Genotyping of Sarawak rice cultivars using microsatellite markers

Genetic diversity of 53 Sarawak rice cultivars, originating from Southern Sarawak, was assessed using 54 microsatellite markers. Initial polymorphism detection was conducted using 54 primer pairs distributed on 12 rice chromosomes. Polymorphic markers were chosen from the initial screening results in order to obtain microsatellite marker panels that can differentiate the rice cultivars undertaken in the study. The chosen microsatellite marker panel consisted of RM1, RM240, RM489, RM252, RM413, RM204, RM11, RM404, RM316, RM271, RM206, and RM19, with one representative from each chromosome. A total of 43 alleles were detected with an average of 3.58 alleles per locus. The polymorphism information content (PIC) values obtained from the microsatellite marker panels ranged from 0.306 to 0.730, with an average of 0.622. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram (r = 0.789) revealed 2 major groups with 6 sub-clusters and the wide range of similarity values (0.24-1.0) obtained showed a high degree of diversity among the cultivars. The results suggest microsatellite markers as a useful tool for the estimation of genetic diversity and cultivar differentiation and present invaluable genetic information for future breeding and association mapping efforts

Stationary Localized States Due to a Nonlinear Dimeric Impurity Embedded in a Perfect 1-D Chain

The formation of Stationary Localized states due to a nonlinear dimeric impurity embedded in a perfect 1-d chain is studied here using the appropriate Discrete Nonlinear Schr$\ddot{o}$dinger Equation. Furthermore, the nonlinearity has the form, $\chi |C|^\sigma$ where $C$ is the complex amplitude. A proper ansatz for the Localized state is introduced in the appropriate Hamiltonian of the system to obtain the reduced effective Hamiltonian. The Hamiltonian contains a parameter, $\beta = \phi_1/\phi_0$ which is the ratio of stationary amplitudes at impurity sites. Relevant equations for Localized states are obtained from the fixed point of the reduced dynamical system. $|\beta|$ = 1 is always a permissible solution. We also find solutions for which $|\beta| \ne 1$. Complete phase diagram in the $(\chi, \sigma)$ plane comprising of both cases is discussed. Several critical lines separating various regions are found. Maximum number of Localized states is found to be six. Furthermore, the phase diagram continuously extrapolates from one region to the other. The importance of our results in relation to solitonic solutions in a fully nonlinear system is discussed.Comment: Seven figures are available on reques

An Introduction to Hyperbolic Barycentric Coordinates and their Applications

Barycentric coordinates are commonly used in Euclidean geometry. The adaptation of barycentric coordinates for use in hyperbolic geometry gives rise to hyperbolic barycentric coordinates, known as gyrobarycentric coordinates. The aim of this article is to present the road from Einstein's velocity addition law of relativistically admissible velocities to hyperbolic barycentric coordinates along with applications.Comment: 66 pages, 3 figure

Clinical course, therapeutic responses and outcomes in relapsing MOG antibody-associated demyelination.

Abstract OBJECTIVE: We characterised the clinical course, treatment and outcomes in 59 patients with relapsing myelin oligodendrocyte glycoprotein (MOG) antibody-associated demyelination. METHODS: We evaluated clinical phenotypes, annualised relapse rates (ARR) prior and on immunotherapy and Expanded Disability Status Scale (EDSS), in 218 demyelinating episodes from 33 paediatric and 26 adult patients. RESULTS: The most common initial presentation in the cohort was optic neuritis (ON) in 54% (bilateral (BON) 32%, unilateral (UON) 22%), followed by acute disseminated encephalomyelitis (ADEM) (20%), which occurred exclusively in children. ON was the dominant phenotype (UON 35%, BON 19%) of all clinical episodes. 109/226 (48%) MRIs had no brain lesions. Patients were steroid responsive, but 70% of episodes treated with oral prednisone relapsed, particularly at doses <10\u2009mg daily or within 2 months of cessation. Immunotherapy, including maintenance prednisone (P=0.0004), intravenous immunoglobulin, rituximab and mycophenolate, all reduced median ARRs on-treatment. Treatment failure rates were lower in patients on maintenance steroids (5%) compared with non-steroidal maintenance immunotherapy (38%) (P=0.016). 58% of patients experienced residual disability (average follow-up 61 months, visual loss in 24%). Patients with ON were less likely to have sustained disability defined by a final EDSS of 652 (OR 0.15, P=0.032), while those who had any myelitis were more likely to have sustained residual deficits (OR 3.56, P=0.077). CONCLUSION: Relapsing MOG antibody-associated demyelination is strongly associated with ON across all age groups and ADEM in children. Patients are highly responsive to steroids, but vulnerable to relapse on steroid reduction and cessation

Lowest-lying Tetra-Quark Hadrons in Anisotropic Lattice QCD

We present a detailed study of lowest-lying $q^{2}\bar{q}^{2}$ hadrons in quenched improved anisotropic lattice QCD. Using the $\pi\pi$ and diquark-antidiquark local and smeared operators, we attempt to isolate the signal for $I(J^{P})=0(0^{+}), 2(0^{+})$ and $1(1^{+})$ states in two flavour QCD. In the chiral limit of light-quark mass region, the lowest scalar $4q$ state is found to have a mass, $m^{I=0}_{4q}=927(12)$ MeV, which is slightly lower than the experimentally observed $f_{0}(980)$. The results from our variational analysis do not indicate a signature of a tetraquark resonance in I=1 and I=2 channels. After the chiral extrapolation the lowest $1(1^{+})$ state is found to have a mass, $m^{I=1}_{4q}=1358(28)$ MeV. We analysed the static $4q$ potential extracted form a tetraquark Wilson loop and illustrated the behaviour of the $4q$ state as a bound state, unbinding at some critical diquark separation. From our analysis we conclude that scalar $4q$ system appears as a two-pion scattering state and that there is no spatially-localised $4q$ state in the light-quark mass region.Comment: 9 pages, 10 figure

A Study of The Formation of Stationary Localized States Due to Nonlinear Impurities Using The Discrete Nonlinear Schr\"odinger Equation

The Discrete Nonlinear Schr$\ddot{o}$dinger Equation is used to study the formation of stationary localized states due to a single nonlinear impurity in a Caley tree and a dimeric nonlinear impurity in the one dimensional system. The rotational nonlinear impurity and the impurity of the form $-\chi \mid C \mid^{\sigma}$ where $\sigma$ is arbitrary and $\chi$ is the nonlinearity parameter are considered. Furthermore, $\mid C \mid$ represents the absolute value of the amplitude. Altogether four cases are studies. The usual Greens function approach and the ansatz approach are coherently blended to obtain phase diagrams showing regions of different number of states in the parameter space. Equations of critical lines separating various regions in phase diagrams are derived analytically. For the dimeric problem with the impurity $-\chi \mid C \mid^{\sigma}$, three values of $\mid \chi_{cr} \mid$, namely, $\mid \chi_{cr} \mid = 2$, at $\sigma = 0$ and $\mid \chi_{cr} \mid = 1$ and $\frac{8}{3}$ for $\sigma = 2$ are obtained. Last two values are lower than the existing values. Energy of the states as a function of parameters is also obtained. A model derivation for the impurities is presented. The implication of our results in relation to disordered systems comprising of nonlinear impurities and perfect sites is discussed.Comment: 10 figures available on reques

State Transition Algorithm

In terms of the concepts of state and state transition, a new heuristic random search algorithm named state transition algorithm is proposed. For continuous function optimization problems, four special transformation operators called rotation, translation, expansion and axesion are designed. Adjusting measures of the transformations are mainly studied to keep the balance of exploration and exploitation. Convergence analysis is also discussed about the algorithm based on random search theory. In the meanwhile, to strengthen the search ability in high dimensional space, communication strategy is introduced into the basic algorithm and intermittent exchange is presented to prevent premature convergence. Finally, experiments are carried out for the algorithms. With 10 common benchmark unconstrained continuous functions used to test the performance, the results show that state transition algorithms are promising algorithms due to their good global search capability and convergence property when compared with some popular algorithms.Comment: 18 pages, 28 figure

Adjacent Nucleotide Dependence in ncRNA and Order-1 SCFG for ncRNA Identification

Background: Non-coding RNAs (ncRNAs) are known to be involved in many critical biological processes, and identification of ncRNAs is an important task in biological research. A popular software, Infernal, is the most successful prediction tool and exhibits high sensitivity. The application of Infernal has been mainly focused on small suspected regions. We tried to apply Infernal on a chromosome level; the results have high sensitivity, yet contain many false positives. Further enhancing Infernal for chromosome level or genome wide study is desirable. Methodology: Based on the conjecture that adjacent nucleotide dependence affects the stability of the secondary structure of an ncRNA, we first conduct a systematic study on human ncRNAs and find that adjacent nucleotide dependence in human ncRNA should be useful for identifying ncRNAs. We then incorporate this dependence in the SCFG model and develop a new order-1 SCFG model for identifying ncRNAs. Conclusions: With respect to our experiments on human chromosomes, the proposed new model can eliminate more than 50 % false positives reported by Infernal while maintaining the same sensitivity. The executable and the source code of programs are freely available a

Optimization of a high work function solution processed vanadium oxide hole-extracting layer for small molecule and polymer organic photovoltaic cells

We report a method of fabricating a high work function, solution processable vanadium oxide (V2Ox(sol)) hole-extracting layer. The atmospheric processing conditions of film preparation have a critical influence on the electronic structure and stoichiometry of the V2Ox(sol), with a direct impact on organic photovoltaic (OPV) cell performance. Combined Kelvin probe (KP) and ultraviolet photoemission spectroscopy (UPS) measurements reveal a high work function, n-type character for the thin films, analogous to previously reported thermally evaporated transition metal oxides. Additional states within the band gap of V2Ox(sol) are observed in the UPS spectra and are demonstrated using X-ray photoelectron spectroscopy (XPS) to be due to the substoichiometric nature of V2Ox(sol). The optimized V2Ox(sol) layer performance is compared directly to bare indium–tin oxide (ITO), poly(ethyleneoxythiophene):poly(styrenesulfonate) (PEDOT:PSS), and thermally evaporated molybdenum oxide (MoOx) interfaces in both small molecule/fullerene and polymer/fullerene structures. OPV cells incorporating V2Ox(sol) are reported to achieve favorable initial cell performance and cell stability attributes

Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy.

OBJECTIVE: To explore the diagnostic utility and cost effectiveness of whole exome sequencing (WES) in a cohort of individuals with peripheral neuropathy. METHODS: Singleton WES was performed in individuals recruited though one pediatric and one adult tertiary center between February 2014 and December 2015. Initial analysis was restricted to a virtual panel of 55 genes associated with peripheral neuropathies. Patients with uninformative results underwent expanded analysis of the WES data. Data on the cost of prior investigations and assessments performed for diagnostic purposes in each patient was collected. RESULTS: Fifty patients with a peripheral neuropathy were recruited (median age 18 years; range 2-68 years). The median time from initial presentation to study enrollment was 6 years 9 months (range 2 months-62 years), and the average cost of prior investigations and assessments for diagnostic purposes AU$4013 per patient. Eleven individuals received a diagnosis from the virtual panel. Eight individuals received a diagnosis following expanded analysis of the WES data, increasing the overall diagnostic yield to 38%. Two additional individuals were diagnosed with pathogenic copy number variants through SNP microarray. CONCLUSIONS: This study provides evidence that WES has a high diagnostic utility and is cost effective in patients with a peripheral neuropathy. Expanded analysis of WES data significantly improves the diagnostic yield in patients in whom a diagnosis is not found on the initial targeted analysis. This is primarily due to diagnosis of conditions caused by newly discovered genes and the resolution of complex and atypical phenotypes