Detecting laterally transferred genes: use of entropic clustering methods and genome position

Most parametric methods for detecting foreign genes in bacterial genomes use a scoring function that measures the atypicality of a gene with respect to the bulk of the genome. Genes whose features are sufficiently atypical—lying beyond a threshold value—are deemed foreign. Yet these methods fail when the range of features of donor genomes overlaps with that of the recipient genome, leading to misclassification of foreign and native genes; existing parametric methods choose threshold parameters to balance these error rates. To circumvent this problem, we have developed a two-pronged approach to minimize the misclassification of genes. First, beyond classifying genes as merely atypical, a gene clustering method based on Jensen–Shannon entropic divergence identifies classes of foreign genes that are also similar to each other. Second, genome position is used to reassign genes among classes whose composition features overlap. This process minimizes the misclassification of either native or foreign genes that are weakly atypical. The performance of this approach was assessed using artificial chimeric genomes and then applied to the well-characterized Escherichia coli K12 genome. Not only were foreign genes identified with a high degree of accuracy, but genes originating from the same donor organism were effectively grouped

Crystallographic and Magnetic Properties of the Spinel-type Ferrites ZnxCo1-xFe2O4 (0.0 <= x <= 0.75)

Ultrahigh frequencies (UHF) have applications in signal and power electronics to minimize product sizes, increase production quantity and lower manufacturing cost. In the UHF range of 300 MHz to 3 GHz, ferrimagnetic iron oxides (ferrites) are especially useful because they combine the properties of a magnetic material with that of an electrical insulator. Ferrites have much higher electrical resistivity than metallic ferromagnetic materials, resulting in minimization of the eddy current losses, and total penetration of the electromagnetic (EM) field. Hence ferrites are frequently applied as circuit elements, magnetic storage media like read/write heads, phase shifters and Faraday rotators. The electromagnetic properties of ferrites are affected by operating conditions such as field strength, temperature and frequency. The spinel system ZnxCo1-xFe2O4 (x= 0.0, 0.25, 0.50 and 0.75) has been prepared by the standard solid state sintering method. X-ray and neutron powder diffraction measurements were performed at room temperature. Neutron diffraction data analysis confirms the cubic symmetry corresponding to the space group Fd3m. The distribution of three cations Zn2+, Co2+ and Fe3+ over the spinel lattice and other crystallographic parameters like lattice constant, oxygen position parameter, overall temperature factor and occupancies of different ions in different lattice sites for the samples have been determined from the analysis of neutron diffraction data. The lattice constant increases with increasing Zn content in the system. The magnetic structure was found to be ferrimagnetic for the samples with x <= 0.50. Magnetization measurements show that with the increase of Zn content in the system the value of saturation magnetization first increases and then decreases. The variation of the magnetic moment with Zn substitution has been discussed in terms of the distribution of magnetic and non-magnetic ions over the A and B sub-lattices and their exchange coupling

Structural and doping effects in the half-metallic double perovskite A2A_2CrWO6_6

he structural, transport, magnetic and optical properties of the double perovskite $A_2$CrWO$_6$ with $A=\text{Sr, Ba, Ca}$ have been studied. By varying the alkaline earth ion on the $A$ site, the influence of steric effects on the Curie temperature $T_C$ and the saturation magnetization has been determined. A maximum $T_C=458$ K was found for Sr$_2$CrWO$_6$ having an almost undistorted perovskite structure with a tolerance factor $f\simeq 1$. For Ca$_2$CrWO$_6$ and Ba$_2$CrWO$_6$ structural changes result in a strong reduction of $T_C$. Our study strongly suggests that for the double perovskites in general an optimum $T_C$ is achieved only for $f \simeq 1$, that is, for an undistorted perovskite structure. Electron doping in Sr$_2$CrWO$_6$ by a partial substitution of Sr$^{2+}$ by La$^{3+}$ was found to reduce both $T_C$ and the saturation magnetization $M_s$. The reduction of $M_s$ could be attributed both to band structure effects and the Cr/W antisites induced by doping. Band structure calculations for Sr$_2$CrWO$_6$ predict an energy gap in the spin-up band, but a finite density of states for the spin-down band. The predictions of the band structure calculation are consistent with our optical measurements. Our experimental results support the presence of a kinetic energy driven mechanism in $A_2$CrWO$_6$, where ferromagnetism is stabilized by a hybridization of states of the nonmagnetic W-site positioned in between the high spin Cr-sites.Comment: 14 pages, 10 figure

Drug-related mutational patterns in hepatitis B virus (HBV) reverse transcriptase proteins from Iranian treatment-Naïve chronic HBV patients

Background: Immunomodulators and Nucleotide analogues have been used globally for the dealing of chronic hepatitis B virus (HBV) infection. However, the development of drug resistance is a major limitation to their long-term effectiveness. Objectives: The aim of this study was to characterize the hepatitis B virus reverse transcriptase (RT) protein variations among Iranian chronic HBV carriers who did not receive any antiviral treatments. Materials and Methods: Hepatitis B virus partial RT genes from 325 chronic in active carrier patients were amplified and directly sequenced. Nucleotide/amino acid substitutions were identified compared to the sequences obtained from the database. Results: All strains belonging to genotype D.365 amino-acid substitutions were found. Mutations related to lamivudine, adefovir, telbivudine, and entecavir occurred in (YMDD) 4% (n = 13), (SVQ) 17.23% (n = 56), (M204I/V + L180M) 2.45% (n = 8) and (M204I) 2.76% (n = 9) of patients, respectively. Conclusions: RT mutants do occur naturally and could be found in HBV carriers who have never received antiviral therapy. However, mutations related to drug resistance in Iranian treatment-naïve chronic HBV patients were found to be higher than other studies published formerly. Chronic HBV patients should be monitored closely prior the commencement of therapy to achieve the best regimen option. © 2013, KOWSAR Corp

Risk Factors for MDR and XDR-TB in a Tertiary Referral Hospital in India

BACKGROUND: India has a high burden of drug resistant TB, although there are few data on XDR-TB. Although XDR-TB has existed previously in India, the definition has not been widely applied, and surveillance using second line drug susceptibility testing has not been performed. Our objective was to analyze clinical and demographic risk factors associated with isolation of MDR and XDR TB as compared to susceptible controls, at a tertiary center. METHODOLOGY/FINDINGS: Retrospective chart review based on positive cultures isolated in a high volume mycobacteriology laboratory between 2002 and 2007. 47 XDR, 30 MDR and 117 susceptible controls were examined. Drug resistant cases were less likely to be extrapulmonary, and had received more previous treatment regimens. Significant risk factors for XDR-TB included residence outside the local state (OR 7.43, 3.07-18.0) and care costs subsidized (OR 0.23, 0.097-0.54) in bivariate analysis and previous use of a fluoroquinolone and injectable agent (other than streptomycin) (OR 7.00, 95% C.I. 1.14-43.03) and an initial treatment regimen which did not follow national guidelines (OR 5.68, 1.24-25.96) in multivariate analysis. Cavitation and HIV did not influence drug resistance. CONCLUSIONS/SIGNIFICANCE: There is significant selection bias in the sample available. Selection pressure from previous treatment and an inadequate initial regimen increases risk of drug resistance. Local patients and those requiring financial subsidies may be at lower risk of XDR-TB

Institutional delivery in public and private sectors in South Asia: A comparative analysis of prospective data from four demographic surveillance sites

__Background:__ Maternity care in South Asia is available in both public and private sectors. Using data from demographic surveillance sites in Bangladesh, Nepal and rural and urban India, we aimed to compare institutional delivery rates and public-private share. __Methods:__ We used records of maternity care collected in socio-economically disadvantaged communities between 2005 and 2011. Institutional delivery was summarized by four potential determinants: household asset index, maternal schooling, maternal age, and parity. We developed logistic regression models for private sector institutional delivery with these as independent covariates. __Results:__ The data described 52 750 deliveries. Institutional delivery proportion varied and there were differences in public-private split. In Bangladesh and urban India, the proportion of deliveries in the private sector increased with wealth, maternal education, and age. The opposite was observed in rural India and Nepal. __Conclusions:__ The proportion of institutional delivery increased with economic status and education. The choice of sector is more complex and provision and perceived quality of public sector services is likely to play a role. Choices for safe maternity are influenced by accessibility, quantity and perceived quality of care. Along with data linkage between privat

A mega-analysis of memory reports from eight peer-reviewed false memory implantation studies

Understanding that suggestive practices can promote false beliefs and false memories forchildhood events is important in many settings (e.g., psychotherapeutic, medical, legal). The generalizability of findings from memory implantation studies has been questioned due to variability in estimates across studies. Such variability is partly due to false memories having been operationalized differently across studies and to differences in memory induction techniques. We explored ways of defining false memory based on memory science and developed a reliable coding system that we applied to reports from eight published implantation studies (N=423). Independent raters coded transcripts using seven criteria: accepting the suggestion, elaboration beyond the suggestion, imagery, coherence, emotion, memory statements, and not rejecting the suggestion. Using this scheme, 30.4% of cases were classified as false memories and another 23% were classified as having accepted the event to some degree. When the suggestion included self-relevant information, an imagination procedure, and was not accompanied by a photo depicting the event, the memory formation rate was 46.1%. Our research demonstrates a useful procedure for systematically combining data that are not amenable to meta-analysis, and provides the most valid estimate of false memory formation and associated moderating factors within the implantation literature to date

Reaching the poor with health interventions: programme-incidence analysis of seven randomised trials of women's groups to reduce newborn mortality in Asia and Africa

Efforts to end preventable newborn deaths will fail if the poor are not reached with effective interventions. To understand what works to reach vulnerable groups, we describe and explain the uptake of a highly effective community-based newborn health intervention across social strata in Asia and Africa