago, the top quark was first observed in experiments at the Tevatron proton sophisticated detectors, the top was hard to find. After a top is made from a proton-antiproton collision, a

  2. Books average previous decade of economic misery.

    Science.gov (United States)

    Bentley, R Alexander; Acerbi, Alberto; Ormerod, Paul; Lampos, Vasileios

    2014-01-01

    For the 20(th) century since the Depression, we find a strong correlation between a 'literary misery index' derived from English language books and a moving average of the previous decade of the annual U.S. economic misery index, which is the sum of inflation and unemployment rates. We find a peak in the goodness of fit at 11 years for the moving average. The fit between the two misery indices holds when using different techniques to measure the literary misery index, and this fit is significantly better than other possible correlations with different emotion indices. To check the robustness of the results, we also analysed books written in German language and obtained very similar correlations with the German economic misery index. The results suggest that millions of books published every year average the authors' shared economic experiences over the past decade.

  3. Books Average Previous Decade of Economic Misery

    Science.gov (United States)

    Bentley, R. Alexander; Acerbi, Alberto; Ormerod, Paul; Lampos, Vasileios

    2014-01-01

    For the 20th century since the Depression, we find a strong correlation between a ‘literary misery index’ derived from English language books and a moving average of the previous decade of the annual U.S. economic misery index, which is the sum of inflation and unemployment rates. We find a peak in the goodness of fit at 11 years for the moving average. The fit between the two misery indices holds when using different techniques to measure the literary misery index, and this fit is significantly better than other possible correlations with different emotion indices. To check the robustness of the results, we also analysed books written in German language and obtained very similar correlations with the German economic misery index. The results suggest that millions of books published every year average the authors' shared economic experiences over the past decade. PMID:24416159

  4. Histologic changes in previously irradiated thyroid glands

    Energy Technology Data Exchange (ETDEWEB)

    Valdiserri, R.O.; Borochovitz, D.

    1980-03-01

    Thyroid tissue from 90 patients with a history of therapeutic irradiation to the head and neck in childhood and adolescence was examined microscopically. In addition to the well-known observation that these individuals have an increased incidence of primary thyroid carcinoma, it was also demonstrated that they have an increased incidence of benign histologic changes. These changes represent a spectrum from nonspecific hyperplastic lesions to benign neoplasis and thyroidltis.

  5. Swallow Event Sequencing: Comparing Healthy Older and Younger Adults.

    Science.gov (United States)

    Herzberg, Erica G; Lazarus, Cathy L; Steele, Catriona M; Molfenter, Sonja M

    2018-04-23

    Previous research has established that a great deal of variation exists in the temporal sequence of swallowing events for healthy adults. Yet, the impact of aging on swallow event sequence is not well understood. Kendall et al. (Dysphagia 18(2):85-91, 2003) suggested there are 4 obligatory paired-event sequences in swallowing. We directly compared adherence to these sequences, as well as event latencies, and quantified the percentage of unique sequences in two samples of healthy adults: young ( 65). The 8 swallowing events that contribute to the sequences were reliably identified from videofluoroscopy in a sample of 23 healthy seniors (10 male, mean age 74.7) and 20 healthy young adults (10 male, mean age 31.5) with no evidence of penetration-aspiration or post-swallow residue. Chi-square analyses compared the proportions of obligatory pairs and unique sequences by age group. Compared to the older subjects, younger subjects had significantly lower adherence to two obligatory sequences: Upper Esophageal Sphincter (UES) opening occurs before (or simultaneous with) the bolus arriving at the UES and UES maximum distention occurs before maximum pharyngeal constriction. The associated latencies were significantly different between age groups as well. Further, significantly fewer unique swallow sequences were observed in the older group (61%) compared with the young (82%) (χ 2  = 31.8; p < 0.001). Our findings suggest that paired swallow event sequences may not be robust across the age continuum and that variation in swallow sequences appears to decrease with aging. These findings provide normative references for comparisons to older individuals with dysphagia.

  6. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

    2009-12-01

    Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with

  7. [Prevalence of previously diagnosed diabetes mellitus in Mexico.

    Science.gov (United States)

    Rojas-Martínez, Rosalba; Basto-Abreu, Ana; Aguilar-Salinas, Carlos A; Zárate-Rojas, Emiliano; Villalpando, Salvador; Barrientos-Gutiérrez, Tonatiuh

    2018-01-01

    To compare the prevalence of previously diagnosed diabetes in 2016 with previous national surveys and to describe treatment and its complications. Mexico's national surveys Ensa 2000, Ensanut 2006, 2012 and 2016 were used. For 2016, logistic regression models and measures of central tendency and dispersion were obtained. The prevalence of previously diagnosed diabetes in 2016 was 9.4%. The increase of 2.2% relative to 2012 was not significant and only observed in patients older than 60 years. While preventive measures have increased, the access to medical treatment and lifestyle has not changed. The treatment has been modified, with an increase in insulin and decrease in hypoglycaemic agents. Population aging, lack of screening actions and the increase in diabetes complications will lead to an increase on the burden of disease. Policy measures targeting primary and secondary prevention of diabetes are crucial.

  8. SOUTH POLE TELESCOPE DETECTIONS OF THE PREVIOUSLY UNCONFIRMED PLANCK EARLY SUNYAEV-ZEL'DOVICH CLUSTERS IN THE SOUTHERN HEMISPHERE

    International Nuclear Information System (INIS)

    Story, K.; Benson, B. A.; Bleem, L. E.; Carlstrom, J. E.; Chang, C. L.; Crawford, T. M.; Crites, A. T.; Aird, K. A.; Andersson, K.; Bazin, G.; Armstrong, R.; Desai, S.; Bonamente, M.; Brodwin, M.; Foley, R. J.; Clocchiatti, A.; De Haan, T.; Dobbs, M. A.; Dudley, J. P.; George, E. M.

    2011-01-01

    We present South Pole Telescope (SPT) observations of the five galaxy cluster candidates in the southern hemisphere which were reported as unconfirmed in the Planck Early Sunyaev-Zel'dovich (ESZ) sample. One cluster candidate, PLCKESZ G255.62-46.16, is located in the 2500 deg 2 SPT SZ survey region and was reported previously as SPT-CL J0411-4819. For the remaining four candidates, which are located outside of the SPT SZ survey region, we performed short, dedicated SPT observations. Each of these four candidates was strongly detected in maps made from these observations, with signal-to-noise ratios ranging from 6.3 to 13.8. We have observed these four candidates on the Magellan-Baade telescope and used these data to estimate cluster redshifts from the red sequence. Resulting redshifts range from 0.24 to 0.46. We report measurements of Y 0.'75 , the integrated Comptonization within a 0.'75 radius, for all five candidates. We also report X-ray luminosities calculated from ROSAT All-Sky Survey catalog counts, as well as optical and improved SZ coordinates for each candidate. The combination of SPT SZ measurements, optical red-sequence measurements, and X-ray luminosity estimates demonstrates that these five Planck ESZ cluster candidates do indeed correspond to real galaxy clusters with redshifts and observable properties consistent with the rest of the ESZ sample.

  9. Unraveling the sequence and structure of the protein osteocalcin from a 42 ka fossil horse

    Science.gov (United States)

    Ostrom, Peggy H.; Gandhi, Hasand; Strahler, John R.; Walker, Angela K.; Andrews, Philip C.; Leykam, Joseph; Stafford, Thomas W.; Kelly, Robert L.; Walker, Danny N.; Buckley, Mike; Humpula, James

    2006-04-01

    We report the first complete amino acid sequence and evidence of secondary structure for osteocalcin from a temperate fossil. The osteocalcin derives from a 42 ka equid bone excavated from Juniper Cave, Wyoming. Results were determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-MS) and Edman sequencing with independent confirmation of the sequence in two laboratories. The ancient sequence was compared to that of three modern taxa: horse ( Equus caballus), zebra ( Equus grevyi), and donkey ( Equus asinus). Although there was no difference in sequence among modern taxa, MALDI-MS and Edman sequencing show that residues 48 and 49 of our modern horse are Thr, Ala rather than Pro, Val as previously reported (Carstanjen B., Wattiez, R., Armory, H., Lepage, O.M., Remy, B., 2002. Isolation and characterization of equine osteocalcin. Ann. Med. Vet.146(1), 31-38). MALDI-MS and Edman sequencing data indicate that the osteocalcin sequence of the 42 ka fossil is similar to that of modern horse. Previously inaccessible structural attributes for ancient osteocalcin were observed. Glu 39 rather than Gln 39 is consistent with deamidation, a process known to occur during fossilization and aging. Two post-translational modifications were documented: Hyp 9 and a disulfide bridge. The latter suggests at least partial retention of secondary structure. As has been done for ancient DNA research, we recommend standards for preparation and criteria for authenticating results of ancient protein sequencing.

  10. Observing participating observation

    DEFF Research Database (Denmark)

    Keiding, Tina Bering

    2011-01-01

    Current methodology concerning participating observation in general leaves the act of observation unobserved. Approaching participating observation from systems theory offers fundamental new insights into the topic. Observation is always participation. There is no way to escape becoming...

  11. Observing participating observation

    DEFF Research Database (Denmark)

    Keiding, Tina Bering

    2010-01-01

    Current methodology concerning participating observation in general leaves the act of observation unobserved. Approaching participating observation from systems theory offers fundamental new insights into the topic. Observation is always participation. There is no way to escape becoming...

  12. Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution.

    Directory of Open Access Journals (Sweden)

    Sara Imari Walker

    Full Text Available Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for

  13. Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database.

    Science.gov (United States)

    Holcomb, C L; Rastrou, M; Williams, T C; Goodridge, D; Lazaro, A M; Tilanus, M; Erlich, H A

    2014-01-01

    The high-resolution human leukocyte antigen (HLA) genotyping assay that we developed using 454 sequencing and Conexio software uses generic polymerase chain reaction (PCR) primers for DRB exon 2. Occasionally, we observed low abundance DRB amplicon sequences that resulted from in vitro PCR 'crossing over' between DRB1 and DRB3/4/5. These hybrid sequences, revealed by the clonal sequencing property of the 454 system, were generally observed at a read depth of 5%-10% of the true alleles. They usually contained at least one mismatch with the IMGT/HLA database, and consequently, were easily recognizable and did not cause a problem for HLA genotyping. Sometimes, however, these artifactual sequences matched a rare allele and the automatic genotype assignment was incorrect. These observations raised two issues: (1) could PCR conditions be modified to reduce such artifacts? and (2) could some of the rare alleles listed in the IMGT/HLA database be artifacts rather than true alleles? Because PCR crossing over occurs during late cycles of PCR, we compared DRB genotypes resulting from 28 and (our standard) 35 cycles of PCR. For all 21 cell line DNAs amplified for 35 cycles, crossover products were detected. In 33% of the cases, these hybrid sequences corresponded to named alleles. With amplification for only 28 cycles, these artifactual sequences were not detectable. To investigate whether some rare alleles in the IMGT/HLA database might be due to PCR artifacts, we analyzed four samples obtained from the investigators who submitted the sequences. In three cases, the sequences were generated from true alleles. In one case, our 454 sequencing revealed an error in the previously submitted sequence. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  14. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  15. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  16. Mediastinal involvement in lymphangiomatosis: a previously unreported MRI sign

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Vikas; Shah, Sachit; Barnacle, Alex; McHugh, Kieran [Great Ormond Street Hospital for Children, Department of Radiology, London (United Kingdom); Sebire, Neil J. [Great Ormond Street Hospital for Children, Department of Histopathology, London (United Kingdom); Brock, Penelope [Great Ormond Street Hospital for Children, Department of Oncology, London (United Kingdom); Harper, John I. [Great Ormond Street Hospital for Children, Department of Dermatology, London (United Kingdom)

    2011-08-15

    Multifocal lymphangiomatosis is a rare systemic disorder affecting children. Due to its rarity and wide spectrum of clinical, histological and imaging features, establishing the diagnosis of multifocal lymphangiomatosis can be challenging. The purpose of this study was to describe a new imaging sign in this disorder: paraspinal soft tissue and signal abnormality at MRI. We retrospectively reviewed the imaging, clinical and histopathological findings in a cohort of eight children with thoracic involvement from this condition. Evidence of paraspinal chest disease was identified at MRI and CT in all eight of these children. The changes comprise heterogeneous intermediate-to-high signal parallel to the thoracic vertebrae on T2-weighted sequences at MRI, with abnormal paraspinal soft tissue at CT and plain radiography. Multifocal lymphangiomatosis is a rare disorder with a broad range of clinicopathological and imaging features. MRI allows complete evaluation of disease extent without the use of ionising radiation and has allowed us to describe a previously unreported imaging sign in this disorder, namely, heterogeneous hyperintense signal in abnormal paraspinal tissue on T2-weighted images. (orig.)

  17. Nonlinear deterministic structures and the randomness of protein sequences

    CERN Document Server

    Huang Yan Zhao

    2003-01-01

    To clarify the randomness of protein sequences, we make a detailed analysis of a set of typical protein sequences representing each structural classes by using nonlinear prediction method. No deterministic structures are found in these protein sequences and this implies that they behave as random sequences. We also give an explanation to the controversial results obtained in previous investigations.

  18. Sensitivity to structure in action sequences: An infant event-related potential study.

    Science.gov (United States)

    Monroy, Claire D; Gerson, Sarah A; Domínguez-Martínez, Estefanía; Kaduk, Katharina; Hunnius, Sabine; Reid, Vincent

    2017-05-06

    Infants are sensitive to structure and patterns within continuous streams of sensory input. This sensitivity relies on statistical learning, the ability to detect predictable regularities in spatial and temporal sequences. Recent evidence has shown that infants can detect statistical regularities in action sequences they observe, but little is known about the neural process that give rise to this ability. In the current experiment, we combined electroencephalography (EEG) with eye-tracking to identify electrophysiological markers that indicate whether 8-11-month-old infants detect violations to learned regularities in action sequences, and to relate these markers to behavioral measures of anticipation during learning. In a learning phase, infants observed an actor performing a sequence featuring two deterministic pairs embedded within an otherwise random sequence. Thus, the first action of each pair was predictive of what would occur next. One of the pairs caused an action-effect, whereas the second did not. In a subsequent test phase, infants observed another sequence that included deviant pairs, violating the previously observed action pairs. Event-related potential (ERP) responses were analyzed and compared between the deviant and the original action pairs. Findings reveal that infants demonstrated a greater Negative central (Nc) ERP response to the deviant actions for the pair that caused the action-effect, which was consistent with their visual anticipations during the learning phase. Findings are discussed in terms of the neural and behavioral processes underlying perception and learning of structured action sequences. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Directed Research in Bone Discipline: Refining Previous Research Observations for Space Medicine

    Science.gov (United States)

    Sibonga, Jean D.

    2015-01-01

    Dual-energy X-ray absorptiometry bone mass density, as a sole index, is an insufficient surrogate for fracture; Clinical Practice Guidelines using bone mass density (both World Health Organization and FRAX) are not specific for complicated subjects such as young, healthy persons following prolonged exposure to skeletal unloading (i.e. an attribute of spaceflight); Research data suggest that spaceflight induces changes to astronaut bones that could be profound, possibly irreversible and unlike age-related bone loss on Earth.; There is a need to objectively assess factors across human physiology that are also influenced by spaceflight (e.g., muscle) that contribute to fracture risk. Some of these objective assessments may require innovative technologies, analyses and modeling.; Astronauts are also exposed to novel situations that may overload their bones highlighting a need integrate biomechanics of physical activities into risk assessments.; As we accumulate data, which reflects the biomechanical competence of bone under specific mechanically-loaded scenarios (even activities of daily living), BONE expects Bone Fracture Module to be more sensitive and/or have less uncertainty in its assessments of fracture probability.; Fracture probability drives the requirement for countermeasures. Level of evidence will unlikely be obtained; hence, the Bone Research and Clinical Advisory Panel (like a Data Safety Monitoring Board) will provide the recommendations.

  20. Neuropsychiatric and cardiometabolic comorbidities in patients with previously diagnosed Cushing's disease: a longitudinal observational study

    OpenAIRE

    Dimopoulou, C; Geraedts, V; Stalla, G K; Sievers, C

    2015-01-01

    INTRODUCTION: Only few studies have systematically investigated neuropsychiatric aspects in patients with Cushing's disease (CD). Pain syndromes have been described in patients with pituitary adenomas, but so far no systematical investigation has been conducted in patients with CD. Additionally, CD has an association with cardiometabolic comorbidities which ultimately leads to increased morbidity and mortality. Long-term treatment of the hypercortisolic state cannot prevent the persistence of...

  1. Situation models and memory: the effects of temporal and causal information on recall sequence.

    Science.gov (United States)

    Brownstein, Aaron L; Read, Stephen J

    2007-10-01

    Participants watched an episode of the television show Cheers on video and then reported free recall. Recall sequence followed the sequence of events in the story; if one concept was observed immediately after another, it was recalled immediately after it. We also made a causal network of the show's story and found that recall sequence followed causal links; effects were recalled immediately after their causes. Recall sequence was more likely to follow causal links than temporal sequence, and most likely to follow causal links that were temporally sequential. Results were similar at 10-minute and 1-week delayed recall. This is the most direct and detailed evidence reported on sequential effects in recall. The causal network also predicted probability of recall; concepts with more links and concepts on the main causal chain were most likely to be recalled. This extends the causal network model to more complex materials than previous research.

  2. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  3. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  4. Radon anomalies prior to earthquakes (1). Review of previous studies

    International Nuclear Information System (INIS)

    Ishikawa, Tetsuo; Tokonami, Shinji; Yasuoka, Yumi; Shinogi, Masaki; Nagahama, Hiroyuki; Omori, Yasutaka; Kawada, Yusuke

    2008-01-01

    The relationship between radon anomalies and earthquakes has been studied for more than 30 years. However, most of the studies dealt with radon in soil gas or in groundwater. Before the 1995 Hyogoken-Nanbu earthquake, an anomalous increase of atmospheric radon was observed at Kobe Pharmaceutical University. The increase was well fitted with a mathematical model related to earthquake fault dynamics. This paper reports the significance of this observation, reviewing previous studies on radon anomaly before earthquakes. Groundwater/soil radon measurements for earthquake prediction began in 1970's in Japan as well as foreign countries. One of the most famous studies in Japan is groundwater radon anomaly before the 1978 Izu-Oshima-kinkai earthquake. We have recognized the significance of radon in earthquake prediction research, but recently its limitation was also pointed out. Some researchers are looking for a better indicator for precursors; simultaneous measurements of radon and other gases are new trials in recent studies. Contrary to soil/groundwater radon, we have not paid much attention to atmospheric radon before earthquakes. However, it might be possible to detect precursors in atmospheric radon before a large earthquake. In the next issues, we will discuss the details of the anomalous atmospheric radon data observed before the Hyogoken-Nanbu earthquake. (author)

  5. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  6. A method for selecting cis-acting regulatory sequences that respond to small molecule effectors

    Directory of Open Access Journals (Sweden)

    Allas Ülar

    2010-08-01

    Full Text Available Abstract Background Several cis-acting regulatory sequences functioning at the level of mRNA or nascent peptide and specifically influencing transcription or translation have been described. These regulatory elements often respond to specific chemicals. Results We have developed a method that allows us to select cis-acting regulatory sequences that respond to diverse chemicals. The method is based on the β-lactamase gene containing a random sequence inserted into the beginning of the ORF. Several rounds of selection are used to isolate sequences that suppress β-lactamase expression in response to the compound under study. We have isolated sequences that respond to erythromycin, troleandomycin, chloramphenicol, meta-toluate and homoserine lactone. By introducing synonymous and non-synonymous mutations we have shown that at least in the case of erythromycin the sequences act at the peptide level. We have also tested the cross-activities of the constructs and found that in most cases the sequences respond most strongly to the compound on which they were isolated. Conclusions Several selected peptides showed ligand-specific changes in amino acid frequencies, but no consensus motif could be identified. This is consistent with previous observations on natural cis-acting peptides, showing that it is often impossible to demonstrate a consensus. Applying the currently developed method on a larger scale, by selecting and comparing an extended set of sequences, might allow the sequence rules underlying the activity of cis-acting regulatory peptides to be identified.

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

    Directory of Open Access Journals (Sweden)

    Ann Ray

    2016-07-01

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

  8. Kidnapping Detection and Recognition in Previous Unknown Environment

    Directory of Open Access Journals (Sweden)

    Yang Tian

    2017-01-01

    Full Text Available An unaware event referred to as kidnapping makes the estimation result of localization incorrect. In a previous unknown environment, incorrect localization result causes incorrect mapping result in Simultaneous Localization and Mapping (SLAM by kidnapping. In this situation, the explored area and unexplored area are divided to make the kidnapping recovery difficult. To provide sufficient information on kidnapping, a framework to judge whether kidnapping has occurred and to identify the type of kidnapping with filter-based SLAM is proposed. The framework is called double kidnapping detection and recognition (DKDR by performing two checks before and after the “update” process with different metrics in real time. To explain one of the principles of DKDR, we describe a property of filter-based SLAM that corrects the mapping result of the environment using the current observations after the “update” process. Two classical filter-based SLAM algorithms, Extend Kalman Filter (EKF SLAM and Particle Filter (PF SLAM, are modified to show that DKDR can be simply and widely applied in existing filter-based SLAM algorithms. Furthermore, a technique to determine the adapted thresholds of metrics in real time without previous data is presented. Both simulated and experimental results demonstrate the validity and accuracy of the proposed method.

  9. The Accident Sequence Precursor program: Methods improvements and current results

    International Nuclear Information System (INIS)

    Minarick, J.W.; Manning, F.M.; Harris, J.D.

    1987-01-01

    Changes in the US NRC Accident Sequence Precursor program methods since the initial program evaluations of 1969-81 operational events are described, along with insights from the review of 1984-85 events. For 1984-85, the number of significant precursors was consistent with the number observed in 1980-81, dominant sequences associated with significant events were reasonably consistent with PRA estimates for BWRs, but lacked the contribution due to small-break LOCAs previously observed and predicted in PWRs, and the frequency of initiating events and non-recoverable system failures exhibited some reduction compared to 1980-81. Operational events which provide information concerning additional PRA modeling needs are also described

  10. Sequence analysis to assess labour market participation following vocational rehabilitation: an observational study among patients sick-listed with low back pain from a randomised clinical trial in Denmark.

    Science.gov (United States)

    Lindholdt, Louise; Labriola, Merete; Nielsen, Claus Vinther; Horsbøl, Trine Allerslev; Lund, Thomas

    2017-07-20

    The return-to-work (RTW) process after long-term sickness absence is often complex and long and implies multiple shifts between different labour market states for the absentee. Standard methods for examining RTW research typically rely on the analysis of one outcome measure at a time, which will not capture the many possible states and transitions the absentee can go through. The purpose of this study was to explore the potential added value of sequence analysis in supplement to standard regression analysis of a multidisciplinary RTW intervention among patients with low back pain (LBP). The study population consisted of 160 patients randomly allocated to either a hospital-based brief or a multidisciplinary intervention. Data on labour market participation following intervention were obtained from a national register and analysed in two ways: as a binary outcome expressed as active or passive relief at a 1-year follow-up and as four different categories for labour market participation. Logistic regression and sequence analysis were performed. The logistic regression analysis showed no difference in labour market participation for patients in the two groups after 1 year. Applying sequence analysis showed differences in subsequent labour market participation after 2 years after baseline in favour of the brief intervention group versus the multidisciplinary intervention group. The study indicated that sequence analysis could provide added analytical value as a supplement to traditional regression analysis in prospective studies of RTW among patients with LBP. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  11. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  12. Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

    Directory of Open Access Journals (Sweden)

    Rebecca M. Davidson

    2011-11-01

    Full Text Available Transcriptome sequencing is a powerful method for studying global expression patterns in large, complex genomes. Evaluation of sequence-based expression profiles during reproductive development would provide functional annotation to genes underlying agronomic traits. We generated transcriptome profiles for 12 diverse maize ( L. reproductive tissues representing male, female, developing seed, and leaf tissues using high throughput transcriptome sequencing. Overall, ∼80% of annotated genes were expressed. Comparative analysis between sequence and hybridization-based methods demonstrated the utility of ribonucleic acid sequencing (RNA-seq for expression determination and differentiation of paralagous genes (∼85% of maize genes. Analysis of 4975 gene families across reproductive tissues revealed expression divergence is proportional to family size. In all pairwise comparisons between tissues, 7 (pre- vs. postemergence cobs to 48% (pollen vs. ovule of genes were differentially expressed. Genes with expression restricted to a single tissue within this study were identified with the highest numbers observed in leaves, endosperm, and pollen. Coexpression network analysis identified 17 gene modules with complex and shared expression patterns containing many previously described maize genes. The data and analyses in this study provide valuable tools through improved gene annotation, gene family characterization, and a core set of candidate genes to further characterize maize reproductive development and improve grain yield potential.

  13. Seismic sequences in the Sombrero Seismic Zone

    Science.gov (United States)

    Pulliam, J.; Huerfano, V. A.; ten Brink, U.; von Hillebrandt, C.

    2007-05-01

    The northeastern Caribbean, in the vicinity of Puerto Rico and the Virgin Islands, has a long and well-documented history of devastating earthquakes and tsunamis, including major events in 1670, 1787, 1867, 1916, 1918, and 1943. Recently, seismicity has been concentrated to the north and west of the British Virgin Islands, in the region referred to as the Sombrero Seismic Zone by the Puerto Rico Seismic Network (PRSN). In the combined seismicity catalog maintained by the PRSN, several hundred small to moderate magnitude events can be found in this region prior to 2006. However, beginning in 2006 and continuing to the present, the rate of seismicity in the Sombrero suddenly increased, and a new locus of activity developed to the east of the previous location. Accurate estimates of seismic hazard, and the tsunamigenic potential of seismic events, depend on an accurate and comprehensive understanding of how strain is being accommodated in this corner region. Are faults locked and accumulating strain for release in a major event? Or is strain being released via slip over a diffuse system of faults? A careful analysis of seismicity patterns in the Sombrero region has the potential to both identify faults and modes of failure, provided the aggregation scheme is tuned to properly identify related events. To this end, we experimented with a scheme to identify seismic sequences based on physical and temporal proximity, under the assumptions that (a) events occur on related fault systems as stress is refocused by immediately previous events and (b) such 'stress waves' die out with time, so that two events that occur on the same system within a relatively short time window can be said to have a similar 'trigger' in ways that two nearby events that occurred years apart cannot. Patterns that emerge from the identification, temporal sequence, and refined locations of such sequences of events carry information about stress accommodation that is obscured by large clouds of

  14. A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius).

    LENUS (Irish Health Repository)

    Edwards, Ceiridwen J

    2010-01-01

    BACKGROUND: The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY: DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+\\/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS: For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified

  15. Is Previous Respiratory Disease a Risk Factor for Lung Cancer?

    Science.gov (United States)

    Denholm, Rachel; Schüz, Joachim; Straif, Kurt; Stücker, Isabelle; Jöckel, Karl-Heinz; Brenner, Darren R.; De Matteis, Sara; Boffetta, Paolo; Guida, Florence; Brüske, Irene; Wichmann, Heinz-Erich; Landi, Maria Teresa; Caporaso, Neil; Siemiatycki, Jack; Ahrens, Wolfgang; Pohlabeln, Hermann; Zaridze, David; Field, John K.; McLaughlin, John; Demers, Paul; Szeszenia-Dabrowska, Neonila; Lissowska, Jolanta; Rudnai, Peter; Fabianova, Eleonora; Dumitru, Rodica Stanescu; Bencko, Vladimir; Foretova, Lenka; Janout, Vladimir; Kendzia, Benjamin; Peters, Susan; Behrens, Thomas; Vermeulen, Roel; Brüning, Thomas; Kromhout, Hans

    2014-01-01

    Rationale: Previous respiratory diseases have been associated with increased risk of lung cancer. Respiratory conditions often co-occur and few studies have investigated multiple conditions simultaneously. Objectives: Investigate lung cancer risk associated with chronic bronchitis, emphysema, tuberculosis, pneumonia, and asthma. Methods: The SYNERGY project pooled information on previous respiratory diseases from 12,739 case subjects and 14,945 control subjects from 7 case–control studies conducted in Europe and Canada. Multivariate logistic regression models were used to investigate the relationship between individual diseases adjusting for co-occurring conditions, and patterns of respiratory disease diagnoses and lung cancer. Analyses were stratified by sex, and adjusted for age, center, ever-employed in a high-risk occupation, education, smoking status, cigarette pack-years, and time since quitting smoking. Measurements and Main Results: Chronic bronchitis and emphysema were positively associated with lung cancer, after accounting for other respiratory diseases and smoking (e.g., in men: odds ratio [OR], 1.33; 95% confidence interval [CI], 1.20–1.48 and OR, 1.50; 95% CI, 1.21–1.87, respectively). A positive relationship was observed between lung cancer and pneumonia diagnosed 2 years or less before lung cancer (OR, 3.31; 95% CI, 2.33–4.70 for men), but not longer. Co-occurrence of chronic bronchitis and emphysema and/or pneumonia had a stronger positive association with lung cancer than chronic bronchitis “only.” Asthma had an inverse association with lung cancer, the association being stronger with an asthma diagnosis 5 years or more before lung cancer compared with shorter. Conclusions: Findings from this large international case–control consortium indicate that after accounting for co-occurring respiratory diseases, chronic bronchitis and emphysema continue to have a positive association with lung cancer. PMID:25054566

  16. Twelve previously unknown phage genera are ubiquitous in global oceans.

    Science.gov (United States)

    Holmfeldt, Karin; Solonenko, Natalie; Shah, Manesh; Corrier, Kristen; Riemann, Lasse; Verberkmoes, Nathan C; Sullivan, Matthew B

    2013-07-30

    Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in "unknowns" dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four well-known viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage-host systems for experimental hypothesis testing.

  17. Urethrotomy has a much lower success rate than previously reported.

    Science.gov (United States)

    Santucci, Richard; Eisenberg, Lauren

    2010-05-01

    We evaluated the success rate of direct vision internal urethrotomy as a treatment for simple male urethral strictures. A retrospective chart review was performed on 136 patients who underwent urethrotomy from January 1994 through March 2009. The Kaplan-Meier method was used to analyze stricture-free probability after the first, second, third, fourth and fifth urethrotomy. Patients with complex strictures (36) were excluded from the study for reasons including previous urethroplasty, neophallus or previous radiation, and 24 patients were lost to followup. Data were available for 76 patients. The stricture-free rate after the first urethrotomy was 8% with a median time to recurrence of 7 months. For the second urethrotomy stricture-free rate was 6% with a median time to recurrence of 9 months. For the third urethrotomy stricture-free rate was 9% with a median time to recurrence of 3 months. For procedures 4 and 5 stricture-free rate was 0% with a median time to recurrence of 20 and 8 months, respectively. Urethrotomy is a popular treatment for male urethral strictures. However, the performance characteristics are poor. Success rates were no higher than 9% in this series for first or subsequent urethrotomy during the observation period. Most of the patients in this series will be expected to experience failure with longer followup and the expected long-term success rate from any (1 through 5) urethrotomy approach is 0%. Urethrotomy should be considered a temporizing measure until definitive curative reconstruction can be planned. 2010 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  18. Impact of previously disadvantaged land-users on sustainable ...

    African Journals Online (AJOL)

    Impact of previously disadvantaged land-users on sustainable agricultural ... about previously disadvantaged land users involved in communal farming systems ... of input, capital, marketing, information and land use planning, with effect on ...

  19. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  20. 22 CFR 40.91 - Certain aliens previously removed.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Certain aliens previously removed. 40.91... IMMIGRANTS UNDER THE IMMIGRATION AND NATIONALITY ACT, AS AMENDED Aliens Previously Removed § 40.91 Certain aliens previously removed. (a) 5-year bar. An alien who has been found inadmissible, whether as a result...

  1. Dinoflagellate phylogeny as inferred from heat shock protein 90 and ribosomal gene sequences.

    Directory of Open Access Journals (Sweden)

    Mona Hoppenrath

    2010-10-01

    evolutionary past. Nonetheless, the more comprehensive analysis of Hsp90 sequences enabled us to infer phylogenetic interrelationships of dinoflagellates more rigorously. For instance, the phylogenetic position of Noctiluca, which possesses several unusual features, was incongruent with previous phylogenetic studies. Therefore, the generation of additional dinoflagellate Hsp90 sequences is expected to refine the stem group of athecate species observed here and contribute to future multi-gene analyses of dinoflagellate interrelationships.

  2. Determining root correspondence between previously and newly detected objects

    Science.gov (United States)

    Paglieroni, David W.; Beer, N Reginald

    2014-06-17

    A system that applies attribute and topology based change detection to networks of objects that were detected on previous scans of a structure, roadway, or area of interest. The attributes capture properties or characteristics of the previously detected objects, such as location, time of detection, size, elongation, orientation, etc. The topology of the network of previously detected objects is maintained in a constellation database that stores attributes of previously detected objects and implicitly captures the geometrical structure of the network. A change detection system detects change by comparing the attributes and topology of new objects detected on the latest scan to the constellation database of previously detected objects.

  3. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  4. Coronary collateral vessels in patients with previous myocardial infarction

    International Nuclear Information System (INIS)

    Nakatsuka, M.; Matsuda, Y.; Ozaki, M.

    1987-01-01

    To assess the degree of collateral vessels after myocardial infarction, coronary angiograms, left ventriculograms, and exercise thallium-201 myocardial scintigrams of 36 patients with previous myocardial infarction were reviewed. All 36 patients had total occlusion of infarct-related coronary artery and no more than 70% stenosis in other coronary arteries. In 19 of 36 patients with transient reduction of thallium-201 uptake in the infarcted area during exercise (Group A), good collaterals were observed in 10 patients, intermediate collaterals in 7 patients, and poor collaterals in 2 patients. In 17 of 36 patients without transient reduction of thallium-201 uptake in the infarcted area during exercise (Group B), good collaterals were seen in 2 patients, intermediate collaterals in 7 patients, and poor collaterals in 8 patients (p less than 0.025). Left ventricular contractions in the infarcted area were normal or hypokinetic in 10 patients and akinetic or dyskinetic in 9 patients in Group A. In Group B, 1 patient had hypokinetic contraction and 16 patients had akinetic or dyskinetic contraction (p less than 0.005). Thus, patients with transient reduction of thallium-201 uptake in the infarcted area during exercise had well developed collaterals and preserved left ventricular contraction, compared to those in patients without transient reduction of thallium-201 uptake in the infarcted area during exercise. These results suggest that the presence of viable myocardium in the infarcted area might be related to the degree of collateral vessels

  5. Culture and the sequence of steps in theory of mind development.

    Science.gov (United States)

    Shahaeian, Ameneh; Peterson, Candida C; Slaughter, Virginia; Wellman, Henry M

    2011-09-01

    To examine cultural contrasts in the ordered sequence of conceptual developments leading to theory of mind (ToM), we compared 135 3- to 6-year-olds (77 Australians; 58 Iranians) on an established 5-step ToM scale (Wellman & Liu, 2004). There was a cross-cultural difference in the sequencing of ToM steps but not in overall rates of ToM mastery. In line with our predictions, the children from Iran conformed to a distinctive sequence previously observed only in children in China. In contrast to the case with children from Australia (and the United States), knowledge access was understood earlier than opinion diversity in children from Iran, consistent with this collectivist culture's emphasis on filial respect, dispute avoidance, and acquiring knowledge. Having a sibling was linked with faster overall ToM progress in Australia only and was not related to scale sequences in either culture.

  6. Milky Way Past Was More Turbulent Than Previously Known

    Science.gov (United States)

    2004-04-01

    Results of 1001 observing nights shed new light on our Galaxy [1] Summary A team of astronomers from Denmark, Switzerland and Sweden [2] has achieved a major breakthrough in our understanding of the Milky Way, the galaxy in which we live. After more than 1,000 nights of observations spread over 15 years, they have determined the spatial motions of more than 14,000 solar-like stars residing in the neighbourhood of the Sun. For the first time, the changing dynamics of the Milky Way since its birth can now be studied in detail and with a stellar sample sufficiently large to allow a sound analysis. The astronomers find that our home galaxy has led a much more turbulent and chaotic life than previously assumed. PR Photo 10a/04: Distribution on the sky of the observed stars. PR Photo 10b/04: Stars in the solar neigbourhood and the Milky Way galaxy (artist's view). PR Video Clip 04/04: The motions of the observed stars during the past 250 million years. Unknown history Home is the place we know best. But not so in the Milky Way - the galaxy in which we live. Our knowledge of our nearest stellar neighbours has long been seriously incomplete and - worse - skewed by prejudice concerning their behaviour. Stars were generally selected for observation because they were thought to be "interesting" in some sense, not because they were typical. This has resulted in a biased view of the evolution of our Galaxy. The Milky Way started out just after the Big Bang as one or more diffuse blobs of gas of almost pure hydrogen and helium. With time, it assembled into the flattened spiral galaxy which we inhabit today. Meanwhile, generation after generation of stars were formed, including our Sun some 4,700 million years ago. But how did all this really happen? Was it a rapid process? Was it violent or calm? When were all the heavier elements formed? How did the Milky Way change its composition and shape with time? Answers to these and many other questions are 'hot' topics for the

  7. Sequence analysis to assess labour market participation following vocational rehabilitation an observational study among patients sick-listed with low back pain from a randomised clinical trial in Denmark

    DEFF Research Database (Denmark)

    Lindholdt, Louise; Labriola, Merete; Nielsen, Claus Vinther

    2017-01-01

    INTRODUCTION: The return-to-work (RTW) process after long-term sickness absence is often complex and long and implies multiple shifts between different labour market states for the absentee. Standard methods for examining RTW research typically rely on the analysis of one outcome measure at a time...... (LBP). METHODS: The study population consisted of 160 patients randomly allocated to either a hospital-based brief or a multidisciplinary intervention. Data on labour market participation following intervention were obtained from a national register and analysed in two ways: as a binary outcome...... expressed as active or passive relief at a 1-year follow-up and as four different categories for labour market participation. Logistic regression and sequence analysis were performed. RESULTS: The logistic regression analysis showed no difference in labour market participation for patients in the two groups...

  8. Hormonal therapy followed by chemotherapy or the reverse sequence as first-line treatment of hormone-responsive, human epidermal growth factor receptor-2 negative metastatic breast cancer patients: results of an observational study.

    Science.gov (United States)

    Bighin, Claudia; Dozin, Beatrice; Poggio, Francesca; Ceppi, Marcello; Bruzzi, Paolo; D'Alonzo, Alessia; Levaggi, Alessia; Giraudi, Sara; Lambertini, Matteo; Miglietta, Loredana; Vaglica, Marina; Fontana, Vincenzo; Iacono, Giuseppina; Pronzato, Paolo; Del Mastro, Lucia

    2017-07-04

    Introduction Although hormonal-therapy is the preferred first-line treatment for hormone-responsive, HER2 negative metastatic breast cancer, no data from clinical trials support the choice between hormonal-therapy and chemotherapy.Methods Patients were divided into two groups according to the treatment: chemotherapy or hormonal-therapy. Outcomes in terms of clinical benefit and median overall survival (OS) were retrospectively evaluated in the two groups. To calculate the time spent in chemotherapy with respect to OS in the two groups, the proportion of patients in chemotherapy relative to those present in either group was computed at every day from the start of therapy.Results From 1999 to 2013, 119 patients received first-line hormonal-therapy (HT-first group) and 100 first-line chemotherapy (CT-first group). Patients in the CT-first group were younger and with poorer prognostic factors as compared to those in HT-first group. Clinical benefit (77 vs 81%) and median OS (50.7 vs 51.1 months) were similar in the two groups. Time spent in chemotherapy was significantly longer during the first 3 years in CT-first group (54-34%) as compared to the HT-first group (11-18%). This difference decreased after the third year and overall was 28% in the CT-first group and 18% in the HT-first group.Conclusions The sequence first-line chemotherapy followed by hormonal-therapy, as compared with the opposite sequence, is associated with a longer time of OS spent in chemotherapy. However, despite the poorer prognostic factors, patients in the CT-first group had a superimposable OS than those in the HT-first group.

  9. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  10. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  11. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  12. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  13. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  14. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  15. Nitrogen chronology of massive main sequence stars

    NARCIS (Netherlands)

    Köhler, K.; Borzyszkowski, M.; Brott, I.; Langer, N.; de Koter, A.

    2012-01-01

    Context. Rotational mixing in massive main sequence stars is predicted to monotonically increase their surface nitrogen abundance with time. Aims. We use this effect to design a method for constraining the age and the inclination angle of massive main sequence stars, given their observed luminosity,

  16. Repeat immigration: A previously unobserved source of heterogeneity?

    Science.gov (United States)

    Aradhya, Siddartha; Scott, Kirk; Smith, Christopher D

    2017-07-01

    Register data allow for nuanced analyses of heterogeneities between sub-groups which are not observable in other data sources. One heterogeneity for which register data is particularly useful is in identifying unique migration histories of immigrant populations, a group of interest across disciplines. Years since migration is a commonly used measure of integration in studies seeking to understand the outcomes of immigrants. This study constructs detailed migration histories to test whether misclassified migrations may mask important heterogeneities. In doing so, we identify a previously understudied group of migrants called repeat immigrants, and show that they differ systematically from permanent immigrants. In addition, we quantify the degree to which migration information is misreported in the registers. The analysis is carried out in two steps. First, we estimate income trajectories for repeat immigrants and permanent immigrants to understand the degree to which they differ. Second, we test data validity by cross-referencing migration information with changes in income to determine whether there are inconsistencies indicating misreporting. From the first part of the analysis, the results indicate that repeat immigrants systematically differ from permanent immigrants in terms of income trajectories. Furthermore, income trajectories differ based on the way in which years since migration is calculated. The second part of the analysis suggests that misreported migration events, while present, are negligible. Repeat immigrants differ in terms of income trajectories, and may differ in terms of other outcomes as well. Furthermore, this study underlines that Swedish registers provide a reliable data source to analyze groups which are unidentifiable in other data sources.

  17. Hydraulic fracturing and the Crooked Lake Sequences: Insights gleaned from regional seismic networks

    Science.gov (United States)

    Schultz, Ryan; Stern, Virginia; Novakovic, Mark; Atkinson, Gail; Gu, Yu Jeffrey

    2015-04-01

    Within central Alberta, Canada, a new sequence of earthquakes has been recognized as of 1 December 2013 in a region of previous seismic quiescence near Crooked Lake, ~30 km west of the town of Fox Creek. We utilize a cross-correlation detection algorithm to detect more than 160 events to the end of 2014, which is temporally distinguished into five subsequences. This observation is corroborated by the uniqueness of waveforms clustered by subsequence. The Crooked Lake Sequences have come under scrutiny due to its strong temporal correlation (>99.99%) to the timing of hydraulic fracturing operations in the Duvernay Formation. We assert that individual subsequences are related to fracturing stimulation and, despite adverse initial station geometry, double-difference techniques allow us to spatially relate each cluster back to a unique horizontal well. Overall, we find that seismicity in the Crooked Lake Sequences is consistent with first-order observations of hydraulic fracturing induced seismicity.

  18. Phylogeny of the Serrasalmidae (Characiformes based on mitochondrial DNA sequences

    Directory of Open Access Journals (Sweden)

    Guillermo Ortí

    2008-01-01

    Full Text Available Previous studies based on DNA sequences of mitochondrial (mt rRNA genes showed three main groups within the subfamily Serrasalminae: (1 a "pacu" clade of herbivores (Colossoma, Mylossoma, Piaractus; (2 the "Myleus" clade (Myleus, Mylesinus, Tometes, Ossubtus; and (3 the "piranha" clade (Serrasalmus, Pygocentrus, Pygopristis, Pristobrycon, Catoprion, Metynnis. The genus Acnodon was placed as the sister taxon of clade (2+3. However, poor resolution within each clade was obtained due to low levels of variation among rRNA gene sequences. Complete sequences of the hypervariable mtDNA control region for a total of 45 taxa, and additional sequences of 12S and 16S rRNA from a total of 74 taxa representing all genera in the family are now presented to address intragroup relationships. Control region sequences of several serrasalmid species exhibit tandem repeats of short motifs (12 to 33 bp in the 3' end of this region, accounting for substantial length variation. Bayesian inference and maximum parsimony analyses of these sequences identify the same groupings as before and provide further evidence to support the following observations: (a Serrasalmus gouldingi and species of Pristobrycon (non-striolatus form a monophyletic group that is the sister group to other species of Serrasalmus and Pygocentrus; (b Catoprion, Pygopristis, and Pristobrycon striolatus form a well supported clade, sister to the group described above; (c some taxa assigned to the genus Myloplus (M. asterias, M tiete, M ternetzi, and M rubripinnis form a well supported group whereas other Myloplus species remain with uncertain affinities (d Mylesinus, Tometes and Myleus setiger form a monophyletic group.

  19. Second generation sequencing of the mesothelioma tumor genome.

    Directory of Open Access Journals (Sweden)

    Raphael Bueno

    2010-05-01

    Full Text Available The current paradigm for elucidating the molecular etiology of cancers relies on the interrogation of small numbers of genes, which limits the scope of investigation. Emerging second-generation massively parallel DNA sequencing technologies have enabled more precise definition of the cancer genome on a global scale. We examined the genome of a human primary malignant pleural mesothelioma (MPM tumor and matched normal tissue by using a combination of sequencing-by-synthesis and pyrosequencing methodologies to a 9.6X depth of coverage. Read density analysis uncovered significant aneuploidy and numerous rearrangements. Method-dependent informatics rules, which combined the results of different sequencing platforms, were developed to identify and validate candidate mutations of multiple types. Many more tumor-specific rearrangements than point mutations were uncovered at this depth of sequencing, resulting in novel, large-scale, inter- and intra-chromosomal deletions, inversions, and translocations. Nearly all candidate point mutations appeared to be previously unknown SNPs. Thirty tumor-specific fusions/translocations were independently validated with PCR and Sanger sequencing. Of these, 15 represented disrupted gene-encoding regions, including kinases, transcription factors, and growth factors. One large deletion in DPP10 resulted in altered transcription and expression of DPP10 transcripts in a set of 53 additional MPM tumors correlated with survival. Additionally, three point mutations were observed in the coding regions of NKX6-2, a transcription regulator, and NFRKB, a DNA-binding protein involved in modulating NFKB1. Several regions containing genes such as PCBD2 and DHFR, which are involved in growth factor signaling and nucleotide synthesis, respectively, were selectively amplified in the tumor. Second-generation sequencing uncovered all types of mutations in this MPM tumor, with DNA rearrangements representing the dominant type.

  20. 49 CFR 173.23 - Previously authorized packaging.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false Previously authorized packaging. 173.23 Section... REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Preparation of Hazardous Materials for Transportation § 173.23 Previously authorized packaging. (a) When the regulations specify a packaging with a specification marking...

  1. 28 CFR 10.5 - Incorporation of papers previously filed.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Incorporation of papers previously filed... CARRYING ON ACTIVITIES WITHIN THE UNITED STATES Registration Statement § 10.5 Incorporation of papers previously filed. Papers and documents already filed with the Attorney General pursuant to the said act and...

  2. 75 FR 76056 - FEDERAL REGISTER CITATION OF PREVIOUS ANNOUNCEMENT:

    Science.gov (United States)

    2010-12-07

    ... SECURITIES AND EXCHANGE COMMISSION Sunshine Act Meeting FEDERAL REGISTER CITATION OF PREVIOUS ANNOUNCEMENT: STATUS: Closed meeting. PLACE: 100 F Street, NE., Washington, DC. DATE AND TIME OF PREVIOUSLY ANNOUNCED MEETING: Thursday, December 9, 2010 at 2 p.m. CHANGE IN THE MEETING: Time change. The closed...

  3. The pathogenicity of genetic variants previously associated with left ventricular non-compaction

    DEFF Research Database (Denmark)

    Abbasi, Yeganeh; Jabbari, Javad; Jabbari, Reza

    2016-01-01

    BACKGROUND: Left ventricular non-compaction (LVNC) is a rare cardiomyopathy. Many genetic variants have been associated with LVNC. However, the number of the previous LVNC-associated variants that are common in the background population remains unknown. The aim of this study was to provide...... an updated list of previously reported LVNC-associated variants with biologic description and investigate the prevalence of LVNC variants in healthy general population to find false-positive LVNC-associated variants. METHODS AND RESULTS: The Human Gene Mutation Database and PubMed were systematically...... searched to identify all previously reported LVNC-associated variants. Thereafter, the Exome Sequencing Project (ESP) and the Exome Aggregation Consortium (ExAC), that both represent the background population, was searched for all variants. Four in silico prediction tools were assessed to determine...

  4. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  5. No discrimination against previous mates in a sexually cannibalistic spider

    Science.gov (United States)

    Fromhage, Lutz; Schneider, Jutta M.

    2005-09-01

    In several animal species, females discriminate against previous mates in subsequent mating decisions, increasing the potential for multiple paternity. In spiders, female choice may take the form of selective sexual cannibalism, which has been shown to bias paternity in favor of particular males. If cannibalistic attacks function to restrict a male's paternity, females may have little interest to remate with males having survived such an attack. We therefore studied the possibility of female discrimination against previous mates in sexually cannibalistic Argiope bruennichi, where females almost always attack their mate at the onset of copulation. We compared mating latency and copulation duration of males having experienced a previous copulation either with the same or with a different female, but found no evidence for discrimination against previous mates. However, males copulated significantly shorter when inserting into a used, compared to a previously unused, genital pore of the female.

  6. Implant breast reconstruction after salvage mastectomy in previously irradiated patients.

    Science.gov (United States)

    Persichetti, Paolo; Cagli, Barbara; Simone, Pierfranco; Cogliandro, Annalisa; Fortunato, Lucio; Altomare, Vittorio; Trodella, Lucio

    2009-04-01

    The most common surgical approach in case of local tumor recurrence after quadrantectomy and radiotherapy is salvage mastectomy. Breast reconstruction is the subsequent phase of the treatment and the plastic surgeon has to operate on previously irradiated and manipulated tissues. The medical literature highlights that breast reconstruction with tissue expanders is not a pursuable option, considering previous radiotherapy a contraindication. The purpose of this retrospective study is to evaluate the influence of previous radiotherapy on 2-stage breast reconstruction (tissue expander/implant). Only patients with analogous timing of radiation therapy and the same demolitive and reconstructive procedures were recruited. The results of this study prove that, after salvage mastectomy in previously irradiated patients, implant reconstruction is still possible. Further comparative studies are, of course, advisable to draw any conclusion on the possibility to perform implant reconstruction in previously irradiated patients.

  7. Perception Enhancement using Visual Attributes in Sequence Motif Visualization

    OpenAIRE

    Oon, Yin; Lee, Nung; Kok, Wei

    2016-01-01

    Sequence logo is a well-accepted scientific method to visualize the conservation characteristics of biological sequence motifs. Previous studies found that using sequence logo graphical representation for scientific evidence reports or arguments could seriously cause biases and misinterpretation by users. This study investigates on the visual attributes performance of a sequence logo in helping users to perceive and interpret the information based on preattentive theories and Gestalt principl...

  8. Nonlinear analysis of sequence repeats of multi-domain proteins

    Energy Technology Data Exchange (ETDEWEB)

    Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail: lmf_bill@sina.com

    2007-11-15

    Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences.

  9. Sequencing Cyclic Peptides by Multistage Mass Spectrometry

    Science.gov (United States)

    Mohimani, Hosein; Yang, Yu-Liang; Liu, Wei-Ting; Hsieh, Pei-Wen; Dorrestein, Pieter C.; Pevzner, Pavel A.

    2012-01-01

    Some of the most effective antibiotics (e.g., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of mass spectrometry based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage mass spectrometry, and show its advantages over single stage mass spectrometry. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria. PMID:21751357

  10. Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae).

    Science.gov (United States)

    Walker, Joseph F; Zanis, Michael J; Emery, Nancy C

    2014-04-01

    Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present the first whole plastome from the Madieae tribe and compare its sequence variation to other chloroplast genomes in Asteraceae. We used high throughput sequencing to obtain the Lasthenia burkei chloroplast genome. We compared sequence structure and rates of molecular evolution in the small single copy (SSC), large single copy (LSC), and inverted repeat (IR) regions to those for eight Asteraceae accessions and one Solanaceae accession. The chloroplast sequence of L. burkei is 150 746 bp and contains 81 unique protein coding genes and 4 coding ribosomal RNA sequences. We identified three major inversions in the L. burkei chloroplast, all of which have been found in other Asteraceae lineages, and a previously unreported inversion in Lactuca sativa. Regions flanking inversions contained tRNA sequences, but did not have particularly high G + C content. Substitution rates varied among the SSC, LSC, and IR regions, and rates of evolution within each region varied among species. Some observed differences in rates of molecular evolution may be explained by the relative proportion of coding to noncoding sequence within regions. Rates of molecular evolution vary substantially within and among chloroplast genomes, and major inversion events may be promoted by the presence of tRNAs. Collectively, these results provide insight into different mechanisms that may promote intramolecular recombination and the inversion of large genomic regions in the plastome.

  11. Arbitrarily accurate twin composite π -pulse sequences

    Science.gov (United States)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2018-04-01

    We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

  12. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  13. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  14. Personality disorders in previously detained adolescent females: a prospective study

    NARCIS (Netherlands)

    Krabbendam, A.; Colins, O.F.; Doreleijers, T.A.H.; van der Molen, E.; Beekman, A.T.F.; Vermeiren, R.R.J.M.

    2015-01-01

    This longitudinal study investigated the predictive value of trauma and mental health problems for the development of antisocial personality disorder (ASPD) and borderline personality disorder (BPD) in previously detained women. The participants were 229 detained adolescent females who were assessed

  15. Payload specialist Reinhard Furrer show evidence of previous blood sampling

    Science.gov (United States)

    1985-01-01

    Payload specialist Reinhard Furrer shows evidence of previous blood sampling while Wubbo J. Ockels, Dutch payload specialist (only partially visible), extends his right arm after a sample has been taken. Both men show bruises on their arms.

  16. Choice of contraception after previous operative delivery at a family ...

    African Journals Online (AJOL)

    Choice of contraception after previous operative delivery at a family planning clinic in Northern Nigeria. Amina Mohammed‑Durosinlorun, Joel Adze, Stephen Bature, Caleb Mohammed, Matthew Taingson, Amina Abubakar, Austin Ojabo, Lydia Airede ...

  17. Previous utilization of service does not improve timely booking in ...

    African Journals Online (AJOL)

    Previous utilization of service does not improve timely booking in antenatal care: Cross sectional study ... Journal Home > Vol 24, No 3 (2010) > ... Results: Past experience on antenatal care service utilization did not come out as a predictor for ...

  18. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  19. Human pro. cap alpha. 1(III) collagen: cDNA sequence for the 3' end

    Energy Technology Data Exchange (ETDEWEB)

    Mankoo, B S; Dalgleish, R

    1988-03-25

    The authors have previously isolated two overlapping cDNA clones, pIII-21 and pIII-33, which encode the C-terminal end of human type III procollagen. They now present the sequence of 2520 bases encoded in these cDNAs which overlaps other previously published sequences for the same gene. The sequence presented differs from previously published sequences at five positions.

  20. Secondary recurrent miscarriage is associated with previous male birth.

    LENUS (Irish Health Repository)

    Ooi, Poh Veh

    2012-01-31

    Secondary recurrent miscarriage (RM) is defined as three or more consecutive pregnancy losses after delivery of a viable infant. Previous reports suggest that a firstborn male child is associated with less favourable subsequent reproductive potential, possibly due to maternal immunisation against male-specific minor histocompatibility antigens. In a retrospective cohort study of 85 cases of secondary RM we aimed to determine if secondary RM was associated with (i) gender of previous child, maternal age, or duration of miscarriage history, and (ii) increased risk of pregnancy complications. Fifty-three women (62.0%; 53\\/85) gave birth to a male child prior to RM compared to 32 (38.0%; 32\\/85) who gave birth to a female child (p=0.002). The majority (91.7%; 78\\/85) had uncomplicated, term deliveries and normal birth weight neonates, with one quarter of the women previously delivered by Caesarean section. All had routine RM investigations and 19.0% (16\\/85) had an abnormal result. Fifty-seven women conceived again and 33.3% (19\\/57) miscarried, but there was no significant difference in failure rates between those with a previous male or female child (13\\/32 vs. 6\\/25, p=0.2). When patients with abnormal results were excluded, or when women with only one previous child were considered, there was still no difference in these rates. A previous male birth may be associated with an increased risk of secondary RM but numbers preclude concluding whether this increases recurrence risk. The suggested association with previous male birth provides a basis for further investigations at a molecular level.

  1. Secondary recurrent miscarriage is associated with previous male birth.

    LENUS (Irish Health Repository)

    Ooi, Poh Veh

    2011-01-01

    Secondary recurrent miscarriage (RM) is defined as three or more consecutive pregnancy losses after delivery of a viable infant. Previous reports suggest that a firstborn male child is associated with less favourable subsequent reproductive potential, possibly due to maternal immunisation against male-specific minor histocompatibility antigens. In a retrospective cohort study of 85 cases of secondary RM we aimed to determine if secondary RM was associated with (i) gender of previous child, maternal age, or duration of miscarriage history, and (ii) increased risk of pregnancy complications. Fifty-three women (62.0%; 53\\/85) gave birth to a male child prior to RM compared to 32 (38.0%; 32\\/85) who gave birth to a female child (p=0.002). The majority (91.7%; 78\\/85) had uncomplicated, term deliveries and normal birth weight neonates, with one quarter of the women previously delivered by Caesarean section. All had routine RM investigations and 19.0% (16\\/85) had an abnormal result. Fifty-seven women conceived again and 33.3% (19\\/57) miscarried, but there was no significant difference in failure rates between those with a previous male or female child (13\\/32 vs. 6\\/25, p=0.2). When patients with abnormal results were excluded, or when women with only one previous child were considered, there was still no difference in these rates. A previous male birth may be associated with an increased risk of secondary RM but numbers preclude concluding whether this increases recurrence risk. The suggested association with previous male birth provides a basis for further investigations at a molecular level.

  2. Previously unclassified bacteria dominate during thermophilic and mesophilic anaerobic pre-treatment of primary sludge.

    Science.gov (United States)

    Pervin, Hasina M; Batstone, Damien J; Bond, Philip L

    2013-06-01

    Thermophilic biological pre-treatment enables enhanced anaerobic digestion for treatment of wastewater sludges but, at present, there is limited understanding of the hydrolytic-acidogenic microbial composition and its contribution to this process. In this study, the process was assessed by comparing the microbiology of thermophilic (50-65 °C) and mesophilic (35 °C) pre-treatment reactors treating primary sludge. A full-cycle approach for the 16S rRNA genes was applied in order to monitor the diversity of bacteria and their abundance in a thermophilic pre-treatment reactor treating primary sludge. For the thermophilic pre-treatment (TP), over 90% of the sequences were previously undetected and these had less than 97% sequence similarity to cultured organisms. During the first 83 days, members of the Betaproteobacteria dominated the community sequences and a newly designed probe was used to monitor a previously unknown bacterium affiliated with the genus Brachymonas. Between days 85 and 183, three phylotypes that affiliated with the genera Comamonas, Clostridium and Lysobacter were persistently dominant in the TP community, as revealed by terminal-restriction fragment length polymorphism (T-RFLP). Hydrolytic and fermentative functions have been speculated for these bacteria. Mesophilic pre-treatment (MP) and TP communities were different but they were both relatively dynamic. Statistical correlation analysis and the function of closely allied reference organisms indicated that previously unclassified bacteria dominated the TP community and may have been functionally involved in the enhanced hydrolytic performance of thermophilic anaerobic pre-treatment. This study is the first to reveal the diversity and dynamics of bacteria during anaerobic digestion of primary sludge. Copyright © 2013 Elsevier GmbH. All rights reserved.

  3. Whole-exome sequencing of a pedigree segregating asthma

    Directory of Open Access Journals (Sweden)

    DeWan Andrew T

    2012-10-01

    Full Text Available Abstract Background Despite the success of genome-wide association studies for asthma, few, if any, definitively causal variants have been identified and there is still a substantial portion of the heritability of the disease yet to be discovered. Some of this “missing heritability” may be accounted for by family-specific coding variants found to be segregating with asthma. Methods To identify family-specific variants segregating with asthma, we recruited one family from a previous study of asthma as reporting multiple asthmatic and non-asthmatic children. We performed whole-exome sequencing on all four children and both parents and identified coding variants segregating with asthma that were not found in other variant databases. Results Ten novel variants were identified that were found in the two affected offspring and affected mother, but absent in the unaffected father and two unaffected offspring. Of these ten, variants in three genes (PDE4DIP, CBLB, and KALRN were deemed of particular interest based on their functional prediction scores and previously reported function or asthma association. We did not identify any common risk variants segregating with asthma, however, we did observe an increase in the number of novel, nonsynonymous variants in asthma candidate genes in the asthmatic children compared to the non-asthmatic children. Conclusions This is the first report applying exome sequencing to identify asthma susceptibility variants. Despite having sequenced only one family segregating asthma, we have identified several potentially functional variants in interesting asthma candidate genes. This will provide the basis for future work in which more families will be sequenced to identify variants across families that cluster within genes.

  4. Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

    DEFF Research Database (Denmark)

    Rettedal, Elizabeth; Gumpert, Heidi; Sommer, Morten

    2014-01-01

    The human gut microbiota is linked to a variety of human health issues and implicated in antibiotic resistance gene dissemination. Most of these associations rely on culture-independent methods, since it is commonly believed that gut microbiota cannot be easily or sufficiently cultured. Here, we...... microbiota. Based on the phenotypic mapping, we tailor antibiotic combinations to specifically select for previously uncultivated bacteria. Utilizing this method we cultivate and sequence the genomes of four isolates, one of which apparently belongs to the genus Oscillibacter; uncultivated Oscillibacter...

  5. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  6. Erlotinib-induced rash spares previously irradiated skin

    International Nuclear Information System (INIS)

    Lips, Irene M.; Vonk, Ernest J.A.; Koster, Mariska E.Y.; Houwing, Ronald H.

    2011-01-01

    Erlotinib is an epidermal growth factor receptor inhibitor prescribed to patients with locally advanced or metastasized non-small cell lung carcinoma after failure of at least one earlier chemotherapy treatment. Approximately 75% of the patients treated with erlotinib develop acneiform skin rashes. A patient treated with erlotinib 3 months after finishing concomitant treatment with chemotherapy and radiotherapy for non-small cell lung cancer is presented. Unexpectedly, the part of the skin that had been included in his previously radiotherapy field was completely spared from the erlotinib-induced acneiform skin rash. The exact mechanism of erlotinib-induced rash sparing in previously irradiated skin is unclear. The underlying mechanism of this phenomenon needs to be explored further, because the number of patients being treated with a combination of both therapeutic modalities is increasing. The therapeutic effect of erlotinib in the area of the previously irradiated lesion should be assessed. (orig.)

  7. Reasoning with Previous Decisions: Beyond the Doctrine of Precedent

    DEFF Research Database (Denmark)

    Komárek, Jan

    2013-01-01

    in different jurisdictions use previous judicial decisions in their argument, we need to move beyond the concept of precedent to a wider notion, which would embrace practices and theories in legal systems outside the Common law tradition. This article presents the concept of ‘reasoning with previous decisions...... law method’, but they are no less rational and intellectually sophisticated. The reason for the rather conceited attitude of some comparatists is in the dominance of the common law paradigm of precedent and the accompanying ‘case law method’. If we want to understand how courts and lawyers......’ as such an alternative and develops its basic models. The article first points out several shortcomings inherent in limiting the inquiry into reasoning with previous decisions by the common law paradigm (1). On the basis of numerous examples provided in section (1), I will present two basic models of reasoning...

  8. Robustness analysis of chiller sequencing control

    International Nuclear Information System (INIS)

    Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

    2015-01-01

    Highlights: • Uncertainties with chiller sequencing control were systematically quantified. • Robustness of chiller sequencing control was systematically analyzed. • Different sequencing control strategies were sensitive to different uncertainties. • A numerical method was developed for easy selection of chiller sequencing control. - Abstract: Multiple-chiller plant is commonly employed in the heating, ventilating and air-conditioning system to increase operational feasibility and energy-efficiency under part load condition. In a multiple-chiller plant, chiller sequencing control plays a key role in achieving overall energy efficiency while not sacrifices the cooling sufficiency for indoor thermal comfort. Various sequencing control strategies have been developed and implemented in practice. Based on the observation that (i) uncertainty, which cannot be avoided in chiller sequencing control, has a significant impact on the control performance and may cause the control fail to achieve the expected control and/or energy performance; and (ii) in current literature few studies have systematically addressed this issue, this paper therefore presents a study on robustness analysis of chiller sequencing control in order to understand the robustness of various chiller sequencing control strategies under different types of uncertainty. Based on the robustness analysis, a simple and applicable method is developed to select the most robust control strategy for a given chiller plant in the presence of uncertainties, which will be verified using case studies

  9. Cardiovascular magnetic resonance in adults with previous cardiovascular surgery.

    Science.gov (United States)

    von Knobelsdorff-Brenkenhoff, Florian; Trauzeddel, Ralf Felix; Schulz-Menger, Jeanette

    2014-03-01

    Cardiovascular magnetic resonance (CMR) is a versatile non-invasive imaging modality that serves a broad spectrum of indications in clinical cardiology and has proven evidence. Most of the numerous applications are appropriate in patients with previous cardiovascular surgery in the same manner as in non-surgical subjects. However, some specifics have to be considered. This review article is intended to provide information about the application of CMR in adults with previous cardiovascular surgery. In particular, the two main scenarios, i.e. following coronary artery bypass surgery and following heart valve surgery, are highlighted. Furthermore, several pictorial descriptions of other potential indications for CMR after cardiovascular surgery are given.

  10. Insights into the sequence parameters for halophilic adaptation.

    Science.gov (United States)

    Nath, Abhigyan

    2016-03-01

    The sequence parameters for halophilic adaptation are still not fully understood. To understand the molecular basis of protein hypersaline adaptation, a detailed analysis is carried out, and investigated the likely association of protein sequence attributes to halophilic adaptation. A two-stage strategy is implemented, where in the first stage a supervised machine learning classifier is build, giving an overall accuracy of 86 % on stratified tenfold cross validation and 90 % on blind testing set, which are better than the previously reported results. The second stage consists of statistical analysis of sequence features and possible extraction of halophilic molecular signatures. The results of this study showed that, halophilic proteins are characterized by lower average charge, lower K content, and lower S content. A statistically significant preference/avoidance list of sequence parameters is also reported giving insights into the molecular basis of halophilic adaptation. D, Q, E, H, P, T, V are significantly preferred while N, C, I, K, M, F, S are significantly avoided. Among amino acid physicochemical groups, small, polar, charged, acidic and hydrophilic groups are preferred over other groups. The halophilic proteins also showed a preference for higher average flexibility, higher average polarity and avoidance for higher average positive charge, average bulkiness and average hydrophobicity. Some interesting trends observed in dipeptide counts are also reported. Further a systematic statistical comparison is undertaken for gaining insights into the sequence feature distribution in different residue structural states. The current analysis may facilitate the understanding of the mechanism of halophilic adaptation clearer, which can be further used for rational design of halophilic proteins.

  11. Impact of Sequencing Targeted Therapies With High-dose Interleukin-2 Immunotherapy: An Analysis of Outcome and Survival of Patients With Metastatic Renal Cell Carcinoma From an On-going Observational IL-2 Clinical Trial: PROCLAIMSM.

    Science.gov (United States)

    Clark, Joseph I; Wong, Michael K K; Kaufman, Howard L; Daniels, Gregory A; Morse, Michael A; McDermott, David F; Agarwala, Sanjiv S; Lewis, Lionel D; Stewart, John H; Vaishampayan, Ulka; Curti, Brendan; Gonzalez, René; Lutzky, Jose; Rudraptna, Venkatesh; Cranmer, Lee D; Jeter, Joanne M; Hauke, Ralph J; Miletello, Gerald; Milhem, Mohammed M; Amin, Asim; Richart, John M; Fishman, Mayer; Hallmeyer, Sigrun; Patel, Sapna P; Van Veldhuizen, Peter; Agarwal, Neeraj; Taback, Bret; Treisman, Jonathan S; Ernstoff, Marc S; Perritt, Jessica C; Hua, Hong; Rao, Tharak B; Dutcher, Janice P; Aung, Sandra

    2017-02-01

    This analysis describes the outcome for patients who received targeted therapy (TT) prior to or following high-dose interleukin-2 (HD IL-2). Patients with renal cell carcinoma (n = 352) receiving HD IL-2 were enrolled in Proleukin R Observational Study to Evaluate the Treatment Patterns and Clinical Response in Malignancy (PROCLAIM SM ) beginning in 2011. Statistical analyses were performed using datasets as of September 24, 2015. Overall, there were 4% complete response (CR), 13% partial response (PR), 39% stable disease (SD), and 43% progressive disease (PD) with HD IL-2. The median overall survival (mOS) was not reached in patients with CR, PR, or SD, and was 15.5 months in patients with PD (median follow-up, 21 months). Sixty-one patients had prior TT before HD IL-2 with an overall response rate (ORR) to HD IL-2 of 19% (1 CR, 9 PR) and an mOS of 22.1 months. One hundred forty-nine patients received TT only after HD IL-2 with an mOS of 35.5 months. One hundred forty-two patients had no TT before or after HD IL-2, and mOS was not reached. The mOS was 8.5 months in PD patients who received HD IL-2 without follow-on TT and 29.7 months in PD patients who received follow-on TT after HD IL-2. HD IL-2 as sole front-line therapy, in the absence of added TT, shows extended clinical benefit (CR, PR, and SD). Patients with PD after HD IL-2 appear to benefit from follow-on TT. Patients who progressed on TT and received follow-on HD IL-2 experienced major clinical benefit. HD IL-2 therapy should be considered in eligible patients. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Squamous cell carcinoma arising in previously burned or irradiated skin

    International Nuclear Information System (INIS)

    Edwards, M.J.; Hirsch, R.M.; Broadwater, J.R.; Netscher, D.T.; Ames, F.C.

    1989-01-01

    Squamous cell carcinoma (SCC) arising in previously burned or irradiated skin was reviewed in 66 patients treated between 1944 and 1986. Healing of the initial injury was complicated in 70% of patients. Mean interval from initial injury to diagnosis of SCC was 37 years. The overwhelming majority of patients presented with a chronic intractable ulcer in previously injured skin. The regional relapse rate after surgical excision was very high, 58% of all patients. Predominant patterns of recurrence were in local skin and regional lymph nodes (93% of recurrences). Survival rates at 5, 10, and 20 years were 52%, 34%, and 23%, respectively. Five-year survival rates in previously burned and irradiated patients were not significantly different (53% and 50%, respectively). This review, one of the largest reported series, better defines SCC arising in previously burned or irradiated skin as a locally aggressive disease that is distinct from SCC arising in sunlight-damaged skin. An increased awareness of the significance of chronic ulceration in scar tissue may allow earlier diagnosis. Regional disease control and survival depend on surgical resection of all known disease and may require radical lymph node dissection or amputation

  13. Outcome Of Pregnancy Following A Previous Lower Segment ...

    African Journals Online (AJOL)

    Background: A previous ceasarean section is an important variable that influences patient management in subsequent pregnancies. A trial of vaginal delivery in such patients is a feasible alternative to a secondary section, thus aiding to reduce the ceasarean section rate and its associated co-morbidities. Objective: To ...

  14. 24 CFR 1710.552 - Previously accepted state filings.

    Science.gov (United States)

    2010-04-01

    ... of Substantially Equivalent State Law § 1710.552 Previously accepted state filings. (a) Materials... and contracts or agreements contain notice of purchaser's revocation rights. In addition see § 1715.15..., unless the developer is obligated to do so in the contract. (b) If any such filing becomes inactive or...

  15. The job satisfaction of principals of previously disadvantaged schools

    African Journals Online (AJOL)

    The aim of this study was to identify influences on the job satisfaction of previously disadvantaged ..... I am still riding the cloud … I hope it lasts. .... as a way of creating a climate and culture in schools where individuals are willing to explore.

  16. Haemophilus influenzae type f meningitis in a previously healthy boy

    DEFF Research Database (Denmark)

    Ronit, Andreas; Berg, Ronan M G; Bruunsgaard, Helle

    2013-01-01

    Non-serotype b strains of Haemophilus influenzae are extremely rare causes of acute bacterial meningitis in immunocompetent individuals. We report a case of acute bacterial meningitis in a 14-year-old boy, who was previously healthy and had been immunised against H influenzae serotype b (Hib...

  17. Research Note Effects of previous cultivation on regeneration of ...

    African Journals Online (AJOL)

    We investigated the effects of previous cultivation on regeneration potential under miombo woodlands in a resettlement area, a spatial product of Zimbabwe's land reforms. We predicted that cultivation would affect population structure, regeneration, recruitment and potential grazing capacity of rangelands. Plant attributes ...

  18. Cryptococcal meningitis in a previously healthy child | Chimowa ...

    African Journals Online (AJOL)

    An 8-year-old previously healthy female presented with a 3 weeks history of headache, neck stiffness, deafness, fever and vomiting and was diagnosed with cryptococcal meningitis. She had documented hearing loss and was referred to tertiary-level care after treatment with fluconazole did not improve her neurological ...

  19. 18 CFR 154.302 - Previously submitted material.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Previously submitted material. 154.302 Section 154.302 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... concurrently with the rate change filing. There must be furnished to the Director, Office of Energy Market...

  20. Process cells dismantling of EUREX pant: previous activities

    International Nuclear Information System (INIS)

    Gili, M.

    1998-01-01

    In the '98-'99 period some process cells of the EUREX pant will be dismantled, in order to place there the liquid wastes conditioning plant 'CORA'. This report resumes the previous activities (plant rinsing campaigns and inactive Cell 014 dismantling), run in the past three years and the drawn experience [it

  1. The job satisfaction of principals of previously disadvantaged schools

    African Journals Online (AJOL)

    The aim of this study was to identify influences on the job satisfaction of previously disadvantaged school principals in North-West Province. Evans's theory of job satisfaction, morale and motivation was useful as a conceptual framework. A mixedmethods explanatory research design was important in discovering issues with ...

  2. Obstructive pulmonary disease in patients with previous tuberculosis ...

    African Journals Online (AJOL)

    Obstructive pulmonary disease in patients with previous tuberculosis: Pathophysiology of a community-based cohort. B.W. Allwood, R Gillespie, M Galperin-Aizenberg, M Bateman, H Olckers, L Taborda-Barata, G.L. Calligaro, Q Said-Hartley, R van Zyl-Smit, C.B. Cooper, E van Rikxoort, J Goldin, N Beyers, E.D. Bateman ...

  3. Abiraterone in metastatic prostate cancer without previous chemotherapy

    NARCIS (Netherlands)

    Ryan, Charles J.; Smith, Matthew R.; de Bono, Johann S.; Molina, Arturo; Logothetis, Christopher J.; de Souza, Paul; Fizazi, Karim; Mainwaring, Paul; Piulats, Josep M.; Ng, Siobhan; Carles, Joan; Mulders, Peter F. A.; Basch, Ethan; Small, Eric J.; Saad, Fred; Schrijvers, Dirk; van Poppel, Hendrik; Mukherjee, Som D.; Suttmann, Henrik; Gerritsen, Winald R.; Flaig, Thomas W.; George, Daniel J.; Yu, Evan Y.; Efstathiou, Eleni; Pantuck, Allan; Winquist, Eric; Higano, Celestia S.; Taplin, Mary-Ellen; Park, Youn; Kheoh, Thian; Griffin, Thomas; Scher, Howard I.; Rathkopf, Dana E.; Boyce, A.; Costello, A.; Davis, I.; Ganju, V.; Horvath, L.; Lynch, R.; Marx, G.; Parnis, F.; Shapiro, J.; Singhal, N.; Slancar, M.; van Hazel, G.; Wong, S.; Yip, D.; Carpentier, P.; Luyten, D.; de Reijke, T.

    2013-01-01

    Abiraterone acetate, an androgen biosynthesis inhibitor, improves overall survival in patients with metastatic castration-resistant prostate cancer after chemotherapy. We evaluated this agent in patients who had not received previous chemotherapy. In this double-blind study, we randomly assigned

  4. Response to health insurance by previously uninsured rural children.

    Science.gov (United States)

    Tilford, J M; Robbins, J M; Shema, S J; Farmer, F L

    1999-08-01

    To examine the healthcare utilization and costs of previously uninsured rural children. Four years of claims data from a school-based health insurance program located in the Mississippi Delta. All children who were not Medicaid-eligible or were uninsured, were eligible for limited benefits under the program. The 1987 National Medical Expenditure Survey (NMES) was used to compare utilization of services. The study represents a natural experiment in the provision of insurance benefits to a previously uninsured population. Premiums for the claims cost were set with little or no information on expected use of services. Claims from the insurer were used to form a panel data set. Mixed model logistic and linear regressions were estimated to determine the response to insurance for several categories of health services. The use of services increased over time and approached the level of utilization in the NMES. Conditional medical expenditures also increased over time. Actuarial estimates of claims cost greatly exceeded actual claims cost. The provision of a limited medical, dental, and optical benefit package cost approximately $20-$24 per member per month in claims paid. An important uncertainty in providing health insurance to previously uninsured populations is whether a pent-up demand exists for health services. Evidence of a pent-up demand for medical services was not supported in this study of rural school-age children. States considering partnerships with private insurers to implement the State Children's Health Insurance Program could lower premium costs by assembling basic data on previously uninsured children.

  5. Sequence variations in C9orf72 downstream of the hexanucleotide repeat region and its effect on repeat-primed PCR interpretation

    DEFF Research Database (Denmark)

    Nordin, Angelica; Akimoto, Chizuru; Wuolikainen, Anna

    2017-01-01

    A large GGGGCC-repeat expansion mutation (HREM) in C9orf72 is the most common known cause of ALS and FTD in European populations. Sequence variations immediately downstream of the HREM region have previously been observed and have been suggested to be one reason for difficulties in interpreting R...

  6. Breaking barriers and halting rupture: the 2016 Amatrice-Visso-Castelluccio earthquake sequence, central Italy

    Science.gov (United States)

    Gregory, L. C.; Walters, R. J.; Wedmore, L. N. J.; Craig, T. J.; McCaffrey, K. J. W.; Wilkinson, M. W.; Livio, F.; Michetti, A.; Goodall, H.; Li, Z.; Chen, J.; De Martini, P. M.

    2017-12-01

    In 2016 the Central Italian Apennines was struck by a sequence of normal faulting earthquakes that ruptured in three separate events on the 24th August (Mw 6.2), the 26th Oct (Mw 6.1), and the 30th Oct (Mw 6.6). We reveal the complex nature of the individual events and the time-evolution of the sequence using multiple datasets. We will present an overview of the results from field geology, satellite geodesy, GNSS (including low-cost short baseline installations), and terrestrial laser scanning (TLS). Sequences of earthquakes of mid to high magnitude 6 are common in historical and seismological records in Italy and other similar tectonic settings globally. Multi-fault rupture during these sequences can occur in seconds, as in the M 6.9 1980 Irpinia earthquake, or can span days, months, or years (e.g. the 1703 Norcia-L'Aquila sequence). It is critical to determine why the causative faults in the 2016 sequence did not rupture simultaneously, and how this relates to fault segmentation and structural barriers. This is the first sequence of this kind to be observed using modern geodetic techniques, and only with all of the datasets combined can we begin to understand how and why the sequence evolved in time and space. We show that earthquake rupture both broke through structural barriers that were thought to exist, but was also inhibited by a previously unknown structure. We will also discuss the logistical challenges in generating datasets on the time-evolving sequence, and show how rapid response and international collaboration within the Open EMERGEO Working Group was critical for gaining a complete picture of the ongoing activity.

  7. Asymptotic behaviour of firmly non expansive sequences

    International Nuclear Information System (INIS)

    Rouhani, B.D.

    1993-04-01

    We introduce the notion of firmly non expansive sequences in a Banach space and present several results concerning their asymptotic behaviour extending previous results and giving an affirmative answer to an open question raised by S. Reich and I. Shafir. Applications to averaged mappings are also given. (author). 16 refs

  8. Reoperative sentinel lymph node biopsy after previous mastectomy.

    Science.gov (United States)

    Karam, Amer; Stempel, Michelle; Cody, Hiram S; Port, Elisa R

    2008-10-01

    Sentinel lymph node (SLN) biopsy is the standard of care for axillary staging in breast cancer, but many clinical scenarios questioning the validity of SLN biopsy remain. Here we describe our experience with reoperative-SLN (re-SLN) biopsy after previous mastectomy. Review of the SLN database from September 1996 to December 2007 yielded 20 procedures done in the setting of previous mastectomy. SLN biopsy was performed using radioisotope with or without blue dye injection superior to the mastectomy incision, in the skin flap in all patients. In 17 of 20 patients (85%), re-SLN biopsy was performed for local or regional recurrence after mastectomy. Re-SLN biopsy was successful in 13 of 20 patients (65%) after previous mastectomy. Of the 13 patients, 2 had positive re-SLN, and completion axillary dissection was performed, with 1 having additional positive nodes. In the 11 patients with negative re-SLN, 2 patients underwent completion axillary dissection demonstrating additional negative nodes. One patient with a negative re-SLN experienced chest wall recurrence combined with axillary recurrence 11 months after re-SLN biopsy. All others remained free of local or axillary recurrence. Re-SLN biopsy was unsuccessful in 7 of 20 patients (35%). In three of seven patients, axillary dissection was performed, yielding positive nodes in two of the three. The remaining four of seven patients all had previous modified radical mastectomy, so underwent no additional axillary surgery. In this small series, re-SLN was successful after previous mastectomy, and this procedure may play some role when axillary staging is warranted after mastectomy.

  9. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  10. Virtual Estimator for Piecewise Linear Systems Based on Observability Analysis

    Science.gov (United States)

    Morales-Morales, Cornelio; Adam-Medina, Manuel; Cervantes, Ilse; Vela-Valdés and, Luis G.; García Beltrán, Carlos Daniel

    2013-01-01

    This article proposes a virtual sensor for piecewise linear systems based on observability analysis that is in function of a commutation law related with the system's outpu. This virtual sensor is also known as a state estimator. Besides, it presents a detector of active mode when the commutation sequences of each linear subsystem are arbitrary and unknown. For the previous, this article proposes a set of virtual estimators that discern the commutation paths of the system and allow estimating their output. In this work a methodology in order to test the observability for piecewise linear systems with discrete time is proposed. An academic example is presented to show the obtained results. PMID:23447007

  11. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  12. Supervised Sequence Labelling with Recurrent Neural Networks

    CERN Document Server

    Graves, Alex

    2012-01-01

    Supervised sequence labelling is a vital area of machine learning, encompassing tasks such as speech, handwriting and gesture recognition, protein secondary structure prediction and part-of-speech tagging. Recurrent neural networks are powerful sequence learning tools—robust to input noise and distortion, able to exploit long-range contextual information—that would seem ideally suited to such problems. However their role in large-scale sequence labelling systems has so far been auxiliary.    The goal of this book is a complete framework for classifying and transcribing sequential data with recurrent neural networks only. Three main innovations are introduced in order to realise this goal. Firstly, the connectionist temporal classification output layer allows the framework to be trained with unsegmented target sequences, such as phoneme-level speech transcriptions; this is in contrast to previous connectionist approaches, which were dependent on error-prone prior segmentation. Secondly, multidimensional...

  13. Identification and functional characterization of a novel bipartite nuclear localization sequence in ARID1A

    Energy Technology Data Exchange (ETDEWEB)

    Bateman, Nicholas W. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD (United States); Shoji, Yutaka [Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids 49503, MI (United States); Conrads, Kelly A.; Stroop, Kevin D. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); Hamilton, Chad A. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD (United States); Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, 8901 Wisconsin Ave, MD, Bethesda, 20889 (United States); Department of Obstetrics and Gynecology, Uniformed Services University of the Health Sciences, Bethesda 20814, MD (United States); Darcy, Kathleen M. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD (United States); Maxwell, George L. [Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, VA 22042 (United States); Risinger, John I. [Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids 49503, MI (United States); and others

    2016-01-01

    AT-rich interactive domain-containing protein 1A (ARID1A) is a recently identified nuclear tumor suppressor frequently altered in solid tumor malignancies. We have identified a bipartite-like nuclear localization sequence (NLS) that contributes to nuclear import of ARID1A not previously described. We functionally confirm activity using GFP constructs fused with wild-type or mutant NLS sequences. We further show that cyto-nuclear localized, bipartite NLS mutant ARID1A exhibits greater stability than nuclear-localized, wild-type ARID1A. Identification of this undescribed functional NLS within ARID1A contributes vital insights to rationalize the impact of ARID1A missense mutations observed in patient tumors. - Highlights: • We have identified a bipartite nuclear localization sequence (NLS) in ARID1A. • Confirmation of the NLS was performed using GFP constructs. • NLS mutant ARID1A exhibits greater stability than wild-type ARID1A.

  14. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  15. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  16. Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica

    Science.gov (United States)

    2011-01-01

    Background Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these cannot easily explain, however, how the diverse mitotypes evolved within each genus or species. We analyzed the evolutionary relationships of Brassica mitotypes by sequencing. Results We sequenced the mitotypes of cam (Brassica rapa), ole (B. oleracea), jun (B. juncea), and car (B. carinata) and analyzed them together with two previously sequenced mitotypes of B. napus (pol and nap). The sizes of whole single circular genomes of cam, jun, ole, and car are 219,747 bp, 219,766 bp, 360,271 bp, and 232,241 bp, respectively. The mitochondrial genome of ole is largest as a resulting of the duplication of a 141.8 kb segment. The jun mitotype is the result of an inherited cam mitotype, and pol is also derived from the cam mitotype with evolutionary modifications. Genes with known functions are conserved in all mitotypes, but clear variation in open reading frames (ORFs) with unknown functions among the six mitotypes was observed. Sequence relationship analysis showed that there has been genome compaction and inheritance in the course of Brassica mitotype evolution. Conclusions We have sequenced four Brassica mitotypes, compared six Brassica mitotypes and suggested a mechanism for mitochondrial genome formation in Brassica, including evolutionary events such as inheritance, duplication, rearrangement, genome compaction, and mutation. PMID:21988783

  17. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae.

    Directory of Open Access Journals (Sweden)

    Isabel A S Bonatelli

    Full Text Available Microsatellite markers (also known as SSRs, Simple Sequence Repeats are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

  18. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).

    Science.gov (United States)

    Bonatelli, Isabel A S; Carstens, Bryan C; Moraes, Evandro M

    2015-01-01

    Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

  19. Bm86 midgut protein sequence variation in South Texas cattle fever ticks

    Directory of Open Access Journals (Sweden)

    Kammlah Diane M

    2010-11-01

    Full Text Available Abstract Background Cattle fever ticks, Rhipicephalus (Boophilus microplus and R. (B. annulatus, vector bovine and equine babesiosis, and have significantly expanded beyond the permanent quarantine zone established in South Texas. Currently, there are no vaccines approved for use within the United States for controlling these vectors. Vaccines developed in Australia and Cuba based on the midgut antigen Bm86 have variable efficacy against cattle fever ticks. A possible explanation for this variation in vaccine efficacy is amino acid sequence divergence between the recombinant Bm86 vaccine component and native Bm86 expressed in ticks from different geographical regions of the world. Results There was 91.8% amino acid sequence identity in Bm86 among R. microplus and R. annulatus sequenced from South Texas infestations. When South Texas isolates were compared to the Australian Yeerongpilly and Cuban Camcord vaccine strains, there was 89.8% and 90.0% identity, respectively. Most of the sequence divergence was focused in one region of the protein, amino acids 206-298. Hydrophilicity profiles revealed that two short regions of Bm86 (amino acids 206-210 and 560-570 appear to be more hydrophilic in South Texas isolates compared to vaccine strains. Only one amino acid difference was found between South Texas and vaccine strains within two previously described B-cell epitopes. A total of 4 amino acid differences were observed within three peptides previously shown to induce protective immune responses in cattle. Conclusions Sequence differences between South Texas isolates and Yeerongpilly and Camcord strains are spread throughout the entire Bm86 sequence, suggesting that geographic variation does exist. Differences within previously described B-cell epitopes between South Texas isolates and vaccine strains are minimal; however, short regions of hydrophilic amino acids found unique to South Texas isolates suggest that additional unique surface exposed

  20. Polymorphism Sequence - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us JSNP Polymorphism Sequence Data detail Data name Polymorphism Sequence DOI 10.18908/lsdba.nb...dc00114-001 Description of data contents Information on polymorphisms (SNPs and insertions/deletions) and th...se Name database name JSNP_SNP: single nucleotide polymorphism JSNP_InsDel_IND: insertion/deletion JSNP_InsD...ved allele observed 3' Flanking Sequence 3' flanking sequence Offset in Flanking Sequence position of the polymorphism...uence Accession No. accession No. of the sequence for polymorphism screening Offset in Record position of the polymorphism

  1. [Fatal amnioinfusion with previous choriocarcinoma in a parturient woman].

    Science.gov (United States)

    Hrgović, Z; Bukovic, D; Mrcela, M; Hrgović, I; Siebzehnrübl, E; Karelovic, D

    2004-04-01

    The case of 36-year-old tercipare is described who developed choriocharcinoma in a previous pregnancy. During the first term labour the patient developed cardiac arrest, so reanimation and sectio cesarea was performed. A male new-born was delivered in good condition, but even after intensive therapy and reanimation occurred death of parturient woman with picture of disseminate intravascular coagulopathia (DIK). On autopsy and on histology there was no sign of malignant disease, so it was not possible to connect previous choricarcinoma with amniotic fluid embolism. Maybe was place of choriocarcinoma "locus minoris resistentiae" which later resulted with failure in placentation what was hard to prove. On autopsy we found embolia of lung with a microthrombosis of terminal circulation with punctiformis bleeding in mucous, what stands for DIK.

  2. Challenging previous conceptions of vegetarianism and eating disorders.

    Science.gov (United States)

    Fisak, B; Peterson, R D; Tantleff-Dunn, S; Molnar, J M

    2006-12-01

    The purpose of this study was to replicate and expand upon previous research that has examined the potential association between vegetarianism and disordered eating. Limitations of previous research studies are addressed, including possible low reliability of measures of eating pathology within vegetarian samples, use of only a few dietary restraint measures, and a paucity of research examining potential differences in body image and food choice motives of vegetarians versus nonvegetarians. Two hundred and fifty-six college students completed a number of measures of eating pathology and body image, and a food choice motives questionnaire. Interestingly, no significant differences were found between vegetarians and nonvegetarians in measures of eating pathology or body image. However, significant differences in food choice motives were found. Implications for both researchers and clinicians are discussed.

  3. Previously unreported abnormalities in Wolfram Syndrome Type 2.

    Science.gov (United States)

    Akturk, Halis Kaan; Yasa, Seda

    2017-01-01

    Wolfram syndrome (WFS) is a rare autosomal recessive disease with non-autoimmune childhood onset insulin dependent diabetes and optic atrophy. WFS type 2 (WFS2) differs from WFS type 1 (WFS1) with upper intestinal ulcers, bleeding tendency and the lack ofdiabetes insipidus. Li-fespan is short due to related comorbidities. Only a few familieshave been reported with this syndrome with the CISD2 mutation. Here we report two siblings with a clinical diagnosis of WFS2, previously misdiagnosed with type 1 diabetes mellitus and diabetic retinopathy-related blindness. We report possible additional clinical and laboratory findings that have not been pre-viously reported, such as asymptomatic hypoparathyroidism, osteomalacia, growth hormone (GH) deficiency and hepatomegaly. Even though not a requirement for the diagnosis of WFS2 currently, our case series confirm hypogonadotropic hypogonadism to be also a feature of this syndrome, as reported before. © Polish Society for Pediatric Endocrinology and Diabetology.

  4. Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas.

    Directory of Open Access Journals (Sweden)

    Christopher DeBoever

    Full Text Available Primary central nervous system lymphomas (PCNSL have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV, JC polyomavirus (JCV, and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples.

  5. A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences.

    Science.gov (United States)

    Groussin, M; Boussau, B; Gouy, M

    2013-07-01

    Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.

  6. Previous climatic alterations are caused by the sun

    International Nuclear Information System (INIS)

    Groenaas, Sigbjoern

    2003-01-01

    The article surveys the scientific results of previous research into the contribution of the sun to climatic alterations. The author concludes that there is evidence of eight cold periods after the last ice age and that the alterations largely were due to climate effects from the sun. However, these effects are only causing a fraction of the registered global warming. It is assumed that the human activities are contributing to the rest of the greenhouse effect

  7. Influence of previous knowledge in Torrance tests of creative thinking

    OpenAIRE

    Aranguren, María; Consejo Nacional de Investigaciones Científicas y Técnicas CONICET

    2015-01-01

    The aim of this work is to analyze the influence of study field, expertise and recreational activities participation in Torrance Tests of Creative Thinking (TTCT, 1974) performance. Several hypotheses were postulated to explore the possible effects of previous knowledge in TTCT verbal and TTCT figural university students’ outcomes. Participants in this study included 418 students from five study fields: Psychology;Philosophy and Literature, Music; Engineering; and Journalism and Advertisin...

  8. In situ hybridization of bat chromosomes with human (TTAGGGn probe, after previous digestion with Alu I

    Directory of Open Access Journals (Sweden)

    Karina de Cassia Faria

    2002-01-01

    Full Text Available The purpose of this work was to verify the ability of the enzyme Alu I to cleave and/or remove satellite DNA sequences from heterochromatic regions in chromosomes of bats, by identifying the occurrence of modifications in the pattern of fluorescence in situ hybridization with telomeric DNA. The localization and fluorescence intensity of the telomeric DNA sites of the Alu-digested and undigested chromosomes of species Eumops glaucinus, Carollia perspicillata, and Platyrrhinus lineatus were analyzed. Telomeric sequences were detected at the termini of chromosomes of all three species, although, in C. perspicillata, the signals were very faint or absent in most chromosomes. This finding was interpreted as being due to a reduced number of copies of the telomeric repeat, resulting from extensive telomeric association and/or rearrangements undergone by the chromosomes of Carollia. Fluorescent signals were also observed in centromeric and pericentromeric regions in several two-arm chromosomes of E. glaucinus and C. perspicillata. In E. glaucinus and P. lineatus, some interstitial and terminal telomeric sites were observed to be in association with regions of constitutive heterochromatin and ribosomal DNA (NORs. After digestion, these telomeric sites showed a significant decrease in signal intensity, indicating that enzyme Alu I cleaves and/or removes part of the satellite DNA present in these regions. These results suggest that the telomeric sequence is a component of the heterochromatin, and that the C-band- positive regions of bat chromosomes have a different DNA composition.

  9. Analysis of previous screening examinations for patients with breast cancer

    International Nuclear Information System (INIS)

    Lee, Eun Hye; Cha, Joo Hee; Han, Dae Hee; Choi, Young Ho; Hwang, Ki Tae; Ryu, Dae Sik; Kwak, Jin Ho; Moon, Woo Kyung

    2007-01-01

    We wanted to improve the quality of subsequent screening by reviewing the previous screening of breast cancer patients. Twenty-four breast cancer patients who underwent previous screening were enrolled. All 24 took mammograms and 15 patients also took sonograms. We reviewed the screening retrospectively according to the BI-RADS criteria and we categorized the results into false negative, true negative, true positive and occult cancers. We also categorized the causes of false negative cancers into misperception, misinterpretation and technical factors and then we analyzed the attributing factors. Review of the previous screening revealed 66.7% (16/24) false negative, 25.0% (6/24) true negative, and 8.3% (2/24) true positive cancers. False negative cancers were caused by the mammogram in 56.3% (9/16) and by the sonogram in 43.7% (7/16). For the false negative cases, all of misperception were related with mammograms and this was attributed to dense breast, a lesion located at the edge of glandular tissue or the image, and findings seen on one view only. Almost all misinterpretations were related with sonograms and attributed to loose application of the final assessment. To improve the quality of breast screening, it is essential to overcome the main causes of false negative examinations, including misperception and misinterpretation. We need systematic education and strict application of final assessment categories of BI-RADS. For effective communication among physicians, it is also necessary to properly educate them about BI-RADS

  10. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  11. WildSpan: mining structured motifs from protein sequences

    Directory of Open Access Journals (Sweden)

    Chen Chien-Yu

    2011-03-01

    Full Text Available Abstract Background Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions that incorporates several pruning strategies to largely reduce the mining cost. Results WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode

  12. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  13. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  14. The 2016 Kumamoto earthquake sequence.

    Science.gov (United States)

    Kato, Aitaro; Nakamura, Kouji; Hiyama, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An M j 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an M j 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest.

  15. The 2016 Kumamoto earthquake sequence

    Science.gov (United States)

    KATO, Aitaro; NAKAMURA, Kouji; HIYAMA, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An Mj 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an Mj 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest. PMID:27725474

  16. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  17. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  18. Ichnology applied to sequence stratigraphic analysis of Siluro-Devonian mud-dominated shelf deposits, Paraná Basin, Brazil

    Science.gov (United States)

    Sedorko, Daniel; Netto, Renata G.; Savrda, Charles E.

    2018-04-01

    Previous studies of the Paraná Supersequence (Furnas and Ponta Grossa formations) of the Paraná Basin in southern Brazil have yielded disparate sequence stratigraphic interpretations. An integrated sedimentological, paleontological, and ichnological model was created to establish a refined sequence stratigraphic framework for this succession, focusing on the Ponta Grossa Formation. Twenty-nine ichnotaxa are recognized in the Ponta Grossa Formation, recurring assemblages of which define five trace fossil suites that represent various expressions of the Skolithos, Glossifungites and Cruziana ichnofacies. Physical sedimentologic characteristics and associated softground ichnofacies provide the basis for recognizing seven facies that reflect a passive relationship to bathymetric gradients from shallow marine (shoreface) to offshore deposition. The vertical distribution of facies provides the basis for dividing the Ponta Grossa Formation into three major (3rd-order) depositional sequences- Siluro-Devonian and Devonian I and II-each containing a record of three to seven higher-order relative sea-level cycles. Major sequence boundaries, commonly coinciding with hiatuses recognized from previously published biostratigraphic data, are locally marked by firmground Glossifungites Ichnofacies associated with submarine erosion. Maximum transgressive horizons are prominently marked by unbioturbated or weakly bioturbated black shales. By integrating observations of the Ponta Grossa Formation with those recently made on the underlying marginal- to shallow-marine Furnas Formation, the entire Paraná Supersequence can be divided into four disconformity-bound sequences: a Lower Silurian (Llandovery-Wenlock) sequence, corresponding to lower and middle units of the Furnas; a Siluro-Devonian sequence (?Pridoli-Early Emsian), and Devonian sequences I (Late Emsian-Late Eifelian) and II (Late Eifelian-Early Givetian). Stratigraphic positions of sequence boundaries generally coincide with

  19. Microbial species delineation using whole genome sequences.

    Science.gov (United States)

    Varghese, Neha J; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T; Mavrommatis, Kostas; Kyrpides, Nikos C; Pati, Amrita

    2015-08-18

    Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Moyamoya disease in a child with previous acute necrotizing encephalopathy

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Taik-Kun; Cha, Sang Hoon; Chung, Kyoo Byung; Kim, Jung Hyuck; Kim, Baek Hyun; Chung, Hwan Hoon [Department of Diagnostic Radiology, Korea University College of Medicine, Ansan Hospital, 516 Kojan-Dong, Ansan City, Kyungki-Do 425-020 (Korea); Eun, Baik-Lin [Department of Pediatrics, Korea University College of Medicine, Seoul (Korea)

    2003-09-01

    A previously healthy 24-day-old boy presented with a 2-day history of fever and had a convulsion on the day of admission. MRI showed abnormal signal in the thalami, caudate nuclei and central white matter. Acute necrotising encephalopathy was diagnosed, other causes having been excluded after biochemical and haematological analysis of blood, urine and CSF. He recovered, but with spastic quadriparesis. At the age of 28 months, he suffered sudden deterioration of consciousness and motor weakness of his right limbs. MRI was consistent with an acute cerebrovascular accident. Angiography showed bilateral middle cerebral artery stenosis or frank occlusion with numerous lenticulostriate collateral vessels consistent with moyamoya disease. (orig.)

  1. MCNP HPGe detector benchmark with previously validated Cyltran model.

    Science.gov (United States)

    Hau, I D; Russ, W R; Bronson, F

    2009-05-01

    An exact copy of the detector model generated for Cyltran was reproduced as an MCNP input file and the detection efficiency was calculated similarly with the methodology used in previous experimental measurements and simulation of a 280 cm(3) HPGe detector. Below 1000 keV the MCNP data correlated to the Cyltran results within 0.5% while above this energy the difference between MCNP and Cyltran increased to about 6% at 4800 keV, depending on the electron cut-off energy.

  2. HEART TRANSPLANTATION IN PATIENTS WITH PREVIOUS OPEN HEART SURGERY

    Directory of Open Access Journals (Sweden)

    R. Sh. Saitgareev

    2016-01-01

    Full Text Available Heart Transplantation (HTx to date remains the most effective and radical method of treatment of patients with end-stage heart failure. The defi cit of donor hearts is forcing to resort increasingly to the use of different longterm mechanical circulatory support systems, including as a «bridge» to the follow-up HTx. According to the ISHLT Registry the number of recipients underwent cardiopulmonary bypass surgery increased from 40% in the period from 2004 to 2008 to 49.6% for the period from 2009 to 2015. HTx performed in repeated patients, on the one hand, involves considerable technical diffi culties and high risks; on the other hand, there is often no alternative medical intervention to HTx, and if not dictated by absolute contradictions the denial of the surgery is equivalent to 100% mortality. This review summarizes the results of a number of published studies aimed at understanding the immediate and late results of HTx in patients, previously underwent open heart surgery. The effect of resternotomy during HTx and that of the specifi c features associated with its implementation in recipients previously operated on open heart, and its effects on the immediate and long-term survival were considered in this review. Results of studies analyzing the risk factors for perioperative complications in repeated recipients were also demonstrated. Separately, HTx risks after implantation of prolonged mechanical circulatory support systems were examined. The literature does not allow to clearly defi ning the impact factor of earlier performed open heart surgery on the course of perioperative period and on the prognosis of survival in recipients who underwent HTx. On the other hand, subject to the regular fl ow of HTx and the perioperative period the risks in this clinical situation are justifi ed as a long-term prognosis of recipients previously conducted open heart surgery and are comparable to those of patients who underwent primary HTx. Studies

  3. Incidence of Acneform Lesions in Previously Chemically Damaged Persons-2004

    Directory of Open Access Journals (Sweden)

    N Dabiri

    2008-04-01

    Full Text Available ABSTRACT: Introduction & Objective: Chemical gas weapons especially nitrogen mustard which was used in Iraq-Iran war against Iranian troops have several harmful effects on skin. Some other chemical agents also can cause acne form lesions on skin. The purpose of this study was to compare the incidence of acneform in previously chemically damaged soldiers and non chemically damaged persons. Materials & Methods: In this descriptive and analytical study, 180 chemically damaged soldiers, who have been referred to dermatology clinic between 2000 – 2004, and forty non-chemically damaged people, were chosen randomly and examined for acneform lesions. SPSS software was used for statistic analysis of the data. Results: The mean age of the experimental group was 37.5 ± 5.2 and that of the control group was 38.7 ± 5.9 years. The mean percentage of chemical damage in cases was 31 percent and the time after the chemical damage was 15.2 ± 1.1 years. Ninety seven cases (53.9 percent of the subjects and 19 people (47.5 percent of the control group had some degree of acne. No significant correlation was found in incidence, degree of lesions, site of lesions and age of subjects between two groups. No significant correlation was noted between percentage of chemical damage and incidence and degree of lesions in case group. Conclusion: Incidence of acneform lesions among previously chemically injured peoples was not higher than the normal cases.

  4. Relationship of deer and moose populations to previous winters' snow

    Science.gov (United States)

    Mech, L.D.; McRoberts, R.E.; Peterson, R.O.; Page, R.E.

    1987-01-01

    (1) Linear regression was used to relate snow accumulation during single and consecutive winters with white-tailed deer (Odocoileus virginianus) fawn:doe ratios, mosse (Alces alces) twinning rates and calf:cow ratios, and annual changes in deer and moose populations. Significant relationships were found between snow accumulation during individual winters and these dependent variables during the following year. However, the strongest relationships were between the dependent variables and the sums of the snow accumulations over the previous three winters. The percentage of the variability explained was 36 to 51. (2) Significant relationships were also found between winter vulnerability of moose calves and the sum of the snow accumulations in the current, and up to seven previous, winters, with about 49% of the variability explained. (3) No relationship was found between wolf numbers and the above dependent variables. (4) These relationships imply that winter influences on maternal nutrition can accumulate for several years and that this cumulative effect strongly determines fecundity and/or calf and fawn survivability. Although wolf (Canis lupus L.) predation is the main direct mortality agent on fawns and calves, wolf density itself appears to be secondary to winter weather in influencing the deer and moose populations.

  5. [ANTITHROMBOTIC MEDICATION IN PREGNANT WOMEN WITH PREVIOUS INTRAUTERINE GROWTH RESTRICTION].

    Science.gov (United States)

    Neykova, K; Dimitrova, V; Dimitrov, R; Vakrilova, L

    2016-01-01

    To analyze pregnancy outcome in patients who were on antithrombotic medication (AM) because of previous pregnancy with fetal intrauterine growth restriction (IUGR). The studied group (SG) included 21 pregnancies in 15 women with history of previous IUGR. The patients were on low dose aspirin (LDA) and/or low molecular weight heparin (LMWH). Pregnancy outcome was compared to the one in two more groups: 1) primary group (PG) including the previous 15 pregnancies with IUGR of the same women; 2) control group (CG) including 45 pregnancies of women matched for parity with the ones in the SG, with no history of IUGR and without medication. The SG, PG and CG were compared for the following: mean gestational age (g.a.) at birth, mean birth weight (BW), proportion of cases with early preeclampsia (PE), IUGR (total, moderate, and severe), intrauterine fetal death (IUFD), neonatal death (NND), admission to NICU, cesarean section (CS) because of chronic or acute fetal distress (FD) related to IUGR, PE or placental abruption. Student's t-test was applied to assess differences between the groups. P values < 0.05 were considered statistically significant. The differences between the SG and the PG regarding mean g. a. at delivery (33.7 and 29.8 w.g. respectively) and the proportion of babies admitted to NICU (66.7% vs. 71.4%) were not statistically significant. The mean BW in the SG (2114,7 g.) was significantly higher than in the PG (1090.8 g.). In the SG compared with the PG there were significantly less cases of IUFD (14.3% and 53.3% respectively), early PE (9.5% vs. 46.7%) moderate and severe IUGR (10.5% and 36.8% vs. 41.7% and 58.3%). Neonatal mortality in the SG (5.6%) was significantly lower than in the PG (57.1%), The proportion of CS for FD was not significantly different--53.3% in the SG and 57.1% in the PG. On the other hand, comparison between the SG and the CG demonstrated significantly lower g.a. at delivery in the SG (33.7 vs. 38 w.g.) an lower BW (2114 vs. 3094 g

  6. The Processing on Different Types of English Formulaic Sequences

    Science.gov (United States)

    Qian, Li

    2015-01-01

    Formulaic sequences are found to be processed faster than their matched novel phrases in previous studies. Given the variety of formulaic types, few studies have compared processing on different types of formulaic sequences. The present study explored the processing among idioms, speech formulae and written formulae. It has been found that in…

  7. Development of simple sequence repeat (SSR) markers that are ...

    African Journals Online (AJOL)

    Simple sequence repeats (SSRs) markers were developed through data mining of 3,803 expressed sequence tags (ESTs) previously published. A total of 144 di- to penta-type SSRs were identified and they were screened for polymorphism between two turnip cultivars, 'Tsuda' and 'Yurugi Akamaru'. Out of 90 EST-SSRs for ...

  8. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

    DEFF Research Database (Denmark)

    Carlton, Jane M.; Hirt, Robert P.; Silva, Joana C.

    2007-01-01

    We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion...... environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria....

  9. Complete genome sequence of a novel pestivirus from sheep.

    Science.gov (United States)

    Becher, Paul; Schmeiser, Stefanie; Oguzoglu, Tuba Cigdem; Postel, Alexander

    2012-10-01

    We report here the complete genome sequence of pestivirus strain Aydin/04-TR, which is the prototype of a group of similar viruses currently present in sheep and goats in Turkey. Sequence data from this virus showed that it clusters separately from the established and previously proposed tentative pestivirus species.

  10. Complete Genome Sequence of a Novel Pestivirus from Sheep

    OpenAIRE

    Becher, Paul; Schmeiser, Stefanie; Oguzoglu, Tuba Cigdem; Postel, Alexander

    2012-01-01

    We report here the complete genome sequence of pestivirus strain Aydin/04-TR, which is the prototype of a group of similar viruses currently present in sheep and goats in Turkey. Sequence data from this virus showed that it clusters separately from the established and previously proposed tentative pestivirus species.

  11. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  12. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  13. Deepwater Gulf of Mexico more profitable than previously thought

    International Nuclear Information System (INIS)

    Craig, M.J.K.; Hyde, S.T.

    1997-01-01

    Economic evaluations and recent experience show that the deepwater Gulf of Mexico (GOM) is much more profitable than previously thought. Four factors contributing to the changed viewpoint are: First, deepwater reservoirs have proved to have excellent productive capacity, distribution, and continuity when compared to correlative-age shelf deltaic sands. Second, improved technologies and lower perceived risks have lowered the cost of floating production systems (FPSs). Third, projects now get on-line quicker. Fourth, a collection of other important factors are: Reduced geologic risk and associated high success rates for deepwater GOM wells due primarily to improved seismic imaging and processing tools (3D, AVO, etc.); absence of any political risk in the deepwater GOM (common overseas, and very significant in some international areas); and positive impact of deepwater federal royalty relief. This article uses hypothetical reserve distributions and price forecasts to illustrate indicative economics of deepwater prospects. Economics of Shell Oil Co.'s three deepwater projects are also discussed

  14. Corneal perforation after conductive keratoplasty with previous refractive surgery.

    Science.gov (United States)

    Kymionis, George D; Titze, Patrik; Markomanolakis, Marinos M; Aslanides, Ioannis M; Pallikaris, Ioannis G

    2003-12-01

    A 56-year-old woman had conductive keratoplasty (CK) for residual hyperopia and astigmatism. Three years before the procedure, the patient had arcuate keratotomy, followed by laser in situ keratomileusis 2 years later for high astigmatism correction in both eyes. During CK, a corneal perforation occurred in the right eye; during the postoperative examination, an iris perforation and anterior subcapsule opacification were seen beneath the perforation site. The perforation was managed with a bandage contact lens and an antibiotic-steroid ointment; it had a negative Seidel sign by the third day. The surgery in the left eye was uneventful. Three months after the procedure, the uncorrected visual acuity was 20/32 and the best corrected visual acuity 20/20 in both eyes with a significant improvement in corneal topography. Care must be taken to prevent CK-treated spots from coinciding with areas in the corneal stroma that might have been altered by previous refractive procedures.

  15. Interference from previous distraction disrupts older adults' memory.

    Science.gov (United States)

    Biss, Renée K; Campbell, Karen L; Hasher, Lynn

    2013-07-01

    Previously relevant information can disrupt the ability of older adults to remember new information. Here, the researchers examined whether prior irrelevant information, or distraction, can also interfere with older adults' memory for new information. Younger and older adults first completed a 1-back task on pictures that were superimposed with distracting words. After a delay, participants learned picture-word paired associates and memory was tested using picture-cued recall. In 1 condition (high interference), some pairs included pictures from the 1-back task now paired with new words. In a low-interference condition, the transfer list used all new items. Older adults had substantially lower cued-recall performance in the high- compared with the low-interference condition. In contrast, younger adults' performance did not vary across conditions. These findings suggest that even never-relevant information from the past can disrupt older adults' memory for new associations.

  16. The long-term consequences of previous hyperthyroidism

    DEFF Research Database (Denmark)

    Hjelm Brandt Kristensen, Frans

    2015-01-01

    Thyroid hormones affect every cell in the human body, and the cardiovascular changes associated with increased levels of thyroid hormones are especially well described. As an example, short-term hyperthyroidism has positive chronotropic and inotropic effects on the heart, leading to a hyperdynamic...... with CVD, LD and DM both before and after the diagnosis of hyperthyroidism. Although the design used does not allow a stringent distinction between cause and effect, the findings indicate a possible direct association between hyperthyroidism and these morbidities, or vice versa....... vascular state. While it is biologically plausible that these changes may induce long-term consequences, the insight into morbidity as well as mortality in patients with previous hyperthyroidism is limited. The reasons for this are a combination of inadequately powered studies, varying definitions...

  17. Typing DNA profiles from previously enhanced fingerprints using direct PCR.

    Science.gov (United States)

    Templeton, Jennifer E L; Taylor, Duncan; Handt, Oliva; Linacre, Adrian

    2017-07-01

    Fingermarks are a source of human identification both through the ridge patterns and DNA profiling. Typing nuclear STR DNA markers from previously enhanced fingermarks provides an alternative method of utilising the limited fingermark deposit that can be left behind during a criminal act. Dusting with fingerprint powders is a standard method used in classical fingermark enhancement and can affect DNA data. The ability to generate informative DNA profiles from powdered fingerprints using direct PCR swabs was investigated. Direct PCR was used as the opportunity to generate usable DNA profiles after performing any of the standard DNA extraction processes is minimal. Omitting the extraction step will, for many samples, be the key to success if there is limited sample DNA. DNA profiles were generated by direct PCR from 160 fingermarks after treatment with one of the following dactyloscopic fingerprint powders: white hadonite; silver aluminium; HiFi Volcano silk black; or black magnetic fingerprint powder. This was achieved by a combination of an optimised double-swabbing technique and swab media, omission of the extraction step to minimise loss of critical low-template DNA, and additional AmpliTaq Gold ® DNA polymerase to boost the PCR. Ninety eight out of 160 samples (61%) were considered 'up-loadable' to the Australian National Criminal Investigation DNA Database (NCIDD). The method described required a minimum of working steps, equipment and reagents, and was completed within 4h. Direct PCR allows the generation of DNA profiles from enhanced prints without the need to increase PCR cycle numbers beyond manufacturer's recommendations. Particular emphasis was placed on preventing contamination by applying strict protocols and avoiding the use of previously used fingerprint brushes. Based on this extensive survey, the data provided indicate minimal effects of any of these four powders on the chance of obtaining DNA profiles from enhanced fingermarks. Copyright © 2017

  18. Approaches for in silico finishing of microbial genome sequences

    Directory of Open Access Journals (Sweden)

    Frederico Schmitt Kremer

    Full Text Available Abstract The introduction of next-generation sequencing (NGS had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases tools that are available to facilitate genome finishing.

  19. Approaches for in silico finishing of microbial genome sequences.

    Science.gov (United States)

    Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

    The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.

  20. In vivo dentate nucleus MRI relaxometry correlates with previous administration of Gadolinium-based contrast agents

    Energy Technology Data Exchange (ETDEWEB)

    Tedeschi, Enrico; Canna, Antonietta; Cocozza, Sirio; Russo, Carmela; Angelini, Valentina; Brunetti, Arturo [University ' ' Federico II' ' , Neuroradiology, Department of Advanced Biomedical Sciences, Naples (Italy); Palma, Giuseppe; Quarantelli, Mario [National Research Council, Institute of Biostructure and Bioimaging, Naples (Italy); Borrelli, Pasquale; Salvatore, Marco [IRCCS SDN, Naples (Italy); Lanzillo, Roberta; Postiglione, Emanuela; Morra, Vincenzo Brescia [University ' ' Federico II' ' , Department of Neurosciences, Reproductive and Odontostomatological Sciences, Naples (Italy)

    2016-12-15

    To evaluate changes in T1 and T2* relaxometry of dentate nuclei (DN) with respect to the number of previous administrations of Gadolinium-based contrast agents (GBCA). In 74 relapsing-remitting multiple sclerosis (RR-MS) patients with variable disease duration (9.8±6.8 years) and severity (Expanded Disability Status Scale scores:3.1±0.9), the DN R1 (1/T1) and R2* (1/T2*) relaxation rates were measured using two unenhanced 3D Dual-Echo spoiled Gradient-Echo sequences with different flip angles. Correlations of the number of previous GBCA administrations with DN R1 and R2* relaxation rates were tested, including gender and age effect, in a multivariate regression analysis. The DN R1 (normalized by brainstem) significantly correlated with the number of GBCA administrations (p<0.001), maintaining the same significance even when including MS-related factors. Instead, the DN R2* values correlated only with age (p=0.003), and not with GBCA administrations (p=0.67). In a subgroup of 35 patients for whom the administered GBCA subtype was known, the effect of GBCA on DN R1 appeared mainly related to linear GBCA. In RR-MS patients, the number of previous GBCA administrations correlates with R1 relaxation rates of DN, while R2* values remain unaffected, suggesting that T1-shortening in these patients is related to the amount of Gadolinium given. (orig.)

  1. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  2. A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius.

    Directory of Open Access Journals (Sweden)

    Ceiridwen J Edwards

    Full Text Available BACKGROUND: The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY: DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer. In total, 289.9 megabases (22.48% of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS: For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously

  3. Seqenv: linking sequences to environments through text mining.

    Science.gov (United States)

    Sinclair, Lucas; Ijaz, Umer Z; Jensen, Lars Juhl; Coolen, Marco J L; Gubry-Rangin, Cecile; Chroňáková, Alica; Oulas, Anastasis; Pavloudi, Christina; Schnetzer, Julia; Weimann, Aaron; Ijaz, Ali; Eiler, Alexander; Quince, Christopher; Pafilis, Evangelos

    2016-01-01

    Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the "nt" nucleotide database provided by NCBI and, out of every hit, extracts-if it is available-the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.

  4. Seqenv: linking sequences to environments through text mining

    Directory of Open Access Journals (Sweden)

    Lucas Sinclair

    2016-12-01

    Full Text Available Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.

  5. Upon Further Review: V. An Examination of Previous Lightcurve Analysis from the Palmer Divide Observatory

    Science.gov (United States)

    Warner, Brian D.

    2011-01-01

    Updated results are given for nine asteroids previously reported from the Palmer Divide Observatory (PDO). The original images were re-measured to obtain new data sets using the latest version of MPO Canopus photometry software, analysis tools, and revised techniques for linking multiple observing runs covering several days to several weeks. Results that were previously not reported or were moderately different were found for 1659 Punkajarju, 1719 Jens, 1987 Kaplan, 2105 Gudy, 2961 Katsurahama, 3285 Ruth Wolfe, 3447 Burckhalter, 7816 Hanoi, and (34817) 2000 SE116. This is one in a series of papers that will examine results obtained during the initial years of the asteroid lightcurve program at PDO.

  6. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  7. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  8. Lung cancer in Hodgkin's disease: association with previous radiotherapy

    International Nuclear Information System (INIS)

    List, A.F.; Doll, D.C.; Greco, F.A.

    1985-01-01

    Seven cases of lung cancer were observed in patients with Hodgkin's disease (HD) since 1970. The risk ratio for the development of lung cancer among HD patients was 5.6 times that expected in the general population. The pertinent clinical data from these patients are described and compared to 28 additional patients reported from other institutions. Small-cell lung cancer represented the predominant histologic type of lung cancer encountered in both smoking and nonsmoking patients with HD, accounting for 42% of cases overall and greater than 55% of cases reported in reviews of second malignancies. Tobacco use was noted in only 53% of patients. Twenty-eight (94%) of 30 patients developing metachronous lung cancer received supradiaphragmatic irradiation as primary therapy for HD. Nineteen (68%) of these patients received subsequent chemotherapy salvage. The median age at diagnosis of HD and lung cancer was 39 and 45 years, respectively. The interval between diagnosis of HD and metachronous lung cancer averaged seven years but appeared to vary inversely with age. HD patients treated with supradiaphragmatic irradiation or combined modality therapy may be at increased risk for developing lung cancer. The high frequency of in-field malignancies that the authors observed and the prevalence of small-cell lung cancer in both smoking and nonsmoking patients suggests that chest irradiation may influence the development of metachronous lung cancer in these patients. The finding of a mean latent interval in excess of seven years emphasizes the need for close long-term observation

  9. A comparative evaluation of sequence classification programs

    Directory of Open Access Journals (Sweden)

    Bazinet Adam L

    2012-05-01

    Full Text Available Abstract Background A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics. Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis. Results We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known. Conclusions We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.

  10. Detection of M-Sequences from Spike Sequence in Neuronal Networks

    Directory of Open Access Journals (Sweden)

    Yoshi Nishitani

    2012-01-01

    Full Text Available In circuit theory, it is well known that a linear feedback shift register (LFSR circuit generates pseudorandom bit sequences (PRBS, including an M-sequence with the maximum period of length. In this study, we tried to detect M-sequences known as a pseudorandom sequence generated by the LFSR circuit from time series patterns of stimulated action potentials. Stimulated action potentials were recorded from dissociated cultures of hippocampal neurons grown on a multielectrode array. We could find several M-sequences from a 3-stage LFSR circuit (M3. These results show the possibility of assembling LFSR circuits or its equivalent ones in a neuronal network. However, since the M3 pattern was composed of only four spike intervals, the possibility of an accidental detection was not zero. Then, we detected M-sequences from random spike sequences which were not generated from an LFSR circuit and compare the result with the number of M-sequences from the originally observed raster data. As a result, a significant difference was confirmed: a greater number of “0–1” reversed the 3-stage M-sequences occurred than would have accidentally be detected. This result suggests that some LFSR equivalent circuits are assembled in neuronal networks.

  11. Cerebral Metastasis from a Previously Undiagnosed Appendiceal Adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Antonio Biroli

    2012-01-01

    Full Text Available Brain metastases arise in 10%–40% of all cancer patients. Up to one third of the patients do not have previous cancer history. We report a case of a 67-years-old male patient who presented with confusion, tremor, and apraxia. A brain MRI revealed an isolated right temporal lobe lesion. A thorax-abdomen-pelvis CT scan showed no primary lesion. The patient underwent a craniotomy with gross-total resection. Histopathology revealed an intestinal-type adenocarcinoma. A colonoscopy found no primary lesion, but a PET-CT scan showed elevated FDG uptake in the appendiceal nodule. A right hemicolectomy was performed, and the specimen showed a moderately differentiated mucinous appendiceal adenocarcinoma. Whole brain radiotherapy was administrated. A subsequent thorax-abdomen CT scan revealed multiple lung and hepatic metastasis. Seven months later, the patient died of disease progression. In cases of undiagnosed primary lesions, patients present in better general condition, but overall survival does not change. Eventual identification of the primary tumor does not affect survival. PET/CT might be a helpful tool in detecting lesions of the appendiceal region. To the best of our knowledge, such a case was never reported in the literature, and an appendiceal malignancy should be suspected in patients with brain metastasis from an undiagnosed primary tumor.

  12. High-Grade Leiomyosarcoma Arising in a Previously Replanted Limb

    Directory of Open Access Journals (Sweden)

    Tiffany J. Pan

    2015-01-01

    Full Text Available Sarcoma development has been associated with genetics, irradiation, viral infections, and immunodeficiency. Reports of sarcomas arising in the setting of prior trauma, as in burn scars or fracture sites, are rare. We report a case of a leiomyosarcoma arising in an arm that had previously been replanted at the level of the elbow joint following traumatic amputation when the patient was eight years old. He presented twenty-four years later with a 10.8 cm mass in the replanted arm located on the volar forearm. The tumor was completely resected and pathology examination showed a high-grade, subfascial spindle cell sarcoma diagnosed as a grade 3 leiomyosarcoma with stage pT2bNxMx. The patient underwent treatment with brachytherapy, reconstruction with a free flap, and subsequently chemotherapy. To the best of our knowledge, this is the first case report of leiomyosarcoma developing in a replanted extremity. Development of leiomyosarcoma in this case could be related to revascularization, scar formation, or chronic injury after replantation. The patient remains healthy without signs of recurrence at three-year follow-up.

  13. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.

    Directory of Open Access Journals (Sweden)

    Pingzhao Hu

    2009-04-01

    Full Text Available One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans. Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a "systems-wide" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.

  14. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.

    Science.gov (United States)

    Hu, Pingzhao; Janga, Sarath Chandra; Babu, Mohan; Díaz-Mejía, J Javier; Butland, Gareth; Yang, Wenhong; Pogoutse, Oxana; Guo, Xinghua; Phanse, Sadhna; Wong, Peter; Chandran, Shamanta; Christopoulos, Constantine; Nazarians-Armavil, Anaies; Nasseri, Negin Karimi; Musso, Gabriel; Ali, Mehrab; Nazemof, Nazila; Eroukova, Veronika; Golshani, Ashkan; Paccanaro, Alberto; Greenblatt, Jack F; Moreno-Hagelsieb, Gabriel; Emili, Andrew

    2009-04-28

    One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a "systems-wide" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.

  15. Influence of Previous Knowledge in Torrance Tests of Creative Thinking

    Directory of Open Access Journals (Sweden)

    María Aranguren

    2015-07-01

    Full Text Available The aim of this work is to analyze the influence of study field, expertise and recreational activities participation in Torrance Tests of Creative Thinking (TTCT, 1974 performance. Several hypotheses were postulated to explore the possible effects of previous knowledge in TTCT verbal and TTCT figural university students’ outcomes. Participants in this study included 418 students from five study fields: Psychology;Philosophy and Literature, Music; Engineering; and Journalism and Advertising (Communication Sciences. Results found in this research seem to indicate that there in none influence of the study field, expertise and recreational activities participation in neither of the TTCT tests. Instead, the findings seem to suggest some kind of interaction between certain skills needed to succeed in specific studies fields and performance on creativity tests, such as the TTCT. These results imply that TTCT is a useful and valid instrument to measure creativity and that some cognitive process involved in innovative thinking can be promoted using different intervention programs in schools and universities regardless the students study field.

  16. Gastrointestinal tolerability with ibandronate after previous weekly bisphosphonate treatment.

    Science.gov (United States)

    Derman, Richard; Kohles, Joseph D; Babbitt, Ann

    2009-01-01

    Data from two open-label trials (PRIOR and CURRENT) of women with postmenopausal osteoporosis or osteopenia were evaluated to assess whether monthly oral and quarterly intravenous (IV) ibandronate dosing improved self-reported gastrointestinal (GI) tolerability for patients who had previously experienced GI irritation with bisphosphonate (BP) use. In PRIOR, women who had discontinued daily or weekly BP treatment due to GI intolerance received monthly oral or quarterly IV ibandronate for 12 months. The CURRENT subanalysis included women receiving weekly BP treatment who switched to monthly oral ibandronate for six months. GI symptom severity and frequency were assessed using the Osteoporosis Patient Satisfaction Questionnaire. In PRIOR, mean GI tolerability scores increased significantly at month 1 from screening for both treatment groups (oral: 79.3 versus 54.1; IV: 84.4 versus 51.0; p 90% at Month 10). In the CURRENT subanalysis >60% of patients reported improvements in heartburn or acid reflux and >70% indicated improvement in other stomach upset at month 6. Postmenopausal women with GI irritability with daily or weekly BPs experienced improvement in symptoms with extended dosing monthly or quarterly ibandronate compared with baseline.

  17. Pertussis-associated persistent cough in previously vaccinated children.

    Science.gov (United States)

    Principi, Nicola; Litt, David; Terranova, Leonardo; Picca, Marina; Malvaso, Concetta; Vitale, Cettina; Fry, Norman K; Esposito, Susanna

    2017-11-01

    To evaluate the role of Bordetella pertussis infection, 96 otherwise healthy 7- to 17-year-old subjects who were suffering from a cough lasting from 2 to 8 weeks were prospectively recruited. At enrolment, a nasopharyngeal swab and an oral fluid sample were obtained to search for pertussis infection by the detection of B. pertussis DNA and/or an elevated titre of anti-pertussis toxin IgG. Evidence of pertussis infection was found in 18 (18.7 %; 95 % confidence interval, 11.5-28.0) cases. In 15 cases, the disease occurred despite booster administration. In two cases, pertussis was diagnosed less than 2 years after the booster injection, whereas in the other cases it was diagnosed between 2 and 9 years after the booster dose. This study used non-invasive testing to show that pertussis is one of the most important causes of long-lasting cough in school-age subjects. Moreover, the protection offered by acellular pertussis vaccines currently wanes more rapidly than previously thought.

  18. Multispecies Coevolution Particle Swarm Optimization Based on Previous Search History

    Directory of Open Access Journals (Sweden)

    Danping Wang

    2017-01-01

    Full Text Available A hybrid coevolution particle swarm optimization algorithm with dynamic multispecies strategy based on K-means clustering and nonrevisit strategy based on Binary Space Partitioning fitness tree (called MCPSO-PSH is proposed. Previous search history memorized into the Binary Space Partitioning fitness tree can effectively restrain the individuals’ revisit phenomenon. The whole population is partitioned into several subspecies and cooperative coevolution is realized by an information communication mechanism between subspecies, which can enhance the global search ability of particles and avoid premature convergence to local optimum. To demonstrate the power of the method, comparisons between the proposed algorithm and state-of-the-art algorithms are grouped into two categories: 10 basic benchmark functions (10-dimensional and 30-dimensional, 10 CEC2005 benchmark functions (30-dimensional, and a real-world problem (multilevel image segmentation problems. Experimental results show that MCPSO-PSH displays a competitive performance compared to the other swarm-based or evolutionary algorithms in terms of solution accuracy and statistical tests.

  19. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  20. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  1. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  2. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  3. A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants.

    Directory of Open Access Journals (Sweden)

    Wai-Ming Lee

    2007-10-01

    Full Text Available Human rhinoviruses (HRVs are the most prevalent human pathogens, and consist of 101 serotypes that are classified into groups A and B according to sequence variations. HRV infections cause a wide spectrum of clinical outcomes ranging from asymptomatic infection to severe lower respiratory symptoms. Defining the role of specific strains in various HRV illnesses has been difficult because traditional serology, which requires viral culture and neutralization tests using 101 serotype-specific antisera, is insensitive and laborious.To directly type HRVs in nasal secretions of infants with frequent respiratory illnesses, we developed a sensitive molecular typing assay based on phylogenetic comparisons of a 260-bp variable sequence in the 5' noncoding region with homologous sequences of the 101 known serotypes. Nasal samples from 26 infants were first tested with a multiplex PCR assay for respiratory viruses, and HRV was the most common virus found (108 of 181 samples. Typing was completed for 101 samples and 103 HRVs were identified. Surprisingly, 54 (52.4% HRVs did not match any of the known serotypes and had 12-35% nucleotide divergence from the nearest reference HRVs. Of these novel viruses, 9 strains (17 HRVs segregated from HRVA, HRVB and human enterovirus into a distinct genetic group ("C". None of these new strains could be cultured in traditional cell lines.By molecular analysis, over 50% of HRV detected in sick infants were previously unrecognized strains, including 9 strains that may represent a new HRV group. These findings indicate that the number of HRV strains is considerably larger than the 101 serotypes identified with traditional diagnostic techniques, and provide evidence of a new HRV group.

  4. Detection and characterization of Pasteuria 16S rRNA gene sequences from nematodes and soils.

    Science.gov (United States)

    Duan, Y P; Castro, H F; Hewlett, T E; White, J H; Ogram, A V

    2003-01-01

    Various bacterial species in the genus Pasteuria have great potential as biocontrol agents against plant-parasitic nematodes, although study of this important genus is hampered by the current inability to cultivate Pasteuria species outside their host. To aid in the study of this genus, an extensive 16S rRNA gene sequence phylogeny was constructed and this information was used to develop cultivation-independent methods for detection of Pasteuria in soils and nematodes. Thirty new clones of Pasteuria 16S rRNA genes were obtained directly from nematodes and soil samples. These were sequenced and used to construct an extensive phylogeny of this genus. These sequences were divided into two deeply branching clades within the low-G + C, Gram-positive division; some sequences appear to represent novel species within the genus Pasteuria. In addition, a surprising degree of 16S rRNA gene sequence diversity was observed within what had previously been designated a single strain of Pasteuria penetrans (P-20). PCR primers specific to Pasteuria 16S rRNA for detection of Pasteuria in soils were also designed and evaluated. Detection limits for soil DNA were 100-10,000 Pasteuria endospores (g soil)(-1).

  5. Eight previously unidentified mutations found in the OA1 ocular albinism gene

    Directory of Open Access Journals (Sweden)

    Dufier Jean-Louis

    2006-04-01

    Full Text Available Abstract Background Ocular albinism type 1 (OA1 is an X-linked ocular disorder characterized by a severe reduction in visual acuity, nystagmus, hypopigmentation of the retinal pigmented epithelium, foveal hypoplasia, macromelanosomes in pigmented skin and eye cells, and misrouting of the optical tracts. This disease is primarily caused by mutations in the OA1 gene. Methods The ophthalmologic phenotype of the patients and their family members was characterized. We screened for mutations in the OA1 gene by direct sequencing of the nine PCR-amplified exons, and for genomic deletions by PCR-amplification of large DNA fragments. Results We sequenced the nine exons of the OA1 gene in 72 individuals and found ten different mutations in seven unrelated families and three sporadic cases. The ten mutations include an amino acid substitution and a premature stop codon previously reported by our team, and eight previously unidentified mutations: three amino acid substitutions, a duplication, a deletion, an insertion and two splice-site mutations. The use of a novel Taq polymerase enabled us to amplify large genomic fragments covering the OA1 gene. and to detect very likely six distinct large deletions. Furthermore, we were able to confirm that there was no deletion in twenty one patients where no mutation had been found. Conclusion The identified mutations affect highly conserved amino acids, cause frameshifts or alternative splicing, thus affecting folding of the OA1 G protein coupled receptor, interactions of OA1 with its G protein and/or binding with its ligand.

  6. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  7. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  8. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  9. Observations on the introduction and dissemination of Salmonella in three previously low prevalence status pig farms in the United Kingdom.

    Science.gov (United States)

    Martelli, Francesca; Andres, Victor M; Davies, Rob; Smith, Richard P

    2018-05-01

    In the United Kingdom a serological Salmonella surveillance scheme was run in pigs up to 2012. Farms that maintained a low seroprevalence (animals. The results of this study suggest that incursion of mST was likely to be the main cause of the loss of "Platinum" status and confirm that mST can persist in pigs and their environment. Copyright © 2017. Published by Elsevier Ltd.

  10. SAGE II observations of a previously unreported stratospheric volcanic aerosol cloud in the northern polar summer of 1990

    Science.gov (United States)

    Yue, Glenn K.; Veiga, Robert E.; Wang, Pi-Huan

    1994-01-01

    Analysis of aerosol extinction profiles obtained by the spaceborne SAGE II sensor reveals that there was an anomalous increase of aerosol extinction below 18.5 km at latitudes poleward of 50 deg N from July 28 to September 9, 1990. This widespread increase of aerosol extinction in the lower stratosphere was apparently due to a remote high-latitude volcanic eruption that has not been reported to date. The increase in stratospheric optical depth in the northern polar region was about 50% in August and had diminished by October 1990. This eruption caused an increase in stratospheric aerosol mass of about 0.33 x 10(exp 5) tons, assuming the aerosol was composed of sulfuric acid and water.

  11. Sacrococcygeal pilonidal disease: analysis of previously proposed risk factors

    Directory of Open Access Journals (Sweden)

    Ali Harlak

    2010-01-01

    Full Text Available PURPOSE: Sacrococcygeal pilonidal disease is a source of one of the most common surgical problems among young adults. While male gender, obesity, occupations requiring sitting, deep natal clefts, excessive body hair, poor body hygiene and excessive sweating are described as the main risk factors for this disease, most of these need to be verified with a clinical trial. The present study aimed to evaluate the value and effect of these factors on pilonidal disease. METHOD: Previously proposed main risk factors were evaluated in a prospective case control study that included 587 patients with pilonidal disease and 2,780 healthy control patients. RESULTS: Stiffness of body hair, number of baths and time spent seated per day were the three most predictive risk factors. Adjusted odds ratios were 9.23, 6.33 and 4.03, respectively (p<0.001. With an adjusted odds ratio of 1.3 (p<.001, body mass index was another risk factor. Family history was not statistically different between the groups and there was no specific occupation associated with the disease. CONCLUSIONS: Hairy people who sit down for more than six hours a day and those who take a bath two or less times per week are at a 219-fold increased risk for sacrococcygeal pilonidal disease than those without these risk factors. For people with a great deal of hair, there is a greater need for them to clean their intergluteal sulcus. People who engage in work that requires sitting in a seat for long periods of time should choose more comfortable seats and should also try to stand whenever possible.

  12. Impact of Students’ Class Attendance on Recalling Previously Acquired Information

    Directory of Open Access Journals (Sweden)

    Camellia Hemyari

    2018-03-01

    Full Text Available Background: In recent years, availability of class material including typed lectures, the professor’s Power Point slides, sound recordings, and even videos made a group of students feel that it is unnecessary to attend the classes. These students usually read and memorize typed lectures within two or three days prior to the exams and usually pass the tests even with low attendance rate. Thus, the question is how effective is this learning system and how long the one-night memorized lessons may last.Methods: A group of medical students (62 out of 106 students, with their class attendance and educational achievements in the Medical Mycology and Parasitology course being recorded since two years ago, was selected and their knowledge about this course was tested by multiple choice questions (MCQ designed based on the previous lectures.Results: Although the mean re-exam score of the students at the end of the externship was lower than the corresponding final score, a significant association was found between the scores of the students in these two exams (r=0.48, P=0.01. Moreover, a significant negative association was predicted between the number of absences and re-exam scores (r=-0.26, P=0.037.Conclusion: As our findings show, the phenomenon of recalling the acquired lessons is preserved for a long period of time and it is associated with the students’ attendance. Many factors including generation effect (by taking notes and cued-recall (via slide picture might play a significant role in the better recalling of the learned information in students with good class attendance.Keywords: STUDENT, MEMORY, LONG-TERM, RECALL, ABSENTEEISM, LEARNING

  13. Gastrointestinal tolerability with ibandronate after previous weekly bisphosphonate treatment

    Directory of Open Access Journals (Sweden)

    Richard Derman

    2009-09-01

    Full Text Available Richard Derman1, Joseph D Kohles2, Ann Babbitt31Department of Obstetrics and Gynecology, Christiana Hospital, Newark, DE, USA; 2Roche, Nutley, NJ, USA; 3Greater Portland Bone and Joint Specialists, Portland, ME, USAAbstract: Data from two open-label trials (PRIOR and CURRENT of women with postmenopausal osteoporosis or osteopenia were evaluated to assess whether monthly oral and quarterly intravenous (IV ibandronate dosing improved self-reported gastrointestinal (GI tolerability for patients who had previously experienced GI irritation with bisphosphonate (BP use. In PRIOR, women who had discontinued daily or weekly BP treatment due to GI intolerance received monthly oral or quarterly IV ibandronate for 12 months. The CURRENT subanalysis included women receiving weekly BP treatment who switched to monthly oral ibandronate for six months. GI symptom severity and frequency were assessed using the Osteoporosis Patient Satisfaction Questionnaire™. In PRIOR, mean GI tolerability scores increased significantly at month 1 from screening for both treatment groups (oral: 79.3 versus 54.1; IV: 84.4 versus 51.0; p < 0.001 for both. Most patients reported improvement in GI symptom severity and frequency from baseline at all post-screening assessments (>90% at Month 10. In the CURRENT subanalysis >60% of patients reported improvements in heartburn or acid reflux and >70% indicated improvement in other stomach upset at month 6. Postmenopausal women with GI irritability with daily or weekly BPs experienced improvement in symptoms with extended dosing monthly or quarterly ibandronate compared with baseline.Keywords: ibandronate, osteoporosis, bisphosphonate, gastrointestinal

  14. Nocturnal Wakefulness as a Previously Unrecognized Risk Factor for Suicide.

    Science.gov (United States)

    Perlis, Michael L; Grandner, Michael A; Brown, Gregory K; Basner, Mathias; Chakravorty, Subhajit; Morales, Knashawn H; Gehrman, Philip R; Chaudhary, Ninad S; Thase, Michael E; Dinges, David F

    2016-06-01

    Suicide is a major public health problem and the 10th leading cause of death in the United States. The identification of modifiable risk factors is essential for reducing the prevalence of suicide. Recently, it has been shown that insomnia and nightmares significantly increase the risk for suicidal ideation, attempted suicide, and death by suicide. While both forms of sleep disturbance may independently confer risk, and potentially be modifiable risk factors, it is also possible that simply being awake at night represents a specific vulnerability for suicide. The present analysis evaluates the frequency of completed suicide per hour while taking into account the percentage of individuals awake at each hour. Archival analyses were conducted estimating the time of fatal injury using the National Violent Death Reporting System for 2003-2010 and the proportion of the American population awake per hour across the 24-hour day using the American Time Use Survey. The mean ± SD incident rate from 06:00-23:59 was 2.2% ± 0.7%, while the mean ± SD incident rate from 00:00-05:59 was 10.3% ± 4.9%. The maximum incident rate was from 02:00-02:59 (16.3%). Hour-by-hour observed values differed from those that would be expected by chance (P < .001), and when 6-hour blocks were examined, the observed frequency at night was 3.6 times higher than would be expected by chance (P < .001). Being awake at night confers greater risk for suicide than being awake at other times of the day, suggesting that disturbances of sleep or circadian neurobiology may potentiate suicide risk. © Copyright 2016 Physicians Postgraduate Press, Inc.

  15. Poly-epiphyseal overgrowth: description of a previously unreported skeletal dysplasia

    Energy Technology Data Exchange (ETDEWEB)

    Pazzaglia, Ugo E.; Bonaspetti, Giovanni [University of Brescia, Orthopaedic Clinic, Brescia (Italy); Beluffi, Giampiero [Fondazione IRCCS Policlinico San Matteo, Department of Paediatric Radiology, Pavia (Italy); Marchi, Antonietta; Bozzola, Mauro; Savasta, Salvatore [Fondazione IRCCS Policlinico San Matteo, Paediatric Clinic, University of Pavia, Pavia (Italy)

    2007-10-15

    A skeletal dysplasia with previously unreported features is presented. Its evolution was characterized by growth abnormalities of bones without involvement of other organs. Advanced bone age, increased stature and irregular epiphyseal ossification with stippling of the main long bones were documented. Physeal overgrowth was massive in the left proximal humerus and femur. Furthermore, the hip joint appeared fused with an abundant mass of pathological calcific tissue extending from the femur to the ilium. Pathological epiphyses were characterized by anarchic cartilaginous proliferation with multiple ossification centres, while lamellar bone apposition and remodelling were normal. The observed bone changes were different from those in any previously reported syndrome, metabolic defect or bone dysplasia. However, they clearly indicated a defect of endochondral ossification with some resemblance to phenotypes observed in dysplasia epiphysealis hemimelica. (orig.)

  16. Poly-epiphyseal overgrowth: description of a previously unreported skeletal dysplasia

    International Nuclear Information System (INIS)

    Pazzaglia, Ugo E.; Bonaspetti, Giovanni; Beluffi, Giampiero; Marchi, Antonietta; Bozzola, Mauro; Savasta, Salvatore

    2007-01-01

    A skeletal dysplasia with previously unreported features is presented. Its evolution was characterized by growth abnormalities of bones without involvement of other organs. Advanced bone age, increased stature and irregular epiphyseal ossification with stippling of the main long bones were documented. Physeal overgrowth was massive in the left proximal humerus and femur. Furthermore, the hip joint appeared fused with an abundant mass of pathological calcific tissue extending from the femur to the ilium. Pathological epiphyses were characterized by anarchic cartilaginous proliferation with multiple ossification centres, while lamellar bone apposition and remodelling were normal. The observed bone changes were different from those in any previously reported syndrome, metabolic defect or bone dysplasia. However, they clearly indicated a defect of endochondral ossification with some resemblance to phenotypes observed in dysplasia epiphysealis hemimelica. (orig.)

  17. Experience of targeted Usher exome sequencing as a clinical test

    Science.gov (United States)

    Besnard, Thomas; García-García, Gema; Baux, David; Vaché, Christel; Faugère, Valérie; Larrieu, Lise; Léonard, Susana; Millan, Jose M; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

    2014-01-01

    We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service. PMID:24498627

  18. Detecting change in stochastic sound sequences.

    Directory of Open Access Journals (Sweden)

    Benjamin Skerritt-Davis

    2018-05-01

    Full Text Available Our ability to parse our acoustic environment relies on the brain's capacity to extract statistical regularities from surrounding sounds. Previous work in regularity extraction has predominantly focused on the brain's sensitivity to predictable patterns in sound sequences. However, natural sound environments are rarely completely predictable, often containing some level of randomness, yet the brain is able to effectively interpret its surroundings by extracting useful information from stochastic sounds. It has been previously shown that the brain is sensitive to the marginal lower-order statistics of sound sequences (i.e., mean and variance. In this work, we investigate the brain's sensitivity to higher-order statistics describing temporal dependencies between sound events through a series of change detection experiments, where listeners are asked to detect changes in randomness in the pitch of tone sequences. Behavioral data indicate listeners collect statistical estimates to process incoming sounds, and a perceptual model based on Bayesian inference shows a capacity in the brain to track higher-order statistics. Further analysis of individual subjects' behavior indicates an important role of perceptual constraints in listeners' ability to track these sensory statistics with high fidelity. In addition, the inference model facilitates analysis of neural electroencephalography (EEG responses, anchoring the analysis relative to the statistics of each stochastic stimulus. This reveals both a deviance response and a change-related disruption in phase of the stimulus-locked response that follow the higher-order statistics. These results shed light on the brain's ability to process stochastic sound sequences.

  19. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  20. Observing nebulae

    CERN Document Server

    Griffiths, Martin

    2016-01-01

    This book enables anyone with suitable instruments to undertake an examination of nebulae and see or photograph them in detail. Nebulae, ethereal clouds of gas and dust, are among the most beautiful objects to view in the night sky. These star-forming regions are a common target for observers and photographers. Griffiths describes many of the brightest and best nebulae and includes some challenges for the more experienced observer. Readers learn the many interesting astrophysical properties of these clouds, which are an important subject of study in astronomy and astrobiology. Non-mathematical in approach, the text is easily accessible to anyone with an interest in the subject. A special feature is the inclusion of an observational guide to 70 objects personally observed or imaged by the author. The guide also includes photographs of each object for ease of identification along with their celestial coordinates, magnitudes and other pertinent information. Observing Nebulae provides a ready resource to allow an...

  1. The phenomenon of claimed memories of previous lives: possible interpretations and importance.

    Science.gov (United States)

    Stevenson, I

    2000-04-01

    Several disorders or abnormalities observed in medicine and psychology are not explicable (or not fully explicable) by genetics and environmental influences, either alone or together. These include phobias and philias observed in early infancy, unusual play in childhood, homosexuality, gender identity disorder, a child's idea of having parents other than its own, differences in temperament manifested soon after birth, unusual birthmarks and their correspondence with wounds on a deceased person, unusual birth defects, and differences (physical and behavioral) between monozygotic twins. The hypothesis of previous lives can contribute to the further understanding of these phenomena. Copyright 2000 Harcourt Publishers Ltd.

  2. Clinical applications of sequencing take center stage

    OpenAIRE

    Glusman, Gustavo

    2013-01-01

    A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013. This year's Advances in Genome Biology and Technology (AGBT) meeting reflected the current state of 'next generation' sequencing (NGS) technologies: significantly reduced competition and innovation, and a strong focus on standardization and application. Announcements of technological breakthroughs - a hallmark of previous AGBT meetings - were markedly absent, but existin...

  3. Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol

    Science.gov (United States)

    Lange, Leslie A.; Hu, Youna; Zhang, He; Xue, Chenyi; Schmidt, Ellen M.; Tang, Zheng-Zheng; Bizon, Chris; Lange, Ethan M.; Smith, Joshua D.; Turner, Emily H.; Jun, Goo; Kang, Hyun Min; Peloso, Gina; Auer, Paul; Li, Kuo-ping; Flannick, Jason; Zhang, Ji; Fuchsberger, Christian; Gaulton, Kyle; Lindgren, Cecilia; Locke, Adam; Manning, Alisa; Sim, Xueling; Rivas, Manuel A.; Holmen, Oddgeir L.; Gottesman, Omri; Lu, Yingchang; Ruderfer, Douglas; Stahl, Eli A.; Duan, Qing; Li, Yun; Durda, Peter; Jiao, Shuo; Isaacs, Aaron; Hofman, Albert; Bis, Joshua C.; Correa, Adolfo; Griswold, Michael E.; Jakobsdottir, Johanna; Smith, Albert V.; Schreiner, Pamela J.; Feitosa, Mary F.; Zhang, Qunyuan; Huffman, Jennifer E.; Crosby, Jacy; Wassel, Christina L.; Do, Ron; Franceschini, Nora; Martin, Lisa W.; Robinson, Jennifer G.; Assimes, Themistocles L.; Crosslin, David R.; Rosenthal, Elisabeth A.; Tsai, Michael; Rieder, Mark J.; Farlow, Deborah N.; Folsom, Aaron R.; Lumley, Thomas; Fox, Ervin R.; Carlson, Christopher S.; Peters, Ulrike; Jackson, Rebecca D.; van Duijn, Cornelia M.; Uitterlinden, André G.; Levy, Daniel; Rotter, Jerome I.; Taylor, Herman A.; Gudnason, Vilmundur; Siscovick, David S.; Fornage, Myriam; Borecki, Ingrid B.; Hayward, Caroline; Rudan, Igor; Chen, Y. Eugene; Bottinger, Erwin P.; Loos, Ruth J.F.; Sætrom, Pål; Hveem, Kristian; Boehnke, Michael; Groop, Leif; McCarthy, Mark; Meitinger, Thomas; Ballantyne, Christie M.; Gabriel, Stacey B.; O’Donnell, Christopher J.; Post, Wendy S.; North, Kari E.; Reiner, Alexander P.; Boerwinkle, Eric; Psaty, Bruce M.; Altshuler, David; Kathiresan, Sekar; Lin, Dan-Yu; Jarvik, Gail P.; Cupples, L. Adrienne; Kooperberg, Charles; Wilson, James G.; Nickerson, Deborah A.; Abecasis, Goncalo R.; Rich, Stephen S.; Tracy, Russell P.; Willer, Cristen J.; Gabriel, Stacey B.; Altshuler, David M.; Abecasis, Gonçalo R.; Allayee, Hooman; Cresci, Sharon; Daly, Mark J.; de Bakker, Paul I.W.; DePristo, Mark A.; Do, Ron; Donnelly, Peter; Farlow, Deborah N.; Fennell, Tim; Garimella, Kiran; Hazen, Stanley L.; Hu, Youna; Jordan, Daniel M.; Jun, Goo; Kathiresan, Sekar; Kang, Hyun Min; Kiezun, Adam; Lettre, Guillaume; Li, Bingshan; Li, Mingyao; Newton-Cheh, Christopher H.; Padmanabhan, Sandosh; Peloso, Gina; Pulit, Sara; Rader, Daniel J.; Reich, David; Reilly, Muredach P.; Rivas, Manuel A.; Schwartz, Steve; Scott, Laura; Siscovick, David S.; Spertus, John A.; Stitziel, Nathaniel O.; Stoletzki, Nina; Sunyaev, Shamil R.; Voight, Benjamin F.; Willer, Cristen J.; Rich, Stephen S.; Akylbekova, Ermeg; Atwood, Larry D.; Ballantyne, Christie M.; Barbalic, Maja; Barr, R. Graham; Benjamin, Emelia J.; Bis, Joshua; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer; Budoff, Matthew; Burke, Greg; Buxbaum, Sarah; Carr, Jeff; Chen, Donna T.; Chen, Ida Y.; Chen, Wei-Min; Concannon, Pat; Crosby, Jacy; Cupples, L. Adrienne; D’Agostino, Ralph; DeStefano, Anita L.; Dreisbach, Albert; Dupuis, Josée; Durda, J. Peter; Ellis, Jaclyn; Folsom, Aaron R.; Fornage, Myriam; Fox, Caroline S.; Fox, Ervin; Funari, Vincent; Ganesh, Santhi K.; Gardin, Julius; Goff, David; Gordon, Ora; Grody, Wayne; Gross, Myron; Guo, Xiuqing; Hall, Ira M.; Heard-Costa, Nancy L.; Heckbert, Susan R.; Heintz, Nicholas; Herrington, David M.; Hickson, DeMarc; Huang, Jie; Hwang, Shih-Jen; Jacobs, David R.; Jenny, Nancy S.; Johnson, Andrew D.; Johnson, Craig W.; Kawut, Steven; Kronmal, Richard; Kurz, Raluca; Lange, Ethan M.; Lange, Leslie A.; Larson, Martin G.; Lawson, Mark; Lewis, Cora E.; Levy, Daniel; Li, Dalin; Lin, Honghuang; Liu, Chunyu; Liu, Jiankang; Liu, Kiang; Liu, Xiaoming; Liu, Yongmei; Longstreth, William T.; Loria, Cay; Lumley, Thomas; Lunetta, Kathryn; Mackey, Aaron J.; Mackey, Rachel; Manichaikul, Ani; Maxwell, Taylor; McKnight, Barbara; Meigs, James B.; Morrison, Alanna C.; Musani, Solomon K.; Mychaleckyj, Josyf C.; Nettleton, Jennifer A.; North, Kari; O’Donnell, Christopher J.; O’Leary, Daniel; Ong, Frank; Palmas, Walter; Pankow, James S.; Pankratz, Nathan D.; Paul, Shom; Perez, Marco; Person, Sharina D.; Polak, Joseph; Post, Wendy S.; Psaty, Bruce M.; Quinlan, Aaron R.; Raffel, Leslie J.; Ramachandran, Vasan S.; Reiner, Alexander P.; Rice, Kenneth; Rotter, Jerome I.; Sanders, Jill P.; Schreiner, Pamela; Seshadri, Sudha; Shea, Steve; Sidney, Stephen; Silverstein, Kevin; Smith, Nicholas L.; Sotoodehnia, Nona; Srinivasan, Asoke; Taylor, Herman A.; Taylor, Kent; Thomas, Fridtjof; Tracy, Russell P.; Tsai, Michael Y.; Volcik, Kelly A.; Wassel, Chrstina L.; Watson, Karol; Wei, Gina; White, Wendy; Wiggins, Kerri L.; Wilk, Jemma B.; Williams, O. Dale; Wilson, Gregory; Wilson, James G.; Wolf, Phillip; Zakai, Neil A.; Hardy, John; Meschia, James F.; Nalls, Michael; Singleton, Andrew; Worrall, Brad; Bamshad, Michael J.; Barnes, Kathleen C.; Abdulhamid, Ibrahim; Accurso, Frank; Anbar, Ran; Beaty, Terri; Bigham, Abigail; Black, Phillip; Bleecker, Eugene; Buckingham, Kati; Cairns, Anne Marie; Caplan, Daniel; Chatfield, Barbara; Chidekel, Aaron; Cho, Michael; Christiani, David C.; Crapo, James D.; Crouch, Julia; Daley, Denise; Dang, Anthony; Dang, Hong; De Paula, Alicia; DeCelie-Germana, Joan; Drumm, Allen DozorMitch; Dyson, Maynard; Emerson, Julia; Emond, Mary J.; Ferkol, Thomas; Fink, Robert; Foster, Cassandra; Froh, Deborah; Gao, Li; Gershan, William; Gibson, Ronald L.; Godwin, Elizabeth; Gondor, Magdalen; Gutierrez, Hector; Hansel, Nadia N.; Hassoun, Paul M.; Hiatt, Peter; Hokanson, John E.; Howenstine, Michelle; Hummer, Laura K.; Kanga, Jamshed; Kim, Yoonhee; Knowles, Michael R.; Konstan, Michael; Lahiri, Thomas; Laird, Nan; Lange, Christoph; Lin, Lin; Lin, Xihong; Louie, Tin L.; Lynch, David; Make, Barry; Martin, Thomas R.; Mathai, Steve C.; Mathias, Rasika A.; McNamara, John; McNamara, Sharon; Meyers, Deborah; Millard, Susan; Mogayzel, Peter; Moss, Richard; Murray, Tanda; Nielson, Dennis; Noyes, Blakeslee; O’Neal, Wanda; Orenstein, David; O’Sullivan, Brian; Pace, Rhonda; Pare, Peter; Parker, H. Worth; Passero, Mary Ann; Perkett, Elizabeth; Prestridge, Adrienne; Rafaels, Nicholas M.; Ramsey, Bonnie; Regan, Elizabeth; Ren, Clement; Retsch-Bogart, George; Rock, Michael; Rosen, Antony; Rosenfeld, Margaret; Ruczinski, Ingo; Sanford, Andrew; Schaeffer, David; Sell, Cindy; Sheehan, Daniel; Silverman, Edwin K.; Sin, Don; Spencer, Terry; Stonebraker, Jackie; Tabor, Holly K.; Varlotta, Laurie; Vergara, Candelaria I.; Weiss, Robert; Wigley, Fred; Wise, Robert A.; Wright, Fred A.; Wurfel, Mark M.; Zanni, Robert; Zou, Fei; Nickerson, Deborah A.; Rieder, Mark J.; Green, Phil; Shendure, Jay; Akey, Joshua M.; Bustamante, Carlos D.; Crosslin, David R.; Eichler, Evan E.; Fox, P. Keolu; Fu, Wenqing; Gordon, Adam; Gravel, Simon; Jarvik, Gail P.; Johnsen, Jill M.; Kan, Mengyuan; Kenny, Eimear E.; Kidd, Jeffrey M.; Lara-Garduno, Fremiet; Leal, Suzanne M.; Liu, Dajiang J.; McGee, Sean; O’Connor, Timothy D.; Paeper, Bryan; Robertson, Peggy D.; Smith, Joshua D.; Staples, Jeffrey C.; Tennessen, Jacob A.; Turner, Emily H.; Wang, Gao; Yi, Qian; Jackson, Rebecca; Peters, Ulrike; Carlson, Christopher S.; Anderson, Garnet; Anton-Culver, Hoda; Assimes, Themistocles L.; Auer, Paul L.; Beresford, Shirley; Bizon, Chris; Black, Henry; Brunner, Robert; Brzyski, Robert; Burwen, Dale; Caan, Bette; Carty, Cara L.; Chlebowski, Rowan; Cummings, Steven; Curb, J. David; Eaton, Charles B.; Ford, Leslie; Franceschini, Nora; Fullerton, Stephanie M.; Gass, Margery; Geller, Nancy; Heiss, Gerardo; Howard, Barbara V.; Hsu, Li; Hutter, Carolyn M.; Ioannidis, John; Jiao, Shuo; Johnson, Karen C.; Kooperberg, Charles; Kuller, Lewis; LaCroix, Andrea; Lakshminarayan, Kamakshi; Lane, Dorothy; Lasser, Norman; LeBlanc, Erin; Li, Kuo-Ping; Limacher, Marian; Lin, Dan-Yu; Logsdon, Benjamin A.; Ludlam, Shari; Manson, JoAnn E.; Margolis, Karen; Martin, Lisa; McGowan, Joan; Monda, Keri L.; Kotchen, Jane Morley; Nathan, Lauren; Ockene, Judith; O’Sullivan, Mary Jo; Phillips, Lawrence S.; Prentice, Ross L.; Robbins, John; Robinson, Jennifer G.; Rossouw, Jacques E.; Sangi-Haghpeykar, Haleh; Sarto, Gloria E.; Shumaker, Sally; Simon, Michael S.; Stefanick, Marcia L.; Stein, Evan; Tang, Hua; Taylor, Kira C.; Thomson, Cynthia A.; Thornton, Timothy A.; Van Horn, Linda; Vitolins, Mara; Wactawski-Wende, Jean; Wallace, Robert; Wassertheil-Smoller, Sylvia; Zeng, Donglin; Applebaum-Bowden, Deborah; Feolo, Michael; Gan, Weiniu; Paltoo, Dina N.; Sholinsky, Phyliss; Sturcke, Anne

    2014-01-01

    Elevated low-density lipoprotein cholesterol (LDL-C) is a treatable, heritable risk factor for cardiovascular disease. Genome-wide association studies (GWASs) have identified 157 variants associated with lipid levels but are not well suited to assess the impact of rare and low-frequency variants. To determine whether rare or low-frequency coding variants are associated with LDL-C, we exome sequenced 2,005 individuals, including 554 individuals selected for extreme LDL-C (>98th or <2nd percentile). Follow-up analyses included sequencing of 1,302 additional individuals and genotype-based analysis of 52,221 individuals. We observed significant evidence of association between LDL-C and the burden of rare or low-frequency variants in PNPLA5, encoding a phospholipase-domain-containing protein, and both known and previously unidentified variants in PCSK9, LDLR and APOB, three known lipid-related genes. The effect sizes for the burden of rare variants for each associated gene were substantially higher than those observed for individual SNPs identified from GWASs. We replicated the PNPLA5 signal in an independent large-scale sequencing study of 2,084 individuals. In conclusion, this large whole-exome-sequencing study for LDL-C identified a gene not known to be implicated in LDL-C and provides unique insight into the design and analysis of similar experiments. PMID:24507775

  4. Dissociation in decision bias mechanism between probabilistic information and previous decision

    Directory of Open Access Journals (Sweden)

    Yoshiyuki eKaneko

    2015-05-01

    Full Text Available Target detection performance is known to be influenced by events in the previous trials. It has not been clear, however, whether this bias effect is due to the previous sensory stimulus, motor response, or decision. Also it remains open whether or not the previous trial effect emerges via the same mechanism as the effect of knowledge about the target probability. In the present study, we asked normal human subjects to make a decision about the presence or absence of a visual target. We presented a pre-cue indicating the target probability before the stimulus, and also a decision-response mapping cue after the stimulus so as to tease apart the effect of decision from that of motor response. We found that the target detection performance was significantly affected by the probability cue in the current trial and also by the decision in the previous trial. While the information about the target probability modulated the decision criteria, the previous decision modulated the sensitivity to target-relevant sensory signals (d-prime. Using functional magnetic resonance imaging, we also found that activation in the left intraparietal sulcus was decreased when the probability cue indicated a high probability of the target. By contrast, activation in the right inferior frontal gyrus was increased when the subjects made a target-present decision in the previous trial, but this change was observed specifically when the target was present in the current trial. Activation in these regions was associated with individual-difference in the decision computation parameters. We argue that the previous decision biases the target detection performance by modulating the processing of target-selective information, and this mechanism is distinct from modulation of decision criteria due to expectation of a target.

  5. A comparison of morbidity associated with placenta previa with and without previous caesarean sections

    International Nuclear Information System (INIS)

    Baqai, S.; Siraj, A.; Noor, N.

    2018-01-01

    To compare the morbidity associated with placenta previa with and without previous caesarean sections. Study Design: Retrospective comparative study. Place and Duration of Study: From March 2014 till March 2016 in the department of Obstetrics and Gynaecology at PNS Shifa hospital Karachi. Material and Methods: After the approval from hospital ethical committee, antenatal patients with singleton pregnancy of gestational age >32 weeks, in the age group of 20-40 years diagnosed to have placenta previa included in the study. All patients with twin pregnancy less than 20 years and more than 40 years of age were excluded. The records of all patients fulfilling the inclusion criteria were reviewed. Data had been collected for demographic and maternal variables, placenta previa, history of previous lower segment caesarean section (LSCS), complications associated with placenta previa and techniques used to control blood loss were recorded. Results: During the study period, 6879 patients were delivered in PNS Shifa, out of these, 2060 (29.9%) had caesarean section out of these, 47.3% patients had previous history of LSCS. Thirty three (1.6%) patients were diagnosed to have placenta previa and frequency of placenta previa was significantly higher in patients with previous history of LSCS than previous normal delivery of LSCS i.e. 22 vs. 11 (p=0.023). It was observed that the frequency of morbidly adherent placenta (MAP) and Intensive care unit (ICU) stay were significantly higher in patients with previous history of LSCS than previous history of normal delivery. Conclusion: Frequency of placenta previa was significantly higher in patients with history of LSCS. Also placenta previa remains a major risk factor for various maternal complications. (author)

  6. Dissociation in decision bias mechanism between probabilistic information and previous decision

    Science.gov (United States)

    Kaneko, Yoshiyuki; Sakai, Katsuyuki

    2015-01-01

    Target detection performance is known to be influenced by events in the previous trials. It has not been clear, however, whether this bias effect is due to the previous sensory stimulus, motor response, or decision. Also it remains open whether or not the previous trial effect emerges via the same mechanism as the effect of knowledge about the target probability. In the present study, we asked normal human subjects to make a decision about the presence or absence of a visual target. We presented a pre-cue indicating the target probability before the stimulus, and also a decision-response mapping cue after the stimulus so as to tease apart the effect of decision from that of motor response. We found that the target detection performance was significantly affected by the probability cue in the current trial and also by the decision in the previous trial. While the information about the target probability modulated the decision criteria, the previous decision modulated the sensitivity to target-relevant sensory signals (d-prime). Using functional magnetic resonance imaging (fMRI), we also found that activation in the left intraparietal sulcus (IPS) was decreased when the probability cue indicated a high probability of the target. By contrast, activation in the right inferior frontal gyrus (IFG) was increased when the subjects made a target-present decision in the previous trial, but this change was observed specifically when the target was present in the current trial. Activation in these regions was associated with individual-difference in the decision computation parameters. We argue that the previous decision biases the target detection performance by modulating the processing of target-selective information, and this mechanism is distinct from modulation of decision criteria due to expectation of a target. PMID:25999844

  7. Memory for sequences of events impaired in typical aging

    Science.gov (United States)

    Allen, Timothy A.; Morris, Andrea M.; Stark, Shauna M.; Fortin, Norbert J.

    2015-01-01

    Typical aging is associated with diminished episodic memory performance. To improve our understanding of the fundamental mechanisms underlying this age-related memory deficit, we previously developed an integrated, cross-species approach to link converging evidence from human and animal research. This novel approach focuses on the ability to remember sequences of events, an important feature of episodic memory. Unlike existing paradigms, this task is nonspatial, nonverbal, and can be used to isolate different cognitive processes that may be differentially affected in aging. Here, we used this task to make a comprehensive comparison of sequence memory performance between younger (18–22 yr) and older adults (62–86 yr). Specifically, participants viewed repeated sequences of six colored, fractal images and indicated whether each item was presented “in sequence” or “out of sequence.” Several out of sequence probe trials were used to provide a detailed assessment of sequence memory, including: (i) repeating an item from earlier in the sequence (“Repeats”; e.g., ABADEF), (ii) skipping ahead in the sequence (“Skips”; e.g., ABDDEF), and (iii) inserting an item from a different sequence into the same ordinal position (“Ordinal Transfers”; e.g., AB3DEF). We found that older adults performed as well as younger controls when tested on well-known and predictable sequences, but were severely impaired when tested using novel sequences. Importantly, overall sequence memory performance in older adults steadily declined with age, a decline not detected with other measures (RAVLT or BPS-O). We further characterized this deficit by showing that performance of older adults was severely impaired on specific probe trials that required detailed knowledge of the sequence (Skips and Ordinal Transfers), and was associated with a shift in their underlying mnemonic representation of the sequences. Collectively, these findings provide unambiguous evidence that the

  8. Emphysema and bronchiectasis in COPD patients with previous pulmonary tuberculosis: computed tomography features and clinical implications

    Directory of Open Access Journals (Sweden)

    Jin J

    2018-01-01

    Full Text Available Jianmin Jin,1 Shuling Li,2 Wenling Yu,2 Xiaofang Liu,1 Yongchang Sun1,3 1Department of Respiratory and Critical Care Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, 2Department of Radiology, Beijing Tongren Hospital, Capital Medical University, Beijing, 3Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China Background: Pulmonary tuberculosis (PTB is a risk factor for COPD, but the clinical characteristics and the chest imaging features (emphysema and bronchiectasis of COPD with previous PTB have not been studied well.Methods: The presence, distribution, and severity of emphysema and bronchiectasis in COPD patients with and without previous PTB were evaluated by high-resolution computed tomography (HRCT and compared. Demographic data, respiratory symptoms, lung function, and sputum culture of Pseudomonas aeruginosa were also compared between patients with and without previous PTB.Results: A total of 231 COPD patients (82.2% ex- or current smokers, 67.5% male were consecutively enrolled. Patients with previous PTB (45.0% had more severe (p=0.045 and longer history (p=0.008 of dyspnea, more exacerbations in the previous year (p=0.011, and more positive culture of P. aeruginosa (p=0.001, compared with those without PTB. Patients with previous PTB showed a higher prevalence of bronchiectasis (p<0.001, which was more significant in lungs with tuberculosis (TB lesions, and a higher percentage of more severe bronchiectasis (Bhalla score ≥2, p=0.031, compared with those without previous PTB. The overall prevalence of emphysema was not different between patients with and without previous PTB, but in those with previous PTB, a higher number of subjects with middle (p=0.001 and lower (p=0.019 lobe emphysema, higher severity score (p=0.028, higher prevalence of panlobular emphysema (p=0.013, and more extensive centrilobular emphysema (p=0.039 were observed. Notably, in patients with

  9. Hepatotoxicity induced by methimazole in a previously healthy patient.

    Science.gov (United States)

    Gallelli, Luca; Staltari, Orietta; Palleria, Caterina; De Sarro, Giovambattista; Ferraro, Maria

    2009-09-01

    We report a case of hepatotoxicity induced by methimazole treatment in a patient affected by hyperthyroidism. A 54-year-old man, presented to our observation for palpitations, excessive sweating, weakness, heat intolerance and weight loss. On physical examination, his blood pressure was 140/90 mmHg and heart beat was 100/min regular. He had mild tremors and left exophthalmos. Laboratory test revealed a significant increase in serum thyroid hormone levels with a decrease in thyroid stimulating hormone levels. A diagnosis of hyperthyroidism was made and he began treatment with methimazole (30 mg/day). Fourteen days later, he returned for the development of scleral icterus, followed by dark urine, and abdominal pain in the right upper quadrant. Laboratory examinations and liver biopsy performed a diagnosis of cholestatic hepatitis, secondary to methimazole usage. Methimazole was promptly withdrawn and cholestyramine, ursodeoxycholic acid, and chlorpheniramine were given. After five days, abdominal pain resolved and laboratory parameters returned to normal. Naranjo probability scale indicated a probable relationship between hepatotoxicity and methimazole therapy. In conclusion physicians should be aware the risk of hepatotoxicity related with methimazole.

  10. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  11. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  12. Songbirds and humans apply different strategies in a sound sequence discrimination task

    Directory of Open Access Journals (Sweden)

    Yoshimasa eSeki

    2013-07-01

    Full Text Available The abilities of animals and humans to extract rules from sound sequences have previously been compared using observation of spontaneous responses and conditioning techniques. However, the results were inconsistently interpreted across studies possibly due to methodological and/or species differences. Therefore, we examined the strategies for discrimination of sound sequences in Bengalese finches and humans using the same protocol. Birds were trained on a GO/NOGO task to discriminate between two categories of sound stimulus generated based on an AAB or ABB rule. The sound elements used were taken from a variety of male (M and female (F calls, such that the sequences could be represented as MMF and MFF. In test sessions, FFM and FMM sequences, which were never presented in the training sessions but conformed to the rule, were presented as probe stimuli. The results suggested two discriminative strategies were being applied: 1 memorizing sound patterns of either GO or NOGO stimuli and generating the appropriate responses for only those sounds; and 2 using the repeated element as a cue. There was no evidence that the birds successfully extracted the abstract rule (i.e. AAB and ABB; MMF-GO subjects did not produce a GO response for FFM and vice versa. Next we examined whether those strategies were also applicable for human participants on the same task. The results and questionnaires revealed that participants extracted the abstract rule, and most of them employed it to discriminate the sequences. This strategy was never observed in bird subjects, although some participants used strategies similar to the birds when responding to the probe stimuli. Our results showed that the human participants applied the abstract rule in the task even without instruction but Bengalese finches did not, thereby reconfirming that humans have to extract abstract rules from sound sequences that is distinct from non-human animals.

  13. Songbirds and humans apply different strategies in a sound sequence discrimination task.

    Science.gov (United States)

    Seki, Yoshimasa; Suzuki, Kenta; Osawa, Ayumi M; Okanoya, Kazuo

    2013-01-01

    The abilities of animals and humans to extract rules from sound sequences have previously been compared using observation of spontaneous responses and conditioning techniques. However, the results were inconsistently interpreted across studies possibly due to methodological and/or species differences. Therefore, we examined the strategies for discrimination of sound sequences in Bengalese finches and humans using the same protocol. Birds were trained on a GO/NOGO task to discriminate between two categories of sound stimulus generated based on an "AAB" or "ABB" rule. The sound elements used were taken from a variety of male (M) and female (F) calls, such that the sequences could be represented as MMF and MFF. In test sessions, FFM and FMM sequences, which were never presented in the training sessions but conformed to the rule, were presented as probe stimuli. The results suggested two discriminative strategies were being applied: (1) memorizing sound patterns of either GO or NOGO stimuli and generating the appropriate responses for only those sounds; and (2) using the repeated element as a cue. There was no evidence that the birds successfully extracted the abstract rule (i.e., AAB and ABB); MMF-GO subjects did not produce a GO response for FFM and vice versa. Next we examined whether those strategies were also applicable for human participants on the same task. The results and questionnaires revealed that participants extracted the abstract rule, and most of them employed it to discriminate the sequences. This strategy was never observed in bird subjects, although some participants used strategies similar to the birds when responding to the probe stimuli. Our results showed that the human participants applied the abstract rule in the task even without instruction but Bengalese finches did not, thereby reconfirming that humans have to extract abstract rules from sound sequences that is distinct from non-human animals.

  14. OTU analysis using metagenomic shotgun sequencing data.

    Directory of Open Access Journals (Sweden)

    Xiaolin Hao

    Full Text Available Because of technological limitations, the primer and amplification biases in targeted sequencing of 16S rRNA genes have veiled the true microbial diversity underlying environmental samples. However, the protocol of metagenomic shotgun sequencing provides 16S rRNA gene fragment data with natural immunity against the biases raised during priming and thus the potential of uncovering the true structure of microbial community by giving more accurate predictions of operational taxonomic units (OTUs. Nonetheless, the lack of statistically rigorous comparison between 16S rRNA gene fragments and other data types makes it difficult to interpret previously reported results using 16S rRNA gene fragments. Therefore, in the present work, we established a standard analysis pipeline that would help confirm if the differences in the data are true or are just due to potential technical bias. This pipeline is built by using simulated data to find optimal mapping and OTU prediction methods. The comparison between simulated datasets revealed a relationship between 16S rRNA gene fragments and full-length 16S rRNA sequences that a 16S rRNA gene fragment having a length >150 bp provides the same accuracy as a full-length 16S rRNA sequence using our proposed pipeline, which could serve as a good starting point for experimental design and making the comparison between 16S rRNA gene fragment-based and targeted 16S rRNA sequencing-based surveys possible.

  15. Hidden Markov models for labeled sequences

    DEFF Research Database (Denmark)

    Krogh, Anders Stærmose

    1994-01-01

    A hidden Markov model for labeled observations, called a class HMM, is introduced and a maximum likelihood method is developed for estimating the parameters of the model. Instead of training it to model the statistics of the training sequences it is trained to optimize recognition. It resembles MMI...

  16. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  17. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Jonas Binladen

    2007-02-01

    Full Text Available The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences. Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis.We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%. Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial

  18. High prevalence of genetic variants previously associated with Brugada syndrome in new exome data

    DEFF Research Database (Denmark)

    Risgaard, B; Jabbari, R; Refsgaard, L

    2013-01-01

    More than 300 variants in 12 genes have been associated with Brugada syndrome (BrS) which has a prevalence ranging between 1:2000 and 1:100,000. Until recently, there has been little knowledge regarding the distribution of genetic variations in the general population. This problem was partly solved......, when exome data from the NHLI GO Exome Sequencing Project (ESP) was published. In this study, we aimed to report the prevalence of previously BrS-associated variants in the ESP population. We performed a search in ESP for variants previously associated with BrS. In addition, four variants in ESP were...... to a surprisingly high genotype prevalence of 1:23 (274:6258). Genotyping the four common ESP-derived variants CACNA2D1 S709N, SCN5A F2004L, CACNB2 S143F, and CACNB2 T450I in the Danish controls, we found a genotype prevalence comparable with that found in ESP. We suggest that exome data are used in research...

  19. Sequence dependent aggregation of peptides and fibril formation

    Science.gov (United States)

    Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X.

    2017-09-01

    Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.

  20. Obstetric Outcomes of Mothers Previously Exposed to Sexual Violence.

    Directory of Open Access Journals (Sweden)

    Agnes Gisladottir

    Full Text Available There is a scarcity of data on the association of sexual violence and women's subsequent obstetric outcomes. Our aim was to investigate whether women exposed to sexual violence as teenagers (12-19 years of age or adults present with different obstetric outcomes than women with no record of such violence.We linked detailed prospectively collected information on women attending a Rape Trauma Service (RTS to the Icelandic Medical Birth Registry (IBR. Women who attended the RTS in 1993-2010 and delivered (on average 5.8 years later at least one singleton infant in Iceland through 2012 formed our exposed cohort (n = 1068. For each exposed woman's delivery, nine deliveries by women with no RTS attendance were randomly selected from the IBR (n = 9126 matched on age, parity, and year and season of delivery. Information on smoking and Body mass index (BMI was available for a sub-sample (n = 792 exposed and n = 1416 non-exposed women. Poisson regression models were used to estimate Relative Risks (RR with 95% confidence intervals (CI.Compared with non-exposed women, exposed women presented with increased risks of maternal distress during labor and delivery (RR 1.68, 95% CI 1.01-2.79, prolonged first stage of labor (RR 1.40, 95% CI 1.03-1.88, antepartum bleeding (RR 1.95, 95% CI 1.22-3.07 and emergency instrumental delivery (RR 1.16, 95% CI 1.00-1.34. Slightly higher risks were seen for women assaulted as teenagers. Overall, we did not observe differences between the groups regarding the risk of elective cesarean section (RR 0.86, 95% CI 0.61-1.21, except for a reduced risk among those assaulted as teenagers (RR 0.56, 95% CI 0.34-0.93. Adjusting for maternal smoking and BMI in a sub-sample did not substantially affect point estimates.Our prospective data suggest that women with a history of sexual assault, particularly as teenagers, are at increased risks of some adverse obstetric outcomes.

  1. Obstetric Outcomes of Mothers Previously Exposed to Sexual Violence.

    Science.gov (United States)

    Gisladottir, Agnes; Luque-Fernandez, Miguel Angel; Harlow, Bernard L; Gudmundsdottir, Berglind; Jonsdottir, Eyrun; Bjarnadottir, Ragnheidur I; Hauksdottir, Arna; Aspelund, Thor; Cnattingius, Sven; Valdimarsdottir, Unnur A

    2016-01-01

    There is a scarcity of data on the association of sexual violence and women's subsequent obstetric outcomes. Our aim was to investigate whether women exposed to sexual violence as teenagers (12-19 years of age) or adults present with different obstetric outcomes than women with no record of such violence. We linked detailed prospectively collected information on women attending a Rape Trauma Service (RTS) to the Icelandic Medical Birth Registry (IBR). Women who attended the RTS in 1993-2010 and delivered (on average 5.8 years later) at least one singleton infant in Iceland through 2012 formed our exposed cohort (n = 1068). For each exposed woman's delivery, nine deliveries by women with no RTS attendance were randomly selected from the IBR (n = 9126) matched on age, parity, and year and season of delivery. Information on smoking and Body mass index (BMI) was available for a sub-sample (n = 792 exposed and n = 1416 non-exposed women). Poisson regression models were used to estimate Relative Risks (RR) with 95% confidence intervals (CI). Compared with non-exposed women, exposed women presented with increased risks of maternal distress during labor and delivery (RR 1.68, 95% CI 1.01-2.79), prolonged first stage of labor (RR 1.40, 95% CI 1.03-1.88), antepartum bleeding (RR 1.95, 95% CI 1.22-3.07) and emergency instrumental delivery (RR 1.16, 95% CI 1.00-1.34). Slightly higher risks were seen for women assaulted as teenagers. Overall, we did not observe differences between the groups regarding the risk of elective cesarean section (RR 0.86, 95% CI 0.61-1.21), except for a reduced risk among those assaulted as teenagers (RR 0.56, 95% CI 0.34-0.93). Adjusting for maternal smoking and BMI in a sub-sample did not substantially affect point estimates. Our prospective data suggest that women with a history of sexual assault, particularly as teenagers, are at increased risks of some adverse obstetric outcomes.

  2. Urinary tract infections in hospital pediatrics: many previous antibiotherapy and antibiotics resistance, including fluoroquinolones.

    Science.gov (United States)

    Garraffo, A; Marguet, C; Checoury, A; Boyer, S; Gardrat, A; Houivet, E; Caron, F

    2014-02-01

    We studied antibiotic resistance in pediatric UTIs and we evaluated the impact of antibiotic exposure in the previous 12 months, very little French data being available for this population. We conducted a multicenter prospective study including children consulting for, or admitted in 2 hospitals. Prior antibiotic exposure was documented from their health record. One hundred and ten patients (73 girls), 11 days to 12 years of age, were included in 10 months. Ninety-six percent presented with pyelonephritis, associated to uropathy for 25%. Escherichia coli was predominant (78%), followed by Proteus spp. and Enterococcus spp. The antibiotic resistance rate of E. coli was high and close to that reported for adults with complicated UTIs: amoxicillin 60%, amoxicillin-clavulanate 35%, cefotaxim 5%, trimethoprim-sulfametoxazole 26%, nalidixic acid 9%, ciprofloxacin 7%, gentamycin 1%, nitrofurantoin and fosfomycin 0%. The antibiotic exposure in the previous 12 months involved 62 children (56%) most frequently with β-lactams (89%) for a respiratory tract infection (56%). A clear relationship between exposure and resistance was observed for amoxicillin (71% vs. 46%), first generation (65% vs. 46%) and third generation (9% vs. 3%) cephalosporins, or trimethoprim-sulfamethoxazole (36% vs. 15%). However, antibiotic exposure could not account alone for the results, as suggested by the 7% of ciprofloxacin resistance, observed without any identified previous treatment. Bacterial species and antibiotic resistance level in children are similar to those reported for adults. Antibiotic exposure in the previous 12 months increases the risk of resistance but other factors are involved (previous antibiotic therapies and fecal-oral or mother-to-child transmission). Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  3. The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

    Science.gov (United States)

    Khoe, Clairine V; Chung, Long H; Murray, Vincent

    2018-06-01

    The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

  4. The frequency of previously undetectable deletions involving 3' Exons of the PMS2 gene.

    Science.gov (United States)

    Vaughn, Cecily P; Baker, Christine L; Samowitz, Wade S; Swensen, Jeffrey J

    2013-01-01

    Lynch syndrome is characterized by mutations in one of four mismatch repair genes, MLH1, MSH2, MSH6, or PMS2. Clinical mutation analysis of these genes includes sequencing of exonic regions and deletion/duplication analysis. However, detection of deletions and duplications in PMS2 has previously been confined to Exons 1-11 due to gene conversion between PMS2 and the pseudogene PMS2CL in the remaining 3' exons (Exons 12-15). We have recently described an MLPA-based method that permits detection of deletions of PMS2 Exons 12-15; however, the frequency of such deletions has not yet been determined. To address this question, we tested for 3' deletions in 58 samples that were reported to be negative for PMS2 mutations using previously available methods. All samples were from individuals whose tumors exhibited loss of PMS2 immunohistochemical staining without concomitant loss of MLH1 immunostaining. We identified seven samples in this cohort with deletions in the 3' region of PMS2, including three previously reported samples with deletions of Exons 13-15 (two samples) and Exons 14-15. Also detected were deletions of Exons 12-15, Exon 13, and Exon 14 (two samples). Breakpoint analysis of the intragenic deletions suggests they occurred through Alu-mediated recombination. Our results indicate that ∼12% of samples suspected of harboring a PMS2 mutation based on immunohistochemical staining, for which mutations have not yet been identified, would benefit from testing using the new methodology. Copyright © 2012 Wiley Periodicals, Inc.

  5. A main sequence for quasars

    Science.gov (United States)

    Marziani, Paola; Dultzin, Deborah; Sulentic, Jack W.; Del Olmo, Ascensión; Negrete, C. A.; Martínez-Aldama, Mary L.; D'Onofrio, Mauro; Bon, Edi; Bon, Natasa; Stirpe, Giovanna M.

    2018-03-01

    The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  6. A Main Sequence for Quasars

    Directory of Open Access Journals (Sweden)

    Paola Marziani

    2018-03-01

    Full Text Available The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  7. Previously unidentified changes in renal cell carcinoma gene expression identified by parametric analysis of microarray data

    International Nuclear Information System (INIS)

    Lenburg, Marc E; Liou, Louis S; Gerry, Norman P; Frampton, Garrett M; Cohen, Herbert T; Christman, Michael F

    2003-01-01

    Renal cell carcinoma is a common malignancy that often presents as a metastatic-disease for which there are no effective treatments. To gain insights into the mechanism of renal cell carcinogenesis, a number of genome-wide expression profiling studies have been performed. Surprisingly, there is very poor agreement among these studies as to which genes are differentially regulated. To better understand this lack of agreement we profiled renal cell tumor gene expression using genome-wide microarrays (45,000 probe sets) and compare our analysis to previous microarray studies. We hybridized total RNA isolated from renal cell tumors and adjacent normal tissue to Affymetrix U133A and U133B arrays. We removed samples with technical defects and removed probesets that failed to exhibit sequence-specific hybridization in any of the samples. We detected differential gene expression in the resulting dataset with parametric methods and identified keywords that are overrepresented in the differentially expressed genes with the Fisher-exact test. We identify 1,234 genes that are more than three-fold changed in renal tumors by t-test, 800 of which have not been previously reported to be altered in renal cell tumors. Of the only 37 genes that have been identified as being differentially expressed in three or more of five previous microarray studies of renal tumor gene expression, our analysis finds 33 of these genes (89%). A key to the sensitivity and power of our analysis is filtering out defective samples and genes that are not reliably detected. The widespread use of sample-wise voting schemes for detecting differential expression that do not control for false positives likely account for the poor overlap among previous studies. Among the many genes we identified using parametric methods that were not previously reported as being differentially expressed in renal cell tumors are several oncogenes and tumor suppressor genes that likely play important roles in renal cell

  8. Order and correlations in genomic DNA sequences. The spectral approach

    International Nuclear Information System (INIS)

    Lobzin, Vasilii V; Chechetkin, Vladimir R

    2000-01-01

    The structural analysis of genomic DNA sequences is discussed in the framework of the spectral approach, which is sufficiently universal due to the reciprocal correspondence and mutual complementarity of Fourier transform length scales. The spectral characteristics of random sequences of the same nucleotide composition possess the property of self-averaging for relatively short sequences of length M≥100-300. Comparison with the characteristics of random sequences determines the statistical significance of the structural features observed. Apart from traditional applications to the search for hidden periodicities, spectral methods are also efficient in studying mutual correlations in DNA sequences. By combining spectra for structure factors and correlation functions, not only integral correlations can be estimated but also their origin identified. Using the structural spectral entropy approach, the regularity of a sequence can be quantitatively assessed. A brief introduction to the problem is also presented and other major methods of DNA sequence analysis described. (reviews of topical problems)

  9. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  10. Amplicon sequencing of bacterial microbiota in abortion material from cattle.

    Science.gov (United States)

    Vidal, Sara; Kegler, Kristel; Posthaus, Horst; Perreten, Vincent; Rodriguez-Campos, Sabrina

    2017-10-10

    Abortions in cattle have a significant economic impact on animal husbandry and require prompt diagnosis for surveillance of epizootic infectious agents. Since most abortions are not epizootic but sporadic with often undetected etiologies, this study examined the bacterial community present in the placenta (PL, n = 32) and fetal abomasal content (AC, n = 49) in 64 cases of bovine abortion by next generation sequencing (NGS) of the 16S rRNA gene. The PL and AC from three fetuses of dams that died from non-infectious reasons were included as controls. All samples were analyzed by bacterial culture, and 17 were examined by histopathology. We observed 922 OTUs overall and 267 taxa at the genus level. No detectable bacterial DNA was present in the control samples. The microbial profiles of the PL and AC differed significantly, both in their composition (PERMANOVA), species richness and Chao-1 (Mann-Whitney test). In both organs, Pseudomonas was the most abundant genus. The combination of NGS and culture identified opportunistic pathogens of interest in placentas with lesions, such as Vibrio metschnikovii, Streptococcus uberis, Lactococcus lactis and Escherichia coli. In placentas with lesions where culturing was unsuccessful, Pseudomonas and unidentified Aeromonadaceae were identified by NGS displaying high number of reads. Three cases with multiple possible etiologies and placentas presenting lesions were detected by NGS. Amplicon sequencing has the potential to uncover unknown etiological agents. These new insights on cattle abortion extend our focus to previously understudied opportunistic abortive bacteria.

  11. Hypervariable minisatellite DNA sequences in the Indian peafowl Pavo cristatus.

    Science.gov (United States)

    Hanotte, O; Burke, T; Armour, J A; Jeffreys, A J

    1991-04-01

    We report here for the first time the large-scale isolation of hypervariable minisatellite DNA sequences from a non-human species, the Indian peafowl (Pavo cristatus). A size-selected genomic DNA fraction, rich in hypervariable minisatellites, was cloned into Charomid 9-36. This library was screened using two multilocus hypervariable probes, 33.6 and 33.15 and also, in a "probe-walking" approach, with five of the peafowl minisatellites initially isolated. Forty-eight positively hybridizing clones were characterized and found to originate from 30 different loci, 18 of which were polymorphic. Five of these variable minisatellite loci were studied further. They all showed Mendelian inheritance. The heterozygosities of these loci were relatively low (range 22-78%) in comparison with those of previously cloned human loci, as expected in view of inbreeding in our semicaptive study population. No new length allele mutations were observed in families and the mean mutation rate per locus is low (less than 0.004, 95% confidence maximum). These loci were also investigated by cross-species hybridization in related taxa. The ability of the probes to detect hypervariable sequences in other species within the same avian family was found to vary, from those probes that are species-specific to those that are apparently general to the family. We also illustrate the potential usefulness of these probes for paternity analysis in a study of sexual selection, and discuss the general application of specific hypervariable probes in behavioral and evolutionary studies.

  12. Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus

    Directory of Open Access Journals (Sweden)

    Claverie Jean-Michel

    2009-10-01

    Full Text Available Abstract Heterocapsa circularisquama DNA virus (HcDNAV; previously designated as HcV is a giant virus (girus with a ~356-kbp double-stranded DNA (dsDNA genome. HcDNAV lytically infects the bivalve-killing marine dinoflagellate H. circularisquama, and currently represents the sole DNA virus isolated from dinoflagellates, one of the most abundant protists in marine ecosystems. Its morphological features, genome type, and host range previously suggested that HcDNAV might be a member of the family Phycodnaviridae of Nucleo-Cytoplasmic Large DNA Viruses (NCLDVs, though no supporting sequence data was available. NCLDVs currently include two families found in aquatic environments (Phycodnaviridae, Mimiviridae, one mostly infecting terrestrial animals (Poxviridae, another isolated from fish, amphibians and insects (Iridoviridae, and the last one (Asfarviridae exclusively represented by the animal pathogen African swine fever virus (ASFV, the agent of a fatal hemorrhagic disease in domestic swine. In this study, we determined the complete sequence of the type B DNA polymerase (PolB gene of HcDNAV. The viral PolB was transcribed at least from 6 h post inoculation (hpi, suggesting its crucial function for viral replication. Most unexpectedly, the HcDNAV PolB sequence was found to be closely related to the PolB sequence of ASFV. In addition, the amino acid sequence of HcDNAV PolB showed a rare amino acid substitution within a motif containing highly conserved motif: YSDTDS was found in HcDNAV PolB instead of YGDTDS in most dsDNA viruses. Together with the previous observation of ASFV-like sequences in the Sorcerer II Global Ocean Sampling metagenomic datasets, our results further reinforce the ideas that the terrestrial ASFV has its evolutionary origin in marine environments.

  13. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  14. Observational astrophysics

    CERN Document Server

    Léna, Pierre; Lebrun, François; Mignard, François; Pelat, Didier

    2012-01-01

    This is the updated, widely revised, restructured and expanded third edition of Léna et al.'s successful work Observational Astrophysics. It presents a synthesis on tools and methods of observational astrophysics of the early 21st century. Written specifically for astrophysicists and graduate students, this textbook focuses on fundamental and sometimes practical limitations on the ultimate performance that an astronomical system may reach, rather than presenting particular systems in detail. In little more than a decade there has been extraordinary progress in imaging and detection technologies, in the fields of adaptive optics, optical interferometry, in the sub-millimetre waveband, observation of neutrinos, discovery of exoplanets, to name but a few examples. The work deals with ground-based and space-based astronomy and their respective fields. And it also presents the ambitious concepts behind space missions aimed for the next decades. Avoiding particulars, it covers the whole of the electromagnetic spec...

  15. Observable supertranslations

    Science.gov (United States)

    Bousso, Raphael; Porrati, Massimo

    2017-10-01

    We show that large gauge transformations in asymptotically flat spacetime can be implemented by sandwiching a shell containing the ingoing hard particles between two finite-width shells of soft gauge excitations. Integration of the graviton Dirac bracket implies that our observable soft degrees of freedom obey the algebra imposed by Strominger et al. on unobservable boundary degrees of freedom. Thus, we provide both a derivation and an observable realization of this algebra. We recently showed that soft charges fail to constrain the hard scattering problem, and so cannot be relevant to the black hole information paradox. By expressing the Bondi-van der Burg-Metzner-Sachs (BMS) algebra in terms of observable quantities, the present work shows that this conclusion was not an artifact of working with strictly zero frequency soft modes. The conservation laws associated with asymptotic symmetries are seen to arise physically from free propagation of infrared modes.

  16. Observational astrophysics

    CERN Document Server

    Smith, Robert C

    1995-01-01

    Combining a critical account of observational methods (telescopes and instrumentation) with a lucid description of the Universe, including stars, galaxies and cosmology, Smith provides a comprehensive introduction to the whole of modern astrophysics beyond the solar system. The first half describes the techniques used by astronomers to observe the Universe: optical telescopes and instruments are discussed in detail, but observations at all wavelengths are covered, from radio to gamma-rays. After a short interlude describing the appearance of the sky at all wavelengths, the role of positional astronomy is highlighted. In the second half, a clear description is given of the contents of the Universe, including accounts of stellar evolution and cosmological models. Fully illustrated throughout, with exercises given in each chapter, this textbook provides a thorough introduction to astrophysics for all physics undergraduates, and a valuable background for physics graduates turning to research in astronomy.

  17. A systematic evaluation of three different cardiac T2-mapping sequences at 1.5 and 3T in healthy volunteers.

    Science.gov (United States)

    Baeßler, Bettina; Schaarschmidt, Frank; Stehning, Christian; Schnackenburg, Bernhard; Maintz, David; Bunck, Alexander C

    2015-11-01

    Previous studies showed that myocardial T2 relaxation times measured by cardiac T2-mapping vary significantly depending on sequence and field strength. Therefore, a systematic comparison of different T2-mapping sequences and the establishment of dedicated T2 reference values is mandatory for diagnostic decision-making. Phantom experiments using gel probes with a range of different T1 and T2 times were performed on a clinical 1.5T and 3T scanner. In addition, 30 healthy volunteers were examined at 1.5 and 3T in immediate succession. In each examination, three different T2-mapping sequences were performed at three short-axis slices: Multi Echo Spin Echo (MESE), T2-prepared balanced SSFP (T2prep), and Gradient Spin Echo with and without fat saturation (GraSEFS/GraSE). Segmented T2-Maps were generated according to the AHA 16-segment model and statistical analysis was performed. Significant intra-individual differences between mean T2 times were observed for all sequences. In general, T2prep resulted in lowest and GraSE in highest T2 times. A significant variation with field strength was observed for mean T2 in phantom as well as in vivo, with higher T2 values at 1.5T compared to 3T, regardless of the sequence used. Segmental T2 values for each sequence at 1.5 and 3T are presented. Despite a careful selection of sequence parameters and volunteers, significant variations of the measured T2 values were observed between field strengths, MR sequences and myocardial segments. Therefore, we present segmental T2 values for each sequence at 1.5 and 3T with the inherent potential to serve as reference values for future studies. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  18. Complete nucleotide sequence of a novel Hibiscus-infecting Cilevirus from Florida and its relationship with closely associated Cileviruses

    Science.gov (United States)

    The complete nucleotide sequence of a recently discovered Florida (FL) isolate of Hibiscus infecting Cilevirus (HiCV) was determined by Sanger sequencing. The movement- and coat- protein gene sequences of the HiCV-FL isolate are more divergent than other genes of the previously sequenced HiCV-HA (Ha...

  19. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  20. Tertiary alphabet for the observable protein structural universe.

    Science.gov (United States)

    Mackenzie, Craig O; Zhou, Jianfu; Grigoryan, Gevorg

    2016-11-22

    Here, we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs). A TERM is a compact backbone fragment that captures the secondary, tertiary, and quaternary environments around a given residue, comprising one or more disjoint segments (three on average). We seek the set of universal TERMs that capture all structure in the Protein Data Bank (PDB), finding remarkable degeneracy. Only ∼600 TERMs are sufficient to describe 50% of the PDB at sub-Angstrom resolution. However, more rare geometries also exist, and the overall structural coverage grows logarithmically with the number of TERMs. We go on to show that universal TERMs provide an effective mapping between sequence and structure. We demonstrate that TERM-based statistics alone are sufficient to recapitulate close-to-native sequences given either NMR or X-ray backbones. Furthermore, sequence variability predicted from TERM data agrees closely with evolutionary variation. Finally, locations of TERMs in protein chains can be predicted from sequence alone based on sequence signatures emergent from TERM instances in the PDB. For multisegment motifs, this method identifies spatially adjacent fragments that are not contiguous in sequence-a major bottleneck in structure prediction. Although all TERMs recur in diverse proteins, some appear specialized for certain functions, such as interface formation, metal coordination, or even water binding. Structural biology has benefited greatly from previously observed degeneracies in structure. The decomposition of the known structural universe into a finite set of compact TERMs offers exciting opportunities toward better understanding, design, and prediction of protein structure.

  1. Polymorphisms and resistance mutations of hepatitis C virus on sequences in the European hepatitis C virus database

    Science.gov (United States)

    Kliemann, Dimas Alexandre; Tovo, Cristiane Valle; da Veiga, Ana Beatriz Gorini; de Mattos, Angelo Alves; Wood, Charles

    2016-01-01

    AIM To evaluate the occurrence of resistant mutations in treatment-naïve hepatitis C virus (HCV) sequences deposited in the European hepatitis C virus database (euHCVdb). METHODS The sequences were downloaded from the euHCVdb (https://euhcvdb.ibcp.fr/euHCVdb/). The search was performed for full-length NS3 protease, NS5A and NS5B polymerase sequences of HCV, separated by genotypes 1a, 1b, 2a, 2b and 3a, and resulted in 798 NS3, 708 NS5A and 535 NS5B sequences from HCV genotypes 1a, 1b, 2a, 2b and 3a, after the exclusion of sequences containing errors and/or gaps or incomplete sequences, and sequences from patients previously treated with direct antiviral agents (DAA). The sequence alignment was performed with MEGA 6.06 MAC and the resulting protein sequences were then analyzed using the BioEdit 7.2.5. for mutations associated with resistance. Only positions that have been described as being associated with failure in treatment in in vivo studies, and/or as conferring a more than 2-fold change in replication in comparison to the wildtype reference strain in in vitro phenotypic assays were included in the analysis. RESULTS The Q80K variant in the NS3 gene was the most prevalent mutation, being found in 44.66% of subtype 1a and 0.25% of subtype 1b. Other frequent mutations observed in more than 2% of the NS3 sequences were: I170V (3.21%) in genotype 1a, and Y56F (15.93%), V132I (23.28%) and I170V (65.20%) in genotype 1b. For the NS5A, 2.21% of the genotype 1a sequences have the P58S mutation, 5.95% of genotype 1b sequences have the R30Q mutation, 15.79% of subtypes 2a sequences have the Q30R mutation, 23.08% of subtype 2b sequences have a L31M mutation, and in subtype 3a sequences, 23.08% have the M31L resistant variants. For the NS5B, the V321L RAV was identified in 0.60% of genotype 1a and in 0.32% of genotype 1b sequences, and the N142T variant was observed in 0.32% of subtype 1b sequences. The C316Y, S556G, D559N RAV were identified in 0.33%, 7.82% and 0.32% of

  2. Polymorphisms and resistance mutations of hepatitis C virus on sequences in the European hepatitis C virus database.

    Science.gov (United States)

    Kliemann, Dimas Alexandre; Tovo, Cristiane Valle; da Veiga, Ana Beatriz Gorini; de Mattos, Angelo Alves; Wood, Charles

    2016-10-28

    To evaluate the occurrence of resistant mutations in treatment-naïve hepatitis C virus (HCV) sequences deposited in the European hepatitis C virus database (euHCVdb). The sequences were downloaded from the euHCVdb (https://euhcvdb.ibcp.fr/euHCVdb/). The search was performed for full-length NS3 protease, NS5A and NS5B polymerase sequences of HCV, separated by genotypes 1a, 1b, 2a, 2b and 3a, and resulted in 798 NS3, 708 NS5A and 535 NS5B sequences from HCV genotypes 1a, 1b, 2a, 2b and 3a, after the exclusion of sequences containing errors and/or gaps or incomplete sequences, and sequences from patients previously treated with direct antiviral agents (DAA). The sequence alignment was performed with MEGA 6.06 MAC and the resulting protein sequences were then analyzed using the BioEdit 7.2.5. for mutations associated with resistance. Only positions that have been described as being associated with failure in treatment in in vivo studies, and/or as conferring a more than 2-fold change in replication in comparison to the wildtype reference strain in in vitro phenotypic assays were included in the analysis. The Q80K variant in the NS3 gene was the most prevalent mutation, being found in 44.66% of subtype 1a and 0.25% of subtype 1b. Other frequent mutations observed in more than 2% of the NS3 sequences were: I170V (3.21%) in genotype 1a, and Y56F (15.93%), V132I (23.28%) and I170V (65.20%) in genotype 1b. For the NS5A, 2.21% of the genotype 1a sequences have the P58S mutation, 5.95% of genotype 1b sequences have the R30Q mutation, 15.79% of subtypes 2a sequences have the Q30R mutation, 23.08% of subtype 2b sequences have a L31M mutation, and in subtype 3a sequences, 23.08% have the M31L resistant variants. For the NS5B, the V321L RAV was identified in 0.60% of genotype 1a and in 0.32% of genotype 1b sequences, and the N142T variant was observed in 0.32% of subtype 1b sequences. The C316Y, S556G, D559N RAV were identified in 0.33%, 7.82% and 0.32% of genotype 1b sequences

  3. Validation of the Online version of the Previous Day Food Questionnaire for schoolchildren

    Directory of Open Access Journals (Sweden)

    Raquel ENGEL

    Full Text Available ABSTRACT Objective To evaluate the validity of the web-based version of the Previous Day Food Questionnaire Online for schoolchildren from the 2nd to 5th grades of elementary school. Methods Participants were 312 schoolchildren aged 7 to 12 years of a public school from the city of Florianópolis, Santa Catarina, Brazil. Validity was assessed by sensitivity, specificity, as well as by agreement rates (match, omission, and intrusion rates of food items reported by children on the Previous Day Food Questionnaire Online, using direct observation of foods/beverages eaten during school meals (mid-morning snack or afternoon snack on the previous day as the reference. Multivariate multinomial logistic regression analysis was used to evaluate the influence of participants’ characteristics on omission and intrusion rates. Results The results showed adequate sensitivity (67.7% and specificity (95.2%. There were low omission and intrusion rates of 22.8% and 29.5%, respectively when all food items were analyzed. Pizza/hamburger showed the highest omission rate, whereas milk and milk products showed the highest intrusion rate. The participants who attended school in the afternoon shift presented a higher probability of intrusion compared to their peers who attended school in the morning. Conclusion The Previous Day Food Questionnaire Online possessed satisfactory validity for the assessment of food intake at the group level in schoolchildren from the 2nd to 5th grades of public school.

  4. Do attitudes of families concerned influence features of children who claim to remember previous lives?

    Science.gov (United States)

    Pasricha, Satwant K

    2011-01-01

    Reported cases of nearly 2600 children (subjects) who claim to remember previous lives have been investigated in cultures with and without belief in reincarnation. The authenticity in most cases has been established. To study the influence of attitudes of parents of the subjects, families of the deceased person with whom they are identified and attention paid by others on the features of the cases. The study is based on field investigations. Data is derived from analysis of a larger series of an ongoing project. Information on initial and subsequent attitudes of subjects' mothers was available for 292 and 136 cases, respectively; attitudes of 227 families of deceased person (previous personality) with whom he is identified, and the extent of attention received from outsiders for 252 cases. Observations and interviews with multiple firsthand informants on both sides of the case as well as some neutral informants supplemented by examination of objective data were the chief methods of investigation. The initial attitude of mothers varied from encouragement (21%) to neutral or tolerance (51%) to discouragement (28%). However, it changed significantly from neutrality to taking measures to induce amnesia in their children for previous life memories due to various psychosocial pressures and prevalent beliefs. Families of the previous personalities, once convinced, showed complete acceptance in a majority of cases. Outside attention was received in 58% cases. The positive attitude of parents might facilitate expression of memories but subsequently attitudes of persons concerned do not seem to alter features of the cases.

  5. Iodine-131 induced hepatotoxicity in previously healthy patients with Grave's disease.

    Science.gov (United States)

    Jhummon, Navina Priya; Tohooloo, Bhavna; Qu, Shen

    2013-01-01

    To describe the association of the rare and serious complication of liver toxicity in previously healthy Grave's disease (GD) patients after the treatment with radioactive iodine (131)I (RAI). We report the clinical, laboratory and pathologic findings of 2 cases of severe liver toxicity associated with the treatment with RAI in previously healthy patients with GD. Clinical examination and laboratory investigations excluded viral hepatitis, autoimmune hepatitis, granulomatous disease, primary biliary disease, extrahepatic biliary obstruction, and heart failure. Case 1: A previously healthy 52-years old man reportedly having a typical GD but following RAI treatment, concomitantly developed severe liver toxicity that required 1 week of treatment in hospital. Case 2: A previously healthy 34-years old woman is reported as having a typical GD but developed jaundice following RAI treatment that required several weeks of in hospital treatment in the hepato-biliary department. In both cases, the liver dysfunction resolved after intensive treatment with hepato-protective agents. In this report the therapeutic considerations as well as the pathogenetic possibilities are reviewed. To the best of our knowledge, this is the first description of the association observed, which is rare but may be severe and should be considered in any case of thyrotoxicosis where a liver dysfunction develops after the treatment with radioactive iodine (131)I.

  6. Iodine-131 induced hepatotoxicity in previously healthy patients with Grave’s disease

    Science.gov (United States)

    2013-01-01

    Objective To describe the association of the rare and serious complication of liver toxicity in previously healthy Grave’s disease (GD) patients after the treatment with radioactive iodine 131I (RAI). Case presentation We report the clinical, laboratory and pathologic findings of 2 cases of severe liver toxicity associated with the treatment with RAI in previously healthy patients with GD. Clinical examination and laboratory investigations excluded viral hepatitis, autoimmune hepatitis, granulomatous disease, primary biliary disease, extrahepatic biliary obstruction, and heart failure. Case 1: A previously healthy 52-years old man reportedly having a typical GD but following RAI treatment, concomitantly developed severe liver toxicity that required 1 week of treatment in hospital. Case 2: A previously healthy 34-years old woman is reported as having a typical GD but developed jaundice following RAI treatment that required several weeks of in hospital treatment in the hepato-biliary department. In both cases, the liver dysfunction resolved after intensive treatment with hepato-protective agents. In this report the therapeutic considerations as well as the pathogenetic possibilities are reviewed. Conclusion To the best of our knowledge, this is the first description of the association observed, which is rare but may be severe and should be considered in any case of thyrotoxicosis where a liver dysfunction develops after the treatment with radioactive iodine 131I. PMID:23497434

  7. Genetic divergence of influenza A NS1 gene in pandemic 2009 H1N1 isolates with respect to H1N1 and H3N2 isolates from previous seasonal epidemics

    Directory of Open Access Journals (Sweden)

    Campanini Giulia

    2010-09-01

    Full Text Available Abstract Background The Influenza A pandemic sustained by a new H1N1 variant (H1N1v started in Mexico and the USA at the end of April 2009 spreading worldwide in a few weeks. In this study we investigate the variability of the NS1 gene of the pandemic H1N1v strain with respect to previous seasonal strains circulating in humans and the potential selection of virus variants through isolation in cell culture. Methods During the period April 27th 2009-Jan 15th 2010, 1633 potential 2009 H1N1v cases have been screened at our center using the CDC detection and typing realtime RT-PCR assays. Virus isolation on MDCK cells was systematically performed in 1/10 positive cases. A subset of 51 H1N1v strains isolated in the period May-September 2009 was selected for NS1 gene sequencing. In addition, 15 H1N1 and 47 H3N2 virus isolates from three previous seasonal epidemics (2006-2009 were analyzed in parallel. Results A low variability in the NS1 amino acid (aa sequence among H1N1v isolates was shown (aa identity 99.5%. A slightly higher NS1 variability was observed among H1N1 and H3N2 strains from previous epidemics (aa identity 98.6% and 98.9%, respectively. The H1N1v strains were closely related (aa identity 92.1% to swine reference strain (A/swine/Oklahoma/042169/2008. In contrast, substantial divergence (aa identity 83.4% with respect to human reference strain A/Brevig Mission/1/1918 and previous epidemic strains H1N1 and H3N2 (aa identity 78.9% and 77.6%, respectively was shown. Specific sequence signatures of uncertain significance in the new virus variant were a C-terminus deletion and a T215P substitution. Conclusions The H1N1v NS1 gene was more conserved than that of previous epidemic strains. In addition, a closer genetic identity of H1N1v with the swine than the human reference strains was shown. Hot-spots were shown in the H1N1v NS1 aa sequence whose biologic relevance remains to be investigated.

  8. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  9. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  10. Low-pass sequencing for microbial comparative genomics

    Directory of Open Access Journals (Sweden)

    Kennedy Sean

    2004-01-01

    Full Text Available Abstract Background We studied four extremely halophilic archaea by low-pass shotgun sequencing: (1 the metabolically versatile Haloarcula marismortui; (2 the non-pigmented Natrialba asiatica; (3 the psychrophile Halorubrum lacusprofundi and (4 the Dead Sea isolate Halobaculum gomorrense. Approximately one thousand single pass genomic sequences per genome were obtained. The data were analyzed by comparative genomic analyses using the completed Halobacterium sp. NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe. Results As expected, the four archaeal halophiles analyzed exhibit both bacterial and eukaryotic characteristics as well as uniquely archaeal traits. All five halophiles exhibit greater than sixty percent GC content and low isoelectric points (pI for their predicted proteins. Multiple insertion sequence (IS elements, often involved in genome rearrangements, were identified in H. lacusprofundi and H. marismortui. The core biological functions that govern cellular and genetic mechanisms of H. sp. NRC-1 appear to be conserved in these four other halophiles. Multiple TATA box binding protein (TBP and transcription factor IIB (TFB homologs were identified from most of the four shotgunned halophiles. The reconstructed molecular tree of all five halophiles shows a large divergence between these species, but with the closest relationship being between H. sp. NRC-1 and H. lacusprofundi. Conclusion Despite the diverse habitats of these species, all five halophiles share (1 high GC content and (2 low protein isoelectric points, which are characteristics associated with environmental exposure to UV radiation and hypersalinity, respectively. Identification of multiple IS elements in the genome of H. lacusprofundi and H. marismortui suggest that genome structure and dynamic genome reorganization might be similar to that previously observed in the

  11. Observational cosmology

    International Nuclear Information System (INIS)

    Partridge, R.B.

    1977-01-01

    Some sixty years after the development of relativistic cosmology by Einstein and his colleagues, observations are finally beginning to have an important impact on our views of the Universe. The available evidence seems to support one of the simplest cosmological models, the hot Big Bang model. The aim of this paper is to assess the observational support for certain assumptions underlying the hot Big Bang model. These are that the Universe is isobaric and homogeneous on a large scale; that it is expanding from an initial state of high density and temperature; and that the proper theory to describe the dynamics of the Universe is unmodified General Relativity. The properties of the cosmic microwave background radiation and recent observations of the abundance of light elements, in particular, support these assumptions. Also examined here are the data bearing on the related questions of the geometry and the future of the Universe (is it ever-expanding, or fated to recollapse). Finally, some difficulties and faults of the standard model are discussed, particularly various aspects of the 'initial condition' problem. It appears that the simplest Big Bang cosmological model calls for a highly specific set of initial conditions to produce the presently observed properties of the Universe. (Auth.)

  12. Flare Observations

    Directory of Open Access Journals (Sweden)

    Benz Arnold O.

    2008-02-01

    Full Text Available Solar flares are observed at all wavelengths from decameter radio waves to gamma-rays at 100 MeV. This review focuses on recent observations in EUV, soft and hard X-rays, white light, and radio waves. Space missions such as RHESSI, Yohkoh, TRACE, and SOHO have enlarged widely the observational base. They have revealed a number of surprises: Coronal sources appear before the hard X-ray emission in chromospheric footpoints, major flare acceleration sites appear to be independent of coronal mass ejections (CMEs, electrons, and ions may be accelerated at different sites, there are at least 3 different magnetic topologies, and basic characteristics vary from small to large flares. Recent progress also includes improved insights into the flare energy partition, on the location(s of energy release, tests of energy release scenarios and particle acceleration. The interplay of observations with theory is important to deduce the geometry and to disentangle the various processes involved. There is increasing evidence supporting reconnection of magnetic field lines as the basic cause. While this process has become generally accepted as the trigger, it is still controversial how it converts a considerable fraction of the energy into non-thermal particles. Flare-like processes may be responsible for large-scale restructuring of the magnetic field in the corona as well as for its heating. Large flares influence interplanetary space and substantially affect the Earth’s lower ionosphere. While flare scenarios have slowly converged over the past decades, every new observation still reveals major unexpected results, demonstrating that solar flares, after 150 years since their discovery, remain a complex problem of astrophysics including major unsolved questions.

  13. Flare Observations

    Science.gov (United States)

    Benz, Arnold O.

    2017-12-01

    Solar flares are observed at all wavelengths from decameter radio waves to gamma-rays beyond 1 GeV. This review focuses on recent observations in EUV, soft and hard X-rays, white light, and radio waves. Space missions such as RHESSI, Yohkoh, TRACE, SOHO, and more recently Hinode and SDO have enlarged widely the observational base. They have revealed a number of surprises: Coronal sources appear before the hard X-ray emission in chromospheric footpoints, major flare acceleration sites appear to be independent of coronal mass ejections, electrons, and ions may be accelerated at different sites, there are at least 3 different magnetic topologies, and basic characteristics vary from small to large flares. Recent progress also includes improved insights into the flare energy partition, on the location(s) of energy release, tests of energy release scenarios and particle acceleration. The interplay of observations with theory is important to deduce the geometry and to disentangle the various processes involved. There is increasing evidence supporting magnetic reconnection as the basic cause. While this process has become generally accepted as the trigger, it is still controversial how it converts a considerable fraction of the energy into non-thermal particles. Flare-like processes may be responsible for large-scale restructuring of the magnetic field in the corona as well as for its heating. Large flares influence interplanetary space and substantially affect the Earth's ionosphere. Flare scenarios have slowly converged over the past decades, but every new observation still reveals major unexpected results, demonstrating that solar flares, after 150 years since their discovery, remain a complex problem of astrophysics including major unsolved questions.

  14. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  15. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.

    Science.gov (United States)

    Lapidoth, Gideon D; Baran, Dror; Pszolla, Gabriele M; Norn, Christoffer; Alon, Assaf; Tyka, Michael D; Fleishman, Sarel J

    2015-08-01

    Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity. © 2015 Wiley Periodicals, Inc.

  16. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  17. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

    An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

  18. Region segmentation along image sequence

    International Nuclear Information System (INIS)

    Monchal, L.; Aubry, P.

    1995-01-01

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs

  19. Perceptions of randomness in binary sequences: Normative, heuristic, or both?

    Science.gov (United States)

    Reimers, Stian; Donkin, Chris; Le Pelley, Mike E

    2018-03-01

    When people consider a series of random binary events, such as tossing an unbiased coin and recording the sequence of heads (H) and tails (T), they tend to erroneously rate sequences with less internal structure or order (such as HTTHT) as more probable than sequences containing more structure or order (such as HHHHH). This is traditionally explained as a local representativeness effect: Participants assume that the properties of long sequences of random outcomes-such as an equal proportion of heads and tails, and little internal structure-should also apply to short sequences. However, recent theoretical work has noted that the probability of a particular sequence of say, heads and tails of length n, occurring within a larger (>n) sequence of coin flips actually differs by sequence, so P(HHHHH) rational norms based on limited experience. We test these accounts. Participants in Experiment 1 rated the likelihood of occurrence for all possible strings of 4, 5, and 6 observations in a sequence of coin flips. Judgments were better explained by representativeness in alternation rate, relative proportion of heads and tails, and sequence complexity, than by objective probabilities. Experiments 2 and 3 gave similar results using incentivized binary choice procedures. Overall the evidence suggests that participants are not sensitive to variation in objective probabilities of a sub-sequence occurring; they appear to use heuristics based on several distinct forms of representativeness. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. The double main sequence of Omega Centauri

    Science.gov (United States)

    Bedin, L. R.; Piotto, G.; Anderson, J.; King, I. R.; Cassisi, S.; Momany, Y.

    Recent, high precision photometry of Omega Centauri, the biggest Galactic globular cluster, has been obtained with Hubble Space Telescope (HST). The color magnitude diagram reveals an unexpected bifurcation of colors in the main sequence (MS). The newly found double MS, the multiple turnoffs and subgiant branches, and other sequences discovered in the past along the red giant branch of this cluster add up to a fascinating but frustrating puzzle. Among the possible explanations for the blue main sequence an anomalous overabundance of helium is suggested. The hypothesis will be tested with a set of FLAMES@VLT data we have recently obtained (ESO DDT program), and with forthcoming ACS@HST images. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS 5-26555.

  1. Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison

    Directory of Open Access Journals (Sweden)

    Saville Barry J

    2007-09-01

    contigs that had previously escaped annotation; 3 evidence is provided that suggests the regulation of nitrogen metabolism in U. maydis differs from that of other model fungi, and 4 Alternative splicing and anti-sense transcription were identified in U. maydis and, amid similar observations in other basidiomycetes, this suggests these phenomena may be widespread in this group of fungi. These advances emphasize the importance of EST analysis in genome annotation.

  2. Inverted temperature sequences: role of deformation partitioning

    Science.gov (United States)

    Grujic, D.; Ashley, K. T.; Coble, M. A.; Coutand, I.; Kellett, D.; Whynot, N.

    2015-12-01

    The inverted metamorphism associated with the Main Central thrust zone in the Himalaya has been historically attributed to a number of tectonic processes. Here we show that there is actually a composite peak and deformation temperature sequence that formed in succession via different tectonic processes. The deformation partitioning seems to the have played a key role, and the magnitude of each process has varied along strike of the orogen. To explain the formation of the inverted metamorphic sequence across the Lesser Himalayan Sequence (LHS) in eastern Bhutan, we used Raman spectroscopy of carbonaceous material (RSCM) to determine the peak metamorphic temperatures and Ti-in-quartz thermobarometry to determine the deformation temperatures combined with thermochronology including published apatite and zircon U-Th/He and fission-track data and new 40Ar/39Ar dating of muscovite. The dataset was inverted using 3D-thermal-kinematic modeling to constrain the ranges of geological parameters such as fault geometry and slip rates, location and rates of localized basal accretion, and thermal properties of the crust. RSCM results indicate that there are two peak temperature sequences separated by a major thrust within the LHS. The internal temperature sequence shows an inverted peak temperature gradient of 12 °C/km; in the external (southern) sequence, the peak temperatures are constant across the structural sequence. Thermo-kinematic modeling suggest that the thermochronologic and thermobarometric data are compatible with a two-stage scenario: an Early-Middle Miocene phase of fast overthrusting of a hot hanging wall over a downgoing footwall and inversion of the synkinematic isotherms, followed by the formation of the external duplex developed by dominant underthrusting and basal accretion. To reconcile our observations with the experimental data, we suggest that pervasive ductile deformation within the upper LHS and along the Main Central thrust zone at its top stopped at

  3. Patterns of presentation of chronic ischemic heart disease with and without previous myocardial infarction

    International Nuclear Information System (INIS)

    Ahmad, R.; Rabbani, A.; Awan, Z.A.

    2009-01-01

    The prevalence of Ischemic Heart Disease (IHD) is on the rise, from increasing lifespan of population and availability of better medical facilities. We studied chronic IHD cases with and without previous myocardial infarction, in Hazara, NWFP, Pakistan to evaluate left ventricular (LV) dysfunction, wall motion abnormalities and complications of IHD. All patients presenting with history of chest pain in Medical 'C' Unit, Ayub Teaching Hospital, Abbottabad from June 2004 to May 2005 were included in the study. Patients with non-cardiac chest pain were excluded from the study. Cases with congenital and rheumatic heart disease, cardiomyopathies, unstable angina and acute MI were excluded. Patients with IHD with or without myocardial infarction (MI) were studied for left ventricular dysfunction (ejection fraction, left atrial size, E/A ratio), wall motion abnormalities and complications of IHD (Mitral regurgitation, Ventricular Septal Defect (VSD), LV aneurysm, LV clot). Clinical and echocardiographic evaluation was done in each case. Out of 183 cases of chronic IHD, 123 patients were without previous MI and 60 had had previous MI. Ejection fraction (EF) was 45%+-15 in the group without MI and 35+-11% in cases with MI. Left Atrium (LA) size was 35+-6 mm and 39+-4 mm in the two groups respectively. LV diastolic dysfunction was seen in 17% in the first and 24% in the second group respectively. Global hypokinesia was seen in 8% and 17% in the 2 groups respectively. Regional Wall Motion Abnormality (RWMA) was observed in 12% in patients without MI and in 58% cases with MI. Mitral regurgitation was seen in 10 and 20% in the 2 groups respectively LV clots, VSD, LV and aneurysm were seen in 8.4, 5, and 6.5% respectively, only in cases with previous MI. LV dysfunction, wall motion abnormalities and mitral regurgitation were more common in IHD cases with previous heart attack. (author)

  4. Initial results of CyberKnife treatment for recurrent previously irradiated head and neck cancer

    International Nuclear Information System (INIS)

    Himei, Kengo; Katsui, Kuniaki; Yoshida, Atsushi

    2003-01-01

    The purpose of this study was to evaluate the efficacy of CyberKnife for recurrent previously irradiated head and neck cancer. Thirty-one patients with recurrent previously irradiated head and neck cancer were treated with a CyberKnife from July 1999 to March 2002 at Okayama Kyokuto Hospital were retrospectively studied. The accumulated dose was 28-80 Gy (median 60 Gy). The interval between CyberKnife treatment and previous radiotherapy was 0.4-429.5 months (median 16.3 months). Primary lesions were nasopharynx: 7, maxillary sinus: 6, tongue: 5, ethmoid sinus: 3, and others: 1. The pathology was squamous cell carcinoma: 25, adenoid cystic carcinoma: 4, and others: 2. Symptoms were pain: 8, and nasal bleeding: 2. The prescribed dose was 15.0-40.3 Gy (median 32.3 Gy) as for the marginal dose. The response rate (complete response (CR)+partial response (PR)) and local control rate (CR+PR+no change (NC)) was 74% and 94% respectively. Pain disappeared for 4 cases, relief was obtained for 4 cases and no change for 2 cases and nasal bleeding disappeared for 2 cases for an improvement of symptoms. An adverse effects were observed as mucositis in 5 cases and neck swelling in one case. Prognosis of recurrent previously irradiated head and neck cancer was estimated as poor. Our early experience shows that CyberKnife is expected to be feasible treatment for recurrent previously irradiated head and neck cancer, and for the reduction adverse effects and maintenance of useful quality of life (QOL) for patients. (author)

  5. Effects of previous ovarian surgery for endometriosis on the outcome of assisted reproduction treatment.

    Science.gov (United States)

    Geber, Selmo; Ferreira, Daniela Parreiras; Spyer Prates, Luis Felipe Víctor; Sales, Liana; Sampaio, Marcos

    2002-01-01

    Endometriosis affects 2-50% of women at reproductive age. Surgery is an option for treatment, but there is no convincing evidence that it promotes a significant improvement in fertility. Also, the removal of ovarian endometrioma might lead to a reduction in the follicular reserve and response to stimulation. Therefore, the aim of this study was to evaluate the effect of previous ovarian surgery for endometriosis on the ovarian response in assisted reproduction treatment cycles and its pregnancy outcome. A total of 61 women, with primary infertility and previously having undergone ovarian surgery for endometriosis, who had received 74 IVF/intracytoplasmic sperm injection (ICSI) cycles, were studied (study group). A further 74 patients with primary infertility who underwent 77 IVF/ICSI cycles within#10; the same period of time, at the same clinic and without previous ovarian surgery or endometriosis were studied as a control group. Patients were matched for age and treatment performed. Patients 35 years with previous ovarian surgery needed more ampoules for ovulation induction (P = 0.017) and had fewer follicles and oocytes than women in the control group (P = 0.001). Duration of folliculogenesis was similar in both groups, as was fertilization rate. A total of 10 patients achieved pregnancy in the study group (34.5%) and 14 (48.3%) in the control group. Although a lower pregnancy rate was observed in patients who had undergone previous ovarian surgery, this difference was not statistically significant (P = 0.424). In conclusion, ovarian surgery for the treatment of endometriosis reduces the ovarian outcome in IVF/ICSI cycles in women >35 years old, and might also decrease pregnancy rates. Therefore, for infertile patients, non-surgical treatment might be a better option to avoid reduction of the ovarian response.

  6. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  7. Science from a glimpse: Hubble SNAPshot observations of massive galaxy clusters

    Science.gov (United States)

    Repp, A.; Ebeling, H.

    2018-06-01

    Hubble Space Telescope SNAPshot surveys of 86 X-ray selected galaxy clusters at 0.3 0.3. Examining the evolution of the slope of the cluster red sequence, we observe at best a slight decrease with redshift, indicating minimal age contribution since z ˜ 1. Congruent to previous studies' findings, we note that the two BCGs which are significantly bluer (≥5σ) than their clusters' red sequences reside in relaxed clusters and exhibit pronounced internal structure. Thanks to our targets' high X-ray luminosity, the subset of our sample observed with Chandra adds valuable leverage to the X-ray luminosity-optical richness relation, which, albeit with substantial scatter, is now clearly established from groups to extremely massive clusters of galaxies. We conclude that SNAPshot observations of MACS clusters stand to continue to play a vital pathfinder role for astrophysical investigations across the entire electromagnetic spectrum.

  8. New MR pulse sequence

    International Nuclear Information System (INIS)

    Harms, S.E.; Flamig, D.P.; Griffey, R.H.

    1990-01-01

    This paper describes a method for fat suppression for three-dimensional MR imaging. The FATS (fat-suppressed acquisition with echo time shortened) sequence employs a pair of opposing adiabatic half-passage RF pulses tuned on fat resonance. The imaging parameters are as follows: TR, 20 msec; TE, 21.7-3.2 msec; 1,024 x 128 x 128 acquired matrix; imaging time, approximately 11 minutes. A series of 54 examinations were performed. Excellent fat suppression with water excitation is achieved in all cases. The orbital images demonstrate superior resolution of small orbital lesions. The high signal-to-noise ratio (SNR) in cranial studies demonstrates excellent petrous bone and internal auditory canal anatomy

  9. 75 FR 39143 - Airworthiness Directives; Arrow Falcon Exporters, Inc. (previously Utah State University); AST...

    Science.gov (United States)

    2010-07-08

    ... (previously Precision Helicopters, LLC); Robinson Air Crane, Inc.; San Joaquin Helicopters (previously Hawkins... (Previously Hawkins & Powers Aviation); S.M. &T. Aircraft (Previously Us Helicopter Inc., UNC Helicopters, Inc...

  10. 75 FR 66009 - Airworthiness Directives; Cessna Aircraft Company (Type Certificate Previously Held by Columbia...

    Science.gov (United States)

    2010-10-27

    ... Company (Type Certificate Previously Held by Columbia Aircraft Manufacturing (Previously the Lancair... Company (Type Certificate Previously Held by Columbia Aircraft Manufacturing (Previously The Lancair...-15895. Applicability (c) This AD applies to the following Cessna Aircraft Company (type certificate...

  11. Effect of previous irradiation of mineral powders on stability of suspensions

    International Nuclear Information System (INIS)

    Kazaryan, G.A.; Polushkin, V.A.; Vlasov, A.V.; Tsetlin, B.L.; Chakhoyan, P.A.; TsNII Khlopchatobumazhnoj Promyshlennosti, Moscow)

    1984-01-01

    One has investigated the influence of the previous irradiation (X-rays and gamma rays) in the viscosity and the aggregative stability of the suspensions of mineral powders (e. g. kaolin, MgO, TiO 2 ) in a number of organic liquids. It has been shown that when the powders have been irradiated at a dose of the order of 10 to 100 Gy, a considerable increase in the stability of suspensions in polar organic liquids is observed. The detected phenomenon is attributed to the formation of additional, positively charged centres on the surface of the particles of mineral substances under the effect of irradiation

  12. DNA sequence analysis of X-ray induced Adh null mutations in Drosophila melanogaster

    International Nuclear Information System (INIS)

    Mahmoud, J.; Fossett, N.G.; Arbour-Reily, P.; McDaniel, M.; Tucker, A.; Chang, S.H.; Lee, W.R.

    1991-01-01

    The mutational spectrum for 28 X-ray induced mutations and 2 spontaneous mutations, previously determined by genetic and cytogenetic methods, consisted of 20 multilocus deficiencies (19 induced and 1 spontaneous) and 10 intragenic mutations (9 induced and 1 spontaneous). One of the X-ray induced intragenic mutations was lost, and another was determined to be a recombinant with the allele used in the recovery scheme. The DNA sequence of two X-ray induced intragenic mutations has been published. This paper reports the results of DNA sequence analysis of the remaining intragenic mutations and a summary of the X-ray induced mutational spectrum. The combination of DNA sequence analysis with genetic complementation analysis shows a continuous distribution in size of deletions rather than two different types of mutations consisting of deletions and 'point mutations'. Sequencing is shown to be essential for detecting intragenic deletions. Of particular importance for future studies is the observation that all of the intragenic deletions consist of a direct repeat adjacent to the breakpoint with one of the repeats deleted

  13. The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4.

    Directory of Open Access Journals (Sweden)

    Jin Duan

    Full Text Available The plant growth-promoting bacterium (PGPB Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated "housekeeping" genes (16S rRNA, gyrB, rpoB and rpoD of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.

  14. The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

    Science.gov (United States)

    Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J.; Glick, Bernard R.

    2013-01-01

    The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup. PMID:23516524

  15. Infants' statistical learning: 2- and 5-month-olds' segmentation of continuous visual sequences.

    Science.gov (United States)

    Slone, Lauren Krogh; Johnson, Scott P

    2015-05-01

    Past research suggests that infants have powerful statistical learning abilities; however, studies of infants' visual statistical learning offer differing accounts of the developmental trajectory of and constraints on this learning. To elucidate this issue, the current study tested the hypothesis that young infants' segmentation of visual sequences depends on redundant statistical cues to segmentation. A sample of 20 2-month-olds and 20 5-month-olds observed a continuous sequence of looming shapes in which unit boundaries were defined by both transitional probability and co-occurrence frequency. Following habituation, only 5-month-olds showed evidence of statistically segmenting the sequence, looking longer to a statistically improbable shape pair than to a probable pair. These results reaffirm the power of statistical learning in infants as young as 5 months but also suggest considerable development of statistical segmentation ability between 2 and 5 months of age. Moreover, the results do not support the idea that infants' ability to segment visual sequences based on transitional probabilities and/or co-occurrence frequencies is functional at the onset of visual experience, as has been suggested previously. Rather, this type of statistical segmentation appears to be constrained by the developmental state of the learner. Factors contributing to the development of statistical segmentation ability during early infancy, including memory and attention, are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

    Directory of Open Access Journals (Sweden)

    Yu-Chih Tsai

    2016-02-01

    Full Text Available Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation.

  17. Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

    Science.gov (United States)

    Tsai, Yu-Chih; Deming, Clayton; Segre, Julia A.; Kong, Heidi H.; Korlach, Jonas

    2016-01-01

    ABSTRACT Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation. PMID:26861018

  18. Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew.

    Science.gov (United States)

    Rabah, Samar O; Lee, Chaehee; Hajrah, Nahid H; Makki, Rania M; Alharby, Hesham F; Alhebshi, Alawiah M; Sabir, Jamal S M; Jansen, Robert K; Ruhlman, Tracey A

    2017-11-01

    In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative in cinnamon ( J. Presl) and other sequenced Lauraceae and an apparent functional transfer of to the nucleus of quinoa ( Willd.). In the orchard tree cashew ( L.), we report the insertion of an ∼6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact open reading frame. Using three plastome markers for five species of , we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated. Copyright © 2017 Crop Science Society of America.

  19. The nucleotide sequence of a Polish isolate of Tomato torrado virus.

    Science.gov (United States)

    Budziszewska, Marta; Obrepalska-Steplowska, Aleksandra; Wieczorek, Przemysław; Pospieszny, Henryk

    2008-12-01

    A new virus was isolated from greenhouse tomato plants showing symptoms of leaf and apex necrosis in Wielkopolska province in Poland in 2003. The observed symptoms and the virus morphology resembled viruses previously reported in Spain called Tomato torrado virus (ToTV) and that in Mexico called Tomato marchitez virus (ToMarV). The complete genome of a Polish isolate Wal'03 was determined using RT-PCR amplification using oligonucleotide primers developed against the ToTV sequences deposited in Genbank, followed by cloning, sequencing, and comparison with the sequence of the type isolate. Phylogenetic analyses, performed on the basis of fragments of polyproteins sequences, established the relationship of Polish isolate Wal'03 with Spanish ToTV and Mexican ToMarV, as well as with other viruses from Sequivirus, Sadwavirus, and Cheravirus genera, reported to be the most similar to the new tomato viruses. Wal'03 genome strands has the same organization and very high homology with the ToTV type isolate, showing only some nucleotide and deduced amino acid changes, in contrast to ToMarV, which was significantly different. The phylogenetic tree clustered aforementioned viruses to the same group, indicating that they have a common origin.

  20. Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association

    Directory of Open Access Journals (Sweden)

    Bannantine John P

    2012-03-01

    Full Text Available Abstract Background The genome of Mycobacterium avium subspecies paratuberculosis (MAP is remarkably homogeneous among the genomes of bovine, human and wildlife isolates. However, previous work in our laboratories with the bovine K-10 strain has revealed substantial differences compared to sheep isolates. To systematically characterize all genomic differences that may be associated with the specific hosts, we sequenced the genomes of three U.S. sheep isolates and also obtained an optical map. Results Our analysis of one of the isolates, MAP S397, revealed a genome 4.8 Mb in size with 4,700 open reading frames (ORFs. Comparative analysis of the MAP S397 isolate showed it acquired approximately 10 large sequence regions that are shared with the human M. avium subsp. hominissuis strain 104 and lost 2 large regions that are present in the bovine strain. In addition, optical mapping defined the presence of 7 large inversions between the bovine and ovine genomes (~ 2.36 Mb. Whole-genome sequencing of 2 additional sheep strains of MAP (JTC1074 and JTC7565 further confirmed genomic homogeneity of the sheep isolates despite the presence of polymorphisms on the nucleotide level. Conclusions Comparative sequence analysis employed here provided a better understanding of the host association, evolution of members of the M. avium complex and could help in deciphering the phenotypic differences observed among sheep and cattle strains of MAP. A similar approach based on whole-genome sequencing combined with optical mapping could be employed to examine closely related pathogens. We propose an evolutionary scenario for M. avium complex strains based on these genome sequences.

  1. Molecular characterization of Fasciola gigantica from Mauritania based on mitochondrial and nuclear ribosomal DNA sequences.

    Science.gov (United States)

    Amor, Nabil; Farjallah, Sarra; Salem, Mohamed; Lamine, Dia Mamadou; Merella, Paolo; Said, Khaled; Ben Slimane, Badreddine

    2011-10-01

    Fasciolosis caused by Fasciola hepatica and Fasciola gigantica (Platyhelminthes: Trematoda: Digenea) is considered the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. From Africa, F. gigantica has been previously characterized from Burkina Faso, Senegal, Kenya, Zambia and Mali, while F. hepatica has been reported from Morocco and Tunisia, and both species have been observed from Ethiopia and Egypt on the basis of morphometric differences, while the use of molecular markers is necessary to distinguish exactly between species. Samples identified morphologically as F. gigantica (n=60) from sheep and cattle from different geographical localities of Mauritania were genetically characterized by sequences of the first (ITS-1), the 5.8S, and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA) genes and the mitochondrial Cytochrome c Oxidase I (COI) gene. Comparison of the sequences of the Mauritanian samples with sequences of Fasciola spp. from GenBank confirmed that all samples belong to the species F. gigantica. The nucleotide sequencing of ITS rDNA of F. gigantica showed no nucleotide variation in the ITS-1, 5.8S, and ITS-2 rDNA sequences among all samples examined and those from Burkina Faso, Kenya, Egypt and Iran. The phylogenetic trees based on the ITS-1 and ITS-2 sequences showed a close relationship of the Mauritanian samples with isolates of F. gigantica from different localities of Africa and Asia. The COI genotypes of the Mauritanian specimens of F. gigantica had a high level of diversity, and they belonged to the F. gigantica phylogenically distinguishable clade. The present study is the first molecular characterization of F. gigantica in sheep and cattle from Mauritania, allowing a reliable approach for the genetic differentiation of Fasciola spp. and providing basis for further studies on liver flukes in the African countries. Copyright © 2011 Elsevier Inc. All

  2. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, Richard Wood [Univ. of California, Berkeley, CA (United States)

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by 31P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 Å of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an α-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  3. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, R.W.

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  4. Functional promoter upstream p53 regulatory sequence of IGFBP3 that is silenced by tumor specific methylation

    International Nuclear Information System (INIS)

    Hanafusa, Tadashi; Shinji, Toshiyuki; Shiraha, Hidenori; Nouso, Kazuhiro; Iwasaki, Yoshiaki; Yumoto, Eichiro; Ono, Toshiro; Koide, Norio

    2005-01-01

    Insulin-like growth factor binding protein (IGFBP)-3 functions as a carrier of insulin-like growth factors (IGFs) in circulation and a mediator of the growth suppression signal in cells. There are two reported p53 regulatory regions in the IGFBP3 gene; one upstream of the promoter and one intronic. We previously reported a hot spot of promoter hypermethylation of IGFBP-3 in human hepatocellular carcinomas and derivative cell lines. As the hot spot locates at the putative upstream p53 consensus sequences, these p53 consensus sequences are really functional is a question to be answered. In this study, we examined the p53 consensus sequences upstream of the IGFBP-3 promoter for the p53 induced expression of IGFBP-3. Deletion, mutagenesis, and methylation constructs of IGFBP-3 promoter were assessed in the human hepatoblastoma cell line HepG2 for promoter activity. Deletions and mutations of these sequences completely abolished the expression of IGFBP-3 in the presence of p53 overexpression. In vitro methylation of these p53 consensus sequences also suppressed IGFBP-3 expression. In contrast, the expression of IGFBP-3 was not affected in the absence of p53 overexpression. Further, we observed by electrophoresis mobility shift assay that p53 binding to the promoter region was diminished when methylated. From these observations, we conclude that four out of eleven p53 consensus sequences upstream of the IGFBP-3 promoter are essential for the p53 induced expression of IGFBP-3, and hypermethylation of these sequences selectively suppresses p53 induced IGFBP-3 expression in HepG2 cells

  5. The Critical Exponent is Computable for Automatic Sequences

    Directory of Open Access Journals (Sweden)

    Jeffrey Shallit

    2011-08-01

    Full Text Available The critical exponent of an infinite word is defined to be the supremum of the exponent of each of its factors. For k-automatic sequences, we show that this critical exponent is always either a rational number or infinite, and its value is computable. This generalizes or recovers previous results of Krieger and others. Our technique is applicable to other situations; e.g., the computation of the optimal recurrence constant for a linearly recurrent k-automatic sequence.

  6. Compilation and analysis of Escherichia coli promoter DNA sequences.

    OpenAIRE

    Hawley, D K; McClure, W R

    1983-01-01

    The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter ...

  7. Observational astrophysics.

    Science.gov (United States)

    Léna, P.; Lebrun, F.; Mignard, F.

    This book is the 2nd edition of an English translation published in 1988 (45.003.105) of the French original "Astrophysique: Méthodes physiques de l'observation" published in 1986 (42.003.048). Written specifically for physicists and graduate students in astronomy, this textbook focuses on astronomical observation and on the basic physical principles that astronomers use to conceive, build and exploit their instruments at their ultimate limits in sensitivity or resolution. This second edition has been entirely restructured and almost doubled in size, in order to improve its clarity and to account for the great progress achieved in the last 15 years. It deals with ground-based and space-based astronomy and their respective fields. It presents the new generation of giant ground-based telescopes, with the new methods of optical interferometry and adaptive optics, and also the ambitious concepts behind planned space missions for the next decades. Avoiding particulars, it covers the whole of the electromagnetic spectrum and touches upon the "new astronomies" becoming possible with gravitational waves and neutrinos.

  8. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  9. Adenylosuccinate lyase (ADSL) and infantile autism: Absence of previously reported point mutation

    Energy Technology Data Exchange (ETDEWEB)

    Fon, E.A.; Sarrazin, J.; Rouleau, G.A. [Montreal General Hospital (Canada)] [and others

    1995-12-18

    Autism is a heterogeneous neuropsychiatric syndrome of unknown etiology. There is evidence that a deficiency in the enzyme adenylosuccinate lyase (ADSL), essential for de novo purine biosynthesis, could be involved in the pathogenesis of certain cases. A point mutation in the ADSL gene, resulting in a predicted serine-to-proline substitution and conferring structural instability to the mutant enzyme, has been reported previously in 3 affected siblings. In order to determine the prevalence of the mutation, we PCR-amplified the exon spanning the site of this mutation from the genomic DNA of patients fulfilling DSM-III-R criteria for autistic disorder. None of the 119 patients tested were found to have this mutation. Furthermore, on preliminary screening using single-strand conformation polymorphism (SSCP), no novel mutations were detected in the coding sequence of four ADSL exons, spanning approximately 50% of the cDNA. In light of these findings, it appears that mutations in the ADSL gene represent a distinctly uncommon cause of autism. 12 refs., 2 figs.

  10. Vaccinia-based influenza vaccine overcomes previously induced immunodominance hierarchy for heterosubtypic protection.

    Science.gov (United States)

    Kwon, Ji-Sun; Yoon, Jungsoon; Kim, Yeon-Jung; Kang, Kyuho; Woo, Sunje; Jung, Dea-Im; Song, Man Ki; Kim, Eun-Ha; Kwon, Hyeok-Il; Choi, Young Ki; Kim, Jihye; Lee, Jeewon; Yoon, Yeup; Shin, Eui-Cheol; Youn, Jin-Won

    2014-08-01

    Growing concerns about unpredictable influenza pandemics require a broadly protective vaccine against diverse influenza strains. One of the promising approaches was a T cell-based vaccine, but the narrow breadth of T-cell immunity due to the immunodominance hierarchy established by previous influenza infection and efficacy against only mild challenge condition are important hurdles to overcome. To model T-cell immunodominance hierarchy in humans in an experimental setting, influenza-primed C57BL/6 mice were chosen and boosted with a mixture of vaccinia recombinants, individually expressing consensus sequences from avian, swine, and human isolates of influenza internal proteins. As determined by IFN-γ ELISPOT and polyfunctional cytokine secretion, the vaccinia recombinants of influenza expanded the breadth of T-cell responses to include subdominant and even minor epitopes. Vaccine groups were successfully protected against 100 LD50 challenges with PR/8/34 and highly pathogenic avian influenza H5N1, which contained the identical dominant NP366 epitope. Interestingly, in challenge with pandemic A/Cal/04/2009 containing mutations in the dominant epitope, only the group vaccinated with rVV-NP + PA showed improved protection. Taken together, a vaccinia-based influenza vaccine expressing conserved internal proteins improved the breadth of influenza-specific T-cell immunity and provided heterosubtypic protection against immunologically close as well as distant influenza strains. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes

    Science.gov (United States)

    Marsh, T. L.; Reich, C. I.; Whitelock, R. B.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1994-01-01

    The first step in transcription initiation in eukaryotes is mediated by the TATA-binding protein, a subunit of the transcription factor IID complex. We have cloned and sequenced the gene for a presumptive homolog of this eukaryotic protein from Thermococcus celer, a member of the Archaea (formerly archaebacteria). The protein encoded by the archaeal gene is a tandem repeat of a conserved domain, corresponding to the repeated domain in its eukaryotic counterparts. Molecular phylogenetic analyses of the two halves of the repeat are consistent with the duplication occurring before the divergence of the archael and eukaryotic domains. In conjunction with previous observations of similarity in RNA polymerase subunit composition and sequences and the finding of a transcription factor IIB-like sequence in Pyrococcus woesei (a relative of T. celer) it appears that major features of the eukaryotic transcription apparatus were well-established before the origin of eukaryotic cellular organization. The divergence between the two halves of the archael protein is less than that between the halves of the individual eukaryotic sequences, indicating that the average rate of sequence change in the archael protein has been less than in its eukaryotic counterparts. To the extent that this lower rate applies to the genome as a whole, a clearer picture of the early genes (and gene families) that gave rise to present-day genomes is more apt to emerge from the study of sequences from the Archaea than from the corresponding sequences from eukaryotes.

  12. Universal sequence map (USM of arbitrary discrete sequences

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2002-02-01

    Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

  13. The genome sequence of four isolates from the family Lichtheimiaceae.

    Science.gov (United States)

    Chibucos, Marcus C; Etienne, Kizee A; Orvis, Joshua; Lee, Hongkyu; Daugherty, Sean; Lockhart, Shawn R; Ibrahim, Ashraf S; Bruno, Vincent M

    2015-07-01

    This study reports the release of draft genome sequences of two isolates of Lichtheimia corymbifera and two isolates of L. ramosa. Phylogenetic analyses indicate that the two L. corymbifera strains (CDC-B2541 and 008-049) are closely related to the previously sequenced L. corymbifera isolate (FSU 9682) while our two L. ramosa strains CDC-B5399 and CDC-B5792 cluster apart from them. These genome sequences will further the understanding of intraspecies and interspecies genetic variation within the Mucoraceae family of pathogenic fungi. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Sequencing of the Hepatitis C Virus: A Systematic Review.

    Directory of Open Access Journals (Sweden)

    Brendan Jacka

    Full Text Available Since the identification of hepatitis C virus (HCV, viral sequencing has been important in understanding HCV classification, epidemiology, evolution, transmission clustering, treatment response and natural history. The length and diversity of the HCV genome has resulted in analysis of certain regions of the virus, however there has been little standardisation of protocols. This systematic review was undertaken to map the location and frequency of sequencing on the HCV genome in peer reviewed publications, with the aim to produce a database of sequencing primers and amplicons to inform future research. Medline and Scopus databases were searched for English language publications based on keyword/MeSH terms related to sequence analysis (9 terms or HCV (3 terms, plus "primer" as a general search term. Exclusion criteria included non-HCV research, review articles, duplicate records, and incomplete description of HCV sequencing methods. The PCR primer locations of accepted publications were noted, and purpose of sequencing was determined. A total of 450 studies were accepted from the 2099 identified, with 629 HCV sequencing amplicons identified and mapped on the HCV genome. The most commonly sequenced region was the HVR-1 region, often utilised for studies of natural history, clustering/transmission, evolution and treatment response. Studies related to genotyping/classification or epidemiology of HCV genotype generally targeted the 5'UTR, Core and NS5B regions, while treatment response/resistance was assessed mainly in the NS3-NS5B region with emphasis on the Interferon sensitivity determining region (ISDR region of NS5A. While the sequencing of HCV is generally constricted to certain regions of the HCV genome there is little consistency in the positioning of sequencing primers, with the exception of a few highly referenced manuscripts. This study demonstrates the heterogeneity of HCV sequencing, providing a comprehensive database of previously

  15. The Release 6 reference sequence of the Drosophila melanogaster genome.

    Science.gov (United States)

    Hoskins, Roger A; Carlson, Joseph W; Wan, Kenneth H; Park, Soo; Mendez, Ivonne; Galle, Samuel E; Booth, Benjamin W; Pfeiffer, Barret D; George, Reed A; Svirskas, Robert; Krzywinski, Martin; Schein, Jacqueline; Accardo, Maria Carmela; Damia, Elisabetta; Messina, Giovanni; Méndez-Lago, María; de Pablos, Beatriz; Demakova, Olga V; Andreyeva, Evgeniya N; Boldyreva, Lidiya V; Marra, Marco; Carvalho, A Bernardo; Dimitri, Patrizio; Villasante, Alfredo; Zhimulev, Igor F; Rubin, Gerald M; Karpen, Gary H; Celniker, Susan E

    2015-03-01

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads. © 2015 Hoskins et al.; Published by Cold Spring Harbor Laboratory Press.

  16. Rapid mineralisation of the herbicide isoproturon in soil from a previously treated Danish agricultural field.

    Science.gov (United States)

    Sørensen, Sebastian R; Aamand, Jens

    2003-10-01

    Mineralisation of the phenylurea herbicide isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea) and two of its known metabolites, 3-(4-isopropylphenyl)-1-methylurea (monodesmethyl-isoproturon) and 4-isopropylaniline, was studied in Danish agricultural soils with or without previous exposure to isoproturon. A potential for rapid mineralisation of isoproturon and the two metabolites was present in soils sampled from three plots within an agricultural field previously treated regularly with the herbicide, with 34-45%, 51-58% and 33-36% of the added [phenyl-U-14C]isoproturon, [phenyl-U-14C]monodesmethyl-isoproturon and [phenyl-U-14C]4-isopropylaniline metabolised to [14C]carbon dioxide within 30 days at 20 degrees C. In contrast, such extensive mineralisation of these three compounds was not observed within this period in soils sampled from two other agricultural fields without previous treatment with isoproturon. The mineralisation patterns indicated growth-linked metabolism of the three compounds in the previously exposed soils, and doubling times for [14C]carbon dioxide production ranged from 1.6 to 3.2, 1.0 to 2.1 and 1.3 to 1.7 days for isoproturon, monodesmethyl-isoproturon and 4-isopropylaniline, respectively. The ability to mineralise [phenyl-U-14C]isoproturon to [14C]carbon dioxide was successfully sub-cultured to a fresh mineral medium which provided isoproturon as sole source of carbon and nitrogen. One of the soils sampled from an agricultural field not previously treated with isoproturon showed accelerated mineralisation of [phenyl-U-14C]4-isopropylaniline toward the end of the experiment, with a doubling time for [14C]carbon dioxide production of 7.4days. This study indicates that the occurrence of rapid mineralisation of the phenyl ring of isoproturon to carbon dioxide is related to previous exposure to the herbicide, which suggests that microbial adaptation upon repeated isoproturon use may occur within agricultural fields.

  17. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

    Directory of Open Access Journals (Sweden)

    Li Kelvin

    2012-11-01

    Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

  18. Economic impact of feeding a phenylalanine-restricted diet to adults with previously untreated phenylketonuria.

    Science.gov (United States)

    Brown, M C; Guest, J F

    1999-02-01

    The aim of the present study was to estimate the direct healthcare cost of managing adults with previously untreated phenylketonuria (PKU) for one year before any dietary restrictions and for the first year after a phenylalanine- (PHE-) restricted diet was introduced. The resource use and corresponding costs were estimated from medical records and interviews with health care professionals experienced in caring for adults with previously untreated PKU. The mean annual cost of caring for a client being fed an unrestricted diet was estimated to be 83 996 pound silver. In the first year after introducing a PHE-restricted diet, the mean annual cost was reduced by 20 647 pound silver to 63 348 pound silver as a result of a reduction in nursing time, hospitalizations, outpatient clinic visits and medications. However, the economic benefit of the diet depended on whether the clients were previously high or low users of nursing care. Nursing time was the key cost-driver, accounting for 79% of the cost of managing high users and 31% of the management cost for low users. In contrast, the acquisition cost of a PHE-restricted diet accounted for up to 6% of the cost for managing high users and 15% of the management cost for low users. Sensitivity analyses showed that introducing a PHE-restricted diet reduces the annual cost of care, provided that annual nursing time was reduced by more than 8% or more than 5% of clients respond to the diet. The clients showed fewer negative behaviours when being fed a PHE-restricted diet, which may account for the observed reduction in nursing time needed to care for these clients. In conclusion, feeding a PHE-restricted diet to adults with previously untreated PKU leads to economic benefits to the UK's National Health Service and society in general.

  19. Does previous abdominal surgery affect the course and outcomes of laparoscopic bariatric surgery?

    Science.gov (United States)

    Major, Piotr; Droś, Jakub; Kacprzyk, Artur; Pędziwiatr, Michał; Małczak, Piotr; Wysocki, Michał; Janik, Michał; Walędziak, Maciej; Paśnik, Krzysztof; Hady, Hady Razak; Dadan, Jacek; Proczko-Stepaniak, Monika; Kaska, Łukasz; Lech, Paweł; Michalik, Maciej; Duchnik, Michał; Kaseja, Krzysztof; Pastuszka, Maciej; Stepuch, Paweł; Budzyński, Andrzej

    2018-03-26

    Global experiences in general surgery suggest that previous abdominal surgery may negatively influence different aspects of perioperative care. As the incidence of bariatric procedures has recently increased, it is essential to assess such correlations in bariatric surgery. To assess whether previous abdominal surgery influences the course and outcomes of laparoscopic bariatric surgery. Seven referral bariatric centers in Poland. We conducted a retrospective analysis of 2413 patients; 1706 patients who underwent laparoscopic sleeve gastrectomy (SG) or Roux-en-Y gastric bypass (RYGB) matched the inclusion criteria. Patients with no history of abdominal surgery were included as group 1, while those who had undergone at least 1 abdominal surgery were included as group 2. Group 2 had a significantly prolonged median operation time for RYGB (P = .012), and the longest operation time was observed in patients who had previously undergone surgeries in both the upper and lower abdomen (P = .002). Such a correlation was not found in SG cases (P = .396). Groups 1 and 2 had similar rates of intraoperative adverse events and postoperative complications (P = .562 and P = .466, respectively). Group 2 had a longer median duration of hospitalization than group 1 (P = .034), while the readmission rate was similar between groups (P = .079). There was no significant difference between groups regarding the influence of the long-term effects of bariatric treatment on weight loss (percentage of follow-up was 55%). Previous abdominal surgery prolongs the operative time of RYGB and the duration of postoperative hospitalization, but does not affect the long-term outcomes of bariatric treatment. Copyright © 2018 American Society for Bariatric Surgery. Published by Elsevier Inc. All rights reserved.

  20. Is the Universe More Transparent to Gamma Rays than Previously Thought?

    Science.gov (United States)

    Stecker, Floyd W.; Scully, Sean T.

    2009-01-01

    The MAGIC collaboration has recently reported the detection of the strong gamma-ray blazar 3C279 during a 1-2 day flare. They have used their spectral observations to draw conclusions regarding upper limits on the opacity of the Universe to high energy gamma-rays and, by implication, upper limits on the extragalactic mid-infrared background radiation. In this paper we examine the effect of gamma-ray absorption by the extragalactic infrared radiation on intrinsic spectra for this blazar and compare our results with the observational data on 3C279. We find agreement with our previous results, contrary to the recent assertion of the MAGIC group that the Universe is more transparent to gamma-rays than our calculations indicate. Our analysis indicates that in the energy range between approx. 80 and approx. 500 GeV, 3C279 has a best-fit intrinsic spectrum with a spectral index approx. 1.78 using our fast evolution model and approx. 2.19 using our baseline model. However, we also find that spectral indices in the range of 1.0 to 3.0 are almost as equally acceptable as the best fit spectral indices. Assuming the same intrinsic spectral index for this flare as for the 1991 flare from 3C279 observed by EGRET, viz., 2.02, which lies between our best fit indeces, we estimate that the MAGIC flare was approx.3 times brighter than the EGRET flare observed 15 years earlier.

  1. Implicity Defined Neural Networks for Sequence Labeling

    Science.gov (United States)

    2017-02-13

    assumption - that a hid- den variable changes its state based only on its current state and observables. In finding maximum likelihood state sequences...this setup, we have the following variables : data X labels Y parameters θ and functions: implicit hidden layer definition H = F (θ, ξ,H) loss function L...tagging task. In future work, we intend to consider implicit varia - tions of other archetectures, such as the LSTM, as well as additional, more challenging

  2. The Sirenomelia Sequence: A Case History

    Directory of Open Access Journals (Sweden)

    Anis Fadhlaoui

    2010-01-01

    Full Text Available We report a case of sirenomelia sequence observed in an incident of preterm labor during the 29th gestational week. According to some authors, this syndrome should be classified separately from caudal regression syndrome and is likely to be the result of an abnormality taking place during the fourth gestational week, causing developmental abnormalities in the lower extremities, pelvis, genitalia, urinary tract and digestive organs. Despite recent progress in pathology, the etiopathogenesis of sirenomelia is still debated.

  3. The Sirenomelia Sequence: A Case History

    Science.gov (United States)

    Fadhlaoui, Anis; Khrouf, Mohamed; Gaigi, Soumaya; Zhioua, Fethi; Chaker, Anis

    2010-01-01

    We report a case of sirenomelia sequence observed in an incident of preterm labor during the 29th gestational week. According to some authors, this syndrome should be classified separately from caudal regression syndrome and is likely to be the result of an abnormality taking place during the fourth gestational week, causing developmental abnormalities in the lower extremities, pelvis, genitalia, urinary tract and digestive organs. Despite recent progress in pathology, the etiopathogenesis of sirenomelia is still debated. PMID:21769253

  4. The sirenomelia sequence: a case history.

    Science.gov (United States)

    Fadhlaoui, Anis; Khrouf, Mohamed; Gaigi, Soumaya; Zhioua, Fethi; Chaker, Anis

    2010-01-01

    We report a case of sirenomelia sequence observed in an incident of preterm labor during the 29th gestational week. According to some authors, this syndrome should be classified separately from caudal regression syndrome and is likely to be the result of an abnormality taking place during the fourth gestational week, causing developmental abnormalities in the lower extremities, pelvis, genitalia, urinary tract and digestive organs. Despite recent progress in pathology, the etiopathogenesis of sirenomelia is still debated.

  5. Post-main-sequence planetary system evolution

    Science.gov (United States)

    Veras, Dimitri

    2016-01-01

    The fates of planetary systems provide unassailable insights into their formation and represent rich cross-disciplinary dynamical laboratories. Mounting observations of post-main-sequence planetary systems necessitate a complementary level of theoretical scrutiny. Here, I review the diverse dynamical processes which affect planets, asteroids, comets and pebbles as their parent stars evolve into giant branch, white dwarf and neutron stars. This reference provides a foundation for the interpretation and modelling of currently known systems and upcoming discoveries. PMID:26998326

  6. Rocket observations

    Science.gov (United States)

    1984-05-01

    The Institute of Space and Astronautical Science (ISAS) sounding rocket experiments were carried out during the periods of August to September, 1982, January to February and August to September, 1983 and January to February, 1984 with sounding rockets. Among 9 rockets, 3 were K-9M, 1 was S-210, 3 were S-310 and 2 were S-520. Two scientific satellites were launched on February 20, 1983 for solar physics and on February 14, 1984 for X-ray astronomy. These satellites were named as TENMA and OHZORA and designated as 1983-011A and 1984-015A, respectively. Their initial orbital elements are also described. A payload recovery was successfully carried out by S-520-6 rocket as a part of MINIX (Microwave Ionosphere Non-linear Interaction Experiment) which is a scientific study of nonlinear plasma phenomena in conjunction with the environmental assessment study for the future SPS project. Near IR observation of the background sky shows a more intense flux than expected possibly coming from some extragalactic origin and this may be related to the evolution of the universe. US-Japan cooperative program of Tether Experiment was done on board US rocket.

  7. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  8. Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

    Directory of Open Access Journals (Sweden)

    Takeru Nakazato

    Full Text Available High-throughput sequencing technology, also called next-generation sequencing (NGS, has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA. As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/. This service will improve accessibility to high-quality data from SRA.

  9. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  10. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  11. Whole Exome Sequencing for a Patient with Rubinstein-Taybi Syndrome Reveals de Novo Variants besides an Overt CREBBP Mutation

    Directory of Open Access Journals (Sweden)

    Hee Jeong Yoo

    2015-03-01

    Full Text Available Rubinstein-Taybi syndrome (RSTS is a rare condition with a prevalence of 1 in 125,000–720,000 births and characterized by clinical features that include facial, dental, and limb dysmorphology and growth retardation. Most cases of RSTS occur sporadically and are caused by de novo mutations. Cytogenetic or molecular abnormalities are detected in only 55% of RSTS cases. Previous genetic studies have yielded inconsistent results due to the variety of methods used for genetic analysis. The purpose of this study was to use whole exome sequencing (WES to evaluate the genetic causes of RSTS in a young girl presenting with an Autism phenotype. We used the Autism diagnostic observation schedule (ADOS and Autism diagnostic interview revised (ADI-R to confirm her diagnosis of Autism. In addition, various questionnaires were used to evaluate other psychiatric features. We used WES to analyze the DNA sequences of the patient and her parents and to search for de novo variants. The patient showed all the typical features of Autism, WES revealed a de novo frameshift mutation in CREBBP and de novo sequence variants in TNC and IGFALS genes. Mutations in the CREBBP gene have been extensively reported in RSTS patients, while potential missense mutations in TNC and IGFALS genes have not previously been associated with RSTS. The TNC and IGFALS genes are involved in central nervous system development and growth. It is possible for patients with RSTS to have additional de novo variants that could account for previously unexplained phenotypes.

  12. Feline leprosy due to Candidatus 'Mycobacterium lepraefelis': Further clinical and molecular characterisation of eight previously reported cases and an additional 30 cases.

    Science.gov (United States)

    O'Brien, Carolyn R; Malik, Richard; Globan, Maria; Reppas, George; McCowan, Christina; Fyfe, Janet A

    2017-09-01

    This paper, the last in a series of three on 'feline leprosy', provides a detailed description of disease referable to the previously unnamed species, Candidatus 'Mycobacterium lepraefelis', a close relative of the human pathogens Mycobacterium leprae and Mycobacterium lepromatosis. Cases were sourced retrospectively and prospectively for this observational study, describing clinical, geographical and molecular microbiological data for cats definitively diagnosed with Candidatus 'M lepraefelis' infection. A total of 145 cases of feline leprosy were scrutinised; 114 'new' cases were sourced from the Victorian Infectious Diseases Reference Laboratory (VIDRL) records, veterinary pathology laboratories or veterinarians, and 31 cases were derived from six published studies. Thirty-eight cats were definitively diagnosed with Candidatus 'M lepraefelis' infection. Typically, cats tended to be middle-aged or older when first infected, with a male predilection. Affected cats typically had widespread cutaneous lesions, in some cases after initially localised disease. Advanced cases were often systemically unwell. All cats had outdoor access. The histological picture was lepromatous in the majority of patients, although two cases had tuberculoid disease. In one case that underwent necropsy, lesions were evident in the liver, spleen and lungs. Treatment was varied, although most cats received a combination of oral clarithromycin and rifampicin. Prognosis for recovery was variable, but typically poor. Candidatus 'M lepraefelis' typically causes high bacterial index (lepromatous) feline leprosy that in some cases progresses to systemic mycobacteriosis. The disease has a variable clinical course and prognosis. Many cases either died or were euthanased due to the infection. Multilocus sequence analysis reveals a heterogeneous picture and further analysis of draft genome sequencing may give clues to the taxonomy and epidemiology of this organism. Prospective treatment trials and

  13. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  14. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  15. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  16. Predictive Place-Cell Sequences for Goal-Finding Emerge from Goal Memory and the Cognitive Map: A Computational Model

    Directory of Open Access Journals (Sweden)

    Lorenz Gönner

    2017-10-01

    Full Text Available Hippocampal place-cell sequences observed during awake immobility often represent previous experience, suggesting a role in memory processes. However, recent reports of goals being overrepresented in sequential activity suggest a role in short-term planning, although a detailed understanding of the origins of hippocampal sequential activity and of its functional role is still lacking. In particular, it is unknown which mechanism could support efficient planning by generating place-cell sequences biased toward known goal locations, in an adaptive and constructive fashion. To address these questions, we propose a model of spatial learning and sequence generation as interdependent processes, integrating cortical contextual coding, synaptic plasticity and neuromodulatory mechanisms into a map-based approach. Following goal learning, sequential activity emerges from continuous attractor network dynamics biased by goal memory inputs. We apply Bayesian decoding on the resulting spike trains, allowing a direct comparison with experimental data. Simulations show that this model (1 explains the generation of never-experienced sequence trajectories in familiar environments, without requiring virtual self-motion signals, (2 accounts for the bias in place-cell sequences toward goal locations, (3 highlights their utility in flexible route planning, and (4 provides specific testable predictions.

  17. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

  18. The Sequence Effect in Parkinson’s Disease

    Directory of Open Access Journals (Sweden)

    Suk Yun Kang

    2011-05-01

    Full Text Available Background and Purpose The sequence effect (SE in Parkinson’s disease (PD denotes progressive slowness in speed or progressive decrease in amplitude of repetitive movements. It is a well-known feature of bradykinesia and is considered unique in PD. Until now, it was well-documented in advanced PD, but not in drug-naïve PD. The aim of this study is to know whether the SE can also be measured in drug-naïve PD. Methods We measured the SE with a computer-based, modified Purdue pegboard in 4 drug-naïve PD patients, which matched our previous study with advanced PD patients. Results We observed progressive slowness during movement, that is, SE. Statistical analysis showed a strong statistical trend toward the SE with the right hand, but no significance with the left hand. There was no statistical significance of SE with either the more or less affected hands. Conclusions These results indicate that the SE can be identified in drug-naïve PD, as well as in advanced PD, with objective measurements and support the idea that the SE is a feature in PD observed during the early stage of the disease without medication.

  19. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  20. SVX Sequencer Board

    International Nuclear Information System (INIS)

    Utes, M.

    1997-01-01

    The SVX Sequencer boards are 9U by 280mm circuit boards that reside in slots 2 through 21 of each of eight Eurocard crates in the D0 Detector Platform. The basic purpose is to control the SVX chips for data acquisition and when a trigger occurs, to gather the SVX data and relay the data to the VRB boards in the Movable Counting House. Functions and features are as follows: (1) Initialization of eight SVX chip strings using the MIL-STD-1553 data bus; (2) Real time manipulation of the SVX control lines to effect data acquisition, digitization, and readout based on the NRZ/Clock signals from the Controller; (3) Conversion of 8-bit electrical SVX readout data to an optical signal operating at 1.062 Gbit/sec, sent to the VRB. Eight HDIs will be serviced per board; (4) Built-in logic analyzer which can record the most important control and data lines during a data acquisition cycle and put this recorded information onto the 1553 bus; (5) Identification header and end of data trailer tacked onto data stream; (6) 1553 register which can read the current values of the control and data lines; (7) 1553 register which can test the optical link; (8) 1553 registers for crossing pulse width, calibration pulse voltage, and calibration pipeline select; (9) 1553 register for reading the optical drivers status link; (10) 1553 register for power control of SVX chips and ignoring bad SVX strings; (11) Front panel displays and LEDs show the board status at a glance; (12) In-system programmable EPLDs are programmed via 1553 or Altera's 'Bitblaster'; (13) Automatic readout abort after 45us; (14) Supplies BUSY signal back to Trigger Framework; (15) Supports a heartbeat system to prevent excessive SVX current draw; and (16) Supports a SVX power trip feature if heartbeat failure occurs.

  1. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    International Nuclear Information System (INIS)

    Rauzy, Antoine B.

    2011-01-01

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  2. Spatio-temporal alignment of pedobarographic image sequences.

    Science.gov (United States)

    Oliveira, Francisco P M; Sousa, Andreia; Santos, Rubim; Tavares, João Manuel R S

    2011-07-01

    This article presents a methodology to align plantar pressure image sequences simultaneously in time and space. The spatial position and orientation of a foot in a sequence are changed to match the foot represented in a second sequence. Simultaneously with the spatial alignment, the temporal scale of the first sequence is transformed with the aim of synchronizing the two input footsteps. Consequently, the spatial correspondence of the foot regions along the sequences as well as the temporal synchronizing is automatically attained, making the study easier and more straightforward. In terms of spatial alignment, the methodology can use one of four possible geometric transformation models: rigid, similarity, affine, or projective. In the temporal alignment, a polynomial transformation up to the 4th degree can be adopted in order to model linear and curved time behaviors. Suitable geometric and temporal transformations are found by minimizing the mean squared error (MSE) between the input sequences. The methodology was tested on a set of real image sequences acquired from a common pedobarographic device. When used in experimental cases generated by applying geometric and temporal control transformations, the methodology revealed high accuracy. In addition, the intra-subject alignment tests from real plantar pressure image sequences showed that the curved temporal models produced better MSE results (P alignment of pedobarographic image data, since previous methods can only be applied on static images.

  3. Optimization of micropillar sequences for fluid flow sculpting

    Energy Technology Data Exchange (ETDEWEB)

    Stoecklein, Daniel; Ganapathysubramanian, Baskar [Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011 (United States); Wu, Chueh-Yu; Kim, Donghyuk; Di Carlo, Dino [Department of Bioengineering, University of California at Los Angeles, Los Angeles, California 90095 (United States)

    2016-01-15

    Inertial fluid flow deformation around pillars in a microchannel is a new method for controlling fluid flow. Sequences of pillars have been shown to produce a rich phase space with a wide variety of flow transformations. Previous work has successfully demonstrated manual design of pillar sequences to achieve desired transformations of the flow cross section, with experimental validation. However, such a method is not ideal for seeking out complex sculpted shapes as the search space quickly becomes too large for efficient manual discovery. We explore fast, automated optimization methods to solve this problem. We formulate the inertial flow physics in microchannels with different micropillar configurations as a set of state transition matrix operations. These state transition matrices are constructed from experimentally validated streamtraces for a fixed channel length per pillar. This facilitates modeling the effect of a sequence of micropillars as nested matrix-matrix products, which have very efficient numerical implementations. With this new forward model, arbitrary micropillar sequences can be rapidly simulated with various inlet configurations, allowing optimization routines quick access to a large search space. We integrate this framework with the genetic algorithm and showcase its applicability by designing micropillar sequences for various useful transformations. We computationally discover micropillar sequences for complex transformations that are substantially shorter than manually designed sequences. We also determine sequences for novel transformations that were difficult to manually design. Finally, we experimentally validate these computational designs by fabricating devices and comparing predictions with the results from confocal microscopy.

  4. Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

    Science.gov (United States)

    Chatterjee, Aniruddha; Rodger, Euan J.; Stockwell, Peter A.; Weeks, Robert J.; Morison, Ian M.

    2012-01-01

    Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background. PMID:23193365

  5. A programmable method for massively parallel targeted sequencing

    Science.gov (United States)

    Hopmans, Erik S.; Natsoulis, Georges; Bell, John M.; Grimes, Susan M.; Sieh, Weiva; Ji, Hanlee P.

    2014-01-01

    We have developed a targeted resequencing approach referred to as Oligonucleotide-Selective Sequencing. In this study, we report a series of significant improvements and novel applications of this method whereby the surface of a sequencing flow cell is modified in situ to capture specific genomic regions of interest from a sample and then sequenced. These improvements include a fully automated targeted sequencing platform through the use of a standard Illumina cBot fluidics station. Targeting optimization increased the yield of total on-target sequencing data 2-fold compared to the previous iteration, while simultaneously increasing the percentage of reads that could be mapped to the human genome. The described assays cover up to 1421 genes with a total coverage of 5.5 Megabases (Mb). We demonstrate a 10-fold abundance uniformity of greater than 90% in 1 log distance from the median and a targeting rate of up to 95%. We also sequenced continuous genomic loci up to 1.5 Mb while simultaneously genotyping SNPs and genes. Variants with low minor allele fraction were sensitively detected at levels of 5%. Finally, we determined the exact breakpoint sequence of cancer rearrangements. Overall, this approach has high performance for selective sequencing of genome targets, configuration flexibility and variant calling accuracy. PMID:24782526

  6. The Iquique 2014 sequence: understanding its nucleation and propagation from the seismicity evolution

    Science.gov (United States)

    Fuenzalida, A.; Rietbrock, A.; Woollam, J.; Tavera, H.; Ruiz, S.

    2017-12-01

    The Northern Chile and Southern Peru region is well known for its high seismic hazard due to the lack of recent major ruptures along long segments of the subduction interface. For this reason the 2014 Iquique Mw 8.1 earthquake that occurred in the Northern Chile seismic gap was expected and high quality seismic and geodetic networks were operating at the time of the event recording the precursory phase of a mega-thrust event with unprecedented detail. In this study we used seismic data collected during the 2014 Iquique sequence to generate a detailed earthquake catalogue. This catalogue consists of more than 15,000 events identified in Northern Chile during the period between 1/3/14 and 31/5/14 and provides full coverage of the immediate foreshock sequence, the main-shock and early after-shock series. The initial catalogue was obtained by automatic data processing and only selecting events with at least two associate S phases to improve the reliability of initial locations. Subsequently, this subset of events was automatically processed again using an optimized STA/LTA triggering algorithm for both P and S-waves and constraining the detection times by estimated arrival times at each station calculated for the preliminary locations. Finally, all events were relocated using a recently developed 1D velocity model and associated station corrections. For events Mw 4 or larger that occurred between the 15/3/14 and 10/04/14, we estimated it regional moment tensor by full-waveform inversion. Our results confirm the seismic activation of the upper plate during the foreshock sequence, as well highlight a crustal activity on the fore-arc during the aftershock series. The seismicity distribution was compared to the previous inter-seismic coupling studies obtained in the region, in which we observe interplay between high and low coupling areas, which are correlated to the seismicity rate. The spatial distribution of the seismicity and the complexities on the mechanisms observed

  7. Identification of a previously undescribed divergent virus from the Flaviviridae family in an outbreak of equine serum hepatitis.

    Science.gov (United States)

    Chandriani, Sanjay; Skewes-Cox, Peter; Zhong, Weidong; Ganem, Donald E; Divers, Thomas J; Van Blaricum, Anita J; Tennant, Bud C; Kistler, Amy L

    2013-04-09

    Theiler's disease is an acute hepatitis in horses that is associated with the administration of equine blood products; its etiologic agent has remained unknown for nearly a century. Here, we used massively parallel sequencing to explore samples from a recent Theiler's disease outbreak. Metatranscriptomic analysis of the short sequence reads identified a 10.5-kb sequence from a previously undescribed virus of the Flaviviridae family, which we designate "Theiler's disease-associated virus" (TDAV). Phylogenetic analysis clusters TDAV with GB viruses of the recently proposed Pegivirus genus, although it shares only 35.3% amino acid identity with its closest relative, GB virus D. An epidemiological survey of additional horses from three separate locations supports an association between TDAV infection and acute serum hepatitis. Experimental inoculation of horses with TDAV-positive plasma provides evidence that several weeks of viremia preceded liver injury and that liver disease may not be directly related to the level of viremia. Like hepatitis C virus, the best characterized Flaviviridae species known to cause hepatitis, we find TDAV is capable of efficient parenteral transmission, engendering acute and chronic infections associated with a diversity of clinical presentations ranging from subclinical infection to clinical hepatitis.

  8. Clinical outcomes of Laparoscopically Assisted Vaginal Hysterectomy at patients who had previous abdominopelvic surgery

    Directory of Open Access Journals (Sweden)

    Ali Riza Odabasi

    2007-03-01

    Full Text Available OBJECTIVE: To determine clinical outcomes of Laparoscopically Assisted Vaginal Hysterectomy (LAVH at patients who had previous abdominopelvic surgery.\tDesign: A clinical observational, prospective, non randomised trial comparing outcomes of 13 patients who had previous abdominopelvic surgery with outcomes of 19 patients who had not surgery.\tSetting: Adnan Menderes University Faculty of Medicine, Department of Obstetrics and Gynecology.\tPatients: Thirty-two subjects [average age 51,1±6,9 (37-66] who had indication of total abdominal hysterectomy and bilateral\tsalpingooferectomy due to benign pathologies.\tInterventions: According to ACOG, LAVH was performed by using the Garry technique at the trocar insertions, the Reich technique\tat the laparoscopic phase and the Heaney technique at the vaginal phase by the same operator. After adhesiolysis and diagnostic procedures, ureters were dissected medially. By coagulating, bilateral round and infundibulopelvic ligaments were cut after the\tmobilisation of bladder. The operation was completed by the same operation team by vaginal approach consequently. At all operations, 80 W unipolar or 150 W bipolar diathermic dissection and 25-35 W unipolar diathermic cutting were performed.\tMain outcome measures: Age, parity, menopausal status, preoperative indications, type of previous abdominopelvic surgey and incision, intraoperative indications, adhesion scores, rate of unintended laparotomy, operative time, uterus weight, loss of blood,\tcomplications, postoperative pain scores and analgesic requirements, time necessary for returning to normal intestinal function, length of hospitalisation and rate of readmission to hospital.\tRESULTS: When compared with the patients who had not previous abdominopelvic surgery, all adhesion scores, uterus weight, operative time and the number of total postoperative complications were found significantly high at patients who had previous\tsurgery. Loss of blood, the rate

  9. An extended sequence specificity for UV-induced DNA damage.

    Science.gov (United States)

    Chung, Long H; Murray, Vincent

    2018-01-01

    The sequence specificity of UV-induced DNA damage was determined with a higher precision and accuracy than previously reported. UV light induces two major damage adducts: cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). Employing capillary electrophoresis with laser-induced fluorescence and taking advantages of the distinct properties of the CPDs and 6-4PPs, we studied the sequence specificity of UV-induced DNA damage in a purified DNA sequence using two approaches: end-labelling and a polymerase stop/linear amplification assay. A mitochondrial DNA sequence that contained a random nucleotide composition was employed as the target DNA sequence. With previous methodology, the UV sequence specificity was determined at a dinucleotide or trinucleotide level; however, in this paper, we have extended the UV sequence specificity to a hexanucleotide level. With the end-labelling technique (for 6-4PPs), the consensus sequence was found to be 5'-GCTC*AC (where C* is the breakage site); while with the linear amplification procedure, it was 5'-TCTT*AC. With end-labelling, the dinucleotide frequency of occurrence was highest for 5'-TC*, 5'-TT* and 5'-CC*; whereas it was 5'-TT* for linear amplification. The influence of neighbouring nucleotides on the degree of UV-induced DNA damage was also examined. The core sequences consisted of pyrimidine nucleotides 5'-CTC* and 5'-CTT* while an A at position "1" and C at position "2" enhanced UV-induced DNA damage. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  10. 75 FR 20933 - Airworthiness Directives; Arrow Falcon Exporters, Inc. (previously Utah State University...

    Science.gov (United States)

    2010-04-22

    ... Hawkins and Powers Aviation, Inc.); S.M.&T. Aircraft (previously US Helicopters, Inc., UNC Helicopter, Inc... Joaquin Helicopters (previously Hawkins and Powers Aviation, Inc.); S.M.&T. Aircraft (previously US...

  11. Chameleon sequences in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-01-01

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  12. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  13. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    Green's function, while the perturbation of a network is investigated in [3]. ... In Theorem 1 below, we employ the Farey sequence to establish a strict .... We next show that the Farey sequence method is applicable for circuits with n or fewer.

  15. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  16. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  17. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  18. Commercial Art: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial art vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  19. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  20. Agaricus bisporus genome sequence: a commentary.

    Science.gov (United States)

    Kerrigan, Richard W; Challen, Michael P; Burton, Kerry S

    2013-06-01

    The genomes of two isolates of Agaricus bisporus have been sequenced recently. This soil-inhabiting fungus has a wide geographical distribution in nature and it is also cultivated in an industrialized indoor process ($4.7bn annual worldwide value) to produce edible mushrooms. Previously this lignocellulosic fungus has resisted precise econutritional classification, i.e. into white- or brown-rot decomposers. The generation of the genome sequence and transcriptomic analyses has revealed a new classification, 'humicolous', for species adapted to grow in humic-rich, partially decomposed leaf material. The Agaricus biporus genomes contain a collection of polysaccharide and lignin-degrading genes and more interestingly an expanded number of genes (relative to other lignocellulosic fungi) that enhance degradation of lignin derivatives, i.e. heme-thiolate peroxidases and β-etherases. A motif that is hypothesized to be a promoter element in the humicolous adaptation suite is present in a large number of genes specifically up-regulated when the mycelium is grown on humic-rich substrate. The genome sequence of A. bisporus offers a platform to explore fungal biology in carbon-rich soil environments and terrestrial cycling of carbon, nitrogen, phosphorus and potassium. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. Evolution of developmental sequences in lepidosaurs

    Directory of Open Access Journals (Sweden)

    Tomasz Skawiński

    2017-04-01

    Full Text Available Background Lepidosaurs, a group including rhynchocephalians and squamates, are one of the major clades of extant vertebrates. Although there has been extensive phylogenetic work on this clade, its interrelationships are a matter of debate. Morphological and molecular data suggest very different relationships within squamates. Despite this, relatively few studies have assessed the utility of other types of data for inferring squamate phylogeny. Methods We used developmental sequences of 20 events in 29 species of lepidosaurs. These sequences were analysed using event-pairing and continuous analysis. They were transformed into cladistic characters and analysed in TNT. Ancestral state reconstructions were performed on two main phylogenetic hypotheses of squamates (morphological and molecular. Results Cladistic analyses conducted using characters generated by these methods do not resemble any previously published phylogeny. Ancestral state reconstructions are equally consistent with both morphological and molecular hypotheses of squamate phylogeny. Only several inferred heterochronic events are common to all methods and phylogenies. Discussion Results of the cladistic analyses, and the fact that reconstructions of heterochronic events show more similarities between certain methods rather than phylogenetic hypotheses, suggest that phylogenetic signal is at best weak in the studied developmental events. Possibly the developmental sequences analysed here evolve too quickly to recover deep divergences within Squamata.

  2. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  3. Accident sequence quantification with KIRAP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

  4. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  5. [Complete genome sequencing and sequence analysis of BCG Tice].

    Science.gov (United States)

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  6. Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.).

    Science.gov (United States)

    Cloutier, Sylvie; Miranda, Evelyn; Ward, Kerry; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Datla, Raju; Rowland, Gordon; Duguid, Scott; Ragupathy, Raja

    2012-08-01

    Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.

  7. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

    Directory of Open Access Journals (Sweden)

    O'Brien Kimberly

    2008-06-01

    Full Text Available Abstract Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC clone library (87 Mb and sequencing of 22 potato BAC clones (2.9 Mb. The GC content of potato is very similar to Solanum lycopersicon (tomato and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that

  8. Subset of Kappa and Lambda Germline Sequences Result in Light Chains with a Higher Molecular Mass Phenotype.

    Science.gov (United States)

    Barnidge, David R; Lundström, Susanna L; Zhang, Bo; Dasari, Surendra; Murray, David L; Zubarev, Roman A

    2015-12-04

    In our previous work, we showed that electrospray ionization of intact polyclonal kappa and lambda light chains isolated from normal serum generates two distinct, Gaussian-shaped, molecular mass distributions representing the light-chain repertoire. During the analysis of a large (>100) patient sample set, we noticed a low-intensity molecular mass distribution with a mean of approximately 24 250 Da, roughly 800 Da higher than the mean of the typical kappa molecular-mass distribution mean of 23 450 Da. We also observed distinct clones in this region that did not appear to contain any typical post-translational modifications that would account for such a large mass shift. To determine the origin of the high molecular mass clones, we performed de novo bottom-up mass spectrometry on a purified IgM monoclonal light chain that had a calculated molecular mass of 24 275.03 Da. The entire sequence of the monoclonal light chain was determined using multienzyme digestion and de novo sequence-alignment software and was found to belong to the germline allele IGKV2-30. The alignment of kappa germline sequences revealed ten IGKV2 and one IGKV4 sequences that contained additional amino acids in their CDR1 region, creating the high-molecular-mass phenotype. We also performed an alignment of lambda germline sequences, which showed additional amino acids in the CDR2 region, and the FR3 region of functional germline sequences that result in a high-molecular-mass phenotype. The work presented here illustrates the ability of mass spectrometry to provide information on the diversity of light-chain molecular mass phenotypes in circulation, which reflects the germline sequences selected by the immunoglobulin-secreting B-cell population.

  9. Chronic impairments in spatial learning and memory in rats previously exposed to chlorpyrfos or diisopropylfluorophosphate.

    Science.gov (United States)

    Terry, A V; Beck, W D; Warner, S; Vandenhuerk, L; Callahan, P M

    2012-01-01

    The acute toxicity of organophosphates (OPs) has been studied extensively; however, much less attention has been given to the subject of repeated exposures that are not associated with overt signs of toxicity (i.e., subthreshold exposures). The objective of this study was to determine if the protracted spatial learning impairments we have observed previously after repeated subthreshold exposures to the insecticide chlorpyrifos (CPF) or the alkylphosphate OP, diisopropylfluorophosphate (DFP) persisted for longer periods after exposure. Male Wistar rats (beginning at two months of age) were initially injected subcutaneously with CPF (10.0 or 18.0mg/kg) or DFP (0.25 or 0.75 mg/kg) every other day for 30 days. After an extended OP-free washout period (behavioral testing begun 50 days after the last OP exposure), rats previously exposed to CPF, but not DFP, were impaired in a radial arm maze (RAM) win-shift task as well as a delayed non-match to position procedure. Later experiments (i.e., beginning 140 days after the last OP exposure) revealed impairments in the acquisition of a water maze hidden platform task associated with both OPs. However, only rats previously exposed to DFP were impaired in a second phase of testing when the platform location was changed (indicative of deficits of cognitive flexibility). These results indicate, therefore, that repeated, subthreshold exposures to CPF and DFP may lead to chronic deficits in spatial learning and memory (i.e., long after cholinesterase inhibition has abated) and that insecticide and alkylphosphate-based OPs may have differential effects depending on the cognitive domain evaluated. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Female Sexual Dysfunction in the Late Postpartum Period Among Women with Previous Gestational Diabetes Mellitus

    International Nuclear Information System (INIS)

    Sargin, M. A.; Yassa, M.; Taymur, B. D.; Akca, G.; Tug, N.; Taymur, B.

    2017-01-01

    Objective: To compare the status of female sexual dysfunction (FSD) between women with a history of previous gestational diabetes mellitus (GDM) and those with follow-up of a healthy pregnancy, using the female sexual function index (FSFI) questionnaire. Study Design: Cross-sectional study. Place and Duration of Study: Department of Obstetrics and Gynecology, Fatih Sultan Mehmet Training and Research Hospital, Istanbul, Turkey, from September to December 2015. Methodology: Healthy sexually active adult parous females were included. Participants were asked to complete the validated Turkish versions of the FSFI and Hospital Anxiety and Depression Scale (HADS) questionnaires. Student's t-test was used for two-group comparisons of normally distributed variables and quantitative data. Mann-Whitney U-test was used for two-group comparisons of non-normally distributed variables. Pearson's chi-squared test, the Fisher-Freeman-Halton test, Fisher's exact test, and Yates' continuity correction test were used for comparison of qualitative data. Results: The mean FSFI scores of the 179 participants was 23.50 +- 3.94. FSFI scores and scores of desire, arousal, lubrication, orgasm, satisfaction, and pain were not statistically significantly different (p>0.05), according to a history of GDM and types of FSD (none, mild, severe). HADS scores and anxiety and depression types did not statistically significantly differ according to the history of GDM (p>0.05). Conclusion: An association could not be found in FSFI scores between participants with both the history of previous GDM and with healthy pregnancy; subclinical sexual dysfunction may be observed in the late postpartum period among women with a history of previous GDM. This may adversely affect their sexual health. (author)

  11. Female Sexual Dysfunction in the Late Postpartum Period Among Women with Previous Gestational Diabetes Mellitus.

    Science.gov (United States)

    Sargin, Mehmet Akif; Yassa, Murat; Taymur, Bilge Dogan; Taymur, Bulent; Akca, Gizem; Tug, Niyazi

    2017-04-01

    To compare the status of female sexual dysfunction (FSD) between women with a history of previous gestational diabetes mellitus (GDM) and those with follow-up of a healthy pregnancy, using the female sexual function index (FSFI) questionnaire. Cross-sectional study. Department of Obstetrics and Gynecology, Fatih Sultan Mehmet Training and Research Hospital, Istanbul, Turkey, from September to December 2015. Healthy sexually active adult parous females were included. Participants were asked to complete the validated Turkish versions of the FSFI and Hospital Anxiety and Depression Scale (HADS) questionnaires. Student's t-test was used for two-group comparisons of normally distributed variables and quantitative data. Mann-Whitney U-test was used for two-group comparisons of non-normally distributed variables. Pearson's chi-squared test, the Fisher-FreemanHalton test, Fisher's exact test, and Yates' continuity correction test were used for comparison of qualitative data. The mean FSFI scores of the 179 participants was 23.50 ±3.94. FSFI scores and scores of desire, arousal, lubrication, orgasm, satisfaction, and pain were not statistically significantly different (p>0.05), according to a history of GDM and types of FSD (none, mild, severe). HADS scores and anxiety and depression types did not statistically significantly differ according to the history of GDM (p>0.05). An association could not be found in FSFI scores between participants with both the history of previous GDM and with healthy pregnancy; subclinical sexual dysfunction may be observed in the late postpartum period among women with a history of previous GDM. This may adversely affect their sexual health.

  12. Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment

    Directory of Open Access Journals (Sweden)

    Jessica M. Labonté

    2015-04-01

    Full Text Available Metagenomic studies have revealed that ssDNA phages from the family Microviridae subfamily Gokushovirinae are widespread in aquatic ecosystems. It is hypothesized that gokushoviruses occupy specialized niches, resulting in differences among genotypes traversing water column gradients. Here, we use degenerate primers that amplify a fragment of the gene encoding the major capsid protein to examine the diversity of gokushoviruses in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia. Amplicon sequencing of samples from the mixed oxic surface (10 m and deeper anoxic (200 m layers indicated a diverse assemblage of gokushoviruses, with greater richness at 10 m than 200 m. A comparison of amplicon sequences with sequences selected on the basis of RFLP patterns from eight surface samples collected over a one-year period revealed that gokushovirus diversity was higher in spring and summer during stratification, and lower in fall and winter after deep-water renewal, consistent with seasonal variability within gokushovirus populations. Phylogenetic analysis of clustered amplicons revealed at least five new phylogenetic clades of previously unknown sequences, with the most abundant group associated with viruses that infect SUP05, a ubiquitous and abundant member of marine oxygen minimum zones. Our results provide persuasive evidence that, while specific gokushovirus genotypes may have a narrow host range, hosts for gokushoviruses in Saanich Inlet consist of a wide range of bacterial taxa, including SUP05, a taxonomic clade of gamma proteobacterial sulfur oxidizers. Members of SUP05 are abundant in Saanich Inlet and involved in carbon, nitrogen, and sulfur cycling along the redoxline; thus, gokushoviruses are likely important mortality agents of these bacteria and have consequent influences on biogeochemical cycling in this system.

  13. Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.

    Science.gov (United States)

    Vincent, Antony T; Trudel, Mélanie V; Freschi, Luca; Nagar, Vandan; Gagné-Thivierge, Cynthia; Levesque, Roger C; Charette, Steve J

    2016-01-12

    Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date. We sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy. Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.

  14. The first complete chloroplast genome sequence of a lycophyte,Huperzia lucidula (Lycopodiaceae)

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, Paul G.; Karol, Kenneth G.; Mandoli, Dina F.; Kuehl,Jennifer V.; Arumuganathan, K.; Ellis, Mark W.; Mishler, Brent D.; Kelch,Dean G.; Olmstead, Richard G.; Boore, Jeffrey L.

    2005-02-01

    We used a unique combination of techniques to sequence the first complete chloroplast genome of a lycophyte, Huperzia lucidula. This plant belongs to a significant clade hypothesized to represent the sister group to all other vascular plants. We used fluorescence-activated cell sorting (FACS) to isolate the organelles, rolling circle amplification (RCA) to amplify the genome, and shotgun sequencing to 8x depth coverage to obtain the complete chloroplast genome sequence. The genome is 154,373bp, containing inverted repeats of 15,314 bp each, a large single-copy region of 104,088 bp, and a small single-copy region of 19,671 bp. Gene order is more similar to those of mosses, liverworts, and hornworts than to gene order for other vascular plants. For example, the Huperziachloroplast genome possesses the bryophyte gene order for a previously characterized 30 kb inversion, thus supporting the hypothesis that lycophytes are sister to all other extant vascular plants. The lycophytechloroplast genome data also enable a better reconstruction of the basaltracheophyte genome, which is useful for inferring relationships among bryophyte lineages. Several unique characters are observed in Huperzia, such as movement of the gene ndhF from the small single copy region into the inverted repeat. We present several analyses of evolutionary relationships among land plants by using nucleotide data, amino acid sequences, and by comparing gene arrangements from chloroplast genomes. The results, while still tentative pending the large number of chloroplast genomes from other key lineages that are soon to be sequenced, are intriguing in themselves, and contribute to a growing comparative database of genomic and morphological data across the green plants.

  15. HLA class I sequence-based typing using DNA recovered from frozen plasma.

    Science.gov (United States)

    Cotton, Laura A; Abdur Rahman, Manal; Ng, Carmond; Le, Anh Q; Milloy, M-J; Mo, Theresa; Brumme, Zabrina L

    2012-08-31

    We describe a rapid, reliable and cost-effective method for intermediate-to-high-resolution sequence-based HLA class I typing using frozen plasma as a source of genomic DNA. The plasma samples investigated had a median age of 8.5 years. Total nucleic acids were isolated from matched frozen PBMC (~2.5 million) and plasma (500 μl) samples from a panel of 25 individuals using commercial silica-based kits. Extractions yielded median [IQR] nucleic acid concentrations of 85.7 [47.0-130.0]ng/μl and 2.2 [1.7-2.6]ng/μl from PBMC and plasma, respectively. Following extraction, ~1000 base pair regions spanning exons 2 and 3 of HLA-A, -B and -C were amplified independently via nested PCR using universal, locus-specific primers and sequenced directly. Chromatogram analysis was performed using commercial DNA sequence analysis software and allele interpretation was performed using a free web-based tool. HLA-A, -B and -C amplification rates were 100% and chromatograms were of uniformly high quality with clearly distinguishable mixed bases regardless of DNA source. Concordance between PBMC and plasma-derived HLA types was 100% at the allele and protein levels. At the nucleotide level, a single partially discordant base (resulting from a failure to call both peaks in a mixed base) was observed out of >46,975 bases sequenced (>99.9% concordance). This protocol has previously been used to perform HLA class I typing from a variety of genomic DNA sources including PBMC, whole blood, granulocyte pellets and serum, from specimens up to 30 years old. This method provides comparable specificity to conventional sequence-based approaches and could be applied in situations where cell samples are unavailable or DNA quantities are limiting. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. THE REST-FRAME OPTICAL LUMINOSITY FUNCTION OF CLUSTER GALAXIES AT z < 0.8 AND THE ASSEMBLY OF THE CLUSTER RED SEQUENCE

    International Nuclear Information System (INIS)

    Rudnick, Gregory; Von der Linden, Anja; De Lucia, Gabriella; White, Simon; Pello, Roser; Aragon-Salamanca, Alfonso; Marchesini, Danilo; Clowe, Douglas; Halliday, Claire; Jablonka, Pascale; Milvang-Jensen, Bo; Poggianti, Bianca; Saglia, Roberto; Simard, Luc; Zaritsky, Dennis

    2009-01-01

    We present the rest-frame optical luminosity function (LF) of red-sequence galaxies in 16 clusters at 0.4 < z < 0.8 drawn from the ESO Distant Cluster Survey (EDisCS). We compare our clusters to an analogous sample from the Sloan Digital Sky Survey (SDSS) and match the EDisCS clusters to their most likely descendants. We measure all LFs down to M ∼ M * + (2.5-3.5). At z < 0.8, the bright end of the LF is consistent with passive evolution but there is a significant buildup of the faint end of the red sequence toward lower redshift. There is a weak dependence of the LF on cluster velocity dispersion for EDisCS but no such dependence for the SDSS clusters. We find tentative evidence that red-sequence galaxies brighter than a threshold magnitude are already in place, and that this threshold evolves to fainter magnitudes toward lower redshifts. We compare the EDisCS LFs with the LF of coeval red-sequence galaxies in the field and find that the bright end of the LFs agree. However, relative to the number of bright red galaxies, the field has more faint red galaxies than clusters at 0.6 < z < 0.8 but fewer at 0.4 < z < 0.6, implying differential evolution. We compare the total light in the EDisCS cluster red sequences to the total red-sequence light in our SDSS cluster sample. Clusters at 0.4 < z < 0.8 must increase their luminosity on the red sequence (and therefore stellar mass in red galaxies) by a factor of 1-3 by z = 0. The necessary processes that add mass to the red sequence in clusters predict local clusters that are overluminous as compared to those observed in the SDSS. The predicted cluster luminosities can be reconciled with observed local cluster luminosities by combining multiple previously known effects.

  17. Emerging Biodegradation of the Previously Persistent Artificial Sweetener Acesulfame in Biological Wastewater Treatment.

    Science.gov (United States)

    Kahl, Stefanie; Kleinsteuber, Sabine; Nivala, Jaime; van Afferden, Manfred; Reemtsma, Thorsten

    2018-03-06

    The persistence of acesulfame (ACE) in wastewater treatment (and subsequently the aquatic environment) has led to its use as a marker substance for wastewater input into surface water and groundwater. However, ACE degradation of >85% during summer and autumn was observed in nine German wastewater treatment plants (WWTPs). Annual removal performance was more stable in larger plants, enhanced by low biological oxygen demand and impeded by water temperatures below 10 °C. Literature data suggest that the potential to degrade ACE emerged in WWTPs around the year 2010. This development is ongoing, as illustrated by ACE content in the German rivers Elbe and Mulde: Between 2013 and 2016 the ACE mass load decreased by 70-80%. In enrichment cultures with ACE as sole carbon source the carbonaceous fraction of ACE was removed completely, indicating catabolic biotransformation and the inorganic compound sulfamic acid formed in quantitative amounts. Sequencing of bacterial 16S rRNA genes suggests that several species are involved in ACE degradation, with proteobacterial species affiliated to Phyllobacteriaceae, Methylophilaceae, Bradyrhizobiaceae, and Pseudomonas becoming specifically enriched. ACE appears to be the first micropollutant for which the evolution of a catabolic pathway in WWTPs has been witnessed. It can yet only be speculated whether the emergence of ACE removal in WWTPs in different regions of the world is due to independent evolution or to global spreading of genes or adapted microorganisms.

  18. Cheilitis in acne vulgaris patients with no previous use of systemic retinoid products.

    Science.gov (United States)

    Balighi, Kamran; Daneshpazhooh, Maryam; Lajevardi, Vahideh; Talebi, Shahin; Azizpour, Arghavan

    2017-08-01

    Isotretinoin is commonly used in the treatment of acne vulgaris. While one of the more common side-effects is cheilitis, we have observed an increased incidence of cheilitis prior to the commencement of systemic isotretinoin. The aim of this study was to assess the prevalence of cheilitis among acne vulgaris patients. A non-interventional cross-sectional study of patients with acne vulgaris. Patients with previous use of systemic retinoids were excluded. The patients were examined for signs and symptoms of cheilitis. Of a total of 400 patients, 134 (34%) had evidence of cheilitis at initial presentation. Two-thirds (63%) were female (P acne excorie, compared with only 8% of patients with no signs of cheilitis. Our findings suggest that cheilitis is quite common among acne vulgaris patients even before treatment with isotretinoin. © 2016 The Australasian College of Dermatologists.

  19. Total brain, cortical and white matter volumes in children previously treated with glucocorticoids

    DEFF Research Database (Denmark)

    Holm, Sara K; Madsen, Kathrine S; Vestergaard, Martin

    2018-01-01

    BACKGROUND: Perinatal exposure to glucocorticoids and elevated endogenous glucocorticoid-levels during childhood can have detrimental effects on the developing brain. Here, we examined the impact of glucocorticoid-treatment during childhood on brain volumes. METHODS: Thirty children and adolescents...... with rheumatic or nephrotic disease previously treated with glucocorticoids and 30 controls matched on age, sex, and parent education underwent magnetic resonance imaging (MRI) of the brain. Total cortical grey and white matter, brain, and intracranial volume, and total cortical thickness and surface area were...... were mainly driven by the children with rheumatic disease. Total cortical thickness and cortical surface area did not significantly differ between groups. We found no significant associations between glucocorticoid-treatment variables and volumetric measures. CONCLUSION: Observed smaller total brain...

  20. Previously Unrecognized Ornithuromorph Bird Diversity in the Early Cretaceous Changma Basin, Gansu Province, Northwestern China

    Science.gov (United States)

    Wang, Ya-Ming; O'Connor, Jingmai K.; Li, Da-Qing; You, Hai-Lu

    2013-01-01

    Here we report on three new species of ornithuromorph birds from the Lower Cretaceous Xiagou Formation in the Changma Basin of Gansu Province, northwestern China: Yumenornis huangi gen. et sp. nov., Changmaornis houi gen. et sp. nov., and Jiuquanornis niui gen. et sp. nov.. The last of these is based on a previously published but unnamed specimen: GSGM-05-CM-021. Although incomplete, the specimens can be clearly distinguished from each other and from Gansus yumenensis Hou and Liu, 1984. Phylogenetic analysis resolves the three new taxa as basal ornithuromorphs. This study reveals previously unrecognized ornithuromorph diversity in the Changma avifauna, which is largely dominated by Gansus but with at least three other ornithuromorphs. Body mass estimates demonstrate that enantiornithines were much smaller than ornithuromorphs in the Changma avifauna. In addition, Changma enantiornithines preserve long and recurved pedal unguals, suggesting an arboreal lifestyle; in contrast, Changma ornithuromorphs tend to show terrestrial or even aquatic adaptions. Similar differences in body mass and ecology are also observed in the Jehol avifauna in northeastern China, suggesting niche partitioning between these two clades developed early in their evolutionary history. PMID:24147058

  1. Jumping performance differences among elite professional handball players with or without previous ACL reconstruction.

    Science.gov (United States)

    Setuain, I; Millor, N; Alfaro, J; Gorostiaga, E; Izquierdo, M

    2015-10-01

    Handball is one of the most challenging sports for the knee joint. Persistent strength and jumping capacity alterations may be observed among athletes who have suffered anterior cruciate ligament (ACL) injury. The aim of this study was to examine unilateral and bilateral jumping ability differences between previously ACL-reconstructed rehabilitated elite handball athletes and sex, age and uninjured sport activity level-pairs of control players. It was a Cross-sectional study with one factor: previous ACL injury. We recruited 22 male (6 ACL-reconstructed and 16 uninjured control players) and 21 female (6 ACL-reconstructed and 15 uninjured control players) elite handball players who were evaluated 6.2±3.4 years after surgical ACL reconstruction. A battery of jump tests, including both bilateral and unilateral maneuvers, was performed. Two-tailed unpaired (intergroup comparison) and paired (intragroup comparison) t-tests were performed for mean comparisons. The P-value cut-off for significance was set at handball athletes demonstrated both lower vertical bilateral drop jump (VBDJ) contact times and lower UTHD scores for the injured leg several years after injury. These deficits could contribute to an increase in ACL re-injury risk.

  2. Prevalence and titers of yellow fever virus neutralizing antibodies in previously vaccinated adults.

    Science.gov (United States)

    Miyaji, Karina Takesaki; Avelino-Silva, Vivian Iida; Simões, Marisol; Freire, Marcos da Silva; Medeiros, Carlos Roberto de; Braga, Patrícia Emilia; Neves, Maria Angélica Acalá; Lopes, Marta Heloisa; Kallas, Esper Georges; Sartori, Ana Marli Christovam

    2017-04-03

    The World Health Organization (WHO) recommends one single dose of the Yellow Fever (YF) vaccine based on studies of antibody persistency in healthy adults. We assessed the prevalence and titers of YF virus neutralizing antibodies in previously vaccinated persons aged  60 years, in comparison to younger adults. We also evaluated the correlation between antibody titers and the time since vaccination among participants who received one vaccine dose, and the seropositivity among participants vaccinated prior to or within the past 10 years. previously vaccinated healthy persons aged  18 years were included. YF virus neutralizing antibody titers were determined by means of the 50% Plaque Reduction Neutralization Test. 46 persons aged  60 years and 48 persons aged 18 to 59 years were enrolled. There was no significant difference in the prevalence of YF virus neutralizing antibodies between the two groups (p = 0.263). However, titers were significantly lower in the elderly (p = 0.022). There was no correlation between YF virus neutralizing antibody titers and the time since vaccination. There was no significant difference in seropositivity among participants vaccinated prior to or within the past 10 years. the clinical relevance of the observed difference in YF virus neutralizing antibody titers between the two groups is not clear.

  3. Main-sequence photometry in NGC 2808

    International Nuclear Information System (INIS)

    Buonanno, R.; Corsi, C.E.; Fusi Pecci, F.; Harris, W.E.

    1984-01-01

    We have obtained a color-magnitude diagram for the southern globular cluster NGC 2808, to V/sub lim/approx. =21 (about 2 mag below the main-sequence turnoff). The internal photographic errors are sigma/sub V/approx. =0.02, sigma/sub B/-Vapprox. =0.03, small enough to permit a precise definition of the turnoff region and an estimate of the ''cosmic scatter'' along the main sequence. Fitting of the CMD to VandenBerg's [Astrophys. J. Suppl. 51, 29 (1983)] isochrones shows that an excellent match to the observations is achieved for model parameters of Yapprox. =0.2, Zapprox. =0.003 ([Fe/H]approx. =-0.8), and an age of (16 +- 2) billion years. All these characteristics are within the expected range from other observational constraints; no new clues from the main-sequence data alone have arisen to help explain the presence of the anomalous blue horizontal-branch stars

  4. Learning by observation: insights from Williams syndrome.

    Science.gov (United States)

    Foti, Francesca; Menghini, Deny; Mandolesi, Laura; Federico, Francesca; Vicari, Stefano; Petrosini, Laura

    2013-01-01

    Observing another person performing a complex action accelerates the observer's acquisition of the same action and limits the time-consuming process of learning by trial and error. Observational learning makes an interesting and potentially important topic in the developmental domain, especially when disorders are considered. The implications of studies aimed at clarifying whether and how this form of learning is spared by pathology are manifold. We focused on a specific population with learning and intellectual disabilities, the individuals with Williams syndrome. The performance of twenty-eight individuals with Williams syndrome was compared with that of mental age- and gender-matched thirty-two typically developing children on tasks of learning of a visuo-motor sequence by observation or by trial and error. Regardless of the learning modality, acquiring the correct sequence involved three main phases: a detection phase, in which participants discovered the correct sequence and learned how to perform the task; an exercise phase, in which they reproduced the sequence until performance was error-free; an automatization phase, in which by repeating the error-free sequence they became accurate and speedy. Participants with Williams syndrome beneficiated of observational training (in which they observed an actor detecting the visuo-motor sequence) in the detection phase, while they performed worse than typically developing children in the exercise and automatization phases. Thus, by exploiting competencies learned by observation, individuals with Williams syndrome detected the visuo-motor sequence, putting into action the appropriate procedural strategies. Conversely, their impaired performances in the exercise phases appeared linked to impaired spatial working memory, while their deficits in automatization phases to deficits in processes increasing efficiency and speed of the response. Overall, observational experience was advantageous for acquiring competencies

  5. Learning by observation: insights from Williams syndrome.

    Directory of Open Access Journals (Sweden)

    Francesca Foti

    Full Text Available Observing another person performing a complex action accelerates the observer's acquisition of the same action and limits the time-consuming process of learning by trial and error. Observational learning makes an interesting and potentially important topic in the developmental domain, especially when disorders are considered. The implications of studies aimed at clarifying whether and how this form of learning is spared by pathology are manifold. We focused on a specific population with learning and intellectual disabilities, the individuals with Williams syndrome. The performance of twenty-eight individuals with Williams syndrome was compared with that of mental age- and gender-matched thirty-two typically developing children on tasks of learning of a visuo-motor sequence by observation or by trial and error. Regardless of the learning modality, acquiring the correct sequence involved three main phases: a detection phase, in which participants discovered the correct sequence and learned how to perform the task; an exercise phase, in which they reproduced the sequence until performance was error-free; an automatization phase, in which by repeating the error-free sequence they became accurate and speedy. Participants with Williams syndrome beneficiated of observational training (in which they observed an actor detecting the visuo-motor sequence in the detection phase, while they performed worse than typically developing children in the exercise and automatization phases. Thus, by exploiting competencies learned by observation, individuals with Williams syndrome detected the visuo-motor sequence, putting into action the appropriate procedural strategies. Conversely, their impaired performances in the exercise phases appeared linked to impaired spatial working memory, while their deficits in automatization phases to deficits in processes increasing efficiency and speed of the response. Overall, observational experience was advantageous for

  6. Effects of hyperthermia applied to previously irradiated cervical spinal cord in the rat

    International Nuclear Information System (INIS)

    Sminia, P.; Haveman, J.; Koedoder, C.

    1991-01-01

    Rat cervical spinal cord was X-ray irradiated at doses of 15, 18, 20 and 26 Gy. Approximately the same part of the spinal cord was heated by means of a 434 MHz microwave applicator 90 days later. After treatment, animals were observed for 18 months, for expression of neurological complications. These could either be result of the heat or of the radiation treatment. The time course showed 3 distinct peaks in the incidence of neurological symptoms. The 1st peak was due to the acute response to hyperthermia. The ED 50 value for neurological complications one day after treatment at 42.3±0.4 o C was 74 ±2 min. Previous X-ray irradiation of spinal cord with 18, 20 and 26 Gy reduced ED 50 to 57±7,65±4 and 55±5 min (12-26% of control), resp. Recovery from heat-induced neurological complications was diminished in previously irradiated animals. The 2nd peak (150-300 days after X-rays) concerned expression of 'early-delayed' radiation damage. Hyperthermia given in 90 days after irradiation did not influence either the percentage of animals with paralysis or the latent period. Neurological symptoms developing after day 300 were due to the late delayed radiation response. Significant difference was not observed in data on paralysis induced by radiation alone or radiation followed by heat. The late radiation-induced minor neurological symptoms, were however, influenced by retreatment with heat. (author). 30 refs., 6 figs., 3 tabs

  7. Next-generation sequencing offers new insights into DNA degradation

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Orlando, Ludovic Antoine Alexandre; Willerslev, Eske

    2012-01-01

    The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation...... rates that previously were obtained only from extrapolations of results from in vitro kinetic experiments performed over short timescales. For example, recent next-generation sequencing of ancient DNA reveals purine bases as one of the main targets of postmortem hydrolytic damage, through base...... elimination and strand breakage. It also shows substantially increased rates of DNA base-loss at guanosine. In this review, we argue that the latter results from an electron resonance structure unique to guanosine rather than adenosine having an extra resonance structure over guanosine as previously suggested....

  8. Car sequencing is NP-hard: a short proof

    OpenAIRE

    B Estellon; F Gardi

    2013-01-01

    In this note, a new proof is given that the car sequencing (CS) problem is NP-hard. Established from the Hamiltonian Path problem, the reduction is direct while closing some gaps remaining in the previous NP-hardness results. Since CS is studied in many operational research courses, this result and its proof are particularly interesting for teaching purposes.

  9. Sequence analysis corresponding to the PPE and PE proteins in ...

    Indian Academy of Sciences (India)

    Unknown

    AB repeats; Mycobacterium tuberculosis genome; PE-PPE domain; PPE, PE proteins; sequence analysis; surface antigens. J. Biosci. | Vol. ... bacterium tuberculosis genomes resulted in the identification of a previously uncharacterized 225 amino acid- ...... Vega Lopez F, Brooks L A, Dockrell H M, De Smet K A,. Thompson ...

  10. Perturbation of frame sequences in shift-invariant spaces

    DEFF Research Database (Denmark)

    Christensen, Ole; Kim, Hong Oh; Kim, Rae Young

    2005-01-01

    We prove a new perturbation criteria for frame sequences, which generalizes previous results and is easier to apply. In the special case of frames infinitely generated shift-invariant subspaces of L2(ℝd) the condition can be formulated in terms of the norm of a finite Gram matrix and a correspond...

  11. Crossover Can Be Constructive When Computing Unique Input Output Sequences

    DEFF Research Database (Denmark)

    Lehre, Per Kristian; Yao, Xin

    2010-01-01

    Unique input output (UIO) sequences have important applications in conformance testing of finite state machines (FSMs). Previous experimental and theoretical research has shown that evolutionary algorithms (EAs) can compute UIOs efficiently on many FSM instance classes, but fail on others. However...

  12. A Population Study of Wide-Separation Brown Dwarf Companions to Main Sequence Stars

    Science.gov (United States)

    Smith, Jeffrey J.

    2005-01-01

    Increased interest in infrared astronomy has opened the frontier to study cooler objects that shed significant light on the formation of planetary systems. Brown dwarf research provides a wealth of information useful for sorting through a myriad of proposed formation theories. Our study combines observational data from 2MASS with rigorous computer simulations to estimate the true population of long-range (greater than 1000 AU) brown dwarf companions in the solar neighborhood (less than 25 pc from Earth). Expanding on Gizis et al. (2001), we have found the margin of error in previous estimates to be significantly underestimated after we included orbit eccentricity, longitude of pericenter, angle of inclination, field star density, and primary and secondary luminosities as parameters influencing the companion systems in observational studies. We apply our simulation results to current L- and T-dwarf catalogs to provide updated estimates on the frequency of wide-separation brown dwarf companions to main sequence stars.

  13. Neural mechanisms of sequence generation in songbirds

    Science.gov (United States)

    Langford, Bruce

    Animal models in research are useful for studying more complex behavior. For example, motor sequence generation of actions requiring good muscle coordination such as writing with a pen, playing an instrument, or speaking, may involve the interaction of many areas in the brain, each a complex system in itself; thus it can be difficult to determine causal relationships between neural behavior and the behavior being studied. Birdsong, however, provides an excellent model behavior for motor sequence learning, memory, and generation. The song consists of learned sequences of notes that are spectrographically stereotyped over multiple renditions of the song, similar to syllables in human speech. The main areas of the songbird brain involve in singing are known, however, the mechanisms by which these systems store and produce song are not well understood. We used a custom built, head-mounted, miniature motorized microdrive to chronically record the neural firing patterns of identified neurons in HVC, a pre-motor cortical nucleus which has been shown to be important in song timing. These were done in Bengalese finch which generate a song made up of stereotyped notes but variable note sequences. We observed song related bursting in neurons projecting to Area X, a homologue to basal ganglia, and tonic firing in HVC interneurons. Interneuron had firing rate patterns that were consistent over multiple renditions of the same note sequence. We also designed and built a light-weight, low-powered wireless programmable neural stimulator using Bluetooth Low Energy Protocol. It was able to generate perturbations in the song when current pulses were administered to RA, which projects to the brainstem nucleus responsible for syringeal muscle control.

  14. Tritium pellet injection sequences for TFTR

    International Nuclear Information System (INIS)

    Houlberg, W.A.; Milora, S.L.; Attenberger, S.E.; Singer, C.E.; Schmidt, G.L.

    1983-01-01

    Tritium pellet injection into neutral deuterium, beam heated deuterium plasmas in the Tokamak Fusion Test Reactor (TFTR) is shown to be an attractive means of (1) minimizing tritium use per tritium discharge and over a sequence of tritium discharges; (2) greatly reducing the tritium load in the walls, limiters, getters, and cryopanels; (3) maintaining or improving instantaneous neutron production (Q); (4) reducing or eliminating deuterium-tritium (D-T) neutron production in non-optimized discharges; and (5) generally adding flexibility to the experimental sequences leading to optimal Q operation. Transport analyses of both compression and full-bore TFTR plasmas are used to support the above observations and to provide the basis for a proposed eight-pellet gas gun injector for the 1986 tritium experiments

  15. Cloning and Sequence Analysis of Vibrio halioticoli Genes Encoding Three Types of Polyguluronate Lyase.

    Science.gov (United States)

    Sugimura; Sawabe; Ezura

    2000-01-01

    The alginate lyase-coding genes of Vibrio halioticoli IAM 14596(T), which was isolated from the gut of the abalone Haliotis discus hannai, were cloned using plasmid vector pUC 18, and expressed in Escherichia coli. Three alginate lyase-positive clones, pVHB, pVHC, and pVHE, were obtained, and all clones expressed the enzyme activity specific for polyguluronate. Three genes, alyVG1, alyVG2, and alyVG3, encoding polyguluronate lyase were sequenced: alyVG1 from pVHB was composed of a 1056-bp open reading frame (ORF) encoding 352 amino acid residues; alyVG2 gene from pVHC was composed of a 993-bp ORF encoding 331 amino acid residues; and alyVG3 gene from pVHE was composed of a 705-bp ORF encoding 235 amino acid residues. Comparison of nucleotide and deduced amino acid sequences among AlyVG1, AlyVG2, and AlyVG3 revealed low homologies. The identity value between AlyVG1 and AlyVG2 was 18.7%, and that between AlyVG2 and AlyVG3 was 17.0%. A higher identity value (26.0%) was observed between AlyVG1 and AlyVG3. Sequence comparison among known polyguluronate lyases including AlyVG1, AlyVG2, and AlyVG3 also did not reveal an identical region in these sequences. However, AlyVG1 showed the highest identity value (36.2%) and the highest similarity (73.3%) to AlyA from Klebsiella pneumoniae. A consensus region comprising nine amino acid (YFKAGXYXQ) in the carboxy-terminal region previously reported by Mallisard and colleagues was observed only in AlyVG1 and AlyVG2.

  16. Osteocalcin protein sequences of Neanderthals and modern primates.

    Science.gov (United States)

    Nielsen-Marsh, Christina M; Richards, Michael P; Hauschka, Peter V; Thomas-Oates, Jane E; Trinkaus, Erik; Pettitt, Paul B; Karavanic, Ivor; Poinar, Hendrik; Collins, Matthew J

    2005-03-22

    We report here protein sequences of fossil hominids, from two Neanderthals dating to approximately 75,000 years old from Shanidar Cave in Iraq. These sequences, the oldest reported fossil primate protein sequences, are of bone osteocalcin, which was extracted and sequenced by using MALDI-TOF/TOF mass spectrometry. Through a combination of direct sequencing and peptide mass mapping, we determined that Neanderthals have an osteocalcin amino acid sequence that is identical to that of modern humans. We also report complete osteocalcin sequences for chimpanzee (Pan troglodytes) and gorilla (Gorilla gorilla gorilla) and a partial sequence for orangutan (Pongo pygmaeus), all of which are previously unreported. We found that the osteocalcin sequences of Neanderthals, modern human, chimpanzee, and orangutan are unusual among mammals in that the ninth amino acid is proline (Pro-9), whereas most species have hydroxyproline (Hyp-9). Posttranslational hydroxylation of Pro-9 in osteocalcin by prolyl-4-hydroxylase requires adequate concentrations of vitamin C (l-ascorbic acid), molecular O(2), Fe(2+), and 2-oxoglutarate, and also depends on enzyme recognition of the target proline substrate consensus sequence Leu-Gly-Ala-Pro-9-Ala-Pro-Tyr occurring in most mammals. In five species with Pro-9-Val-10, hydroxylation is blocked, whereas in gorilla there is a mixture of Pro-9 and Hyp-9. We suggest that the absence of hydroxylation of Pro-9 in Pan, Pongo, and Homo may reflect response to a selective pressure related to a decline in vitamin C in the diet during omnivorous dietary adaptation, either independently or through the common ancestor of these species.

  17. Previously unknown and highly divergent ssDNA viruses populate the oceans.

    Science.gov (United States)

    Labonté, Jessica M; Suttle, Curtis A

    2013-11-01

    Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.

  18. Inverse statistical physics of protein sequences: a key issues review.

    Science.gov (United States)

    Cocco, Simona; Feinauer, Christoph; Figliuzzi, Matteo; Monasson, Rémi; Weigt, Martin

    2018-03-01

    In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques, sequence data accumulate at unprecedented pace. This provides large sets of so-called homologous, i.e. evolutionarily related protein sequences, to which methods of inverse statistical physics can be applied. Using sequence data as the basis for the inference of Boltzmann distributions from samples of microscopic configurations or observables, it is possible to extract information about evolutionary constraints and thus protein function and structure. Here we give an overview over some biologically important questions, and how statistical-mechanics inspired modeling approaches can help to answer them. Finally, we discuss some open questions, which we expect to be addressed over the next years.

  19. Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives

    Directory of Open Access Journals (Sweden)

    Michael Knapp

    2010-07-01

    Full Text Available The invention of next-generation-sequencing has revolutionized almost all fields of genetics, but few have profited from it as much as the field of ancient DNA research. From its beginnings as an interesting but rather marginal discipline, ancient DNA research is now on its way into the centre of evolutionary biology. In less than a year from its invention next-generation-sequencing had increased the amount of DNA sequence data available from extinct organisms by several orders of magnitude. Ancient DNA  research is now not only adding a temporal aspect to evolutionary studies and allowing for the observation of evolution in real time, it also provides important data to help understand the origins of our own species. Here we review progress that has been made in next-generation-sequencing of ancient DNA over the past five years and evaluate sequencing strategies and future directions.

  20. Solving Assembly Sequence Planning using Angle Modulated Simulated Kalman Filter

    Science.gov (United States)

    Mustapa, Ainizar; Yusof, Zulkifli Md.; Adam, Asrul; Muhammad, Badaruddin; Ibrahim, Zuwairie

    2018-03-01

    This paper presents an implementation of Simulated Kalman Filter (SKF) algorithm for optimizing an Assembly Sequence Planning (ASP) problem. The SKF search strategy contains three simple steps; predict-measure-estimate. The main objective of the ASP is to determine the sequence of component installation to shorten assembly time or save assembly costs. Initially, permutation sequence is generated to represent each agent. Each agent is then subjected to a precedence matrix constraint to produce feasible assembly sequence. Next, the Angle Modulated SKF (AMSKF) is proposed for solving ASP problem. The main idea of the angle modulated approach in solving combinatorial optimization problem is to use a function, g(x), to create a continuous signal. The performance of the proposed AMSKF is compared against previous works in solving ASP by applying BGSA, BPSO, and MSPSO. Using a case study of ASP, the results show that AMSKF outperformed all the algorithms in obtaining the best solution.

  1. GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

    OpenAIRE

    BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

    2011-01-01

    In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

  2. 76 FR 1349 - Airworthiness Directives; Cessna Aircraft Company (Cessna) (Type Certificate A00003SE Previously...

    Science.gov (United States)

    2011-01-10

    ... Airworthiness Directives; Cessna Aircraft Company (Cessna) (Type Certificate A00003SE Previously Held by... Company (Type Certificate A00003SE previously held by Columbia Aircraft Manufacturing (previously The... Cessna Aircraft Company (Cessna) (Type Certificate A00003SE previously held by Columbia Aircraft...

  3. LPTAU, Quasi Random Sequence Generator

    International Nuclear Information System (INIS)

    Sobol, Ilya M.

    1993-01-01

    1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

  4. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  5. Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems.

    Science.gov (United States)

    Yao, Yining; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui

    2018-01-01

    Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex ® 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR ® . Identifiler ® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex ® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data.

    Science.gov (United States)

    Perry, George H; Kistler, Logan; Kelaita, Mary A; Sams, Aaron J

    2015-02-01

    Nuclear genome sequence data from Neandertals, Denisovans, and archaic anatomically modern humans can be used to complement our understanding of hominin evolutionary biology and ecology through i) direct inference of archaic hominin phenotypes, ii) indirect inference of those phenotypes by identifying the effects of previously-introgressed alleles still present among modern humans, or iii) determining the evolutionary timing of relevant hominin-specific genetic changes. Here we review and reanalyze published Neandertal and Denisovan genome sequence data to illustrate an example of the third approach. Specifically, we infer the timing of five human gene presence/absence changes that may be related to particular hominin-specific dietary changes and discuss these results in the context of our broader reconstructions of hominin evolutionary ecology. We show that pseudogenizing (gene loss) mutations in the TAS2R62 and TAS2R64 bitter taste receptor genes and the MYH16 masticatory myosin gene occurred after the hominin-chimpanzee divergence but before the divergence of the human and Neandertal/Denisovan lineages. The absence of a functional MYH16 protein may explain our relatively reduced jaw muscles; this gene loss may have followed the adoption of cooking behavior. In contrast, salivary amylase gene (AMY1) duplications were not observed in the Neandertal and Denisovan genomes, suggesting a relatively recent origin for the AMY1 copy number gains that are observed in modern humans. Thus, if earlier hominins were consuming large quantities of starch-rich underground storage organs, as previously hypothesized, then they were likely doing so without the digestive benefits of increased salivary amylase production. Our most surprising result was the observation of a heterozygous mutation in the first codon of the TAS2R38 bitter taste receptor gene in the Neandertal individual, which likely would have resulted in a non-functional protein and inter-individual PTC

  7. Highly multiplexed targeted DNA sequencing from single nuclei.

    Science.gov (United States)

    Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

    2016-02-01

    Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

  8. Beryllium abundances along the evolutionary sequence of the open cluster IC 4651 - A new test for hydrodynamical stellar models

    Science.gov (United States)

    Smiljanic, R.; Pasquini, L.; Charbonnel, C.; Lagarde, N.

    2010-02-01

    Context. Previous analyses of lithium abundances in main sequence and red giant stars have revealed the action of mixing mechanisms other than convection in stellar interiors. Beryllium abundances in stars with Li abundance determinations can offer valuable complementary information on the nature of these mechanisms. Aims: Our aim is to derive Be abundances along the whole evolutionary sequence of an open cluster. We focus on the well-studied open cluster IC 4651. These Be abundances are used with previously determined Li abundances, in the same sample stars, to investigate the mixing mechanisms in a range of stellar masses and evolutionary stages. Methods: Atmospheric parameters were adopted from a previous abundance analysis by the same authors. New Be abundances have been determined from high-resolution, high signal-to-noise UVES spectra using spectrum synthesis and model atmospheres. The careful synthetic modeling of the Be lines region is used to calculate reliable abundances in rapidly rotating stars. The observed behavior of Be and Li is compared to theoretical predictions from stellar models including rotation-induced mixing, internal gravity waves, atomic diffusion, and thermohaline mixing. Results: Beryllium is detected in all the main sequence and turn-off sample stars, both slow- and fast-rotating stars, including the Li-dip stars, but is not detected in the red giants. Confirming previous results, we find that the Li dip is also a Be dip, although the depletion of Be is more modest than for Li in the corresponding effective temperature range. For post-main-sequence stars, the Be dilution starts earlier within the Hertzsprung gap than expected from classical predictions, as does the Li dilution. A clear dispersion in the Be abundances is also observed. Theoretical stellar models including the hydrodynamical transport processes mentioned above are able to reproduce all the observed features well. These results show a good theoretical understanding of the

  9. Isolation and sequence characterization of DNA-A genome of a new begomovirus strain associated with severe leaf curling symptoms of Jatropha curcas L.

    KAUST Repository

    Chauhan, Sushma

    2018-04-22

    Begomoviruses belong to the family Geminiviridae are associated with several disease symptoms, such as mosaic and leaf curling in Jatropha curcas. The molecular characterization of these viral strains will help in developing management strategies to control the disease. In this study, J. curcas that was infected with begomovirus and showed acute leaf curling symptoms were identified. DNA-A segment from pathogenic viral strain was isolated and sequenced. The sequenced genome was assembled and characterized in detail. The full-length DNA-A sequence was covered by primer walking. The genome sequence showed the general organization of DNA-A from begomovirus by the distribution of ORFs in both viral and anti-viral strands. The genome size ranged from 2844 bp–2852 bp. Three strains with minor nucleotide variations were identified, and a phylogenetic analysis was performed by comparing the DNA-A segments from other reported begomovirus isolates. The maximum sequence similarity was observed with Euphorbia yellow mosaic virus (FN435995). In the phylogenetic tree, no clustering was observed with previously reported begomovirus strains isolated from J. curcas host. The strains isolated in this study belong to new begomoviral strain that elicits symptoms of leaf curling in J. curcas. The results indicate that the probable origin of the strains is from Jatropha mosaic virus infecting J. gassypifolia. The strains isolated in this study are referred as Jatropha curcas leaf curl India virus (JCLCIV) based on the major symptoms exhibited by host J. curcas.

  10. Abnormal flow behavior and necklace microstructure of powder metallurgy superalloys with previous particle boundaries (PPBs)

    Energy Technology Data Exchange (ETDEWEB)

    Ning, Yongquan, E-mail: luckyning@nwpu.edu.cn [School of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072 (China); Zhou, Cong; Liang, Houquan [School of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072 (China); Fu, M.W., E-mail: mmmwfu@polyu.edu.hk [Department of Mechanical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong (China)

    2016-01-15

    Powder metallurgy (P/M) has been introduced as an innovative process to manufacture high performance components with fine, homogenous and segregation-free microstructure. Unfortunately, previous particle boundary (PPB) precipitated during the powder metallurgy process. Since undesirable PPB is detrimental to mechanical properties, hot extrusion or/and isothermal forging are needed. In present research, isothermal compression tests were conducted on P/M FGH4096 superalloys with typical PPBs. Abnormal flow behavior during high-speed deformation has been quantitatively investigated. Caused by the competition mechanism between work-hardening and dynamic-softening, abnormal flow behaves typical four stages (viz., work-hardening, stable, softening and steady). Microstructure observation for hardening or/and softening mechanism has been investigated. Meanwhile, necklace microstructure was observed by scanning electron microscope, and the grain fraction analysis was performed by using electron backscatter diffraction. Transmission electron microscopy was used for characterizing the boundary structure. Necklace microstructural mechanism for processing P/M superalloys has been developed, and the dynamic recrystallization model has also been conducted. Bulge–corrugation model is the primary nucleation mechanism for P/M superalloys with PPBs. When PPB is entirely covered with new grains, necklace microstructure has formed. Bulge–corrugation mechanism can repeatedly take place in the following necklace DRX.

  11. Visual working memory supports the inhibition of previously processed information: evidence from preview search.

    Science.gov (United States)

    Al-Aidroos, Naseem; Emrich, Stephen M; Ferber, Susanne; Pratt, Jay

    2012-06-01

    In four experiments we assessed whether visual working memory (VWM) maintains a record of previously processed visual information, allowing old information to be inhibited, and new information to be prioritized. Specifically, we evaluated whether VWM contributes to the inhibition (i.e., visual marking) of previewed distractors in a preview search. We evaluated this proposal by testing three predictions. First, Experiments 1 and 2 demonstrate that preview inhibition is more effective when the number of previewed distractors is below VWM capacity than above; an effect that can only be observed at small preview set sizes (Experiment 2A) and when observers are allowed to move their eyes freely (Experiment 2B). Second, Experiment 3 shows that, when quantified as the number of inhibited distractors, the magnitude of the preview effect is stable across different search difficulties. Third, Experiment 4 demonstrates that individual differences in preview inhibition are correlated with individual differences in VWM capacity. These findings provide converging evidence that VWM supports the inhibition of previewed distractors. More generally, these findings demonstrate how VWM contributes to the efficiency of human visual information processing--VWM prioritizes new information by inhibiting old information from being reselected for attention.

  12. The effectiveness of external beam radiotherapy for acromegaly is not affected by previous pituitary ablative treatments

    International Nuclear Information System (INIS)

    Reed, P.I.; Joplin, G.F.; Speirs, C.J.; Morrison, R.; Aber, V.

    1990-01-01

    Thirty-three acromegalic patients were treated with radiotherapy and followed up for at least 3 years (mean 6 years, range 3 to 12). Seventeen had not had previous pituitary ablative therapy and 16 had. The mean GH level for these two groups before radiotherapy was comparable at 98 and 119 mlU/l. The observed frequency of reaching <10 mlU/L was 53% and 75% of patients in the two groups, respectively, the mean observed falls in growth hormone level were 81 and 85% of the initial level, and the calculated exponential decline rate of GH level was 72 and 52% per fyear. Considering all 35 patients, requirement for pituitary hormone replacement therapy increased from 15 patients before radiotherapy to 20 after radiotherapy, being mostly those who had had prior ablative therapies. There were no complications attributable to the radiotherapy treatment. It appears that radiotherapy is equally efficacious whether a prior unsuccessful ablative procedure had been used or not. (author)

  13. The effectiveness of external beam radiotherapy for acromegaly is not affected by previous pituitary ablative treatments

    Energy Technology Data Exchange (ETDEWEB)

    Reed, P.I.; Joplin, G.F. (Department of Medicine, Royal Postgraduate Medical School, Hammersmith Hospital, London (UK)); Speirs, C.J. (Department of Clinical Pharmacology, Royal Postgraduate Medical School, Hammersmith Hospital, London (UK)); Morrison, R. (Department of Radiotherapy, Royal Postgraduate Medical School, Hammersmith Hospital, London (UK)); Aber, V. (Department of Medical Physics, Royal Postgraduate Medical School, Hammersmith Hospital, London (UK))

    1990-01-01

    Thirty-three acromegalic patients were treated with radiotherapy and followed up for at least 3 years (mean 6 years, range 3 to 12). Seventeen had not had previous pituitary ablative therapy and 16 had. The mean GH level for these two groups before radiotherapy was comparable at 98 and 119 mlU/l. The observed frequency of reaching <10 mlU/L was 53% and 75% of patients in the two groups, respectively, the mean observed falls in growth hormone level were 81 and 85% of the initial level, and the calculated exponential decline rate of GH level was 72 and 52% per fyear. Considering all 35 patients, requirement for pituitary hormone replacement therapy increased from 15 patients before radiotherapy to 20 after radiotherapy, being mostly those who had had prior ablative therapies. There were no complications attributable to the radiotherapy treatment. It appears that radiotherapy is equally efficacious whether a prior unsuccessful ablative procedure had been used or not. (author).

  14. The presence of five nifH-like sequences in Clostridium pasteurianum: sequence divergence and transcription properties.

    OpenAIRE

    Wang, S Z; Chen, J S; Johnson, J L

    1988-01-01

    The nifH gene encodes the iron protein (component II) of the nitrogenase complex. We have