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https://www.readbyqxmd.com/read/28092777/controlling-the-3d-architecture-of-self-lifting-auto-generated-tissue-equivalents-slates-for-optimized-corneal-graft-composition-and-stability
#1
Ricardo M Gouveia, Elena González-Andrades, Juan C Cardona, Carmen González-Gallardo, Ana M Ionescu, Ingrid Garzon, Miguel Alaminos, Miguel González-Andrades, Che J Connon
Ideally, biomaterials designed to play specific physical and physiological roles in vivo should comprise components and microarchitectures analogous to those of the native tissues they intend to replace. For that, implantable biomaterials need to be carefully designed to have the correct structural and compositional properties, which consequently impart their bio-function. In this study, we showed that the control of such properties can be defined from the bottom-up, using smart surface templates to modulate the structure, composition, and bio-mechanics of human transplantable tissues...
December 23, 2016: Biomaterials
https://www.readbyqxmd.com/read/28088762/the-super-n-motifs-model-a-novel-alignment-free-approach-for-representing-and-comparing-rna-secondary-structures
#2
Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang
MOTIVATION: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28087396/influence-of-coronal-bowing-on-the-lower-alignment-and-the-positioning-of-component-in-navigation-and-conventional-total-knee-arthroplasty
#3
Hideo Kobayashi, Yasushi Akamatsu, Ken Kumagai, Yoshihiro Kusayama, Masato Aratake, Tomoyuki Saito
BACKGROUND: Coronal alignment is an important factor for the function and longevity of total knee arthroplasty (TKA). Coronal bowing of the lower extremity is common among Asians and it may pose a risk for malalignment of the lower leg and malposition of component. HYPOTHESIS: We hypothesized that coronal bowing itself has a risk for malalignment of the lower leg and malposition of femoral / tibial components and that navigation TKA is beneficial for patients with coronal bowing...
January 10, 2017: Orthopaedics & Traumatology, Surgery & Research: OTSR
https://www.readbyqxmd.com/read/28081367/ordered-mesoporous-titanium-nitride-as-a-promising-carbon-free-cathode-for-aprotic-lithium-oxygen-batteries
#4
Byung Gon Kim, Changshin Jo, Jaeho Shin, Yeongdong Mun, Jinwoo Lee, Jang Wook Choi
Despite the extraordinary gravimetric energy densities, Li-O2 batteries are still facing a technological challenge; limited round trip efficiency leading to insufficient cycle life. Recently, carbonaceous electrode materials were found to be one of the primary origins of the limited cycle life, as they produce irreversible side products during discharge. A few investigations based on non-carbonaceous materials have demonstrated largely suppressed accumulation of irreversible side products but such studies have focused mainly on the materials themselves rather than delicate morphology control...
January 12, 2017: ACS Nano
https://www.readbyqxmd.com/read/28078717/a-whole-lamella-perspective-on-the-origin-of-the-epidermal-free-margin-of-anolis-reptilia-dactyloidae-toe-pads
#5
Anthony P Russell, Alyssa Eslinger
Anoline lamellae terminate in an epidermal free margin carrying the majority of its setae. How the free margin is extruded from the body of the scale is not well understood. Two hypotheses have been advanced to account for it, one advocating distal migration of the outer epidermal layers relative to the body of the lamella, and the other proposing regression of the dermal core. Available evidence provides partial support for both. We assembled a series of specimens of Anolis grahami representing all shedding cycle stages, and prepared histological sections of the toe pads to allow measurement of appropriate lamellar components through the shedding cycle...
January 12, 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28077565/mahmi-database-a-comprehensive-metahit-based-resource-for-the-study-of-the-mechanism-of-action-of-the-human-microbiota
#6
Aitor Blanco-Míguez, Alberto Gutiérrez-Jácome, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez
The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28075041/engineering-matrix-free-laser-desorption-ionization-mass-spectrometry-using-glancing-angle-deposition-films
#7
Reshma Singh, Louis W Bezuidenhout, Abebaw Jemere, Zhen Wang, Michael Brett, D Jed Harrison
Thin, nanoporous films fabricated using Glancing Angle Deposition (GLAD) technology are demonstrated for solid matrix laser desorption ionization mass spectrometry (SMALDI-MS). GLAD allows facile engineering of naonporosity, film thickness, post alignment, and material composition, as demonstrated here by the fabrication of Co-GLAD and Si-GLAD films for SMALDI, and by exploration of the SMALDI performance as a function of thickness, post density, and angle of the post relative to surface normal. GLAD films were prepared by electron beam evaporation onto silicon substrates, using steep angles of incidence for the vacuum deposition, with computer controlled substrate rotation...
January 11, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28074911/further-evidence-for-microtubule-independent-dimerization-of-tppp-p25
#8
J Oláh, T Szénási, S Szunyogh, A Szabó, A Lehotzky, J Ovádi
Tubulin Polymerization Promoting Protein (TPPP/p25) is a brain-specific disordered protein that modulates the dynamics and stability of the microtubule network by its assembly promoting, cross-linking and acetylation enhancing activities. In normal brain it is expressed primarily in differentiated oligodendrocytes; however, at pathological conditions it is enriched in inclusions of both neurons and oligodendrocytes characteristic for Parkinson's disease and multiple system atrophy, respectively. The objective of this paper is to highlight a critical point of a recently published Skoufias's paper in which the crucial role of the microtubules in TPPP/p25 dimerization leading to microtubule bundling was suggested...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28073754/fast-and-accurate-phylogeny-reconstruction-using-filtered-spaced-word-matches
#9
Chris-André Leimeister, Salma Sohrabi-Jahromi, Burkhard Morgenstern
MOTIVATION: Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. RESULTS: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28071341/identification-of-novel-hits-as-highly-prospective-dual-agonists-for-mu-and-kappa-opioid-receptors-an-integrated-in-silico-approach
#10
Indrani Bera, Mrinal Vishwas Marathe, Pavan V Payghan, Nanda Ghoshal
Opioid agonists are used clinically for the treatment of acute and chronic pain, however, their clinical use is limited due to the presence of undesired side effects. Dual agonists, simultaneously targeting mu and kappa opioid receptors, show fewer side effects than that of selective agonists. In the present work, 2D- and 3D- Quantitative Structure Activity Relationship studies were performed on a series of aminomorphinan derivatives as dual agonists, using a wide range of descriptors. The aim of the study was to identify the structural requirements for the activity of these compounds towards mu and kappa opioid receptors and using the models, with best external predictability, for predicting the activities of new hits obtained from shape based virtual screening of drug like compounds from ZINC database...
January 10, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28063445/influence-of-dy-3-and-tb-3-doping-on-13-c-dynamic-nuclear-polarization
#11
Peter Niedbalski, Christopher Parish, Andhika Kiswandhi, Leila Fidelino, Chalermchai Khemtong, Zahra Hayati, Likai Song, André Martins, A Dean Sherry, Lloyd Lumata
Dynamic nuclear polarization (DNP) is a technique that uses a microwave-driven transfer of high spin alignment from electrons to nuclear spins. This is most effective at low temperature and high magnetic field, and with the invention of the dissolution method, the amplified nuclear magnetic resonance (NMR) signals in the frozen state in DNP can be harnessed in the liquid-state at physiologically acceptable temperature for in vitro and in vivo metabolic studies. A current optimization practice in dissolution DNP is to dope the sample with trace amounts of lanthanides such as Gd(3+) or Ho(3+), which further improves the polarization...
January 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28060880/accelerated-wound-closure-differently-organized-nanofibers-affect-cell-migration-and-hence-the-closure-of-artificial-wounds-in-a-cell-based-in-vitro-model
#12
Maximilian Ottosson, Albin Jakobsson, Fredrik Johansson
Nanofiber meshes holds great promise in wound healing applications by mimicking the topography of extracellular matrix, hence providing guidance for crucial cells involved in the regenerative processes. Here we explored the influence of nanofiber alignment on fibroblast behavior in a novel in vitro wound model. The model included electrospun poly-ε-caprolactone scaffolds with different nanofiber orientation. Fibroblasts were cultured to confluency for 24h before custom-made inserts were removed, creating cell-free zones serving as artificial wounds...
2017: PloS One
https://www.readbyqxmd.com/read/28059411/spray-assisted-alignment-of-layer-by-layer-assembled-silver-nanowires-a-general-approach-for-the-preparation-of-highly-anisotropic-nano-composite-films
#13
H Hu, M Pauly, O Felix, G Decher
The present article focuses on the build-up and the properties of oriented silver nanowire monolayer films and Layer-by-Layer assembled multilayer films. We describe the template-free oriented spray-assisted assembly of silver nanowires at solid/air-interfaces using Grazing Incidence Spraying, a simple and versatile approach that allows the formation of highly oriented thin films with a tunable density and in-plane orientation. Depending on the spraying conditions the nematic order parameter, which describes the angular spread of misaligned nanowires, can be as high as 0...
January 6, 2017: Nanoscale
https://www.readbyqxmd.com/read/28058085/microfluidic-cytometers-with-integrated-on-chip-optical-systems-for-red-blood-cell-and-platelet-counting
#14
Yingying Zhao, Qin Li, Xiaoming Hu, Yuhwa Lo
A microfluidic cytometer with integrated on-chip optical systems was designed for red blood cell (RBC) and platelet (PLT) counting. The design, fabrication, and characterization of the microfluidic cytometer with on-chip optical signal detection were described. With process using only a single mask, the device that integrates optical fibers and on-chip microlens with microfluidic channels on a polydimethylsiloxane layer by standard soft photolithography. This compact structure increased the sensitivity of the device and eliminated time-consuming free-space optical alignments...
November 2016: Biomicrofluidics
https://www.readbyqxmd.com/read/28056555/a-prospective-clinical-trial-to-compare-the-performance-of-dried-blood-spots-prenatal-screening-for-down-s-syndrome-with-conventional-non-invasive-testing-technology
#15
Huiying Hu, Yulin Jiang, Minghui Zhang, Shanying Liu, Na Hao, Jing Zhou, Juntao Liu, Xiaojin Zhang, Liangkun Ma
To evaluate, side by side, the efficiency of dried blood spots (DBSs) against serum screening for Down's syndrome, and then, to construct a two-tier strategy by topping up the fetal cell-free DNA (cfDNA) secondary screening over the high-risk women marked by the primary blood testing to build a practical screening tactic to identify fetal Down's syndrome. One thousand eight hundred and thirty-seven low-risk Chinese women, with singleton pregnancy, were enrolled for the study. Alpha-fetoprotein and free beta human chorionic gonadotropin were measured for the serum as well as for the parallel DBS samples...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28053114/feelnc-a-tool-for-long-non-coding-rna-annotation-and-its-application-to-the-dog-transcriptome
#16
Valentin Wucher, Fabrice Legeai, Benoît Hédan, Guillaume Rizk, Lætitia Lagoutte, Tosso Leeb, Vidhya Jagannathan, Edouard Cadieu, Audrey David, Hannes Lohi, Susanna Cirera, Merete Fredholm, Nadine Botherel, Peter A J Leegwater, Céline Le Béguec, Hille Fieten, Jeremy Johnson, Jessica Alföldi, Catherine André, Kerstin Lindblad-Toh, Christophe Hitte, Thomas Derrien
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28049316/system-size-dependence-of-the-structure-and-rheology-in-a-sheared-lamellar-liquid-crystalline-medium
#17
S J Jaju, V Kumaran
The structural and rheological evolution of an initially disordered lamellar phase system under a shear flow is examined using a mesoscale model based on a free energy functional for the concentration field, which is the scaled difference in the concentration between the hydrophilic and hydrophobic components. The dimensionless numbers which affect the shear evolution are the Reynolds number (γ˙¯L(2)/ν), the Schmidt number (ν/D), a dimensionless parameter Σ=(Aλ(2)/ρν(2)), a parameter μr which represents the viscosity contrast between the hydrophilic and hydrophobic components, and (L/λ), the ratio of system size and layer spacing...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28048300/th-cd-206-10-clinical-application-of-the-mind-demons-algorithm-for-symmetric-diffeomorphic-deformable-mr-to-ct-image-registration-in-spinal-interventions
#18
S Reaungamornrat, T De Silva, A Uneri, J Wolinsky, A Khanna, G Kleinszig, S Vogt, J Prince, J Siewerdsen
PURPOSE: Accurate intraoperative localization of target anatomy (e.g., tumors and vertebral levels) and critical structures (e.g., nerves and vessels) is essential to safe, effective surgery. Preoperative CT/MR images can be used to identify such vital anatomy in intraoperative images through multimodality deformable registration. We proposed a deformable registration method to align preoperative MR to intraoperative CT using modality-independent neighborhood descriptors (MIND) and a Huber metric for robust registration...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047810/su-f-t-592-a-delivery-qa-free-approach-for-adaptive-therapy-of-prostate-cancer-with-static-intensity-modulated-radiotherapy
#19
T Roth, J Dooley, T Zhu, R Woods, P Mavroidis, J Lian
PURPOSE: Clinical implementations of adaptive radiotherapy (ART) are limited mainly by the requirement of delivery QA (DQA) prior to the treatment. Small segment size and small segment MU are two dominant factors causing failures of DQA. The aim of this project is to explore the feasibility of ART treatment without DQA by using a partial optimization approach. METHODS: A retrospective simulation study was performed on two prostate cancer patients treated with SMLC-IMRT...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047353/su-f-j-53-a-3d-printed-phantom-for-the-use-of-daily-quality-assurance-alignment-tests
#20
K Woods, A Ayan, J Woollard, N Gardner, N Gupta
PURPOSE: To discuss experiences and results for a 3D printed QA phantom used for daily alignment purposes for a six degrees-of-freedom (6DoF) table METHODS: A 3D model was created using a fused deposition modeling (FDM) printer using free online computer-aided design (CAD) software. The model has been under use for daily QA alignment tests for a 6DoF couch. An aligned and angled baseplate were also printed in order to introduce known angles for 6DoF corrections during image-guidance. Unique registration contours were created on the faces of the phantom in order to achieve a better cone-beam computed tomography (CBCT) match using an auto-registration algorithm...
June 2016: Medical Physics
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