The Effects of Air Pollution on Mortality in Socially Deprived Urban Areas in Hong Kong, China

Background: Poverty is a major determinant of population health, but little is known about its role in modifying air pollution effects. Objectives: We set out to examine whether people residing in socially deprived communities are at higher mortality risk from ambient air pollution. Methods: This study included 209 tertiary planning units (TPUs), the smallest units for town planning in the Special Administrative Region of Hong Kong, China. The socioeconomic status of each TPU was measured by a social deprivation index (SDI) derived from the proportions of the population with a) unemployment, b) monthly household income < US$250, c) no schooling at all, d) one-person household, e) never-married status, and f) subtenancy, from the 2001 Population Census. TPUs were classified into three levels of SDI: low, middle, and high. We performed time-series analysis with Poisson regression to examine the association between changes in daily concentrations of ambient air pollution and daily number of deaths in each SDI group for the period from January 1996 to December 2002. We evaluated the differences in pollution effects between different SDI groups using a case-only approach with logistic regression. Results: We found significant associations of nitrogen dioxide, sulfur dioxide, particulate matter with aerodynamic diameter < 10 μm, and ozone with all nonaccidental and cardiovascular mortality in areas of middle or high SDI (p < 0.05). Health outcomes, measured as all nonaccidental, cardiovascular, and respiratory mortality, in people residing in high SDI areas were more strongly associated with SO 2 and NO 2 compared with those in middle or low SDI areas. Conclusions: Neighborhood socioeconomic deprivation increases mortality risks associated with air pollution.published_or_final_versio

The SAURON project. II. Sample and early results

Early results are reported from the SAURON survey of the kinematics and stellar populations of a representative sample of nearby E, S0 and Sa galaxies. The survey is aimed at determining the intrinsic shape of the galaxies, their orbital structure, the mass-to-light ratio as a function of radius, the age and metallicity of the stellar populations, and the frequency of kinematically decoupled cores and nuclear black holes. The construction of the representative sample is described, and its properties are illustrated. A comparison with long-slit spectroscopic data establishes that the SAURON measurements are comparable to, or better than, the highest-quality determinations. Comparisons are presented for NGC 3384 and NGC 4365 where stellar velocities and velocity dispersions are determined to a precision of 6 km/s, and the h3 and h4 parameters of the line-of-sight velocity distribution to a precision of better than 0.02. Extraction of accurate gas emission-line intensities, velocities and line widths from the datacubes is illustrated for NGC 5813. Comparisons with published line-strengths for NGC 3384 and NGC 5813 reveal uncertainties of < 0.1 A on the measurements of the Hbeta, Mgb and Fe5270 indices. Integral-field mapping uniquely connects measurements of the kinematics and stellar populations to the galaxy morphology. The maps presented here illustrate the rich stellar kinematics, gaseous kinematics, and line-strength distributions of early-type galaxies. The results include the discovery of a thin, edge-on, disk in NGC 3623, confirm the axisymmetric shape of the central region of M32, illustrate the LINER nucleus and surrounding counter-rotating star-forming ring in NGC 7742, and suggest a uniform stellar population in the decoupled core galaxy NGC 5813.Comment: 20 pages, 17 figures. To be published in MNRAS. Version with full resolution images available at http://www.strw.leidenuniv.nl/~dynamics/Instruments/Sauron/pub_list.htm

A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data

<p>Abstract</p> <p>Background</p> <p>Mosaicism for copy number and copy neutral chromosomal rearrangements has been recently identified as a relatively common source of genetic variation in the normal population. However its prevalence is poorly defined since it has been only studied systematically in one large-scale study and by using non optimal <it>ad-hoc </it>SNP array data analysis tools, uncovering rather large alterations (> 1 Mb) and affecting a high proportion of cells. Here we propose a novel methodology, Mosaic Alteration Detection-MAD, by providing a software tool that is effective for capturing previously described alterations as wells as new variants that are smaller in size and/or affecting a low percentage of cells.</p> <p>Results</p> <p>The developed method identified all previously known mosaic abnormalities reported in SNP array data obtained from controls, bladder cancer and HapMap individuals. In addition MAD tool was able to detect new mosaic variants not reported before that were smaller in size and with lower percentage of cells affected. The performance of the tool was analysed by studying simulated data for different scenarios. Our method showed high sensitivity and specificity for all assessed scenarios.</p> <p>Conclusions</p> <p>The tool presented here has the ability to identify mosaic abnormalities with high sensitivity and specificity. Our results confirm the lack of sensitivity of former methods by identifying new mosaic variants not reported in previously utilised datasets. Our work suggests that the prevalence of mosaic alterations could be higher than initially thought. The use of appropriate SNP array data analysis methods would help in defining the human genome mosaic map.</p

Orbital decay in an accreting and eclipsing 13.7 minute orbital period binary with a luminous donor

We report the discovery of ZTF J0127+5258, a compact mass-transferring binary with an orbital period of 13.7 minutes. The system contains a white dwarf accretor, which likely originated as a post-common envelope carbon-oxygen (CO) white dwarf, and a warm donor ($T_{\rm eff,\,donor}= 16,400\pm1000\,\rm K$). The donor probably formed during a common envelope phase between the CO white dwarf and an evolving giant which left behind a helium star or helium white dwarf in a close orbit with the CO white dwarf. We measure gravitational wave-driven orbital inspiral with $\sim 35\sigma$ significance, which yields a joint constraint on the component masses and mass transfer rate. While the accretion disk in the system is dominated by ionized helium emission, the donor exhibits a mixture of hydrogen and helium absorption lines. Phase-resolved spectroscopy yields a donor radial-velocity semi-amplitude of $771\pm27\,\rm km\, s^{-1}$, and high-speed photometry reveals that the system is eclipsing. We detect a {\it Chandra} X-ray counterpart with $L_{X}\sim 3\times 10^{31}\,\rm erg\,s^{-1}$. Depending on the mass-transfer rate, the system will likely evolve into either a stably mass-transferring helium CV, merge to become an R Crb star, or explode as a Type Ia supernova in the next million years. We predict that the Laser Space Interferometer Antenna (LISA) will detect the source with a signal-to-noise ratio of $24\pm6$ after 4 years of observations. The system is the first \emph{LISA}-loud mass-transferring binary with an intrinsically luminous donor, a class of sources that provide the opportunity to leverage the synergy between optical and infrared time domain surveys, X-ray facilities, and gravitational-wave observatories to probe general relativity, accretion physics, and binary evolution.Comment: 13 pages, 7 figures, 2 tables, submitted to ApJ

Inhibition of HIV virus by neutralizing Vhh attached to dual functional liposomes encapsulating dapivirine

Although highly active antiretroviral therapy (HAART) has greatly improved the life expectancy of HIV/AIDS patients, the treatment is not curative. It is a global challenge which fosters an urgent need to develop an effective drug or neutralizing antibody delivery approach for the prevention and treatment of this disease. Due to the low density of envelope spikes with restricted mobility present on the surface of HIV virus, which limit the antibody potency and allow virus mutation and escape from the immune system, it is important for a neutralizing antibody to form bivalent or multivalent bonds with the virus. Liposome constructs could fulfil this need due to the flexible mobility of the membrane with its attached antibodies and the capacity for drug encapsulation. In this study, we evaluated the neutralization activity of a range of liposome formulations in different sizes coated with anti-gp120 llama antibody fragments (Vhhs) conjugated via either non-covalent metal chelation or a covalent linkage. The non-covalent construct demonstrated identical binding affinity to HIV-1 envelope glycoprotein gp120 and neutralizing ability for HIV virus as free Vhh. Although covalently linked Vhh showed significant binding affinity to gp120, it unexpectedly had a lower neutralization potency. This may be due to the comparability in size of the viral and liposome particles restricting the number which can be bound to the liposome surface so involving only a fraction of the antibodies, whereas non-covalently attached antibodies dissociate from the surface after acting with gp120 and free the remainder to bind further viruses. Covalently conjugated Vhh might also trigger the cellular uptake of a liposome-virion complex. To explore the possible ability of the antibody-coated liposomes to have a further function, we encapsulated the hydrophobic antiviral drug dapivirine into both of the non-covalently and covalently conjugated liposome formulations, both of which revealed high efficacy in reducing viral replication in vitro. Thus, dual function liposomes may lead to a novel strategy for the prophylaxis of HIV/AIDS by combining the neutralizing activity of Vhh with antiviral effects of high drug concentrations

Test performance of faecal occult blood testing for the detection of bowel cancer in people with chronic kidney disease (DETECT) protocol

<p>Abstract</p> <p>Background</p> <p>Cancer is a major cause of mortality and morbidity in patients with chronic kidney disease (CKD). In patients without kidney disease, screening is a major strategy for reducing the risk of cancer and improving the health outcomes for those who developed cancers by detecting treatable cancers at an early stage. Among those with CKD, the effectiveness, the efficacy and patients' preferences for cancer screening are unknown.</p> <p>Methods/Design</p> <p>This work describes the protocol for the DETECT study examining the effectiveness, efficiency and patient's perspectives of colorectal cancer screening using immunochemical faecal occult blood testing (iFOBT) for people with CKD. The aims of the DETECT study are 1) to determine the test performance characteristics of iFOBT screening in individuals with CKD, 2) to estimate the incremental costs and health benefits of iFOBT screening in CKD compared to no screening and 3) to elicit patients' perspective for colorectal cancer screening in the CKD population. Three different study designs will be used to explore the uncertainties surrounding colorectal cancer screening in CKD. A diagnostic test accuracy study of iFOBT screening will be conducted across all stages of CKD in patients ages 35-70. Using individually collected direct healthcare costs and outcomes from the diagnostic test accuracy study, cost-utility and cost-effective analyses will be performed to estimate the costs and health benefits of iFOBT screening in CKD. Qualitative in-depth interviews will be undertaken in a subset of participants from the diagnostic test accuracy study to investigate the perspectives, experiences, attitudes and beliefs about colorectal cancer screening among individuals with CKD.</p> <p>Discussion</p> <p>The DETECT study will target the three major unknowns about early cancer detection in CKD. Findings from our study will provide accurate and definitive estimates of screening efficacy and efficiency for colorectal cancer, and will allow better service planning and budgeting for early cancer detection in this at-risk population.</p> <p>The DETECT study is also registered with the Australia New Zealand Clinical Trials Registry <a href="http://www.anzctr.org.au/ACTRN12611000538943.aspx">ACTRN12611000538943</a></p

Reproducing the manual annotation of multiple sequence alignments using a SVM classifier

Motivation: Aligning protein sequences with the best possible accuracy requires sophisticated algorithms. Since the optimal alignment is not guaranteed to be the correct one, it is expected that even the best alignment will contain sites that do not respect the assumption of positional homology. Because formulating rules to identify these sites is difficult, it is common practice to manually remove them. Although considered necessary in some cases, manual editing is time consuming and not reproducible. We present here an automated editing method based on the classification of ‘valid’ and ‘invalid’ sites