eScience for molecular-scale simulations and the eMinerals project.

We review the work carried out within the eMinerals project to develop eScience solutions that facilitate a new generation of molecular-scale simulation work. Technological developments include integration of compute and data systems, developing of collaborative frameworks and new researcher-friendly tools for grid job submission, XML data representation, information delivery, metadata harvesting and metadata management. A number of diverse science applications will illustrate how these tools are being used for large parameter-sweep studies, an emerging type of study for which the integration of computing, data and collaboration is essential.

The SIESTA method; developments and applicability.

Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.

Ferrodistortive instability at the (001) surface of half-metallic manganites.

We present the structure of the fully relaxed (001) surface of the half-metallic manganite La0.7Sr0.3MnO3, calculated using density functional theory. Two relevant ferroelastic order parameters are identified and characterized. The known tilting of the oxygen octahedra, which is present in the bulk phase, decreases towards the surface. A ferrodistortive Mn off-centering, triggered by the surface and not reported before, decays monotonically into the bulk. This distortion affects neither the half-metallicity nor the zero-temperature magnetization, but does change the effective spin-spin interactions, and thus the temperature dependence of the magnetic properties.

Electronic stopping power in LiF from first principles.

Using time-dependent density-functional theory we calculate from first principles the rate of energy transfer from a moving proton or antiproton to the electrons of an insulating material, LiF. The behavior of the electronic stopping power versus projectile velocity displays an effective threshold velocity of approximately 0.2 a.u. for the proton, consistent with recent experimental observations, and also for the antiproton. The calculated proton/antiproton stopping-power ratio is approximately 2.4 at velocities slightly above the threshold (v approximately 0.4 a.u.), as compared to the experimental value of 2.1. The projectile energy loss mechanism is observed to be extremely local.

Detection with MR imaging of residual tumor in the breast soon after surgery.

OBJECTIVE: Difficulties in the preoperative assessment of tumor size and extent result in a positive pathologic margin in up to 70% of patients undergoing breast conservation surgery. Although positive margins usually require reexcision, the location and extent of surgery required are often difficult to establish by current imaging techniques. We investigated the accuracy of three-dimensional rotating delivery of excitation off resonance (3D RODEO) MR imaging of the breast in revealing the presence and extent of residual tumor within the breast soon after surgery. MATERIALS AND METHODS: Nineteen patients who had undergone lumpectomy or excisional biopsy were evaluated with contrast-enhanced 3D RODEO MR imaging of the breast within 10 months after surgery. The MR imaging results were correlated with serial-sectioned mastectomy or partial mastectomy specimens from 18 patients and with a clinical and mammographic follow-up examination in one patient. RESULTS: We found that 3D RODEO MR imaging accurately revealed the presence or absence and the location and extent of recurrent tumor in 15 of the 18 patients who had pathologic confirmation. Of the three MR imaging-pathology mismatches, two had irregular or nodular enhancement that corresponded to microabscesses. The third mismatch showed multicentric disease on MR imaging but only single-quadrant lobular carcinoma at pathologic examination. Our 19th patient showed no evidence of recurrent tumor on MR imaging or at 2-year follow-up clinical and mammographic examinations. CONCLUSION: MR imaging with 3D RODEO technique correctly revealed the presence or absence, the location, and the extent of recurrent tumor in 84% of patients who had recently undergone breast surgery.

MR imaging in the management before surgery of lobular carcinoma of the breast: correlation with pathology.

OBJECTIVE: Our objective was to investigate the use of MR imaging in preoperative staging and characterization of lobular carcinoma. MATERIALS AND METHODS: MR imaging studies and mammographic studies in 20 patients with infiltrating lobular carcinoma were evaluated and correlated with pathology findings on serially sectioned tissue. The MR images and mammograms were reviewed retrospectively by three independent examiners unaware of the clinical, imaging, and pathology findings. RESULTS: The extent of disease found pathologically correlated with that predicted by MR imaging studies in 85% of patients, compared with a 32% correlation (p < .0001) with mammographic studies. Interobserver agreement on lesion morphology and extent of disease was higher for MR imaging (91% and 100%, respectively) than for mammography (64% and 91%, respectively). The retrospective MR readings did not differ from the prospective reports. No false-positive lymphadenopathy was interpreted on MR imaging. Lymph nodes having metastatic lobular carcinoma on the pathology examination were missed on MR imaging in four patients. CONCLUSION: MR imaging is significantly more accurate than mammography in determining the extent of disease and characterizing the morphology of infiltrating lobular carcinoma. MR imaging may play a role in preoperative planning, especially when breast conservation is being considered.

Computer-aided mammographic screening for spiculated lesions.

PURPOSE: To study the use of a computer vision method as a second reader for the detection of spiculated lesions on screening mammograms. MATERIALS AND METHODS: An algorithmic computer process for the detection of spiculated lesions on digitized screen-film mammograms was applied to 85 four-view clinical cases: 36 cases with cancer proved by means of biopsy and 49 cases with negative findings at examination and follow-up. The computer detections were printed as film with added outlines that indicated the suspected cancers. Four radiologists screened the 85 cases twice, once without and once with the computer reports as ancillary films. RESULTS: The algorithm alone achieved 100% sensitivity, with a specificity of 82%. The computer reports increased the average radiologist sensitivity by 9.7% (P = .005), moving from 80.6% to 90.3%, with no decrease in average specificity. CONCLUSION: The study demonstrated that computer analysis of mammograms can provide a substantial and statistically significant increase in radiologist screening efficacy.