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https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#1
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28430266/machine-learning-approach-to-oam-beam-demultiplexing-via-convolutional-neural-networks
#2
Timothy Doster, Abbie T Watnik
Orbital angular momentum (OAM) beams allow for increased channel capacity in free-space optical communication. Conventionally, these OAM beams are multiplexed together at a transmitter and then propagated through the atmosphere to a receiver where, due to their orthogonality properties, they are demultiplexed. We propose a technique to demultiplex these OAM-carrying beams by capturing an image of the unique multiplexing intensity pattern and training a convolutional neural network (CNN) as a classifier. This CNN-based demultiplexing method allows for simplicity of operation as alignment is unnecessary, orthogonality constraints are loosened, and costly optical hardware is not required...
April 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/28429018/force-induced-elastic-matrix-mediated-interactions-in-the-presence-of-a-rigid-wall
#3
Andreas M Menzel
We consider a soft elastic matrix that contains particulate inclusions and is bounded by a rigid wall, e.g., the substrate. Such a situation arises in elastic composite materials. They may serve as soft actuators when forces are imposed on or induced between the embedded particles. We investigate how the presence of the rigid wall affects the interactions between the inclusions. First, for no-slip boundary conditions, we transfer Blake's derivation of a corresponding Green's function from low-Reynolds-number hydrodynamics to the linearly elastic case...
April 21, 2017: Soft Matter
https://www.readbyqxmd.com/read/28426163/lipid-flip-flop-and-pore-nucleation-on-zwitterionic-bilayers-are-asymmetric-under-ionic-imbalance
#4
Jiaqi Lin, Roozbeh Dargazany, Alfredo Alexander-Katz
Lipid flip-flop and its associated transient pore formation are key thermodynamic properties of living cell membranes. However, there is a lack of understanding of whether ionic imbalance that exists ubiquitously across cell membranes affects lipid flip-flop and its associated functions. Potential of mean force calculations show that the free-energy barrier of lipid flip-flop on the extracellular leaflet reduces with the presence of ionic imbalance, whereas the barrier on the intracellular leaflet is generally not affected...
April 20, 2017: Small
https://www.readbyqxmd.com/read/28422500/influence-of-13-c-isotopic-labeling-location-on-dynamic-nuclear-polarization-of-acetate
#5
Peter NIedbalski, Christopher Parish, Andhika Kiswandhi, Zoltán Kovács, Lloyd Laporca Lumata
Dynamic nuclear polarization (DNP) via the dissolution method has alleviated the insensitivity problem in liquid-state nuclear magnetic resonance (NMR) spectroscopy by amplifying the signals by several thousand-fold. This NMR signal amplification process emanates from the microwave-mediated transfer of high electron spin alignment to the nuclear spins at high magnetic field and cryogenic temperature. Since the interplay between the electrons and nuclei is crucial, the chemical composition of a DNP sample such as the type of free radical used, glassing solvents, or the nature of the target nuclei can significantly affect the NMR signal enhancement levels that can be attained with DNP...
April 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28422050/k-mer-content-correlation-and-position-analysis-of-genome-dna-sequences-for-the-identification-of-function-and-evolutionary-features
#6
Aaron Sievers, Katharina Bosiek, Marc Bisch, Chris Dreessen, Jascha Riedel, Patrick Froß, Michael Hausmann, Georg Hildenbrand
In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used...
April 19, 2017: Genes
https://www.readbyqxmd.com/read/28415220/multistage-modeling-of-protein-dynamics-with-monomeric-myc-oncoprotein-as-an-example
#7
Jiaojiao Liu, Jin Dai, Jianfeng He, Antti J Niemi, Nevena Ilieva
We propose to combine a mean-field approach with all-atom molecular dynamics (MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28414421/shape-controlled-metal-free-catalysts-facet-sensitive-catalytic-activity-induced-by-the-arrangement-pattern-of-noncovalent-supramolecular-chains
#8
Guangwei Geng, Penglei Chen, Bo Guan, Lang Jiang, Zhongfei Xu, Dawei Di, Zeyi Tu, Weichang Hao, Yuanping Yi, Chuncheng Chen, Minghua Liu, Wenping Hu
Metal-free catalytic materials have recently received broad attention as promising alternatives to metal-involved catalysts. This is owing to their inherent capability to overcome the inevitable limitations of metal-involved catalysts, such as high sensitivity to poisoning, the limited reserves, high cost and scarcity of metals (especially noble metals), etc. However, the lack of shape-controlled metal-free catalysts with well-defined facets is a formidable bottleneck limiting our understandings on the underlying structure-activity relationship at atomic/molecular level, which thereby restrains their rational design...
April 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28412106/radial-notch-labralization-for-proximal-radioulnar-joint-dysplasia
#9
Enrico Bellato, Shawn W O'Driscoll
BACKGROUND: Chronic posterior subluxation or dislocation of the radial head is uncommon and difficult to treat. To restore radiocapitellar alignment, procedures such as deepening of the notch using a high-speed burr have been described, but they can result in cartilage damage. We hypothesized that a radial notch labralization using soft tissue could improve radiocapitellar tracking without violating the joint surface. METHODS: A radial notch labralization was performed in 3 patients with chronic posterior subluxation of the radial head and developmental dysplasia of the radial notch in the setting of complex recurrent instability of the elbow...
April 12, 2017: Journal of Shoulder and Elbow Surgery
https://www.readbyqxmd.com/read/28409507/fasparser-a-package-for-manipulating-sequence-data
#10
Yan-Bo Sun
A computer software package called 'FasParser' was developed for manipulating sequence data. It can be used on personal computers to perform series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identifying overlapping regions between two alignments, sorting of sequences according to their IDs or lengths, concatenating sequences of multiple loci for a particular set of samples, translating nucleotide sequences to amino acids, and constructing alignments in several different formats, as well as some extracting and filtrating of data for a particular FASTA file...
March 18, 2017: Zoological Research
https://www.readbyqxmd.com/read/28404839/coverage-of-nutrition-interventions-intended-for-infants-and-young-children-varies-greatly-across-programs-results-from-coverage-surveys-in-5-countries
#11
REVIEW
Magali Leyvraz, Grant J Aaron, Alia Poonawala, Marti J van Liere, Dominic Schofield, Mark Myatt, Lynnette M Neufeld
Background: The efficacy of a number of interventions that include fortified complementary foods (FCFs) or other products to improve infant and young child feeding (IYCF) is well established. Programs that provide such products free or at a subsidized price are implemented in many countries around the world. Demonstrating the impact at scale of these programs has been challenging, and rigorous information on coverage and utilization is lacking.Objective: The objective of this article is to review key findings from 11 coverage surveys of IYCF programs distributing or selling FCFs or micronutrient powders in 5 countries...
April 12, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28401221/synthesis-of-two-titanosilicates-with-distinct-interlayer-connections-from-similar-gels
#12
Peng Ji, Kun Lu, Xinqing Lu, Hao Xu, Peng Wu
Ti-SSZ-70 and Ti-ECNU-6, with identical intralayer structures but distinct interlayer connections, were prepared from similar synthetic gels free of alkali metal ions and boric acid. Ti-SSZ-70, composed of vertically misaligned MWW layers, was transferred to Ti-ECNU-6, structurally analogous to the Ti-MWW zeolite with a well-aligned layer stacking, upon the addition of an appropriate amount of hexamethyleneimine to the gel. These two titanosilicate catalysts exhibited outstanding catalytic activities in the liquid-phase alkene epoxidation...
April 12, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28400671/distraction-osteogenesis-using-combined-locking-plate-and-ilizarov-fixator-in-the-treatment-of-bone-defect-a-report-of-2-cases
#13
John Mukhopadhaya, Manish Raj
Distraction osteogenesis and bone transport has been used to reconstruct bone loss defect by allowing new bone to form in the gap. Plate-guided bone transport has been successfully described in literature to treat bone loss defect in the femur, tibia, and mandible. This study reports two cases of fracture of femur with segmental bone loss treated with locking plate fixation and bone transport with Ilizarov ring fixator. At the time of docking, when the transport segment is compressed with bone fragment, the bone fragment is fixed with additional locking or nonlocking screws through the plate...
March 2017: Indian Journal of Orthopaedics
https://www.readbyqxmd.com/read/28400101/overcoming-the-exacerbating-effects-of-ranitidine-on-nsaid-induced-small-intestinal-toxicity-with-quercetin-providing-a-complete-gi-solution
#14
Devendra Pratap Singh, Swapnil P Borse, Manish Nivsarkar
There is a need to find/discover novel leads to treat complex and/or multi-factorial-pathogenic disease(s) like Nonsteroidal anti-inflammatory drugs (NSAID)-induced gastroenteropathy or gastrointestinal (GI) toxicity as it has emerged as an important medical and socioeconomic problem. There is no approved therapeutic strategy to prevent NSAID-induced small intestinal toxicity and highly effective gastro-protective drugs such as ranitidine hydrochloride (RAN) exacerbate it. In this purview, the multi target drug discovery approach (MTDD), combination approach and hit to lead strategies based on the foundation of ethnopharmacology and/or reverse pharmacology holds strong potential...
April 8, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28398992/translating-technical-support-into-country-action-the-role-of-the-interagency-task-team-on-the-prevention-and-treatment-of-hiv-infection-in-pregnant-women-mothers-and-children-in-the-global-plan-era
#15
Chewe Luo, Gottfried Hirnschall, Jessica Rodrigues, Sostena Romano, Shaffiq Essajee, Braeden Rogers, Elizabeth McCarthy, Albert Mwango, Nalinee Sangrujee, Michelle R Adler, James C Houston, Judite O Langa, Marilena Urso, Omotayo Bolu, Gilbert Tene, Jean B Elat Nfetam, Etienne Kembou, Benjamin R Phelps
While the Interagency Task Team on the Prevention and Treatment of HIV Infection in Pregnant Women, Mothers, and Children (IATT) partnership existed before the Global Plan Towards the Elimination of New HIV Infections Among Children by 2015 and Keeping Their Mothers Alive (Global Plan), its reconfiguration was critical to coordinating provision of technical assistance that positively influenced country decision-making and program performance. This article describes how the Global Plan anchored the work of the IATT and, in turn, how the IATT's technical assistance helped to accelerate achievement of the Global Plan targets and milestones...
May 1, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/28397885/oxygen-promoted-catalyst-sintering-influences-number-density-alignment-and-wall-number-of-vertically-aligned-carbon-nanotubes
#16
Wenbo Shi, Jinjing Li, Erik S Polsen, C Ryan Oliver, Yikun Zhao, Eric R Meshot, Michael Barclay, D Howard Fairbrother, A John Hart, Desiree L Plata
A lack of synthetic control and reproducibility during vertically aligned carbon nanotube (CNT) synthesis has stifled many promising applications of organic nanomaterials. Oxygen-containing species are particularly precarious in that they have both beneficial and deleterious effects and are notoriously difficult to control. Here, we demonstrated diatomic oxygen's ability, independent of water, to tune oxide-supported catalyst thin film dewetting and influence nanoscale (diameter and wall number) and macro-scale (alignment and density) properties for as-grown vertically aligned CNTs...
April 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28397083/cephalometric-and-dental-arch-changes-to-haas-type-rapid-maxillary-expander-anchored-to-deciduous-vs-permanent-molars-a-multicenter-randomized-controlled-trial
#17
Carmen Cerruto, Alessandro Ugolini, Luca Di Vece, Tiziana Doldo, Alberto Caprioglio, Armando Silvestrini-Biavati
OBJECTIVE: To assess radiographic changes and dental arch changes with Haas-type rapid maxillary expansion (H-RME) anchored to deciduous versus permanent molars in children with unilateral posterior crossbite. METHODS: In all, 70 patients with unilateral posterior crossbite were randomly allocated to group GrE (H-RME on second deciduous molars) or Gr6 (H-RME on first permanent molars) and compared between T0 (before treatment) and T1 (at the RME removal; i.e., 10 months after the end of the activation of the screw)...
April 10, 2017: Journal of Orofacial Orthopedics, Fortschritte der Kieferorthopädie
https://www.readbyqxmd.com/read/28393762/engineering-a-functional-three-dimensional-human-cardiac-tissue-model-for-drug-toxicity-screening
#18
Hong Fang Lu, Meng Leong, Tze Lim, Ying Ping Chua, Jia Kai Lim, Chan Du, Andrew C A Wan
Cardiotoxicity is one of the major reasons for clinical drug attrition. In vitro tissue models that can provide efficient and accurate drug toxicity screening are highly desired for preclinical drug development and personalized therapy. Here, we report the fabrication and characterization of a human cardiac tissue model for high throughput drug toxicity studies. Cardiac tissues were fabricated via cellular self-assembly of human transgene-free iPSC-derived cardiomyocytes in pre-fabricated polydimethylsiloxane molds...
April 10, 2017: Biofabrication
https://www.readbyqxmd.com/read/28391694/molecular-characterization-and-variation-of-the-celiac-disease-epitope-domains-among-%C3%AE-gliadin-genes-in-aegilops-tauschii
#19
YuGe Li, HuiHui Liang, Sheng-Long Bai, Yun Zhou, Guiling Sun, Ya-Rui Su, An-Li Gao, DaLe Zhang, SuoPing Li
To explore the distribution and quantity of toxic epitopes in α-gliadins from Aegilops tauschii, a total of 133 complete α-gliadin coding sequences were obtained, including 69 pseudogenes with at least one premature stop codon and 64 genes with complete open reading frames (ORFs). Plenty of deletions and single amino acid substitutions were found in the 4 celiac disease (CD) toxic epitope domains through multiple alignments, in which the sequence of DQ2.5-glia-α2 demonstrated the most significant changes...
April 10, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28391192/estimation-of-large-motion-in-lung-ct-by-integrating-regularized-keypoint-correspondences-into-dense-deformable-registration
#20
Jan Ruhaak, Thomas Polzin, Stefan Heldmann, Ivor Simpson, Heinz Handels, Jan Modersitzki, Mattias Paul Heinrich
We present a novel algorithm for the registration of pulmonary CT scans. Our method is designed for large respiratory motion by integrating sparse keypoint correspondences into a dense continuous optimization framework. The detection of keypoint correspondences enables robustness against large deformations by jointly optimizing over a large number of potential discrete displacements, whereas the dense continuous registration achieves sub-voxel alignment with smooth transformations. Both steps are driven by the same normalized gradient fields data term...
April 5, 2017: IEEE Transactions on Medical Imaging
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