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https://www.readbyqxmd.com/read/28334343/pathwaymapper-a-collaborative-visual-web-editor-for-cancer-pathways-and-genomic-data
#1
Istemi Bahceci, Ugur Dogrusoz, Konnor C La, Özgün Babur, Jianjiong Gao, Nikolaus Schultz
Motivation: While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer Genome Atlas (TCGA). These pathway diagrams typically summarize how a pathway is altered in individual cancer types, including alteration frequencies for each gene. Results: To address this need, we developed the web-based tool PathwayMapper, which runs in most common web browsers...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334310/different-from-trees-more-than-metaphors-branching-silhouettes-corals-cacti-and-the-oaks
#2
János Podani
There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like visualization of phylogeny may also be done via other types of graphics, especially botanical (or literal) tree drawings. As a consequence, the meaning of such diagrams is not always clear: a given picture may have multiple interpretations in its different parts and two figures that look similar may actually carry quite different information...
March 11, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28334247/genetic-population-structure-of-dastarcus-helophoroides-coleoptera-bothrideridae-from-different-long-horned-beetle-hosts-based-on-complete-sequences-of-mitochondrial-coi
#3
Zhengqing Zhang, Yong Chang, Menglou Li
Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) is an important natural enemy of long-horned beetles in China, Japan, and Korea. In this study, the genetic sequence of cytochrome oxidase subunit Ι was used to investigate the genetics and relationships within and among D. helophoroides populations collected from five different geographic locations. We used principal component analysis, heatmap, and Venn diagram results to determine the relationship between haplotypes and populations. In total, 26 haplotypes with 51 nucleotide polymorphic sites were defined, and low genetic diversity was found among the different populations...
March 3, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28334105/biojava-modfinder-identification-of-protein-modifications-in-3d-structures-from-the-protein-data-bank
#4
Jianjiong Gao, Andreas Prlic, Chunxiao Bi, Wolfgang F Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E Bourne, Peter W Rose
Summary: We developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). Information on more than 400 types of protein modifications were collected and curated from annotations in PDB, RESID, and PSI-MOD. We divided these modifications into three categories: modified residues, attachment modifications, and cross-links. We have developed a systematic method to identify these modifications in 3D protein structures...
February 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28331293/risk-assessment-and-experimental-design-in-the-development-of-a-prolonged-release-drug-delivery-system-with-paliperidone
#5
Sonia Iurian, Luana Turdean, Ioan Tomuta
This study focuses on the development of a drug product based on a risk assessment-based approach, within the quality by design paradigm. A prolonged release system was proposed for paliperidone (Pal) delivery, containing Kollidon(®) SR as an insoluble matrix agent and hydroxypropyl cellulose, hydroxypropyl methylcellulose (HPMC), or sodium carboxymethyl cellulose as a hydrophilic polymer. The experimental part was preceded by the identification of potential sources of variability through Ishikawa diagrams, and failure mode and effects analysis was used to deliver the critical process parameters that were further optimized by design of experiments...
2017: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/28330990/on-the-growth-and-form-of-shoots
#6
Raghunath Chelakkot, L Mahadevan
Growing plant stems and shoots exhibit a variety of shapes that embody growth in response to various stimuli. Building on experimental observations, we provide a quantitative biophysical theory for these shapes by accounting for the inherent observed passive and active effects: (i) the active controllable growth response of the shoot in response to its orientation relative to gravity, (ii) proprioception, the shoot's growth response to its own observable current shape, and (iii) the passive elastic deflection of the shoot due to its own weight, which determines the current shape of the shoot...
March 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28330366/phase-behaviour-of-quasicrystal-forming-systems-of-core-corona-particles
#7
Harini Pattabhiraman, Marjolein Dijkstra
Using Monte Carlo simulations and free-energy calculations, we study the phase behaviour of a two-dimensional system of particles interacting with a hard core of diameter σHD and a repulsive square shoulder potential. The interest in this system lies in the formation of quasicrystals of different symmetries at specific square-shoulder widths δ as previously reported by Dotera et al. [Nature 506, 208 (2014)]. However, an insight into other possible periodic phases formed in these systems and the thermodynamic stability of both the periodic and quasicrystal phases is yet to be addressed...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28329938/-research-of-prevalence-of-schistosomiasis-in-hunan-province-1984-2015
#8
F Y Li, H Z Tan, G H Ren, Q Jiang, H L Wang
Objective: To analyze the prevalence of schistosomiasis in Hunan province, and provide scientific evidence for the control and elimination of schistosomiasis. Methods: The changes of infection rates of Schistosoma (S.) japonicum among residents and cattle in Hunan from 1984 to 2015 were analyzed by using dynamic trend diagram; and the time regression model was used to fit the infection rates of S. japonicum, and predict the recent infection rate. Results: The overall infection rates of S. japonicum in Hunan from 1984 to 2015 showed downward trend (95...
March 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28327186/clinical-behavioural-and-pharmacogenomic-factors-influencing-the-response-to-levothyroxine-therapy-in-patients-with-primary-hypothyroidism-protocol-for-a-systematic-review
#9
Rosie Dew, Onyebuchi Okosieme, Colin Dayan, Vinay Eligar, Ishrat Khan, Salman Razvi, Simon Pearce, Scott Wilkes
BACKGROUND: Suboptimal thyroid hormone therapy including under-replacement and over-replacement is common amongst patients with hypothyroidism. This is a significant health concern as affected patients are at risk of adverse cardiovascular or metabolic consequences. Despite a growing body of evidence on the effects of various factors on thyroid hormone replacement, a systematic appraisal of the evidence is lacking. This review aims to appraise and quantify the extent to which clinical, behavioural and pharmacogenomic factors affect levothyroxine therapy in patients with primary hypothyroidism...
March 21, 2017: Systematic Reviews
https://www.readbyqxmd.com/read/28325707/leaching-process-for-recovering-valuable-metals-from-the-lini1-3co1-3mn1-3o2-cathode-of-lithium-ion-batteries
#10
Li-Po He, Shu-Ying Sun, Xing-Fu Song, Jian-Guo Yu
In view of the importance of environmental protection and resource recovery, recycling of spent lithium-ion batteries (LIBs) and electrode scraps generated during manufacturing processes is quite necessary. An environmentally sound leaching process for the recovery of Li, Ni, Co, and Mn from spent LiNi1/3Co1/3Mn1/3O2-based LIBs and cathode scraps was investigated in this study. Eh-pH diagrams were used to determine suitable leaching conditions. Operating variables affecting the leaching efficiencies for Li, Ni, Co, and Mn from LiNi1/3Co1/3Mn1/3O2, such as the H2SO4 concentration, temperature, H2O2 concentration, stirring speed, and pulp density, were investigated to determine the most efficient conditions for leaching...
March 18, 2017: Waste Management
https://www.readbyqxmd.com/read/28325035/calculation-of-energy-diagram-of-asymmetric-graded-band-gap-semiconductor-superlattices
#11
Liubomyr S Monastyrskii, Bogdan S Sokolovskii, Mariya P Alekseichyk
The paper theoretically investigates the peculiarities of energy diagram of asymmetric graded-band-gap superlattices with linear coordinate dependences of band gap and electron affinity. For calculating the energy diagram of asymmetric graded-band-gap superlattices, linearized Poisson's equation has been solved for the two layers forming a period of the superlattice. The obtained coordinate dependences of edges of the conduction and valence bands demonstrate substantial transformation of the shape of the energy diagram at changing the period of the lattice and the ratio of width of the adjacent layers...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28324782/two-dimensional-bismuth-oxybromide-coupled-with-molybdenum-disulphide-for-enhanced-dye-degradation-using-low-power-energy-saving-light-bulb
#12
W P Cathie Lee, Fhu-Hin Wong, Nicole K Attenborough, Xin Ying Kong, Lling-Lling Tan, S Sumathi, Siang-Piao Chai
In the present work, two-dimensional bismuth oxybromide (BiOBr) was synthesized and coupled with co-catalyst molybdenum disulphide (MoS2) via a simple hydrothermal process. The photoactivity of the resulting hybrid photocatalyst (MoS2/BiOBr) was evaluated under the irradiation of 15 W energy-saving light bulb at ambient condition using Reactive Black 5 (RB5) as model dye solution. The photo-degradation of RB5 by BiOBr loaded with 0.2 wt% MoS2 (MoBi-2) exhibited more than 1.4 and 5.0 folds of enhancement over pristine BiOBr and titanium dioxide (Degussa, P25), respectively...
March 18, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28324242/numerical-insights-into-the-phase-diagram-of-p-atic-membranes-with-spherical-topology
#13
A G Hansen, N Ramakrishnan, P B Sunil Kumar, J H Ipsen
The properties of self-avoiding p-atic membranes restricted to spherical topology have been studied by Monte Carlo simulations of a triangulated random surface model. Spherically shaped p-atic membranes undergo a Kosterlitz-Thouless transition as expected with topology induced mutually repelling disclinations of the p-atic ordered phase. For flexible membranes the phase behaviour bears some resemblance to the spherically shaped case with a p-atic disordered crumpled phase and p-atic ordered, conformationally ordered (crinkled) phase separated by a KT-like transition with proliferation of disclinations...
March 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/28323940/thyroid-signaling-insulin-resistance-and-type-2-diabetes-mellitus-a-mendelian-randomization-study
#14
Maxime M Bos, Roelof Aj Smit, Stella Trompet, Diana van Heemst, Raymond Noordam
CONTEXT: Increasing evidence suggests an association between thyroid stimulating hormone (TSH), free thyroxine (fT4) and deiodinases with insulin resistance and type 2 diabetes mellitus (T2D). OBJECTIVE: We examined whether TSH and fT4 levels and deiodinases are causally associated with insulin resistance and T2D using Mendelian randomization (MR). METHODS: We selected twenty genetic variants for TSH level and four for fT4 level (identified in a GWAS meta-analysis of European-ancestry cohorts) as instrumental variables for TSH and fT4 level, respectively...
March 9, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28322542/rectifying-characteristics-and-semiconductor-metal-transition-induced-by-interfacial-potential-in-mn3cun-n-si-intermetallic-heterojunction
#15
Kewen Shi, Cong Wang, Ying Sun, Lei Wang, Sihao Deng, Pengwei Hu, Huiqing Lu, Weichang Hao, Tianmin Wang, Weihua Tang
Mn3CuN/n-Si heterojunction device is firstly designed in antiperovskite compound and excellent rectifying characteristics are obtained. The rectification ratio (RR) reaches as large as 38.9 at 10 V and the open-circuit voltage Voc of 1.13 V is observed under temperature 410 K. The rectifying behaviors can be well described by the Shockley equation, indicating the existence of Schottky diode. Simultaneously, a particular semiconductor-metal transition (SMT) behavior at 250 K is also observed in the Mn3CuN/n-Si heterojunction...
March 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28320456/thiolation-of-arabinoxylan-and-its-application-in-the-fabrication-of-controlled-release-mucoadhesive-oral-films
#16
Muhammad Hanif, Muhammad Zaman
BACKGROUND: Mucoadhesion is an important property that helps oral drug delivery system to remain attached with buccal mucosa and hence to improve the delivery of the drug. The current study was designed to achieve the thiol modification of Arabinoxylan (ARX) and to develop a mucoadhesive oral film for the improved delivery of tizanidine hydrochloride (TZN HCl). METHOD: Synthesis of thiolated arabinoxylan (TARX) was accomplished by esterification of ARX with thioglycolic acid (TGA)...
March 20, 2017: Daru: Journal of Faculty of Pharmacy, Tehran University of Medical Sciences
https://www.readbyqxmd.com/read/28320113/alzheimer-s-disease-elevated-pigment-epithelium-derived-factor-in-the-cerebrospinal-fluid-is-mostly-of-systemic-origin
#17
Veronika Lang, Marietta Zille, Carmen Infante-Duarte, Sven Jarius, Holger Jahn, Friedemann Paul, Klemens Ruprecht, Ana Luisa Pina
Pigment-epithelium derived factor (PEDF) is a neurotrophic factor with neuroprotective, anti-tumorigenic, and anti-angiogenic effects. Elevated levels of PEDF have previously been proposed as a cerebrospinal fluid (CSF) biomarker for Alzheimer's disease. However, the origin of PEDF in CSF, i.e. whether it is derived from the brain or from the systemic circulation, and the specificity of this finding hitherto remained unclear. Here, we analyzed levels of PEDF in paired CSF and serum samples by ELISA in patients with Alzheimer's disease (AD, n=12), frontotemporal dementia (FTD, n=6), vascular dementia (n=4), bacterial meningitis (n=8), multiple sclerosis (n=32), pseudotumor cerebri (n=36), and diverse non-inflammatory neurological diseases (n=19)...
April 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28319375/dissociative-photoionization-of-dimethyl-carbonate-the-more-it-is-cut-the-bigger-the-fragment-ion
#18
Xiangkun Wu, Xiaoguo Zhou, Patrick Hemberger, Andras Bodi
The dissociation of internal energy selected dimethyl carbonate (DMC) cations was studied by imaging photoelectron photoion coincidence spectroscopy (iPEPICO) in the 10.3-12.5 eV photon energy range. Vibrational fine structure is observed in the ground state band of the threshold photoelectron spectrum up to the dissociation threshold, and Franck-Condon simulations identify the O-C-O bend mode, in particular in combination with the C=O stretch mode, to be active. The DMC ionization energy was determined to be 10...
March 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28319367/structural-stability-from-crystallographic-shear-in-tio2-nb2o5-phases-cation-ordering-and-lithiation-behavior-of-tinb24o62
#19
Kent J Griffith, Anatoliy Senyshyn, Clare P Grey
The host structure and reversible lithium insertion and extraction of an intercalation compound, TiNb24O62, are described. Neutron diffraction, applied for the first time to TiNb24O62, allowed an accurate refinement of the complex block superstructure, particularly with respect to the oxygen sublattice. Analysis of the transition-metal sites revealed significant cation ordering in the mixed-metal oxide. Electrochemical analysis demonstrated highly reversible lithium intercalation with ca. 190 mA·h·g(-1) after 100 cycles (C/10 rate, 3 months)...
March 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28318028/study-of-the-cold-charge-transfer-state-separation-at-the-tq1-pc71-bm-interface
#20
Riccardo Volpi, Mathieu Linares
Charge transfer (CT) state separation is one of the most critical processes in the functioning of an organic solar cell. In this article, we study a bilayer of TQ1 and PC71 BM molecules presenting disorder at the interface, obtained by means of Molecular Dynamics. The study of the CT state splitting can be first analyzed through the CT state splitting diagram, introduced in a previous work. Through this analysis, we identify the possibility of CT state splitting within Marcus Theory in function of the electric field...
March 20, 2017: Journal of Computational Chemistry
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