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Alignment free

Prachi Mehrotra, Vimla Kany G Ami, Narayanaswamy Srinivasan
The overall function of a multi-domain protein is determined by the functional and structural interplay of its constituent domains. Traditional sequence alignment-based methods commonly utilize domain-level information and provide classification only at the level of domains. Such methods are not capable of taking into account the contributions of other domains in the proteins, and domain-linker regions and classify multi-domain proteins. An alignment-free protein sequence comparison tool, CLAP (CLAssification of Proteins) was previously developed in our laboratory to especially handle multi-domain protein sequences without a requirement of defining domain boundaries and sequential order of domains...
April 20, 2018: Proteins
Kok Hong Tan, Fang Sheng Lim, Alfred Zhen Yang Toh, Xia-Xi Zheng, Chang Fu Dee, Burhanuddin Yeop Majlis, Siang-Piao Chai, Wei Sea Chang
Observation of visible light trapping in zinc oxide (ZnO) nanorods (NRs) correlated to the optical and photoelectrochemical properties is reported. In this study, ZnO NR diameter and c-axis length respond primarily at two different regions, UV and visible light, respectively. ZnO NR diameter exhibits UV absorption where large ZnO NR diameter area increases light absorption ability leading to high efficient electron-hole pair separation. On the other hand, ZnO NR c-axis length has a dominant effect in visible light resulting from a multiphoton absorption mechanism due to light reflection and trapping behavior in the free space between adjacent ZnO NRs...
April 17, 2018: Small
Weipeng Zhang, Ren-Mao Tian, Jin Sun, Salim Bougouffa, Wei Ding, Lin Cai, Yi Lan, Haoya Tong, Yongxin Li, Alan J Jamieson, Vladimir B Bajic, Jeffrey C Drazen, Douglas Bartlett, Pei-Yuan Qian
Amphipods are the dominant scavenging metazoan species in the Mariana Trench, the deepest known point in Earth's oceans. Here the gut microbiota of the amphipod Hirondellea gigas collected from the Challenger and Sirena Deeps of the Mariana Trench were investigated. The 11 amphipod individuals included for analyses were dominated by Psychromonas , of which a nearly complete genome was successfully recovered (designated CDP1). Compared with previously reported free-living Psychromonas strains, CDP1 has a highly reduced genome...
May 2018: MSystems
Deepal Dalal, Christian Curry, Ryan Carter, Colin Zdenek, Nicholas W Todd, Shannon M Rush, Richard Jensen
Midfoot injuries are the second most common athletic foot injury documented in the published data. High-energy Lisfranc dislocations are commonly seen secondary to traumatic etiologies and disrupt the strong midfoot ligaments supporting the arch. These injuries require immediate surgical intervention to prevent serious complications such as compartment syndrome and amputation. The present case series reports a new Lapidus plate system used in 3 patients who underwent arthrodesis procedures for Lisfranc joint dislocation...
April 11, 2018: Journal of Foot and Ankle Surgery: Official Publication of the American College of Foot and Ankle Surgeons
Hervé Seligmann
Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data...
April 2, 2018: Bio Systems
Ronaldo Correia da Silva, Andrei Santos Siqueira, Alex Ranieri Jerônimo Lima, Adonis de Melo Lima, Alberdan Silva Santos, Délia Cristina Figueira Aguiar, Evonnildo Costa Gonçalves
Asparaginases are found in a range of organisms, although those found in cyanobacteria have been little studied, in spite of their great potential for biotechnological application. This study therefore sought to characterize the molecular structure of an L-asparaginase from the cyanobacterium Limnothrix sp. CACIAM 69d, which was isolated from a freshwater Amazonian environment. After homology modeling, model validation was performed using a Ramachandran plot, VERIFY3D, and the RMSD. We also performed molecular docking and dynamics simulations based on binding free-energy analysis...
April 4, 2018: Journal of Molecular Modeling
Lynda Jones, Diana Gordon, Mary Zelinski
Students tend to be very interested in medical issues that affect them and their friends and family. Using cancer as a hook, the ART of Reproductive Medicine: Oncofertility curriculum (free, online, and NIH sponsored) has been developed to supplement the teaching of basic biological concepts and to connect biology and biomedical research. This approach allows integration of up-to-date information on cancer and cancer treatment, cell division, male and female reproductive anatomy and physiology, cryopreservation, fertility preservation, stem cells, ethics, and epigenetics into an existing biology curriculum...
March 2018: American Biology Teacher
Orly B Tarun, Christof Hannesschläger, Peter Pohl, Sylvie Roke
Biological membranes are highly dynamic and complex lipid bilayers, responsible for the fate of living cells. To achieve this function, the hydrating environment is crucial. However, membrane imaging typically neglects water, focusing on the insertion of probes, resonant responses of lipids, or the hydrophobic core. Owing to a recent improvement of second-harmonic (SH) imaging throughput by three orders of magnitude, we show here that we can use SH microscopy to follow membrane hydration of freestanding lipid bilayers on millisecond time scales...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
M Tulik, D Kabat, R A Kycia, Z Tabor, A Woszczyna, Z Latała
PURPOSE: To develop an assumption-free methodology for aligning the geometry of on-board imagers with the geometry of medical linear accelerators applied in image-guided radiotherapy (IGRT). MATERIAL: Alignment of the on-board imaging (OBI) system with respect to the accelerator system is achieved using a multi-modular phantom described elsewhere (Tabor et al., 2017), enabling the geometry of the linear accelerator to be specified without any pre-assumptions. METHODS: The placement of two isocentres (of the on-board imager and of the therapeutic system) and of three frames of reference (those of the on-board imager, of the therapeutic system, and of the treatment table) is formulated as an optimization problem...
March 2018: Physica Medica: PM
Zexiao Li, Xianlei Liu, Fengzhou Fang, Xiaodong Zhang, Zhen Zeng, Linlin Zhu, Ning Yan
Multi-reflective imaging systems find wide applications in optical imaging and space detection. However, it is faced with difficulties in adjusting the freeform mirrors with high accuracy to guarantee the optical function. Motivated by this, an alignment-free manufacture approach is proposed to machine the optical system. The direct optical performance-guided manufacture route is established without measuring the form error of freeform optics. An analytical model is established to investigate the effects of machine errors to serve the error identification and compensation in machining...
March 19, 2018: Optics Express
H Zhang, F Billard, X Yu, O Faucher, B Lavorel
The field-free molecular alignment of symmetric-top molecules, ethane, induced by intense non-resonant linearly polarized femtosecond laser pulses is investigated experimentally in the presence of collisional relaxation. The dissipation dynamics of field-free molecular alignment are measured by the balanced detection of ultrafast molecular birefringence of ethane gas samples at high pressures. By separating the molecular alignment into the permanent alignment and the transient alignment, the decay time-constants of both components are quantified at the same pressure...
March 28, 2018: Journal of Chemical Physics
Hai-Jeon Yoon, Yemi Kim, Jin Chung, Bom Sahn Kim
Predicting response to neo-adjuvant chemotherapy (NAC) and survival in locally advanced breast cancer (LABC) is important. This study investigated the prognostic value of tumor heterogeneity evaluated with textural analysis through F-18 fluorodeoxyglucose (FDG) positron emission tomography (PET) and diffusion-weighted imaging (DWI). We enrolled 83 patients with LABC who had completed NAC and curative surgery. Tumor texture indices from pretreatment FDG PET and DWI were extracted from histogram analysis and 7 different parent matrices: co-occurrence matrix, the voxel-alignment matrix, neighborhood intensity difference matrix, intensity size-zone matrix (ISZM), normalized gray-level co-occurrence matrix (NGLCM), neighboring gray-level dependence matrix (NGLDM), and texture spectrum matrix...
March 30, 2018: Breast Journal
Abdulrahman Altin, Maciej Krzywiecki, Adnan Sarfraz, Cigdem Toparli, Claudius Laska, Philipp Kerger, Aleksandar Zeradjanin, Karl J J Mayrhofer, Michael Rohwerder, Andreas Erbe
Corrosion inhibitors are added in low concentrations to corrosive solutions for reducing the corrosion rate of a metallic material. Their mechanism of action is typically the blocking of free metal surface by adsorption, thus slowing down dissolution. This work uses electrochemical impedance spectroscopy to show the cyclic oligosaccharide β-cyclodextrin (β-CD) to inhibit corrosion of zinc in 0.1M chloride with an inhibition efficiency of up to 85%. Only a monomolecular adsorption layer of β-CD is present on the surface of the oxide covered metal, with Raman spectra of the interface proving the adsorption of the intact β-CD...
2018: Beilstein Journal of Nanotechnology
Sang Hyun Ji, Ji Sun Yun
Flexible lead-free piezoelectric nanofibers, based on BNT-ST (0.78Bi0.5 Na0.5 TiO₃-0.22SrTiO₃) ceramic and poly(vinylidene fluoride-trifluoroethylene) (PVDF-TrFE) copolymers, were fabricated by an electrospinning method and the effects of the degree of alignment in the nanofibers on the piezoelectric characteristics were investigated. The microstructure of the lead-free piezoelectric nanofibers was observed by field emission scanning electron microscope (FE-SEM) and the orientation was analyzed by fast Fourier transform (FFT) images...
March 29, 2018: Nanomaterials
Peter Wehrwein
The insurer's vice president of provider alignment solutions says: "We're going to start to signal to providers that if you are going to stay an upside-only arrangement, we're not going to give you free money forever in the form of the care-coordination fees that we've been paying out. They're not an entitlement."
March 2018: Managed Care
Soroush Samadian, Jeff P Bruce, Trevor J Pugh
Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments...
March 28, 2018: PLoS Computational Biology
Sadra Sadeghi, Houman Bahmani Jalali, Rustamzhon Melikov, Baskaran Ganesh Kumar, Mohammad Mohammadi Aria, Cleva W Ow-Yang, Sedat Nizamoğlu
Luminescent solar concentrators (LSCs) show promise due to its potential for low-cost, large-area and high-efficiency energy harvesting. Stokes shift engineering of luminescent quantum dots is a favorable approach to suppress reabsorption losses in LSCs; however, the use of highly-toxic heavy metals in quantum dots constitutes a serious concern for environmental sustainability. Here, we report LSCs based on cadmium-free InP/ZnO core/shell quantum dots with Type-II band alignment that allow for suppression of reabsorption by Stokes shift engineering...
March 28, 2018: ACS Applied Materials & Interfaces
Seon-Min Jang, Su Chul Yang
Low-dimensional piezoelectric nanostructures such as nanoparticles, nanotubes, nanowires, nanoribbons and nanosheets have been developed for potential applications of energy harvesters, tunable sensors, functional transducers and low-power actuators. In this study, lead-free BaTiO3 Nanorod Bundle Arrays (NBA) for high piezoelectric property were successfully synthesized on Fluorine-doped Tin Oxide (FTO) substrate via two-step process, consisting of TiO2 epitaxial growth and BaTiO3 conversion. Through the TiO2 epitaxial growth on FTO substrate, (001) oriented TiO2 nanostructures were formed vertically-aligned NBA with bundle diameter of 80 nm and aspect ratio of 6...
March 27, 2018: Nanotechnology
Ian J Neeland, Paul Poirier, Jean-Pierre Després
The prevalence of obesity has increased globally over the last 2 decades. Although the body mass index has been a convenient and simple index of obesity at the population level, studies have shown that obesity defined by body mass index alone is a remarkably heterogeneous condition with varying cardiovascular and metabolic manifestations across individuals. Adipose tissue is an exquisitely active metabolic organ engaged in cross-talk between various systems; perturbation of adipose tissue results in a pathological response to positive caloric balance in susceptible individuals that directly and indirectly contributes to cardiovascular and metabolic disease...
March 27, 2018: Circulation
Wencai Fan, Ying Yang, Zhiquan Wang, Yunlong Yin, Chaoguang Yu, Qin Shi, Jinbo Guo, Lei Xuan, Jianfeng Hua
As a subfamily of the APETALA 2/ethylene response element binding protein (AP2/EREBP) transcription factor superfamily, the ethylene response factor (ERF) is widely involved in the regulation of growth and response to various abiotic stresses in plants, and has been shown to be the main transcription factor regulating transcription of the genes related to hypoxia and waterlogging stress. In this study, three ThERF genes, with significant differences in expression profile in response to flooding stress, were identified from the transcriptomics data acquired from Taxodium hybrid 'Zhongshanshan 406' ( T...
2018: PeerJ
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