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https://www.readbyqxmd.com/read/27936033/automated-detection-of-cancer-associated-genes-using-a-combined-fuzzy-rough-set-based-f-information-and-water-swirl-algorithm-of-human-gene-expression-data
#1
Pugalendhi Ganesh Kumar, Muthu Subash Kavitha, Byeong-Cheol Ahn
This study describes a novel approach to reducing the challenges of highly nonlinear multiclass gene expression values for cancer diagnosis. To build a fruitful system for cancer diagnosis, in this study, we introduced two levels of gene selection such as filtering and embedding for selection of potential genes and the most relevant genes associated with cancer, respectively. The filter procedure was implemented by developing a fuzzy rough set (FR)-based method for redefining the criterion function of f-information (FI) to identify the potential genes without discretizing the continuous gene expression values...
2016: PloS One
https://www.readbyqxmd.com/read/27934325/ab-initio-study-of-ionized-water-radical-cation-h2o-8-in-combination-with-the-particle-swarm-optimization-method
#2
Mei Tang, Cui-E Hu, Zhen-Long Lv, Xiang-Rong Chen, Ling-Cang Cai
The structures of cationic water clusters (H2O)8(+) have been globally explored by the particle swarm optimization method in combination with quantum chemical calculations. Geometry optimization and vibrational analysis for the 15 most interesting clusters were computed at the MP2/aug-cc-pVDZ level and infrared spectrum calculation at MPW1K/6-311++G** level. Special attention was paid to the relationships between their configurations and energies. Both MP2 and B3LYP-D3 calculations revealed that the cage-like structure is the most stable, which is different from a five-membered ring lowest energy structure but agrees well with a cage-like structure in the literature...
December 1, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27933270/compliance-control-based-on-pso-algorithm-to-improve-the-feeling-during-physical-human-robot-interaction
#3
Zhongliang Jiang, Yu Sun, Peng Gao, Ying Hu, Jianwei Zhang
Robots play more important roles in daily life and bring us a lot of convenience. But when people work with robots, there remain some significant differences in human-human interactions and human-robot interaction. It is our goal to make robots look even more human-like. We design a controller which can sense the force acting on any point of a robot and ensure the robot can move according to the force. First, a spring-mass-dashpot system was used to describe the physical model, and the second-order system is the kernel of the controller...
2016: Robotics and Biomimetics
https://www.readbyqxmd.com/read/27926379/a-comparative-analysis-of-chaotic-particle-swarm-optimizations-for-detecting-single-nucleotide-polymorphism-barcodes
#4
Li-Yeh Chuang, Sin-Hua Moi, Yu-Da Lin, Cheng-Hong Yang
OBJECTIVE: Evolutionary algorithms could overcome the computational limitations for the statistical evaluation of large datasets for high-order single nucleotide polymorphism (SNP) barcodes. Previous studies have proposed several chaotic particle swarm optimization (CPSO) methods to detect SNP barcodes for disease analysis (e.g., for breast cancer and chronic diseases). This work evaluated additional chaotic maps combined with the particle swarm optimization (PSO) method to detect SNP barcodes using a high-dimensional dataset...
October 2016: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/27925297/swarm-intelligence-inspired-spontaneous-fabrication-of-optimal-interconnect-at-the-micro-nanoscale
#5
Meng Su, Zhandong Huang, Yong Huang, Shuoran Chen, Xin Qian, Wenbo Li, Yifan Li, Weihua Pei, Hongda Chen, Fengyu Li, Yanlin Song
A spontaneous process is demonstrated to assemble nanoparticles into optimal interconnect, as natural systems spontaneously figuring out the shortest path. The optimal interconnect leads to a 65.9% decrease in electromagnetic interference, a 17.1% decrease in delay, and a 24.5% decrease in energy-delay. It will be of great significance for interconnect fabrication of versatile electronic circuits.
December 7, 2016: Advanced Materials
https://www.readbyqxmd.com/read/27924254/genetic-analysis-of-revertants-isolated-from-the-rod-fragile-flif-mutant-of-salmonella
#6
Hitomi Komatsu, Fumio Hayashi, Masahiro Sasa, Koji Shikata, Shigeru Yamaguchi, Keiichi Namba, Kenji Oosawa
FliF is the protein comprising the MS-ring of the bacterial flagellar basal body, which is the base for the assembly of flagellar axial structures. From a fliF mutant that easily releases the rod-hook-filament in viscous environments, more than 400 revertants that recovered their swarming ability in viscous conditions, were isolated. The second-site mutations were determined for approximately 70% of them. There were three regions where the mutations were localized: two in Region I, 112 in Region II, and 71 in Region III including the true reversion...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27920788/vegetative-and-adaptive-traits-predict-different-outcomes-for-restoration-using-hybrids
#7
Philip A Crystal, Nathanael I Lichti, Keith E Woeste, Douglass F Jacobs
Hybridization has been implicated as a driver of speciation, extinction, and invasiveness, but can also provide resistant breeding stock following epidemics. However, evaluating the appropriateness of hybrids for use in restoration programs is difficult. Past the F1 generation, the proportion of a progenitor's genome can vary widely, as can the combinations of parental genomes. Detailed genetic analysis can reveal this information, but cannot expose phenotypic alterations due to heterosis, transgressive traits, or changes in metabolism or development...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27902425/virulence-adaptations-of-pseudomonas-aeruginosa-isolated-from-patients-with-non-cystic-fibrosis-bronchiectasis
#8
Taylor Evart Woo, Jessica Duong, Nicole M Jervis, Harvey R Rabin, Michael D Parkins, Douglas Gordon Storey
Pseudomonas aeruginosa is a major pathogen in chronic lung diseases such as cystic fibrosis (CF) and non-cystic fibrosis bronchiectasis (nCFB). Much of our understanding regarding infections in nCFB patients is extrapolated from findings in CF with little direct investigation on the adaptation of P. aeruginosa in nCFB patients. As such, we investigated whether the adaptation of P. aeruginosa was indeed similar between nCFB and CF. From our prospectively collected biobank we identified 40 nCFB patients who had repeated P...
November 8, 2016: Microbiology
https://www.readbyqxmd.com/read/27901586/long-single-molecule-reads-can-resolve-the-complexity-of-the-influenza-virus-composed-of-rare-closely-related-mutant-variants
#9
Alexander Artyomenko, Nicholas C Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
As a result of a high rate of mutations and recombination events, an RNA-virus exists as a heterogeneous "swarm" of mutant variants. The long read length offered by single-molecule sequencing technologies allows each mutant variant to be sequenced in a single pass. However, high error rate limits the ability to reconstruct heterogeneous viral population composed of rare, related mutant variants. In this article, we present two single-nucleotide variants (2SNV), a method able to tolerate the high error rate of the single-molecule protocol and reconstruct mutant variants...
November 30, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27901295/nonparametric-de-noising-filter-optimization-using-structure-based-microscopic-image-classification
#10
Samsad Beagum, Nilanjan Dey, Amira S Ashour, Dimitra Sifaki-Pistolla, Valentina E Balas
The Local Polynomial Approximation (LPA) is a nonparametric filter that performs pixel-wise polynomial fit on a certain neighborhood. This filter can be supported by the Intersection of Confidence Interval rule (ICI) as an adaptation algorithm to identify the most suited neighborhood at which the polynomial assumptions provide superior fit for the observations. However, the LPA-ICI is considered to be a near-optimal de-noising filter. Moreover, the ICI rule has several parameters that affect its performance...
November 30, 2016: Microscopy Research and Technique
https://www.readbyqxmd.com/read/27898691/a-personalized-electronic-movie-recommendation-system-based-on-support-vector-machine-and-improved-particle-swarm-optimization
#11
Xibin Wang, Fengji Luo, Ying Qian, Gianluca Ranzi
With the rapid development of ICT and Web technologies, a large an amount of information is becoming available and this is producing, in some instances, a condition of information overload. Under these conditions, it is difficult for a person to locate and access useful information for making decisions. To address this problem, there are information filtering systems, such as the personalized recommendation system (PRS) considered in this paper, that assist a person in identifying possible products or services of interest based on his/her preferences...
2016: PloS One
https://www.readbyqxmd.com/read/27893374/differential-evolution-optimization-of-the-sar-distribution-for-head-and-neck-hyperthermia
#12
Grazia Cappiello, Brian Mc Ginley, Muhammad Adnan Elahi, Tomas Drizdal, Margarethus M Paulides, Martin Glavin, Martin O'Halloran, Edward Jones
Hyperthermia is an emerging cancer treatment modality which involves applying heat to the malignant tumor. The heating can be delivered using electromagnetic (EM) energy, mostly in the radiofrequency (RF) or microwave range. Accurate patient-specific hyperthermia treatment planning (HTP) is essential for effective and safe treatments, in particular for deep and loco-regional hyperthermia. An important aspect of HTP is the ability to focus microwave energy into the tumor and reduce the occurrence of hot spots in healthy tissue...
November 14, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27892524/vectorized-magnetometer-for-space-applications-using-electrical-readout-of-atomic-scale-defects-in-silicon-carbide
#13
Corey J Cochrane, Jordana Blacksberg, Mark A Anders, Patrick M Lenahan
Magnetometers are essential for scientific investigation of planetary bodies and are therefore ubiquitous on missions in space. Fluxgate and optically pumped atomic gas based magnetometers are typically flown because of their proven performance, reliability, and ability to adhere to the strict requirements associated with space missions. However, their complexity, size, and cost prevent their applicability in smaller missions involving cubesats. Conventional solid-state based magnetometers pose a viable solution, though many are prone to radiation damage and plagued with temperature instabilities...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27879336/beyond-antimicrobial-resistance-evidence-for-a-distinct-role-of-the-acrd-efflux-pump-in-salmonella-biology
#14
Michelle M C Buckner, Jessica M A Blair, Roberto M La Ragione, Jane Newcombe, Daniel J Dwyer, Alasdair Ivens, Laura J V Piddock
: For over 20 years, bacterial multidrug resistance (MDR) efflux pumps have been studied because of their impact on resistance to antimicrobials. However, critical questions remain, including why produce efflux pumps under non-antimicrobial treatment conditions, and why have multiple pumps if their only purpose is antimicrobial efflux? Salmonella spp. possess five efflux pump families, including the resistance-nodulation-division (RND) efflux pumps. Notably, the RND efflux pump AcrD has a unique substrate profile, distinct from other Salmonella efflux pumps...
November 22, 2016: MBio
https://www.readbyqxmd.com/read/27874229/exopolysaccharides-promote-myxococcus-xanthus-social-motility-by-inhibiting-cellular-reversals
#15
Tianyi Zhou, Beiyan Nan
The biofilm-forming bacterium Myxococcus xanthus moves on surfaces as structured swarms utilizing type IV pili-dependent social (S-) motility. In contrast to isolated cells that reverse their moving direction frequently, individual cells within swarms rarely reverse. The regulatory mechanisms that inhibit cellular reversal and promote the formation of swarms are not well understood. Here we show that exopolysaccharides (EPS), the major extracellular components of M. xanthus swarms, inhibit cellular reversal in a concentration-dependent manner...
November 22, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27873565/patterns-of-virulence-factor-expression-and-antimicrobial-resistance-in-achromobacter-xylosoxidans-and-achromobacter-ruhlandii-isolates-from-patients-with-cystic-fibrosis
#16
R H V Pereira, R S Leão, A P Carvalho-Assef, R M Albano, E R A Rodrigues, M C Firmida, T W Folescu, M C Plotkowski, V G Bernardo, E A Marques
Achromobacter spp. are opportunistic pathogens increasingly recovered from adult patients with cystic fibrosis (CF). We report the characterization of 122 Achromobacter spp. isolates recovered from 39 CF patients by multilocus sequence typing, virulence traits, and susceptibility to antimicrobials. Two species, A. xylosoxidans (77%) and A. ruhlandii (23%) were identified. All isolates showed a similar biofilm formation ability, and a positive swimming phenotype. By contrast, 4·3% and 44·4% of A. xylosoxidans and A...
November 22, 2016: Epidemiology and Infection
https://www.readbyqxmd.com/read/27868330/structural-and-functional-analysis-of-cyclophilin-ppib-mutants-supports-an-in%C3%A2-vivo-function-not-limited-to-prolyl-isomerization-activity
#17
Aggeliki Skagia, Eleni Vezyri, Markezina Sigala, Areti Kokkinou, Michael Karpusas, Anastasia Venieraki, Panagiotis Katinakis, Maria Dimou
Escherichia coli cyclophilin PpiB is a peptidyl-prolyl cis/trans isomerase (PPIase, EC: 5.2.1.8), involved in the negative modulation of various bacterial processes, such as swimming and swarming motility and biofilm formation ability. In this study, we show that PpiB possesses also a chaperone function as it can prevent the thermal denaturation of citrate synthase even with essentially eliminated PPIase activity. We demonstrate, using active site mutations, that the PPIase activity of PpiB is required in all processes, except for the negative effect on swimming, indicating a possible isomerase-independent function...
November 21, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/27862537/pervasive-yet-idiosyncratic-epistatic-pleiotropy-during-adaptation-in-a-behaviourally-complex-microbe
#18
P C Zee, J Liu, G J Velicer
Understanding how multiple mutations interact to jointly impact multiple ecologically important traits is critical for creating a robust picture of organismal fitness and the process of adaptation. However, this is complicated by both environmental heterogeneity and the complexity of genotype-to-phenotype relationships generated by pleiotropy and epistasis. Moreover, little is known about how pleiotropic and epistatic relationships themselves change over evolutionary time. The soil bacterium Myxococcus xanthus employs several distinct social traits across a range of environments...
October 19, 2016: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/27860087/the-effect-of-burdock-leaf-fraction-on-adhesion-biofilm-formation-quorum-sensing-and-virulence-factors-of-p-aeruginosa
#19
Zaixiang Lou, Hongxin Wang, Yuxia Tang
AIMS: This study aimed to evaluate the effect of a fraction of burdock (Arctium lappa L.) leaf on the initial adhesion, biofilm formation, quorum sensing and virulence factors of P. aeruginosa. METHODS AND RESULTS: Anti-biofilm activity of the burdock leaf fraction was studied by the method of crystal violet staining. When the concentration of the burdock leaf fraction was 2.0 mg mL(-1) , the inhibition rates on biofilm formation of P. aeruginosa were 100%. The burdock leaf fraction was found to inhibit the formation of biofilm by reducing bacterial surface hydrophobicity, decreasing bacterial aggregation ability and inhibiting swarming motility Interestingly, the burdock leaf fraction inhibited the secretion of quorum sensing (QS) signaling molecule 3-oxo-C12-HSL and interfered quorum sensing...
November 12, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27859130/stream-thermal-heterogeneity-prolongs-aquatic-terrestrial-subsidy-and-enhances-riparian-spider-growth
#20
Hiromi Uno
Emerging aquatic insects from streams are important food sources for riparian predators, yet their availability is seasonally limited. Spatial heterogeneity in stream water temperature was found to spatially desynchronize the emergence timing of aquatic insects, and prolong their flight period, potentially enhancing consumer growth. While a mayfly Ephemerella maculata emergence lasted for 12-22 d in local sites along a river, mayflies emerged 19 days earlier from warmer than cooler sites. Therefore, the overall emergence of E...
October 2016: Ecology
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