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  • 1
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    Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment (2015)
    Oxford University Press
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    Publication Date: 2015-05-09
    Description: There are two known mRNA degradation pathways, 3' to 5' and 5' to 3'. We identified likely pathogenic variants in two genes involved in these two pathways in individuals with intellectual disability. In a large family with multiple branches, we identified biallelic variants in DCPS in three affected individuals; a splice site variant (c.636+1G〉A) that results in an in-frame insertion of 45 nucleotides and a missense variant (c.947C〉T; p.Thr316Met). DCPS decaps the cap structure generated by 3' to 5' exonucleolytic degradation of mRNA. In vitro decapping assays showed an ablation of decapping function for both variants in DCPS. In another family, we identified a homozygous mutation (c.161T〉C; p.Phe54Ser) in EDC3 in two affected children. EDC3 stimulates DCP2, which decaps mRNAs at the beginning of the 5' to 3' degradation pathway. In vitro decapping assays showed that altered EDC3 is unable to enhance DCP2 decapping at low concentrations and even inhibits DCP2 decapping at high concentration. We show that individuals with biallelic mutations in these genes of seemingly central functions are viable and that these possibly lead to impairment of neurological functions linking mRNA decapping to normal cognition. Our results further affirm an emerging theme linking aberrant mRNA metabolism to neurological defects.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    A 0.24+0.18 M{odot} double-lined eclipsing binary from the HATSouth survey (2015)
    Oxford University Press
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    Publication Date: 2015-06-15
    Description: We report the discovery and characterization of a new M-dwarf binary, with component masses and radii of $M_1 = 0.244_{-0.003}^{+0.003} \, \mathrm{M}_{\odot }$ , $R_1 = 0.261_{-0.009}^{+0.006} \, \mathrm{R}_{\odot }$ , $M_2 = 0.179_{-0.001}^{+0.002} \, \mathrm{M}_{\odot }$ , $R_2 = 0.218 _{-0.011}^{+0.007} \, \mathrm{R}_{\odot }$ , and orbital period of ~4.1 d. The M-dwarf binary HATS551–027 (LP 837–20) was identified as an eclipsing binary by the HATSouth survey, and characterized by a series of high-precision photometric observations of the eclipse events, and spectroscopic determinations of the atmospheric parameters and radial velocity orbits. HATS551–027 is one of few systems with both stellar components lying in the fully convective regime of very low mass stars, and can serve as a test for stellar interior models. The radius of HATS551–027A is consistent with models to 1, whilst HATS551–027B is inflated by 9 per cent at 2 significance. We measure the effective temperatures for the two stellar components to be T eff, 1  = 3190 ± 100 K and T eff, 2  = 2990 ± 110 K; both are slightly cooler than theoretical models predict, but consistent with other M-dwarfs of similar masses that have previously been studied. We also measure significant H α emission from both components of the binary system, and discuss this in the context of the correlation between stellar activity and the discrepancies between the observed and model temperatures.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Antioxidant and phytochemical analysis of Ranunculus arvensis L. extracts (2015)
    BioMed Central
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    Publication Date: 2015-07-01
    Description: Background: Ranunculus arvensis L. (R. arvensis) has long been used to treat a variety of medical conditions such as arthritis, asthma, hay fever, rheumatism, psoriasis, gut diseases and rheumatic pain. Here, we screened R. arvensis for antioxidant activity, phytochemical and high performance liquid chromatography (HPLC) analyses. Methods: The chloroform, chloroform:methanol, methanol, methanol:acetone, acetone, methanol:water and water extracts of R. arvensis were examined for DPPH (1, 1-diphenyl-2-picrylhydrazyl) free radical scavenging assay, hydrogen peroxide scavenging assay, phosphomolybdenum assay, reducing power assay, flavonoid content, phenolic content and high performance liquid chromatography analysis. Results: Significant antioxidant activity was displayed by methanol extract (IC 50 34.71 ± 0.02) in DPPH free radical scavenging assay. Total flavonoids and phenolics ranged 0.96–6.0 mg/g of extract calculated as rutin equivalent and 0.48–1.43 mg/g of extract calculated as gallic acid equivalent respectively. Significant value of rutin and caffeic acid was observed via high performance liquid chromatography. Conclusions: These results showed that extracts of R. arvensis exhibited significant antioxidant activities. Moreover, R. arvensis is a rich source of rutin, flavonoids and phenolics.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 4
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    Down-weighting overlapping genes improves gene set analysis (2012)
    BioMed Central
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    Publication Date: 2012-06-20
    Description: Background: The identification of gene sets that are significantly impacted in a given condition based on microarray data is acrucial step in current life science research. Most gene set analysis methods treat genes equally, regardless howspecific they are to a given gene set. Results: In this work we propose a new gene set analysis method that computes a gene set score as the mean of absolutevalues of weighted moderated gene t-scores. The gene weights are designed to emphasize the genes appearing infew gene sets, versus genes that appear in many gene sets. We demonstrate the usefulness of the method whenanalyzing gene sets that correspond to the KEGG pathways, and hence we called our method Pathway Analysiswith Down-weighting of Overlapping Genes (PADOG). Unlike most gene set analysis methods which arevalidated through the analysis of 2-3 data sets followed by a human interpretation of the results, the validationemployed here uses 24 different data sets and a completely objective assessment scheme that makes minimalassumptions and eliminates the need for possibly biased human assessments of the analysis results. Conclusions: PADOG significantly improves gene set ranking and boosts sensitivity of analysis using information alreadyavailable in the gene expression profiles and the collection of gene sets to be analyzed. The advantages ofPADOG over other existing approaches are shown to be stable to changes in the database of gene sets to beanalyzed. PADOG was implemented as an R package available at:http://bioinformaticsprb.med.wayne.edu/PADOG/ or www.bioconductor.org.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
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  • 5
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    Stellar rotational periods in the planet hosting open cluster Praesepe (2014)
    Oxford University Press
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    Publication Date: 2014-06-20
    Description: By using the dense coverage of the extrasolar planet survey project HATNet (Hungarian-made Automated Telescope Network), we Fourier analyse 381 high-probability members of the nearby open cluster Praesepe (Beehive/M44/NGC 2632). In addition to the detection of 10 variables (of Scuti and other types), we identify 180 rotational variables (including the two known planet hosts). This sample increases the number of known rotational variables in this cluster for spectral classes earlier than M by more than a factor of 3. These stars closely follow a colour/magnitude–period relation from early F to late K stars. We approximate this relation by polynomials for an easier reference to the rotational characteristics in different colours. The total (peak-to-peak) amplitudes of the large majority (94 per cent) of these variables span the range of 0.005–0.04 mag. The periods cover a range from 2.5 to 15 d. These data strongly confirm that Praesepe and the Hyades have the same gyrochronological ages. Regarding the two planet hosts, Pr0211 (the one with the shorter orbital period) has a rotational period that is ~2 d shorter than the one expected from the main rotational pattern in this cluster. This, together with other examples discussed in the paper, may hint that star–planet interaction via tidal dissipation can be significant in some cases in the rotational evolution of stars hosting hot Jupiters.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Electromagnetic field and cylindrical compact objects in modified gravity (2016)
    Oxford University Press
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    Publication Date: 2016-03-18
    Description: In this paper, we have investigated the role of different fluid parameters particularly electromagnetic field and f ( R ) corrections on the evolution of cylindrical compact object. We have explored the modified field equations, kinematical quantities and dynamical equations. An expression for the mass function has been found in comparison with the Misner–Sharp formalism in modified gravity, after which different mass–radius diagrams are drawn. The coupled dynamical transport equation have been formulated to discuss the role of thermoinertial effects on the inertial mass density of the cylindrical relativistic interior. Finally, we have presented a framework, according to which all possible solutions of the metric f ( R )-Maxwell field equations coupled with static fluid can be written through set of scalar functions. It is found that modified gravity induced by Lagrangians f ( R ) = α R 2 , f ( R ) = α R 2 – β R and $f(R)=\frac{\alpha R^2-\beta R}{1+\gamma R}$ are likely to host more massive cylindrical compact objects with smaller radii as compared to general relativity.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    School-based injury outcomes in children from a low-income setting: results from the pilot injury surveillance in Rawalpindi city, Pakistan (2013)
    BioMed Central
    Details
    Publication Date: 2013-03-08
    Description: Background: School-based injuries account for one in five unintentional childhood injuries. Little is known about the epidemiology of school-based injuries in low-income settings. The objective of our study was to compare emergency department (ED) outcomes of the school-based injuries with respect to age, sex, and injury mechanisms in a Pakistani urban setting.FindingsA pilot injury surveillance study was conducted at the EDs of three major tertiary-care hospitals of Rawalpindi city from July 2007 to June 2008 and included children of less than 15 years injured at school. The World Health Organization's questionnaire for injury surveillance was used. There were 923 school injury cases. Mean age of children involved was 8.3 years (SD +/- 3.3) with male female ratio 2.9:1. Most injuries occurred while playing 85.6% (n = 789); of which the most common mechanism was falls (n = 797, 86.4%). Nineteen of twenty cases were directly discharged home from the ED (N = 861). Compared to ED discharged cases, injury characteristics overrepresented in hospital admitted cases (n = 46) were age 10--14 years (65.2% vs. 40.9%, p = 0.005), male (88.6% vs. 25.9%), involved in educational activities (39.1% vs. 5.3%), injured from fire/heat (37.8% vs. 0.6%), had burns (39.5% vs. 0.9%) and head injuries (27.9% vs. 6.4%). Conclusion: Falls while playing are the commonest injury mechanism in school-based injuries reported in our ED sample. School officials need to prevent these injuries. Studying injury hazards present in school environment in Pakistan might facilitate developing specific prevention strategies.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 8
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    School-based injury outcomes in children from a low-income setting: results from the pilot injury surveillance in Rawalpindi city, Pakistan (2013)
    BioMed Central
    Details
    Publication Date: 2013-03-15
    Description: Background: School-based injuries account for one in five unintentional childhood injuries. Little is known about the epidemiology of school-based injuries in low-income settings. The objective of our study was to compare emergency department (ED) outcomes of the school-based injuries with respect to age, sex, and injury mechanisms in a Pakistani urban setting.FindingsA pilot injury surveillance study was conducted at the EDs of three major tertiary-care hospitals of Rawalpindi city from July 2007 to June 2008 and included children of less than 15 years injured at school. The World Health Organization’s questionnaire for injury surveillance was used. There were 923 school injury cases. Mean age of children involved was 8.3 years (SD ± 3.3) with male female ratio 2.9:1. Most injuries occurred while playing 85.6% (n = 789); of which the most common mechanism was falls (n = 797, 86.4%). Nineteen of twenty cases were directly discharged home from the ED (N = 861). Compared to ED discharged cases, injury characteristics overrepresented in hospital admitted cases (n = 46) were age 10–14 years (65.2% vs. 40.9%, p = 0.005), male (88.6% vs. 25.9%), involved in educational activities (39.1% vs. 5.3%), injured from fire/heat (37.8% vs. 0.6%), had burns (39.5% vs. 0.9%) and head injuries (27.9% vs. 6.4%). Conclusion: Falls while playing are the commonest injury mechanism in school-based injuries reported in our ED sample. School officials need to prevent these injuries. Studying injury hazards present in school environment in Pakistan might facilitate developing specific prevention strategies.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 9
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    Stability analysis of axial reflection symmetric spacetime (2015)
    Oxford University Press
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    Publication Date: 2015-11-12
    Description: In this paper, we explore instability regions of non-static axial reflection symmetric spacetime with anisotropic source in the interior. We impose linear perturbation on the Einstein field equations and dynamical equations to establish the collapse equation. The effects of different physical factors like energy density and anisotropic stresses on the instability regions are studied under Newtonian and post-Newtonian limits. We conclude that stiffness parameter has a significant role in this analysis while the reflection terms increase instability ranges of non-static axial collapse.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    High-precision photometry for K2 Campaign 1 (2015)
    Oxford University Press
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    Publication Date: 2015-10-30
    Description: The two reaction wheel K2 mission promises and has delivered new discoveries in the stellar and exoplanet fields. However, due to the loss of accurate pointing, it also brings new challenges for the data reduction processes. In this paper, we describe a new reduction pipeline for extracting high-precision photometry from the K2 data set, and present public light curves for the K2 Campaign 1 target pixel data set. Key to our reduction is the derivation of global astrometric solutions from the target stamps, from which accurate centroids are passed on for high-precision photometry extraction. We extract target light curves for sources from a combined UCAC4 and EPIC catalogue – this includes not only primary targets of the K2 campaign 1, but also any other stars that happen to fall on the pixel stamps. We provide the raw light curves, and the products of various detrending processes aimed at removing different types of systematics. Our astrometric solutions achieve a median residual of ~0.127 arcsec. For bright stars, our best 6.5 h precision for raw light curves is ~20 parts per million (ppm). For our detrended light curves, the best 6.5 h precision achieved is ~15 ppm. We show that our detrended light curves have fewer systematic effects (or trends, or red-noise) than light curves produced by other groups from the same observations. Example light curves of transiting planets and a Cepheid variable candidate, are also presented. We make all light curves public, including the raw and detrended photometry, at http://k2.hatsurveys.org .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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