Security and confidentiality approach for the Clinical E-Science Framework (CLEF)

CLEF is an MRC sponsored project in the E-Science programme that aims to establish policies and infrastructure for the next generation of integrated clinical and bioscience research. One of the major goals of the project is to provide a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies are needed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research. This paper summarises the overall approach adopted by CLEF to meet data protection requirements, including the data flows and pseudonymisation mechanisms that are currently being developed. Intended constraints and monitoring policies that will apply to research interrogation of the repository are also outlined. Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research

Security and confidentiality approach for the Clinical E-Science Framework (CLEF)

Objectives: CLEF is an MRC sponsored project in the E-Science programme that aims to establish methodologies and a technical infrastructure for the next generation of integrated clinical and bioscience research. Methods: The heart of the CLEF approach to this challenge is to design and develop a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies have been developed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research. Results: This paper summarises the overall approach adopted by CLEF to meet data protection requirements, including the data flows, pseudonymisation measures and additional monitoring policies that are currently being developed. Conclusion: Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research

eHealth Applications in Health Care Management

© 2002 Svensson; licensee BioMed Central Ltd. This article is published in Open Access: verbatim copying and redistribution of this article are permitted in all media for any non-commercial purpose, provided this notice is preserved along with the article's original URL

Helium in superstrong magnetic fields

We investigate the helium atom embedded in a superstrong magnetic field gamma=100-10000 au. All effects due to the finite nuclear mass for vanishing pseudomomentum are taken into account. The influence and the magnitude of the different finite mass effects are analyzed and discussed. Within our full configuration interaction approach calculations are performed for the magnetic quantum numbers M=0,-1,-2,-3, singlet and triplet states, as well as positive and negative z parities. Up to six excited states for each symmetry are studied. With increasing field strength the number of bound states decreases rapidly and we remain with a comparatively small number of bound states for gamma=10^4 au within the symmetries investigated here.Comment: 16 pages, including 14 eps figures, submitted to Phys. Rev.

Hydrogen molecule in a magnetic field: The lowest states of the Pi manifold and the global ground state of the parallel configuration

The electronic structure of the hydrogen molecule in a magnetic field is investigated for parallel internuclear and magnetic field axes. The lowest states of the $\Pi$ manifold are studied for spin singlet and triplet$(M_s = -1)$ as well as gerade and ungerade parity for a broad range of field strengths $0 \leq B \leq 100 a.u.$ For both states with gerade parity we observe a monotonous decrease in the dissociation energy with increasing field strength up to $B = 0.1 a.u.$ and metastable states with respect to the dissociation into two H atoms occur for a certain range of field strengths. For both states with ungerade parity we observe a strong increase in the dissociation energy with increasing field strength above some critical field strength $B_c$. As a major result we determine the transition field strengths for the crossings among the lowest $^1\Sigma_g$, $^3\Sigma_u$ and $^3\Pi_u$ states. The global ground state for $B \lesssim 0.18 a.u.$ is the strongly bound $^1\Sigma_g$ state. The crossings of the $^1\Sigma_g$ with the $^3\Sigma_u$ and $^3\Pi_u$ state occur at $B \approx 0.18$ and $B \approx0.39 a.u.$, respectively. The transition between the $^3\Sigma_u$ and $^3\Pi_u$ state occurs at $B \approx 12.3 a.u.$ Therefore, the global ground state of the hydrogen molecule for the parallel configuration is the unbound $^3\Sigma_u$ state for $0.18 \lesssim B \lesssim 12.3 a.u.$ The ground state for $B \gtrsim 12.3 a.u.$ is the strongly bound $^3\Pi_u$ state. This result is of great relevance to the chemistry in the atmospheres of magnetic white dwarfs and neutron stars.Comment: submitted to Physical Review

Exchange and correlation energies of ground states of atoms and molecules in strong magnetic fields

Using a Hartree-Fock mesh method and a configuration interaction approach based on a generalized Gaussian basis set we investigate the behaviour of the exchange and correlation energies of small atoms and molecules, namely th e helium and lithium atom as well as the hydrogen molecule, in the presence of a magnetic field covering the regime B=0-100a.u. In general the importance of the exchange energy to the binding properties of at oms or molecules increases strongly with increasing field strength. This is due to the spin-flip transitions and in particular due to the contributions of the tightly bound hydrogenic state s which are involved in the corresponding ground states of different symmetries. In contrast to the exchange energy the correlation energy becomes less relevant with increasing field strength. This holds for the individual configurations constituting the ground state and for the crossovers of the global ground state.Comment: 4 Figures acc.f.publ.in Phys.Rev.

P20-16. Ultra-deep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in SIV-infected macaques

Background A complex population of viral variants exists within each individual infected with immunodeficiency virus. Deciphering the breadth and frequency of accruing viral mutations provides insight into immune responses, drug resistance, and potential vaccine targets. Contemporary sequencing methods are limited to detection of high frequency variants, leading to an incomplete assessment of the overall viral population. Here, we use ultra-deep pyrosequencing to create a comprehensive picture of CD8+ T-lymphocyte (CD8-TL) escape in two epitopes in SIV-infected rhesus and cynomolgus macaques, revealing a complex pattern of viral variants previously undetected. Methods Plasma was collected from SIV-infected rhesus and cynomolgus macaques at multiple timepoints between weeks 1 and 20 post-infection. Viral RNA was isolated and amplicons spanning the epitopes of interest were generated by RT-PCR, using primers that incorporated a unique 10 bp molecular barcode into each sample. Amplicons were pooled and sequenced on a Roche Genome Sequencer FLX instrument and analyzed using Roche Amplicon Variant Analyzer software. Results The increased sensitivity of ultra-deep pyrosequencing enabled detection of acute CD8-TL escape as early as 17 days post-infection, representing the earliest published example of CD8-TL escape in intrarectally infected macaques. Conversely, we observed the continued presence of a complex viral population well into chronic infection, indicating that viral mutations deemed ''fixed'' by Sanger sequencing are instead complemented by a broad array of viral variants. Additionally, we show that these methods can be applied to sequencing of the entire SIVmac239 genome, supporting the continued use of pyrosequencing in comprehensive SIV infection studies. Conclusion Overall, these findings demonstrate that pyrosequencing can be used to study viral evolution during HIV/SIV infection with an unprecedented degree of sensitivity. Utilizing newly emerging molecular tools is essential and will further our understanding of how viral pathogens evade the immune system

Development and Initial Validation of an Instrument to Measure Physicians' Use of, Knowledge about, and Attitudes Toward Computers

This paper describes details of four scales of a questionnaire—“Computers in Medical Care”—measuring attributes of computer use, self-reported computer knowledge, computer feature demand, and computer optimism of academic physicians. The reliability (i.e., precision, or degree to which the scale's result is reproducible) and validity (i.e., accuracy, or degree to which the scale actually measures what it is supposed to measure) of each scale were examined by analysis of the responses of 771 full-time academic physicians across four departments at five academic medical centers in the United States. The objectives of this paper were to define the psychometric properties of the scales as the basis for a future demonstration study and, pending the results of further validity studies, to provide the questionnaire and scales to the medical informatics community as a tool for measuring the attitudes of health care providers

Guided random walk calculation of energies and <\sq {r^2} > values of the 1Σg^1\Sigma_g state of H_2 in a magnetic field

Energies and spatial observables for the $^1\Sigma_g$ state of the hydrogen molecule in magnetic fields parallel to the proton-proton axis are calculated with a guided random walk Feynman-Kac algorithm. We demonstrate that the accuracy of the results and the simplicity of the method may prove it a viable alternative to large basis set expansions for small molecules in applied fields.Comment: 10 pages, no figure

Confirmation that “Brachyspira hampsonii” clade I (Canadian strain 30599) causes mucohemorrhagic diarrhea and colitis in experimentally infected pigs

BACKGROUND: “Brachyspira hampsonii”, discovered in North America in 2010 associated with dysentery-like illness, is an economically relevant swine pathogen resulting in decreased feed efficiency and increased morbidity, mortality and medication usage. “B. hampsonii” clade II strain 30446 has been shown to be causally associated with mucohemorrhagic diarrhea and colitis. Our objectives were to determine if “Brachyspira hampsonii” clade I strain 30599 is pathogenic to pigs, and to evaluate the relative diagnostic performance of three ante mortem sampling methodologies (direct PCR on feces, PCR on rectal GenoTube Livestock swabs, Brachyspira culture from rectal swabs). Five-week old pigs were intragastrically inoculated thrice with 10(8) genomic equivalents "B. hampsonii" (n = 12), or served as sham controls (n = 6). Feces were sampled and consistency assessed daily. Necropsies were performed 24 h after peak clinical signs. RESULTS: One pig died due to unrelated illness. Nine of 11 inoculated pigs, but no controls, developed mucoid or mucohemorrhagic diarrhea (MHD). Characteristic lesions of swine dysentery were observed in large intestine. “B. hampsonii” strain 30599 DNA was detected by qPCR in feces of all inoculated pigs for up to 6 days prior to the onset of MHD. The organism was isolated from the feces and colons of pigs demonstrating MHD, but not from controls. B. intermedia was isolated from inoculated pigs without MHD, and from 5 of 6 controls. CONCLUSIONS: We conclude that “Brachyspira hampsonii” clade I strain 30599 is pathogenic and causes mucohemorrhagic diarrhea and colitis in susceptible pigs. Moreover, the three sampling methodologies performed similarly. GenoTube Livestock, a forensic swab designed to preserve DNA during shipping is a useful tool especially in settings where timely transport of diagnostic samples is challenging