Domain-mediated interactions for protein subfamily identification

Within a protein family, proteins with the same domain often exhibit different cellular functions, despite the shared evolutionary history and molecular function of the domain. We hypothesized that domain-mediated interactions (DMIs) may categorize a protein family into subfamilies because the diversified functions of a single domain often depend on interacting partners of domains. Here we systematically identified DMI subfamilies, in which proteins share domains with DMI partners, as well as with various functional and physical interaction networks in individual species. In humans, DMI subfamily members are associated with similar diseases, including cancers, and are frequently co-associated with the same diseases. DMI information relates to the functional and evolutionary subdivisions of human kinases. In yeast, DMI subfamilies contain proteins with similar phenotypic outcomes from specific chemical treatments. Therefore, the systematic investigation here provides insights into the diverse functions of subfamilies derived from a protein family with a link-centric approach and suggests a useful resource for annotating the functions and phenotypic outcomes of proteins.11Ysciescopu

Determining clinical pharmacy workload by patient disease classification in medical and surgical patients

Aim: To determine the time needed to provide clinical pharmacy services to individual patient episodes for medical and surgical patients and the effect of patient presentation and complexity on the clinical pharmacy workload. Method: During a 5-month period in 2006 at two general hospitals, pharmacists recorded a defined range of activities that they provided for patients, including the actual times required for these tasks. A customised database linked to the two hospitals\u27 patient administration systems stored the data according to the specific patient episode number. The influence of patient presentation and complexity on the clinical pharmacy activities provided was also examined. Results: The average time required by pharmacists to undertake a medication history interview and medication reconciliation was 9.6 (SD 4.9) minutes. Interventions required 5.7 (SD 4.6) minutes, clinical review of the medical record 5.5 (SD 4.0) minutes and medication order review 3.5 (SD 2.0) minutes. For all of these activities, the time required for medical patients was greater than for surgical patients and greater for \u27complicated\u27 patients. The average time required to perform all clinical pharmacy activities for 1071 completed patient episodes was 14.4 (SD 10.9) minutes and was greater for medical and \u27complicated\u27 patients. Conclusion: The time needed to provide clinical pharmacy services was affected by whether the patients were medical or surgical. The existence of comorbidities or complications affected these times. The times required to perform clinical pharmacy activities may not be consistent with recently proposed staff ratios for the provision of a basic clinical pharmacy service.<br /

Electronic structure, electron-phonon coupling and superconductivity of isotypic noncentrosymmetric crystals Li2_2Pd3_3B and Li2_2Pt3_3B

Electronic structure of recently discovered isotypic ternary borides Li$_2$Pd$_3$B and Li$_2$Pt$_3$B, with noncentrosymmetric crystal structures, is studied with a view to understanding their superconducting properties. Estimates of the Fermi-surface averaged electron-phonon matrix element and Hopfield parameter are obtained in the rigid ion approximation of Gaspari and Gyorffy [Phys. Rev. Lett. {\bf 28} (1972) 801]. The contribution of the lithium atoms to the electron-phonon coupling is found to be negligible, while both boron and palladium atoms contribute equally strongly to the Hopfield parameter. There is a significant transfer of charge from lithium, almost the entire valence charge, to the B-Pd(Pt) complex. The electronic structure and superconducting properties of Li$_2$Pd$_3$B, thus, can be understood from the viewpoint of the compound being composed of a connected array of B-Pd tetrahedra decoupled from the backbone of Li atoms, which are connected by relatively short bonds. Our results suggest that conventional s-wave electron-phonon interaction without explicit consideration of SO coupling can explain qualitatively the observed $T_c$ in Li$_2$Pd$_3$B. However, such an approach is likely to fail to describe superconductivity in Li$_2$Pt$_3$B.Comment: 14 pages, 4 figures An erroneous statement following Eq. 6 in version 1 has been deleted. A statement regarding the possible inadequacy of Eq. 6 has been added following Eq. 6. At two places in the discussion Refs. 37,39 has been changed to 37-39, as it should b

Neon ion Irradiation studies on MgB2 Superconductor

160 MeV Neon ion irradiation has been carried out on MgB2 polycrystalline pellets at various doses. There has not been any significant change in Tc except at the highest dose of 1x10^15 ions/cm^2. Increase in resistivity has been noticed. Resistivity data has been fitted with Bloch-Gruneisen function and the values of Debye temperature, residual resistivity and temperature coefficient of resistivity have been extracted for irradiated as well as unirradiated samples. The increase in the resistivity of irradiated samples has been explained in the light of damage in the 3D pi bonding network of B.Comment: 15 pages, 3 figure

Point defect induced incommensurate dipole moments in the KCa2Nb3O10 Dion-Jacobson layered perovskite

Local structural distortions due to isolated atomic defects and defect complexes strongly affect the macroscopic properties of oxide ceramics. While the characterization of local defect structures is more common in simple ABO3 perovskites, unambiguous determination of the same in layered perovskites is more difficult due to their complex crystal structures. Here, we combined x-ray pair distribution function and density functional theory calculations to characterize the structure of cation-oxygen divacancy pairs in a Dion-Jacobson (D-J) layered perovskite. Our results indicate that local incommensurate dipole moments with polarization density in the range of ∼0.1–17μC/cm2 are created due to divacancy-induced structural distortions in the D-J phase KCa2Nb3O10. This is comparable with defect dipole moments observed in well-known perovskite ferroelectrics. The current results imply that controlling the atomic defects can potentially lead to significant control of dielectric properties in D-J layered perovskites

Comparing benefits from many possible computed tomography lung cancer screening programs: Extrapolating from the National Lung Screening Trial using comparative modeling

Background: The National Lung Screening Trial (NLST) demonstrated that in current and former smokers aged 55 to 74 years, with at least 30 pack-years of cigarette smoking history and who had quit smoking no more than 15 years ago, 3 annual computed tomography (CT) screens reduced lung cancer-specific mortality by 20% relative to 3 annual chest X-ray screens. We compared the benefits achievable with 576 lung cancer screening programs that varied CT screen number and frequency, ages of screening, and eligibility based on smoking. Methods and Findings: We used five independent microsimulation models with lung cancer natural history parameters previously calibrated to the NLST to simulate life histories of the US cohort born in 1950 under all 576 programs. 'Efficient' (within model) programs prevented the greatest number of lung cancer deaths, compared to no screening, for a given number of CT screens. Among 120 'consensus efficient' (identified as efficient across models) programs, the average starting age was 55 years, the stopping age was 80 or 85 years, the average minimum pack-years was 27, and the maximum years since quitting was 20. Among consensus efficient programs, 11% to 40% of the cohort was screened, and 153 to 846 lung cancer deaths were averted per 100,000 people. In all models, annual screening based on age and smoking eligibility in NLST was not efficient; continuing screening to age 80 or 85 years was more efficient. Conclusions: Consensus results from five models identified a set of efficient screening programs that include annual CT lung cancer screening using criteria like NLST eligibility but extended to older ages. Guidelines for screening should also consider harms of screening and individual patient characteristics

Comparative analysis of the genes UL1 through UL7 of the duck enteritis virus and other herpesviruses of the subfamily Alphaherpesvirinae

The nucleotide sequences of eight open reading frames (ORFs) located at the 5' end of the unique long region of the duck enteritis virus (DEV) Clone-03 strain were determined. The genes identified were designated UL1, UL2, UL3, UL4, UL5, UL6 and UL7 homologues of the herpes simplex virus 1 (HSV-1). The DEV UL3.5 located between UL3 and UL4 had no homologue in the HSV-1. The arrangement and transcription orientation of the eight genes were collinear with their homologues in the HSV-1. Phylogenetic trees were constructed based on the alignments of the deduced amino acids of eight proteins with their homologues in 12 alpha-herpesviruses. In the UL1, UL3, UL3.5, UL5 and UL7 proteins trees, the branches were more closely related to the genus Mardivirus. However, the UL2, UL4, and UL6 proteins phylogenetic trees indicated a large distance from Mardivirus, indicating that the DEV evolved differently from other viruses in the subfamily Alphaherpesvirinae and formed a single branch within this subfamily

Fitting the integrated Spectral Energy Distributions of Galaxies

Fitting the spectral energy distributions (SEDs) of galaxies is an almost universally used technique that has matured significantly in the last decade. Model predictions and fitting procedures have improved significantly over this time, attempting to keep up with the vastly increased volume and quality of available data. We review here the field of SED fitting, describing the modelling of ultraviolet to infrared galaxy SEDs, the creation of multiwavelength data sets, and the methods used to fit model SEDs to observed galaxy data sets. We touch upon the achievements and challenges in the major ingredients of SED fitting, with a special emphasis on describing the interplay between the quality of the available data, the quality of the available models, and the best fitting technique to use in order to obtain a realistic measurement as well as realistic uncertainties. We conclude that SED fitting can be used effectively to derive a range of physical properties of galaxies, such as redshift, stellar masses, star formation rates, dust masses, and metallicities, with care taken not to over-interpret the available data. Yet there still exist many issues such as estimating the age of the oldest stars in a galaxy, finer details ofdust properties and dust-star geometry, and the influences of poorly understood, luminous stellar types and phases. The challenge for the coming years will be to improve both the models and the observational data sets to resolve these uncertainties. The present review will be made available on an interactive, moderated web page (sedfitting.org), where the community can access and change the text. The intention is to expand the text and keep it up to date over the coming years.Comment: 54 pages, 26 figures, Accepted for publication in Astrophysics & Space Scienc