110 research outputs found
Practical Tools to Implement Massive Parallel Pyrosequencing of PCR Products in Next Generation Molecular Diagnostics
Despite improvements in terms of sequence quality and price per basepair, Sanger sequencing remains restricted to screening of individual disease genes. The development of massively parallel sequencing (MPS) technologies heralded an era in which molecular diagnostics for multigenic disorders becomes reality. Here, we outline different PCR amplification based strategies for the screening of a multitude of genes in a patient cohort. We performed a thorough evaluation in terms of set-up, coverage and sequencing variants on the data of 10 GS-FLX experiments (over 200 patients). Crucially, we determined the actual coverage that is required for reliable diagnostic results using MPS, and provide a tool to calculate the number of patients that can be screened in a single run. Finally, we provide an overview of factors contributing to false negative or false positive mutation calls and suggest ways to maximize sensitivity and specificity, both important in a routine setting. By describing practical strategies for screening of multigenic disorders in a multitude of samples and providing answers to questions about minimum required coverage, the number of patients that can be screened in a single run and the factors that may affect sensitivity and specificity we hope to facilitate the implementation of MPS technology in molecular diagnostics
Soil Inorganic N Leaching in Edges of Different Forest Types Subject to High N Deposition Loads
X-Ray Spectroscopy of Stars
(abridged) Non-degenerate stars of essentially all spectral classes are soft
X-ray sources. Low-mass stars on the cooler part of the main sequence and their
pre-main sequence predecessors define the dominant stellar population in the
galaxy by number. Their X-ray spectra are reminiscent, in the broadest sense,
of X-ray spectra from the solar corona. X-ray emission from cool stars is
indeed ascribed to magnetically trapped hot gas analogous to the solar coronal
plasma. Coronal structure, its thermal stratification and geometric extent can
be interpreted based on various spectral diagnostics. New features have been
identified in pre-main sequence stars; some of these may be related to
accretion shocks on the stellar surface, fluorescence on circumstellar disks
due to X-ray irradiation, or shock heating in stellar outflows. Massive, hot
stars clearly dominate the interaction with the galactic interstellar medium:
they are the main sources of ionizing radiation, mechanical energy and chemical
enrichment in galaxies. High-energy emission permits to probe some of the most
important processes at work in these stars, and put constraints on their most
peculiar feature: the stellar wind. Here, we review recent advances in our
understanding of cool and hot stars through the study of X-ray spectra, in
particular high-resolution spectra now available from XMM-Newton and Chandra.
We address issues related to coronal structure, flares, the composition of
coronal plasma, X-ray production in accretion streams and outflows, X-rays from
single OB-type stars, massive binaries, magnetic hot objects and evolved WR
stars.Comment: accepted for Astron. Astrophys. Rev., 98 journal pages, 30 figures
(partly multiple); some corrections made after proof stag
Solar Spectroscopy and (Pseudo-)Diagnostics of the Solar Chromosphere
I first review trends in current solar spectrometry and then concentrate on
comparing various spectroscopic diagnostics of the solar chromosphere. Some are
actually not at all chromospheric but just photospheric or clapotispheric and
do not convey information on chromospheric heating, even though this is often
assumed. Balmer Halpha is the principal displayer of the closed-field
chromosphere, but it is unclear how chromospheric fibrils gain their large
Halpha opacity. The open-field chromosphere seems to harbor most if not all
coronal heating and solar wind driving, but is hardly seen in optical
diagnostics.Comment: To appear in "Recent Advances in Spectroscopy: Astrophysical,
Theoretical and Experimental Perspectives", eds. R.K. Chaudhuri, M.V.
Mekkaden, A.V. Raveendran and A. Satya Narayanan, Astrophysics and Space
Science Proceedings, Springer, Heidelberg, 2009. Revision: references
corrected, new references added, minor text correction
Review of Coronal Oscillations - An Observer's View
Recent observations show a variety of oscillation modes in the corona. Early
non-imaging observations in radio wavelengths showed a number of fast-period
oscillations in the order of seconds, which have been interpreted as fast
sausage mode oscillations. TRACE observations from 1998 have for the first time
revealed the lateral displacements of fast kink mode oscillations, with periods
of ~3-5 minutes, apparently triggered by nearby flares and destabilizing
filaments. Recently, SUMER discovered with Doppler shift measurements loop
oscillations with longer periods (10-30 minutes) and relatively short damping
times in hot (7 MK) loops, which seem to correspond to longitudinal slow
magnetoacoustic waves. In addition, propagating longitudinal waves have also
been detected with EIT and TRACE in the lowest density scale height of loops
near sunspots. All these new observations seem to confirm the theoretically
predicted oscillation modes and can now be used as a powerful tool for
``coronal seismology'' diagnostic.Comment: 5 Figure
Restaurant outbreak of Legionnaires' disease associated with a decorative fountain: an environmental and case-control study
BACKGROUND: From June to November 2005, 18 cases of community-acquired Legionnaires' disease (LD) were reported in Rapid City South Dakota. We conducted epidemiologic and environmental investigations to identify the source of the outbreak. METHODS: We conducted a case-control study that included the first 13 cases and 52 controls randomly selected from emergency department records and matched on underlying illness. We collected information about activities of case-patients and controls during the 14 days before symptom onset. Environmental samples (n = 291) were cultured for Legionella. Clinical and environmental isolates were compared using monoclonal antibody subtyping and sequence based typing (SBT). RESULTS: Case-patients were significantly more likely than controls to have passed through several city areas that contained or were adjacent to areas with cooling towers positive for Legionella. Six of 11 case-patients (matched odds ratio (mOR) 32.7, 95% CI 4.7-infinity) reported eating in Restaurant A versus 0 controls. Legionella pneumophila serogroup 1 was isolated from four clinical specimens: 3 were Benidorm type strains and 1 was a Denver type strain. Legionella were identified from several environmental sites including 24 (56%) of 43 cooling towers tested, but only one site, a small decorative fountain in Restaurant A, contained Benidorm, the outbreak strain. Clinical and environmental Benidorm isolates had identical SBT patterns. CONCLUSION: This is the first time that small fountain without obvious aerosol-generating capability has been implicated as the source of a LD outbreak. Removal of the fountain halted transmission
Trans Fat Consumption and Aggression
Background: Dietary trans fatty acids (dTFA) are primarily synthetic compounds that have been introduced only recently; little is known about their behavioral effects. dTFA inhibit production of omega-3 fatty acids, which experimentally have been shown to reduce aggression. Potential behavioral effects of dTFA merit investigation. We sought to determine whether dTFA are associated with aggression/irritability. Methodolgy/Prinicpal Findings: We capitalized on baseline dietary and behavioral assessments in an existing clinical trial to analyze the relationship of dTFA to aggression. Of 1,018 broadly sampled baseline subjects, the 945 adult men and women who brought a completed dietary survey to their baseline visit are the target of this analysis. Subjects (seen 1999– 2004) were not on lipid medications, and were without LDL-cholesterol extremes, diabetes, HIV, cancer or heart disease. Outcomes assessed adverse behaviors with impact on others: Overt Aggression Scale Modified-aggression subscale (primary behavioral endpoint); Life History of Aggression; Conflict Tactics Scale; and self-rated impatience and irritability. The association of dTFA to aggression was analyzed via regression and ordinal logit, unadjusted and adjusted for potential confounders (sex, age, education, alcohol, and smoking). Additional analyses stratified on sex, age, and ethnicity, and examined the prospective association. Greater dTFA were strongly significantly associated with greater aggression, with dTFA more consistently predictive than other assessed aggression predictors. The relationship was upheld wit
Exploiting solar visible-range observations by inversion techniques: from flows in the solar subsurface to a flaring atmosphere
Observations of the Sun in the visible spectral range belong to standard
measurements obtained by instruments both on the ground and in the space.
Nowadays, both nearly continuous full-disc observations with medium resolution
and dedicated campaigns of high spatial, spectral and/or temporal resolution
constitute a holy grail for studies that can capture (both) the long- and
short-term changes in the dynamics and energetics of the solar atmosphere.
Observations of photospheric spectral lines allow us to estimate not only the
intensity at small regions, but also various derived data products, such as the
Doppler velocity and/or the components of the magnetic field vector. We show
that these measurements contain not only direct information about the dynamics
of solar plasmas at the surface of the Sun but also imprints of regions below
and above it. Here, we discuss two examples: First, the local time-distance
helioseismology as a tool for plasma dynamic diagnostics in the near subsurface
and second, the determination of the solar atmosphere structure during flares.
The methodology in both cases involves the technique of inverse modelling.Comment: 29 pages, 15 figures. Accepted for publication in the book "Reviews
in Frontiers of Modern Astrophysics: From Space Debris to Cosmology" (eds
Kabath, Jones and Skarka; publisher Springer Nature) funded by the European
Union Erasmus+ Strategic Partnership grant "Per Aspera Ad Astra Simul"
2017-1-CZ01-KA203-03556
Evidence for Hitchhiking of Deleterious Mutations within the Human Genome
Deleterious mutations present a significant obstacle to adaptive evolution. Deleterious mutations can inhibit the spread of linked adaptive mutations through a population; conversely, adaptive substitutions can increase the frequency of linked deleterious mutations and even result in their fixation. To assess the impact of adaptive mutations on linked deleterious mutations, we examined the distribution of deleterious and neutral amino acid polymorphism in the human genome. Within genomic regions that show evidence of recent hitchhiking, we find fewer neutral but a similar number of deleterious SNPs compared to other genomic regions. The higher ratio of deleterious to neutral SNPs is consistent with simulated hitchhiking events and implies that positive selection eliminates some deleterious alleles and increases the frequency of others. The distribution of disease-associated alleles is also altered in hitchhiking regions. Disease alleles within hitchhiking regions have been associated with auto-immune disorders, metabolic diseases, cancers, and mental disorders. Our results suggest that positive selection has had a significant impact on deleterious polymorphism and may be partly responsible for the high frequency of certain human disease alleles
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