81 research outputs found
Patients with severe mental illness: A new approach to testing for HIV
Background. The prevalence of HIV infection in South Africa
is approaching 20% of young adults. In severely mentally ill
people it is probably higher. Testing for infection is subject
to stringent ethical principles. Undiagnosed HIV infection in
people with severe mental illness increases costs and morbidity.
Since effective treatments are available, it is imperative to
diagnose HIV infection early in this high-risk population.
Methods. A literature review established the prevalence of HIV
infection in inpatient populations with HIV infection. The
pattern of testing for HIV over 3 years at a major psychiatric
hospital was investigated. We surveyed public sector
psychiatrists in the Western Cape to establish their attitudes to
HIV in their patients.
Results. The reported HIV seroprevalence in psychiatric
inpatients ranges from 0 to 59.3%, with a mean of 10%. Data
show a clear trend towards an increase in prevalence: before
1996 the mean HIV seroprevalence was 7.4%, while after 1996
the mean was 15%. State psychiatrists in the Western Cape do
not test routinely for HIV infection, mainly owing to ethical
constraints: 14.6% of patients at Lentegeur Hospital were tested
in 2006.
Conclusions. The high prevalence of HIV infection in South
Africa, which is probably higher in patients with severe mental
illness (most of whom are not competent to provide informed
consent), and the availability of effective treatment require
debate and a clear policy regarding testing for HIV infection
to be implemented. We recommend a new approach to HIV
testing in these patients. South African Medical Journal Vol. 98 (3) 2008: pp. 213-21
Quantum resource estimates for computing elliptic curve discrete logarithms
We give precise quantum resource estimates for Shor's algorithm to compute
discrete logarithms on elliptic curves over prime fields. The estimates are
derived from a simulation of a Toffoli gate network for controlled elliptic
curve point addition, implemented within the framework of the quantum computing
software tool suite LIQ. We determine circuit implementations for
reversible modular arithmetic, including modular addition, multiplication and
inversion, as well as reversible elliptic curve point addition. We conclude
that elliptic curve discrete logarithms on an elliptic curve defined over an
-bit prime field can be computed on a quantum computer with at most qubits using a quantum circuit of at most Toffoli gates. We are able to classically simulate the
Toffoli networks corresponding to the controlled elliptic curve point addition
as the core piece of Shor's algorithm for the NIST standard curves P-192,
P-224, P-256, P-384 and P-521. Our approach allows gate-level comparisons to
recent resource estimates for Shor's factoring algorithm. The results also
support estimates given earlier by Proos and Zalka and indicate that, for
current parameters at comparable classical security levels, the number of
qubits required to tackle elliptic curves is less than for attacking RSA,
suggesting that indeed ECC is an easier target than RSA.Comment: 24 pages, 2 tables, 11 figures. v2: typos fixed and reference added.
ASIACRYPT 201
Non-Negative Matrix Factorization for Learning Alignment-Specific Models of Protein Evolution
Models of protein evolution currently come in two flavors: generalist and specialist. Generalist models (e.g. PAM, JTT, WAG) adopt a one-size-fits-all approach, where a single model is estimated from a number of different protein alignments. Specialist models (e.g. mtREV, rtREV, HIVbetween) can be estimated when a large quantity of data are available for a single organism or gene, and are intended for use on that organism or gene only. Unsurprisingly, specialist models outperform generalist models, but in most instances there simply are not enough data available to estimate them. We propose a method for estimating alignment-specific models of protein evolution in which the complexity of the model is adapted to suit the richness of the data. Our method uses non-negative matrix factorization (NNMF) to learn a set of basis matrices from a general dataset containing a large number of alignments of different proteins, thus capturing the dimensions of important variation. It then learns a set of weights that are specific to the organism or gene of interest and for which only a smaller dataset is available. Thus the alignment-specific model is obtained as a weighted sum of the basis matrices. Having been constrained to vary along only as many dimensions as the data justify, the model has far fewer parameters than would be required to estimate a specialist model. We show that our NNMF procedure produces models that outperform existing methods on all but one of 50 test alignments. The basis matrices we obtain confirm the expectation that amino acid properties tend to be conserved, and allow us to quantify, on specific alignments, how the strength of conservation varies across different properties. We also apply our new models to phylogeny inference and show that the resulting phylogenies are different from, and have improved likelihood over, those inferred under standard models
Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans
Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have
fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in
25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16
regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of
correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP,
while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in
Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium
(LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region.
Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant
enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the
refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa,
an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of
PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent
signals within the same regio
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