1,042 research outputs found
Genetic Classification of Populations using Supervised Learning
There are many instances in genetics in which we wish to determine whether
two candidate populations are distinguishable on the basis of their genetic
structure. Examples include populations which are geographically separated,
case--control studies and quality control (when participants in a study have
been genotyped at different laboratories). This latter application is of
particular importance in the era of large scale genome wide association
studies, when collections of individuals genotyped at different locations are
being merged to provide increased power. The traditional method for detecting
structure within a population is some form of exploratory technique such as
principal components analysis. Such methods, which do not utilise our prior
knowledge of the membership of the candidate populations. are termed
\emph{unsupervised}. Supervised methods, on the other hand are able to utilise
this prior knowledge when it is available.
In this paper we demonstrate that in such cases modern supervised approaches
are a more appropriate tool for detecting genetic differences between
populations. We apply two such methods, (neural networks and support vector
machines) to the classification of three populations (two from Scotland and one
from Bulgaria). The sensitivity exhibited by both these methods is considerably
higher than that attained by principal components analysis and in fact
comfortably exceeds a recently conjectured theoretical limit on the sensitivity
of unsupervised methods. In particular, our methods can distinguish between the
two Scottish populations, where principal components analysis cannot. We
suggest, on the basis of our results that a supervised learning approach should
be the method of choice when classifying individuals into pre-defined
populations, particularly in quality control for large scale genome wide
association studies.Comment: Accepted PLOS On
The Parkes multibeam pulsar survey: IV. Discovery of 180 pulsars and parameters for 281 previously known pulsars
The Parkes multibeam pulsar survey has led to the discovery of more than 700
pulsars. In this paper, we provide timing solutions, flux densities and pulse
profiles for 180 of these new discoveries. Two pulsars, PSRs J1736-2843 and
J1847-0130 have rotational periods P > 6s and are therefore among the slowest
rotating radio pulsars known. Conversely, with P = 1.8ms, PSR J1843-1113 has
the third shortest period of pulsars currently known. This pulsar and PSR
J1905+0400 (P = 3.8ms) are both solitary. We also provide orbital parameters
for a new binary system, PSR J1420-5625, which has P = 34ms, an orbital period
of 40 days and a minimum companion mass of 0.4 solar masses. The 10 degree-wide
strip along the Galactic plane that was surveyed is known to contain 264 radio
pulsars that were discovered prior to the multibeam pulsar survey. We have
redetected almost all of these pulsars and provide new dispersion measure
values and flux densities at 20cm for the redetected pulsars.Comment: 35 pages, accepted for publication in MNRAS, a high quality image of
the figure on page 32 is available from
http://www.atnf.csiro.au/research/pulsar/images/pmsurvey_fig.p
Milestones in the Observations of Cosmic Magnetic Fields
Magnetic fields are observed everywhere in the universe. In this review, we
concentrate on the observational aspects of the magnetic fields of Galactic and
extragalactic objects. Readers can follow the milestones in the observations of
cosmic magnetic fields obtained from the most important tracers of magnetic
fields, namely, the star-light polarization, the Zeeman effect, the rotation
measures (RMs, hereafter) of extragalactic radio sources, the pulsar RMs, radio
polarization observations, as well as the newly implemented sub-mm and mm
polarization capabilities.
(Another long paragraph is omitted due to the limited space here)Comment: Invited Review (ChJA&A); 32 pages. Sorry if your significant
contributions in this area were not mentioned. Published pdf & ps files (with
high quality figures) now availble at http://www.chjaa.org/2002_2_4.ht
Recommended from our members
A systematic review of frameworks for the interrelationships of mental health evidence and policy in low- and middle-income countries
Background: The interrelationships between research evidence and policy-making are complex. Different theoretical frameworks exist to explain general evidenceâpolicy interactions. One largely unexplored element of these interrelationships is how evidence interrelates with, and influences, policy/political agenda-setting. This review aims to identify the elements and processes of theories, frameworks and models on interrelationships of research evidence and health policy-making, with a focus on actionability and agenda-setting in the context of mental health in low- and middle-income countries (LMICs).
Methods: A systematic review of theories was conducted based on the BeHeMOTh search method, using a tested and refined search strategy. Nine electronic databases and other relevant sources were searched for peer-reviewed and grey literature. Two reviewers screened the abstracts, reviewed full-text articles, extracted data and performed quality assessments. Analysis was based on a thematic analysis. The included papers had to present an actionable theoretical framework/model on evidence and policy interrelationships, such as knowledge translation or evidence-based policy, specifically target the agenda-setting process, focus on mental health, be from LMICs and published in English.
Results: From 236 publications included in the full text analysis, no studies fully complied with our inclusion criteria. Widening the focus by leaving out âagenda-settingâ, we included ten studies, four of which had unique conceptual frameworks focusing on mental health and LMICs but not agenda-setting. The four analysed frameworks confirmed research gaps from LMICs and mental health, and a lack of focus on agenda-setting. Frameworks and models from other health and policy areas provide interesting conceptual approaches and lessons with regards to agenda-setting.
Conclusion: Our systematic review identified frameworks on evidence and policy interrelations that differ in their elements and processes. No framework fulfilled all inclusion criteria. Four actionable frameworks are applicable to mental health and LMICs, but none specifically target agenda-setting. We have identified agenda-setting as a research theory gap in the context of mental health knowledge translation in LMICs. Frameworks from other health/policy areas could offer lessons on agenda-setting and new approaches for creating policy impact for mental health and to tackle the translational gap in LMICs
Gigahertz (GHz) hard x-ray imaging using fast scintillators
Gigahertz (GHz) imaging technology will be needed at high-luminosity X-ray and charged particle sources. It is plausible to combine fast scintillators with the latest picosecond detectors and GHz electronics for multi-frame hard Xray imaging and achieve an inter-frame time of less than 10 ns. The time responses and light yield of LYSO, LaBr_3, BaF_2 and ZnO are measured using an MCP-PMT detector. Zinc Oxide (ZnO) is an attractive material for fast hard X-ray imaging based on GEANT4 simulations and previous studies, but the measured light yield from the samples is much lower than expected
Gender Differences in Russian Colour Naming
In the present study we explored Russian colour naming in a web-based psycholinguistic experiment
(http://www.colournaming.com). Colour singletons representing the Munsell Color Solid (N=600 in total) were presented on a computer monitor and named using an unconstrained colour-naming method. Respondents were
Russian speakers (N=713). For gender-split equal-size samples (NF=333, NM=333) we estimated and compared (i)
location of centroids of 12 Russian basic colour terms (BCTs); (ii) the number of words in colour descriptors; (iii) occurrences of BCTs most frequent non-BCTs. We found a close correspondence between femalesâ and malesâ
BCT centroids. Among individual BCTs, the highest inter-gender agreement was for seryj âgreyâ and goluboj
âlight blueâ, while the lowest was for sinij âdark blueâ and krasnyj âredâ. Females revealed a significantly richer repertory of distinct colour descriptors, with great variety of monolexemic non-BCTs and âfancyâ colour names; in comparison, males offered relatively more BCTs or their compounds. Along with these measures, we gauged
denotata of most frequent CTs, reflected by linguistic segmentation of colour space, by employing a synthetic
observer trained by gender-specific responses. This psycholinguistic representation revealed femalesâ more
refined linguistic segmentation, compared to males, with higher linguistic density predominantly along the redgreen axis of colour space
Quantifying serum antibody in bird fanciers' hypersensitivity pneumonitis
BACKGROUND: Detecting serum antibody against inhaled antigens is an important diagnostic adjunct for hypersensitivity pneumonitis (HP). We sought to validate a quantitative fluorimetric assay testing serum from bird fanciers. METHODS: Antibody activity was assessed in bird fanciers and control subjects using various avian antigens and serological methods, and the titer was compared with symptoms of HP. RESULTS: IgG antibody against pigeon serum antigens, quantified by fluorimetry, provided a good discriminator of disease. Levels below 10 mg/L were insignificant, and increasing titers were associated with disease. The assay was unaffected by total IgG, autoantibodies and antibody to dietary hen's egg antigens. Antigens from pigeon serum seem sufficient to recognize immune sensitivity to most common pet avian species. Decreasing antibody titers confirmed antigen avoidance. CONCLUSION: Increasing antibody titer reflected the likelihood of HP, and decreasing titers confirmed antigen avoidance. Quantifying antibody was rapid and the increased sensitivity will improve the rate of false-negative reporting and obviate the need for invasive diagnostic procedures. Automated fluorimetry provides a method for the international standardization of HP serology thereby improving quality control and improving its suitability as a diagnostic adjunct
CD33 Alzheimerâs disease locus: Altered monocyte function and amyloid biology
In our functional dissection of the CD33 Alzheimerâs disease susceptibility locus, we find that the rs3865444C risk allele is associated with greater cell surface expression of CD33 in monocytes (t50 = 10.06, pjoint=1.3Ă10â13) of young and older individuals. It is also associated with (1) diminished internalization of Aβ42) (2) accumulation of neuritic amyloid pathology and fibrillar amyloid on in vivo imaging and (3), increased numbers of activated human microglia
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