A statistical model describing temperature dependent gettering of Cu in p-type Si

A model is proposed describing quantitatively the temperature dependent gettering of Cu atoms in p-type Si wafers by taking into account the densities and the binding energies of all types of occupying sites, including the gettering ones. Binding energy in this context is defined as the decrease of the formation energy from the reference energy of the Cu atom when it is located at the T-site through which Cu atoms wander through the silicon lattice. By using a statistical approach, the model allows to predict the thermal equilibrium concentration of Cu atoms in each part of a wafer structure. The calculated results show good agreement with reported experimental observations. This model can also be applied to calculate thermal equilibrium concentrations of any contaminant

Conspiracy in bacterial genomes

The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two parabolically) from the total GC content. The rank ordered distribution of the amino acids is fitted by a straight line. The Shannon entropy computed over all the codons is well fitted by a parabola in the GC content, while the partial entropies computed over subsets of the codons show peculiar different behavior, exhibiting therefore a first conspiracy effect. Moreover the sum of the codon usage frequencies over particular sets, e.g. with C and A (respectively G and U) as i-th nucleotide, shows a clear linear dependence from the GC content, exhibiting another conspiracy effect.Comment: revised version: introduction and conclusion enhanced, references added, figures added, some tables remove

Depression Treatment in HIV-infected and Uninfected Veterans: Do Treatment Rates Vary by HIV Status?

Background: Despite a higher prevalence of depression among HIV-infected veterans, previous research has shown that infectious disease (ID) providers report substantially less comfort with depression treatment than do general medicine (GM) providers. We examined whether HIV-infected veterans who are treated by ID providers are less likely to have their depressive symptoms treated compared to uninfected controls managed by GM providers. Methods: We used survey, service utilization, and pharmacy data on veterans from the Veterans Aging Cohort Study (VACS), a prospective cohort study of HIV-infected and age-, race- and site-matched uninfected subjects at 8 Veterans Affairs Healthcare Centers. We used the Patient Health Questionnaire (PHQ-9) to identify veterans with depressive symptoms. Each of nine survey items was rated by the veteran as being present 0 (not at all) to 3 (nearly every day). Veterans were considered to have active depressive symptoms if they had a PHQ-9 score of 10 or greater, which constituted a positive screen for major depressive disorder. Of the 5998 VACS patients, 19.7% of uninfected and 21.3% of HIV-infected veterans had PHQ-9 scores of 10 or greater. Of these veterans with active depressive symptoms, those receiving mono-amine oxidase inhibitors (MAOIs) (n=3), female veterans, and men with diagnoses of schizophrenia (n=511) or PTSD (n=689), were excluded. A small number of patients receiving tricyclic antidepressants (TCAs) were excluded for criteria other than TCA use. Depression treatment was defined as receipt of a selective serotonin reuptake inhibitor (SSRI) or any VA mental health utilization in the 6 months prior to or after survey. Bivariate comparisons by clinic type were assessed using chi-square and t-tests. Logistic regression was used to determine whether clinic type was associated with receipt of SSRI, adjusting for potential confounding variables such as demographics and clinical factors. Results: Of the 5998 veterans in VACS, 732 met our criteria with PHQ-9 scores greater than 10, male gender, without schizophrenia, PTSD or MAOI use. Of the 732 eligible veterans, 59% were HIV-infected and 41% were uninfected. The sample was predominantly African-American (58%) and had a median age of 48 years. There was no significant difference in the proportion of veterans with depressive symptoms who were treated by HIV status (38% of HIV-infected veterans vs. 34% of uninfected veterans, p=0.4). This remained true even when mental health service utilization was included (48% vs. 49%, p=0.8). Caucasian veterans were significantly more likely than African-Americans to have received SSRI (48% vs. 30%, p\u3c0.01). After controlling for veteran age, race, and comorbid conditions, HIV-infected veterans did not differ significantly in receipt of SSRI (OR=1.16, 95% CI=0.84, 1.58). However, there were significant differences in treatment rates by site and by individual clinic. Conclusions: Despite previous analysis demonstrating substantial differences in provider comfort with depression treatment, both HIV-infected and uninfected veterans were equally unlikely to be treated for depressive symptoms. While treatment rates did not vary by HIV status, they varied significantly by geographic site and individual clinic, suggesting that provider practices have considerable influence over receipt of treatment

Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons

Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between the two DNA strands, a model with at most 6 different parameters instead of 12 is sufficient to study the evolutionary relationship between homologous sequences derived from a common ancestor. On the other hand the same symmetry reduces the number of independent observations which can be made. Such a reduction can in some cases invalidate the calculation of the parameters. A compromise between biologically acceptable hypotheses and tractability is introduced and a five parameter reversible no-strand-bias condition (RNSB) is presented. The identifiability of the parameters under this model is shown by examples.Comment: 12 pages, 4 figures, corrected typo

Isochores Merit the Prefix 'Iso'

The isochore concept in human genome sequence was challenged in an analysis by the International Human Genome Sequencing Consortium (IHGSC). We argue here that a statement in IGHSC analysis concerning the existence of isochore is incorrect, because it had applied an inappropriate statistical test. To test the existence of isochores should be equivalent to a test of homogeneity of windowed GC%. The statistical test applied in the IHGSC's analysis, the binomial test, is however a test of a sequence being random on the base level. For testing the existence of isochore, or homogeneity in GC%, we propose to use another statistical test: the analysis of variance (ANOVA). It can be shown that DNA sequences that are rejected by binomial test may not be rejected by the ANOVA test.Comment: 14 pages (including 1 figure), submitte

Polarization Modeling and Predictions for DKIST Part 2: Application of the Berreman Calculus to Spectral Polarization Fringes of Beamsplitters and Crystal Retarders

We outline polarization fringe predictions derived from a new application of the Berreman calculus for the Daniel K. Inouye Solar Telescope (DKIST) retarder optics. The DKIST retarder baseline design used 6 crystals, single-layer anti-reflection coatings, thick cover windows and oil between all optical interfaces. This new tool estimates polarization fringes and optic Mueller matrices as functions of all optical design choices. The amplitude and period of polarized fringes under design changes, manufacturing errors, tolerances and several physical factors can now be estimated. This tool compares well with observations of fringes for data collected with the SPINOR spectropolarimeter at the Dunn Solar Telescope using bi-crystalline achromatic retarders as well as laboratory tests. With this new tool, we show impacts of design decisions on polarization fringes as impacted by anti-reflection coatings, oil refractive indices, cover window presence and part thicknesses. This tool helped DKIST decide to remove retarder cover windows and also recommends reconsideration of coating strategies for DKIST. We anticipate this tool to be essential in designing future retarders for mitigation of polarization and intensity fringe errors in other high spectral resolution astronomical systems.Comment: Accepted for publication in JATI