Linear scaling computation of the Fock matrix VII. Periodic Density Functional Theory at the Γ\Gamma-point

Linear scaling quantum chemical methods for Density Functional Theory are extended to the condensed phase at the $\Gamma$-point. For the two-electron Coulomb matrix, this is achieved with a tree-code algorithm for fast Coulomb summation [J. Chem. Phys. {\bf 106}, 5526 (1997)], together with multipole representation of the crystal field [J. Chem. Phys. {\bf 107}, 10131 (1997)]. A periodic version of the hierarchical cubature algorithm [J. Chem. Phys. {\bf 113}, 10037 (2000)], which builds a telescoping adaptive grid for numerical integration of the exchange-correlation matrix, is shown to be efficient when the problem is posed as integration over the unit cell. Commonalities between the Coulomb and exchange-correlation algorithms are discussed, with an emphasis on achieving linear scaling through the use of modern data structures. With these developments, convergence of the $\Gamma$-point supercell approximation to the ${\bf k}$-space integration limit is demonstrated for MgO and NaCl. Linear scaling construction of the Fockian and control of error is demonstrated for RBLYP/6-21G* diamond up to 512 atoms

Ab initio linear scaling response theory: Electric polarizability by perturbed projection

A linear scaling method for calculation of the static {\em ab inito} response within self-consistent field theory is developed and applied to calculation of the static electric polarizability. The method is based on density matrix perturbation theory [Niklasson and Challacombe, cond-mat/0311591], obtaining response functions directly via a perturbative approach to spectral projection. The accuracy and efficiency of the linear scaling method is demonstrated for a series of three-dimensional water clusters at the RHF/6-31G** level of theory. Locality of the response under a global electric field perturbation is numerically demonstrated by approximate exponential decay of derivative density matrix elements.Comment: 4.25 pages in PRL format, 2 figure

Molecular-orbital-free algorithm for excited states in time-dependent perturbation theory

A non-linear conjugate gradient optimization scheme is used to obtain excitation energies within the Random Phase Approximation (RPA). The solutions to the RPA eigenvalue equation are located through a variational characterization using a modified Thouless functional, which is based upon an asymmetric Rayleigh quotient, in an orthogonalized atomic orbital representation. In this way, the computational bottleneck of calculating molecular orbitals is avoided. The variational space is reduced to the physically-relevant transitions by projections. The feasibility of an RPA implementation scaling linearly with system size, N, is investigated by monitoring convergence behavior with respect to the quality of initial guess and sensitivity to noise under thresholding, both for well- and ill-conditioned problems. The molecular- orbital-free algorithm is found to be robust and computationally efficient providing a first step toward a large-scale, reduced complexity calculation of time-dependent optical properties and linear response. The algorithm is extensible to other forms of time-dependent perturbation theory including, but not limited to, time-dependent Density Functional theory.Comment: 9 pages, 7 figure

CXCL13, CCL21, and CXCL12 expression in salivary glands of patients with Sjogren's syndrome and MALT lymphoma: Association with reactive and malignant areas of lymphoid organization

The chemokines (CKs) CXCL13, CCL21, and CXCL12 are known to play differential roles in the organization of the lymphoid tissues and the development of lymphoid malignancies. We investigated the expression of these CKs and their receptors in the salivary glands of Sjogren's syndrome patients with lymphoepithelial lesions (lymphoepithelial sialadenitis or LESA) and in MALT lymphoma to understand their involvement in salivary gland lymphomagenesis. We demonstrate that within salivary glands with LESA and MALT lymphoma the lymphoid CKs CXCL13 and CCL21 are selectively associated with areas of reactive lymphoid proliferation, whereas no significant expression of these molecules was detected in the malignant lymphoid aggregate. Conversely, CXCL12 was observed predominantly in infiltrated ducts and malignant B cells. Accordingly, CXCL13 and CCL21 transcript levels were significantly increased in LESA samples while CXCL12 levels were increased in MALT lymphoma and isolated tumor cells. Low levels of CK receptors were detected on lymphoma-extracted lymphocytes, suggesting down-regulation in the abundance of ligands. Our findings suggest that in salivary gland MALT lymphoma the lymphoid CKs CXCL13 and CCL21 are directly implicated in the organization of ectopic reactive lymphoid tissue, whereas CXCL12 is associated with the infiltrated epithelium and malignant B cell component and is possibly involved in the regulation of malignant B cell survival

A cross sectional study of water quality from dental unit water lines in dental practices in the West of Scotland

OBJECTIVE: To determine the microbiological quality of water from dental units in a general practice setting and current practice for disinfection of units. DESIGN: A cross-sectional study of the water quality from 40 dental units in 39 general practices and a questionnaire of the disinfection protocols used in those practices. SETTING: NHS practices in primarydental care. SUBJECTS: Thirty-nine general practices from the West of Scotland. METHODS: Water samples were collected on two separate occasions from dental units and analysed for microbiological quality by the total viable count (TVC) method. Water specimens were collected from the triple syringe, high speed outlet, cup filler and surgery tap. Each participating practitioner was asked to complete a questionnaire. Results Microbial contamination was highest from the high speed outlet followed by the triple syringe and cup filler. On average, the TVC counts from the high speed water lines at 37 degrees C and for the high speed lines, triple syringe and cup filler at 22 degrees C were significantly higher than that from the control tap water specimens. The study included units from 11 different manufacturers with ages ranging from under one year to over eight years. The age of the dental unit analysed did not appear to influence the level of microbial contamination. Five of the practices surveyed used disinfectants to clean the dental units but these had no significant effect on the microbiological quality of the water. The majority of dental units (25 out of 40) were never flushed with water between patients. A number of different non-sterile irrigants were used for surgical procedures. CONCLUSION: The microbiological quality of water from dental units in general dental practice is poor compared with that from drinking water sources. Suitable sterile irrigants should be used for surgical procedures in dental practice. Further work is required for pragmatic decontamination regimens of dental unit water lines in a general dental practice setting

O(N) methods in electronic structure calculations

Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high performance computers. The linear scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas is then discussed. The applications of linear scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear scaling methods are discussed.Comment: 85 pages, 15 figures, 488 references. Resubmitted to Rep. Prog. Phys (small changes

Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae

Background: In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study. Results: Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15% divergence (88 to 85% ANI and 92 to 91% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95% and AAI <96% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59%) and 2058 ORFs (56%) with the published core genome of V. cholerae and 2956 (82%) and 3048 ORFs (84%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81% Vibrio sp. RC341 and 81% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp. Conclusions: Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.

Evaluation of the efficacy of Alpron disinfectant for dental unit water lines

AIMS: To assess the efficacy of a disinfectant, Alpron, for controlling microbial contamination within dental unit water lines. METHODS: The microbiological quality of water emerging from the triple syringe, high speed handpiece, cup filler and surgery hand wash basin from six dental units was assessed for microbiological total viable counts at 22 degrees C and 37 degrees C before and after treatment with Alpron solutions. RESULTS: The study found that the use of Alpron disinfectant solutions could reduce microbial counts in dental unit water lines to similar levels for drinking water. This effect was maintained in all units for up to six weeks following one course of treatment. In four out of six units the low microbial counts were maintained for 13 weeks. CONCLUSIONS: Disinfectants may have a short term role to play in controlling microbial contamination of dental unit water lines to drinking water quality. However, in the longer term attention must be paid to redesigning dental units to discourage the build up of microbial biofilms

Intensive hog farming operations and self-reported health among nearby rural residents in Ottawa, Canada

<p>Abstract</p> <p>Background</p> <p>In 2004, hog farming operations were introduced in the village of Sarsfield in the eastern part of Ottawa, Canada. This study evaluates the health-related quality of life (HRQOL), and the prevalence of respiratory conditions among adults and children who lived in proximity to this farm.</p> <p>Methods</p> <p>A cross-sectional survey was administered to a random sample of residents from seven rural communities in the eastern part of Ottawa, Canada. We analyzed self-reported questionnaire data obtained from 723 adults and 285 children/adolescents. HRQOL was assessed using the SF-36 survey instrument, while data were also collected for sociodemographic characteristics, the prevalence of selected health conditions, and lifestyle related behaviours (e.g., smoking) of participants. Variations in self-reported health according to the residential distance to the hog farm were evaluated using logistic regression and analysis of variance methods.</p> <p>Results</p> <p>For the most part, the prevalence of selected health conditions among adults and children was not associated with how far they lived from the farm. No associations were observed with migraines, respiratory conditions (asthma, rhinitis, sinusitis, and chronic bronchitis), and allergies. However, a higher prevalence of depression was noted among those who lived within 3 km of the farm relative to those who lived more than 9 km away (odds ratio = 2.01, 95% CI = 1.11, 3.65). Furthermore, individuals who lived closer to the IHF were more likely to worry about environmental issues such as water quality, outdoor and indoor smells, and air pollution. This level of worry also contributed to lower HRQOL scores for individuals who lived closer to the farm. It was also observed that the prevalence of depression was much higher among those who indicated a concern about environmental issues (18.2%) when compared to those who did not (8.0%).</p> <p>Conclusion</p> <p>While our findings suggest that living in close proximity to an IHF may adversely affect HRQOL these should be interpreted cautiously due to a lack of direct measures of environmental exposures, and possible biases inherent in the use of self-reported health measures.</p

Suitability of PSA-detected localised prostate cancers for focal therapy: Experience from the ProtecT study

This article is available through a Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License. Copyright @ 2011 Cancer Research UK.Background: Contemporary screening for prostate cancer frequently identifies small volume, low-grade lesions. Some clinicians have advocated focal prostatic ablation as an alternative to more aggressive interventions to manage these lesions. To identify which patients might benefit from focal ablative techniques, we analysed the surgical specimens of a large sample of population-detected men undergoing radical prostatectomy as part of a randomised clinical trial. Methods: Surgical specimens from 525 men who underwent prostatectomy within the ProtecT study were analysed to determine tumour volume, location and grade. These findings were compared with information available in the biopsy specimen to examine whether focal therapy could be provided appropriately. Results: Solitary cancers were found in prostatectomy specimens from 19% (100 out of 525) of men. In addition, 73 out of 425 (17%) men had multiple cancers with a solitary significant tumour focus. Thus, 173 out of 525 (33%) men had tumours potentially suitable for focal therapy. The majority of these were small, well-differentiated lesions that appeared to be pathologically insignificant (38–66%). Criteria used to select patients for focal prostatic ablation underestimated the cancer's significance in 26% (34 out of 130) of men and resulted in overtreatment in more than half. Only 18% (24 out of 130) of men presumed eligible for focal therapy, actually had significant solitary lesions. Conclusion: Focal therapy appears inappropriate for the majority of men presenting with prostate-specific antigen-detected localised prostate cancer. Unifocal prostate cancers suitable for focal ablation are difficult to identify pre-operatively using biopsy alone. Most lesions meeting criteria for focal ablation were either more aggressive than expected or posed little threat of progression.National Institute for Health Researc