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https://www.readbyqxmd.com/read/28102960/nine-degrees-of-freedom-flexmap-for-a-cone-beam-computed-tomography-imaging-device-with-independently-movable-source-and-detector
#1
Peter Keuschnigg, Daniel Kellner, Karl Fritscher, Andrea Zechner, Ulrich Mayer, Philipp Huber, Felix Sedlmayer, Heinz Deutschmann, Philipp Steininger
PURPOSE: Couch-mounted cone-beam computed tomography (CBCT) imaging devices with independently rotatable x-ray source and flat-panel detector arms for acquisitions of arbitrary regions of interest (ROI) have recently been introduced in image-guided radiotherapy (IGRT). This work analyzes mechanical limitations and gravity-induced effects influencing the geometric accuracy of images acquired with arbitrary angular constellations of source and detector in nonisocentric trajectories, which is considered essential for IGRT...
January 2017: Medical Physics
https://www.readbyqxmd.com/read/28102945/learning-based-deformable-image-registration-for-infant-mr-images-in-the-first-year-of-life
#2
Shunbo Hu, Lifang Wei, Yaozong Gao, Yanrong Guo, Guorong Wu, Dinggang Shen
PURPOSE: Many brain development studies have been devoted to investigate dynamic structural and functional changes in the first year of life. To quantitatively measure brain development in such a dynamic period, accurate image registration for different infant subjects with possible large age gap is of high demand. Although many state-of-the-art image registration methods have been proposed for young and elderly brain images, very few registration methods work for infant brain images acquired in the first year of life, because of (a) large anatomical changes due to fast brain development and (b) dynamic appearance changes due to white-matter myelination...
January 2017: Medical Physics
https://www.readbyqxmd.com/read/28102868/control-and-automation-of-multilayered-integrated-microfluidic-device-fabrication
#3
Sarit Kipper, Ludmila Frolov, Ortal Guy, Michal Pellach, Yair Glick, Asaf Malichi, Binyamin A Knisbacher, Efrat Barbiro-Michaely, Dorit Avrahami, Yehuda Yavets-Chen, Erez Y Levanon, Doron Gerber
Integrated microfluidics is a sophisticated three-dimensional (multi layer) solution for high complexity serial or parallel processes. Fabrication of integrated microfluidic devices requires soft lithography and the stacking of thin-patterned PDMS layers. Precise layer alignment and bonding is crucial. There are no previously reported standards for alignment of the layers, which is mostly performed using uncontrolled processes with very low alignment success. As a result, integrated microfluidics is mostly used in academia rather than in the many potential industrial applications...
January 19, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28102825/versatile-modular-three-dimensional-microelectrode-arrays-for-neuronal-ensemble-recordings-from-design-to-fabrication-assembly-and-functional-validation-in-non-human-primates
#4
Falk Barz, Alessandro Livi, Marco Lanzilotto, Monica Maranesi, Luca Bonini, Oliver Paul, Patrick Ruther
<i>Objective. </i>Application-specific designs of electrode arrays offer an improved effectiveness for providing access to targeted brain regions in neuroscientific research and brain machine interfaces. The simultaneous and stable recording of neuronal ensembles is the main goal in the design of advanced neural interfaces. Here, we describe the development and assembly of highly customizable three-dimensional microelectrode arrays and demonstrate their recording performance in chronic applications in non-human primates...
January 19, 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#5
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101989/diagnosis-of-peste-des-petits-ruminants-in-wild-and-domestic-animals-in-xinjiang-china-2013-2016
#6
J Li, L Li, X Wu, F Liu, Y Zou, Q Wang, C Liu, J Bao, W Wang, W Ma, H Lin, J Huang, X Zheng, Z Wang
Peste des petits ruminants viruses (PPRVs) re-emerged in China at the end of 2013 and then spread rapidly into 22 provinces through movement of live goats and sheep. In this study, 96 samples of domestic animals and 13 samples of wildlife were analysed for the presence of PPRV infection by ELISA or RT-PCR. Of 96 samples from sheep and goats, 91 were PPRV positive, whereas all of the 13 samples from three wild species, Capra ibex (Capra ibex sibirica), argali (Ovis ammon) and Goitered gazelle (Gazella subgutturosa), were found to be positive...
January 18, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28101861/structural-transition-of-trichocyte-keratin-intermediate-filaments-during-development-in-the-hair-follicle
#7
R D Bruce Fraser, David A D Parry
The intermediate filaments (IF) in trichocyte (hard α-) keratin are unique amongst the various classes of IF in having not one but two topologically-distinct structures. The first is formed at an early stage of hair development in a reducing environment within the cells in the lower part of the follicle. The second structure occurs at a later stage of hair development in the upper part of the follicle, where there is a transition to an oxidizing environment. Crosslinking studies reveal that molecular slippage occurs within the IF upon oxidation and that this results in many cysteine residues lying in near axial alignment, thereby facilitating disulphide bond formation...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101855/improving-morphological-quality-and-uniformity-of-hydrothermally-grown-zno-nanowires-by-surface-activation-of-catalyst-layer
#8
Gonzalo Murillo, Helena Lozano, Joana Cases-Utrera, Minbaek Lee, Jaume Esteve
This paper presents a study about the dependence of the hydrothermal growth of ZnO nanowires (NWs) with the passivation level of the active surface of the Au catalyst layer. The hydrothermal method has many potential applications because of its low processing temperature, feasibility, and low cost. However, when a gold thin film is utilized as the seed material, the grown NWs often lack morphological homogeneity; their distribution is not uniform and the reproducibility of the growth is low. We hypothesize that the state or condition of the active surface of the Au catalyst layer has a critical effect on the uniformity of the NWs...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28101590/-minimally-invasive-treatment-of-intra-articular-calcaneal-fractures-with-the-2%C3%A2-point-distractor
#9
G Mattiassich, W Litzlbauer, M Ponschab, R Ortmaier, C Rodemund
OBJECTIVE: Open treatment of calcaneus fractures often has an increased risk of wound healing. Minimally invasive treatment with small incisions reduces complications. INDICATIONS: Calcaneal fractures with malalignment/comminution >1-2 mm; broadening, varus alignment of the calcaneal length axis or shortening; emergency surgery for open fractures or compartment syndrome. CONTRAINDICATIONS: Local or general contraindications. SURGICAL TECHNIQUE: Standardised positioning; restoration of length/axis with 2‑point distractor under fluoroscopic control...
January 18, 2017: Operative Orthopädie und Traumatologie
https://www.readbyqxmd.com/read/28101462/identification-and-molecular-characterization-of-genes-coding-pharmaceutically-important-enzymes-from-halo-thermo-tolerant-bacillus
#10
Azam Safary, Rezvan Moniri, Maryam Hamzeh-Mivehroud, Siavoush Dastmalchi
Purpose: Robust pharmaceutical and industrial enzymes from extremophile microorganisms are main source of enzymes with tremendous stability under harsh conditions which make them potential tools for commercial and biotechnological applications. Methods: The genome of a Gram-positive halo-thermotolerant Bacillus sp. SL1, new isolate from Saline Lake, was investigated for the presence of genes coding for potentially pharmaceutical enzymes. We determined gene sequences for the enzymes laccase (CotA), l-asparaginase (ansA3, ansA1), glutamate-specific endopeptidase (blaSE), l-arabinose isomerase (araA2), endo-1,4-β mannosidase (gmuG), glutaminase (glsA), pectate lyase (pelA), cellulase (bglC1), aldehyde dehydrogenase (ycbD) and allantoinases (pucH) in the genome of Bacillus sp...
December 2016: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28101273/who-scared-the-cat-a-molecular-crime-scene-investigation-laboratory-exercise
#11
Laura E Ott, Susan D Carson
This introductory laboratory exercise gives first-year life science majors or nonmajors an opportunity to gain knowledge and experience in basic bioinformatics and molecular biology laboratory techniques and analysis in the context of a mock crime scene investigation. In this laboratory, students determine if a human (Lady) or dog (Kona) committed the fictional crime of scaring a cat. Students begin by performing in silico PCR using provided dog- and human-specific PCR primers to determine the sequences to be amplified and predict PCR amplicon sizes...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28101268/traditional-versus-online-biology-courses-connecting-course-design-and-student-learning-in-an-online-setting
#12
Rachel Biel, Cynthia J Brame
Online courses are a large and growing part of the undergraduate education landscape, but many biology instructors are skeptical about the effectiveness of online instruction. We reviewed studies comparing the effectiveness of online and face-to-face (F2F) undergraduate biology courses. Five studies compared student performance in multiple course sections at community colleges, while eight were smaller scale and compared student performance in particular biology courses at a variety of types of institutions...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28101266/how-to-assess-your-cure-a-practical-guide-for-instructors-of-course-based-undergraduate-research-experiences
#13
Erin E Shortlidge, Sara E Brownell
Integrating research experiences into undergraduate life sciences curricula in the form of course-based undergraduate research experiences (CUREs) can meet national calls for education reform by giving students the chance to "do science." In this article, we provide a step-by-step practical guide to help instructors assess their CUREs using best practices in assessment. We recommend that instructors first identify their anticipated CURE learning outcomes, then work to identify an assessment instrument that aligns to those learning outcomes and critically evaluate the results from their course assessment...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28100789/complex-evolutionary-history-of-the-mammalian-histone-h1-1-h1-5-gene-family
#14
Inma Ponte, Devani Romero, Daniel Yero, Pedro Suau, Alicia Roque
H1 is involved in chromatin higher-order structure and gene regulation. H1 has a tripartite structure. The central domain is stably folded in solution, while the N- and C-terminal domains are intrinsically disordered. The terminal domains are encoded by DNA of low sequence complexity, and are thus prone to short insertions/deletions. We have examined the evolution of the H1.1 to H1.5 gene family from 27 mammalian species. Multiple sequence alignment has revealed a strong preferential conservation of the number and position of basic residues among paralogs, suggesting that overall H1 basicity is under a strong purifying selection...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100776/crystallographic-snapshots-of-class-a-%C3%AE-lactamase-catalysis-reveal-structural-changes-that-facilitate-%C3%AE-lactam-hydrolysis
#15
Xuehua Pan, Yunjiao He, Jinping Lei, Xuhui Huang, Yanxiang Zhao
β-lactamases confer resistance to β-lactam-based antibiotics. There is great interest in understanding their mechanisms to enable the development of β-lactamase-specific inhibitors. The mechanism of Class A β-lactamases has been studied extensively, revealing Lys73 and Glu166 as general bases that assist the catalytic residue Ser70. However, the specific roles of these two residues within the catalytic cycle remains not fully understood. To help resolve this question, we first identified a Glu166His mutant that is functional but kinetically slowed...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100585/fast-and-accurate-de-novo-genome-assembly-from-long-uncorrected-reads
#16
Robert Vaser, Ivan Sovic, Niranjan Nagarajan, Mile Sikic
The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource intensive error correction and consensus generation steps to obtain high quality assemblies. We show that the error correction step can be omitted and high quality consensus sequences can be generated efficiently with a SIMD accelerated, partial order alignment based stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore datasets we show that Racon coupled with Miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster...
January 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28100479/evidence-of-central-sensitisation-in-those-with-dry-eye-symptoms-and-neuropathic-like-ocular-pain-complaints-incomplete-response-to-topical-anaesthesia-and-generalised-heightened-sensitivity-to-evoked-pain
#17
Ashley M Crane, William Feuer, Elizabeth R Felix, Roy C Levitt, Allison L McClellan, Konstantinos D Sarantopoulos, Anat Galor
OBJECTIVE: To evaluate how closely neuropathic-like ocular pain (NOP) symptoms align with a metric of central sensitisation (ie, the presence of persistent ocular pain after topical anaesthetic placement) in individuals with dry eye (DE) symptoms. DESIGN: Cross-sectional study of 224 individuals with DE symptoms seen in the Miami Veterans Affairs eye clinic. An evaluation was performed consisting of questionnaires regarding DE symptoms, NOP descriptors and evoked pain sensitivity testing on the forehead and forearm, followed by a comprehensive ocular surface examination including corneal mechanical sensitivity testing...
January 18, 2017: British Journal of Ophthalmology
https://www.readbyqxmd.com/read/28099991/bayescat-bayesian-co-estimation-of-alignment-and-tree
#18
Heejung Shim, Bret Larget
Traditionally, phylogeny and sequence alignment are estimated separately: first estimate a multiple sequence alignment and then infer a phylogeny based on the sequence alignment estimated in the previous step. However, uncertainty in the alignment is ignored, resulting, possibly, in overstated certainty in phylogeny estimates. We develop a joint model for co-estimating phylogeny and sequence alignment which improves estimates from the traditional approach by accounting for uncertainty in the alignment in phylogenetic inferences...
January 18, 2017: Biometrics
https://www.readbyqxmd.com/read/28099810/anisotropic-self-assembly-of-supramolecular-polymers-and-plasmonic-nanoparticles-at-the-liquid-liquid-interface
#19
Joseph J Armao, Irina Nyrkova, Gad Fuks, Artem Osypenko, Mounir Maaloum, Emilie Moulin, Raul Arenal, Odile Gavat, Alexander N Semenov, Nicolas Giuseppone
The study of supramolecular polymers in the bulk, in solution, and at the solid-liquid interface has recently become a major topic of interest, going from fundamental aspects to applications in materials science. However, examples of 1D supramolecular polymers at the liquid-liquid interface are mostly unexplored. Here we describe the light-assisted supramolecular polymerization of triarylamine molecules and their organization at a chloroform-water interface. The resulting interfacial nematic layer of these 1D supramolecular polymers is further used as a template for the precise alignment of spherical gold nanoparticles coming from the water phase...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28099799/hierarchically-porous-electrocatalyst-with-vertically-aligned-defect-rich-comos-nanosheets-for-her-in-alkaline-medium
#20
Zexing Wu, Junpo Guo, Jie Wang, Rong Liu, Weiping Xiao, Cuijuan Xuan, Kedong Xia, Deli Wang
Effective electrocatalysts for hydrogen evolution reaction (HER) in alkaline electrolytes can be developed via a simple solvothermal process. In this work, firstly, the prepared CoMoS nanomaterials through solvothermal treatment have a porous, defect-rich, and vertically aligned nanostructure, which is beneficial for HER in an alkaline medium. Secondly, the electron transfer from Co to MoS2 that reduces the unoccupied d-orbitals of Mo, can also enhance the HER kinetics in an alkaline medium. This has been demonstrated via comparison of catalytic performances of CoMoS, CoS, and MoS2...
January 18, 2017: ACS Applied Materials & Interfaces
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