Improved Core Genes Prediction for Constructing well-supported Phylogenetic Trees in large sets of Plant Species

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies, many similarity based algorithms, mainly dependent on calculating sequence alignment matrices, have been proposed to find them. In these kinds of approaches, a significantly high similarity score between two coding sequences extracted from a given annotation tool means that one has the same genes. In a previous work article, we presented a quality test approach (QTA) that improves the core genes quality by combining two annotation tools (namely NCBI, a partially human-curated database, and DOGMA, an efficient annotation algorithm for chloroplasts). This method takes the advantages from both sequence similarity and gene features to guarantee that the core genome contains correct and well-clustered coding sequences (\emph{i.e.}, genes). We then show in this article how useful are such well-defined core genes for biomolecular phylogenetic reconstructions, by investigating various subsets of core genes at various family or genus levels, leading to subtrees with strong bootstraps that are finally merged in a well-supported supertree.Comment: 12 pages, 7 figures, IWBBIO 2015 (3rd International Work-Conference on Bioinformatics and Biomedical Engineering

Event by Event Analysis of High Multiplicity Events Produced in 158 A GeV/c 208 Pb- 208 Pb Collisions

An extensive analysis of individual high multiplicity events produced in 158 A GeV /c 208Pb- 208Pb collisions is carried by adopting different methods to examine the anomalous behavior of these rare events. A method of selecting the events with densely populated narrow regions or spikes out of a given sample of collision events is discussed.Employing this approach two events with large spikes in their eta- and phi- distributions are selected for further analysis. For the sake of comparison, another two events which do not exhibit such spikes are simultaneously analyzed. The findings suggest that the systematic studies of particle density fluctuations in one- and two-dimensional phase-spaces and comparison with those obtained from the studies of correlation free Monte Carlo events, would be useful for identifying the events with large dynamical fluctuations. Formation of clusters or jet like phenomena in multihadronic final states in individual events is also discussed and the experimental findings are compared with the independent particle emission hypothesis by carrying out Monte Carlo simulations

Correlation of Atrial Fibrillation with Left Atrial Volume in Patients with Mitral Stenosis. a Single Centre Study From Pakistan

Background: Rheumatic heart disease has a strong association with mitral valve stenosis. Atrial fibrillation is one of the most common complications of this condition and is a poor prognostic factor. Early detection and prompt management of atrial fibrillation can help to improve the quality of life and increase the life expectancy of the patients. We carried out this study to investigate the significance of left atrial volumetric changes in mitral stenosis and its correlation with atrial fibrillation. Methodology: We audited the data of 60 patients of rheumatic heart disease who had mitral valve stenosis. The patients were randomized into atrial fibrillation (Group A) and normal sinus rhythm (Group B). We conducted this cross-sectional analytical study at Cardiology Department, Mayo Hospital, Lahore, from 1st February 2017 to 31st January 2018. We only included those patients who consented to be a part of this study and fulfilled our predefined inclusion criteria. Left atrial volume was measured by prolate ellipse method and biplane methods on echocardiography. The Data was analyzed on SPSS v20. Results: Sixty patients were included in the study. Among the subjects, thirty-six (60%) were males, and twenty-four (40%) were females. Atrial fibrillation was noted in 43.33% of the patients of mitral valve stenosis. There was a marked difference in the mean volume of the left atrium among the two groups. We observed that the mean area of the mitral valve for Group A patients was larger than that of patients in Group B. Our study showed an inverse correlation between left atrial volume and mitral valve area among Group A patients. Conclusion: Patients of mitral stenosis are at an increased risk of developing atrial fibrillation if the left atrial volume is increasing. All patients with mitral stenosis should have routine echocardiography & measurement of left atrial volumes, so that proper treatment can be started if the left atrial volume is increasing, to prevent atrial fibrillation

New features of scattering from a one-dimensional non-Hermitian (complex) potential

For complex one-dimensional potentials, we propose the asymmetry of both reflectivity and transmitivity under time-reversal: $R(-k)\ne R(k)$ and $T(-k) \ne T(k)$, unless the potentials are real or PT-symmetric. For complex PT-symmetric scattering potentials, we propose that $R_{left}(-k)=R_{right}(k)$ and $T(-k)=T(k)$. So far, the spectral singularities (SS) of a one-dimensional non-Hermitian scattering potential are witnessed/conjectured to be at most one. We present a new non-Hermitian parametrization of Scarf II potential to reveal its four new features. Firstly, it displays the just acclaimed (in)variances. Secondly, it can support two spectral singularities at two pre-assigned real energies ($E_*=\alpha^2,\beta^2$) either in $T(k)$ or in $T(-k)$, when $\alpha\beta>0$. Thirdly, when $\alpha \beta <0$ it possesses one SS in $T(k)$ and the other in $T(-k)$. Fourthly, when the potential becomes PT-symmetric $[(\alpha+\beta)=0]$, we get $T(k)=T(-k)$, it possesses a unique SS at $E=\alpha^2$ in both $T(-k)$ and $T(k)$. Lastly, for completeness, when $\alpha=i\gamma$ and $\beta=i\delta$, there are no SS, instead we get two negative energies $-\gamma^2$ and $-\delta^2$ of the complex PT-symmetric Scarf II belonging to the two well-known branches of discrete bound state eigenvalues and no spectral singularity exists in this case. We find them as $E^{+}_{M}=-(\gamma-M)^2$ and $E^{-}_{N}=-(\delta-N)^2$; $M(N)=0,1,2,...$ with $0 \le M (N)< \gamma (\delta)$. {PACS: 03.65.Nk,11.30.Er,42.25.Bs}Comment: 10 pages, one Table, one Figure, important changes, appeared as an FTC (J. Phys. A: Math. Theor. 45(2012) 032004

Hypophyseal Growth Hormone II. Interaction with Other Hormones

Growth hormone (GH) synthesis and release is controlled by hypothalamic GH releasing factor. Thyroid hormones, androgens and estrogens in physiologic concentrations enhance GH secretion but a controlling role for glucagon and vasopressin in GH release is not established. Under stress, ACTH directly facilitates GH release while the similar action of the catecholamines is mediated by the a-adrenergic receptors. Though physiologic doses of glucorticoids and progestins do not affect GH liberation, prolonged administration of medroxyprogesterone acetate or of glucocorticoids in high dosage will decrease blood levels or blunt Gti responsiveness. GH enhances the release of insulin. A shift in adrenal steroid biosynthesis from the glucocorticoid to the androgenic pathway may also be an effect of GH administration. Prolonged elevated GH levels decrease serum thyroid binding globulin but increase the turnover of free thyroxine. Decreased thyroidal iodine uptake is probably secondary to these changes in thyroxine metabolism. In hypothyroidism and severe Cushing\u27s syndrome GH release is blunted. In most cases of acromegaly as well as in hyperthyroidism GH is nonsuppressible, while in diabetes its response to stimuli other than hypoglycemia is exaggerated

The Effectiveness of Oxandrolone in Promoting Linear Growth in Growth Hormone Deficient Children

This two-year study consisted of a comparison of oxandrolone and growth hormone for the treatment of five children with documented growth hormone deficiency. Previously, androgens have been reported to be relatively ineffective in accelerating linear growth In growth hormone deficient children. Oxandrolone was administered for one year. Growth hormone was added in the second six months and then was given as a single agent in the third six months. Growth accelerated markedly in all patients. Only one child showed more rapid growth with the addition of growth hormone while two children actually grew more rapidly under the Influence of oxandrolone alone. Growth was poor and diminished when growth hormone was given as a single agent in the third six-month period for three children but improved when oxandrolone was re-instituted in a fourth six-month treatment period. These results suggest that oxandrolone may prove to be an effective and safe substitute for growth hormone in the management of selected cases of hypopituitarism

Fairness Beyond Disparate Treatment & Disparate Impact: Learning Classification without Disparate Mistreatment

Automated data-driven decision making systems are increasingly being used to assist, or even replace humans in many settings. These systems function by learning from historical decisions, often taken by humans. In order to maximize the utility of these systems (or, classifiers), their training involves minimizing the errors (or, misclassifications) over the given historical data. However, it is quite possible that the optimally trained classifier makes decisions for people belonging to different social groups with different misclassification rates (e.g., misclassification rates for females are higher than for males), thereby placing these groups at an unfair disadvantage. To account for and avoid such unfairness, in this paper, we introduce a new notion of unfairness, disparate mistreatment, which is defined in terms of misclassification rates. We then propose intuitive measures of disparate mistreatment for decision boundary-based classifiers, which can be easily incorporated into their formulation as convex-concave constraints. Experiments on synthetic as well as real world datasets show that our methodology is effective at avoiding disparate mistreatment, often at a small cost in terms of accuracy.Comment: To appear in Proceedings of the 26th International World Wide Web Conference (WWW), 2017. Code available at: https://github.com/mbilalzafar/fair-classificatio

The ESO UVES Advanced Data Products Quasar Sample - VI. Sub-Damped Lyman-α\alpha Metallicity Measurements and the Circum-Galactic Medium

The Circum-Galactic Medium (CGM) can be probed through the analysis of absorbing systems in the line-of-sight to bright background quasars. We present measurements of the metallicity of a new sample of 15 sub-damped Lyman-$\alpha$ absorbers (sub-DLAs, defined as absorbers with 19.0 < log N(H I) < 20.3) with redshift 0.584 < $\rm z_{abs}$ < 3.104 from the ESO Ultra-Violet Echelle Spectrograph (UVES) Advanced Data Products Quasar Sample (EUADP). We combine these results with other measurements from the literature to produce a compilation of metallicity measurements for 92 sub-DLAs as well as a sample of 362 DLAs. We apply a multi-element analysis to quantify the amount of dust in these two classes of systems. We find that either the element depletion patterns in these systems differ from the Galactic depletion patterns or they have a different nucleosynthetic history than our own Galaxy. We propose a new method to derive the velocity width of absorption profiles, using the modeled Voigt profile features. The correlation between the velocity width delta_V90 of the absorption profile and the metallicity is found to be tighter for DLAs than for sub-DLAs. We report hints of a bimodal distribution in the [Fe/H] metallicity of low redshift (z < 1.25) sub-DLAs, which is unseen at higher redshifts. This feature can be interpreted as a signature from the metal-poor, accreting gas and the metal-rich, outflowing gas, both being traced by sub-DLAs at low redshifts.Comment: 64 pages, 31 figures, 27 tables. Submitted to MNRA

Reflectionless Potentials and PT Symmetry

Large families of Hamiltonians that are non-Hermitian in the conventional sense have been found to have all eigenvalues real, a fact attributed to an unbroken PT symmetry. The corresponding quantum theories possess an unconventional scalar product. The eigenvalues are determined by differential equations with boundary conditions imposed in wedges in the complex plane. For a special class of such systems, it is possible to impose the PT-symmetric boundary conditions on the real axis, which lies on the edges of the wedges. The PT-symmetric spectrum can then be obtained by imposing the more transparent requirement that the potential be reflectionless.Comment: 4 Page