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Biomedical subjects

Brian D Athey

Publications and source records attributed to Brian D Athey.

8 recordsLinked to original sources
PubMed2006

An 'Honest Broker' mechanism to maintain privacy for patient care and academic medical research.

PURPOSE: From the Hippocratic Oath to the World Medical Association's Declaration of Geneva, physicians have sworn to protect patients' privacy. However, as systems move to more integrated architectures, protecting this medical data becomes more of a challenge. The increase in complexity of IT environments, the aggregation of data, and the desire of other entities to access this data, often 24 h/day x 7 day/week x 365 day/year, is putting serious strains on our ability to maintain its security. This problem cuts across all electronic record sources from patient care records to academic medical research records. APPROACH: In order to address this issue, we are rethinking the way we store, transmit, process, access, and federate patient data from clinical and research applications. Our groups at the University of Michigan are developing a system called the "Honest Broker" to help manage this problem. The Honest Broker will offload the burden of housing identifiable data elements of protected health information (PHI) (e.g., name and address) as well as manage data transfer between clinical and research systems. Lab results and other non-identifiable data will be stored in separate systems with either a research study ID or clinical ID number. This two-component architecture increases the burden on attackers who now need to compromise two systems, one of which is seriously hardened, in order to match health data with a patient's actual identity. CONCLUSIONS: While no security system is truly intrusion-proof, this architecture provides a high security choke point reducing the likelihood of a breach. By redesigning the method of integrating clinical care and research, we have enabled projects that would be cost prohibitive to conduct otherwise. The scalability of this mechanism is dependant on nature of the heterogenous nature of the clinical systems serving patients.

Biomedical Research↗
PubMed2005

miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST.

A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Existing tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example, miBLAST aligned 247 965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users.

Algorithms↗
PubMed2005

The "Honest Broker" method of integrating interdisciplinary research data.

Multiple clinical informatics systems have been developed within separate departments of the University of Michigan Medical School. We are in the process of creating an "Honest Broker" method of safely and securely linking together data from different clinical systems for a research project studying the co-morbidity of depression and cardiovascular disease. The Michigan Clinical Research Collaboratory (MCRC) is an NIH/NHLBI Roadmap initiative funded to re-engineer the clinical research enterprise.

Biomedical Research↗
PubMed2004

Noise suppression and optical sectioning by non-phase-recording interferometry.

It has long been known that image plane holography with low-coherence illumination achieves optical sectioning of a volume object. A method is analyzed that is similar to image plane holography, but the interferometric arrangement utilizes the interference between two object-bearing beams instead of the basic object and reference beams.

Journal Article↗
PubMed2004

Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray.

Sequence-specific oligonucleotide probes play a crucial role in hybridization techniques including PCR, DNA microarray and RNA interference. Once the entire genome becomes the search space for target genes/genomic sequences, however, cross-hybridization to non-target sequences becomes a problem. Large gene families with significant similarity among family members, such as the P450s, are particularly problematic. Additionally, accurate single nucleotide polymorphism (SNP) detection depends on probes that can distinguish between nearly identical sequences. Conventional oligonucleotide probes that are perfectly matched to target genes/genomic sequences are often unsuitable in such cases. Carefully designed mismatches can be used to decrease cross-hybridization potential, but implementing all possible mismatch probes is impractical. Our study provides guidelines for designing non-perfectly matched DNA probes to target DNA sequences as desired throughout the genome. These guidelines are based on the analysis of hybridization data between perfectly matched and non-perfectly matched DNA sequences (single-point or double-point mutated) calculated in silico. Large changes in hybridization temperature predicted by these guidelines for non-matched oligonucleotides fit independent experimental data very well. Applying the guidelines to find oligonucleotide microarray probes for P450 genes, we confirmed the ability of our point mutation method to differentiate the individual genes in terms of thermodynamic calculations of hybridization and sequence similarity.

Base Sequence↗
PubMed2002

Correlations among angular wave component amplitudes in elastic multiple-scattering random media.

The propagation of scalar waves through random media that provide multiple elastic scattering is considered by derivation of an expression for the angular correlation of the scattered wave amplitudes. Coherent wave transmission is shown to occur through a mechanism similar to that responsible for coherent backscattering. While the properties of the scattered wave are generally consistent with radiative-transfer theory for sufficiently small incident and scattering angles, coherent transmission provides corrections to radiative-transfer results at larger angles. The theoretical angular correlation curves are fit, by specifying the probability densities of two random variables that correspond to material parameters, to measured data of laser light scattering from various polymer microsphere suspensions.

Light↗
PubMed2002

Analysis of time-gated imaging through scattering media by a Fourier optics approach.

The method of Fourier optics is applied to the problem of time-gated imaging through scattering media. Tb adapt the problem to this treatment, appropriate alterations are made: The continuous medium is replaced by a cascade of thin scatterers, and a spatial filtering process is substituted for the conventional gating processes. Closed-form solutions are derived.

Journal Article↗