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Bryan D Merrill, Andy T Ward, Julianne H Grose, Sandra Hope
BACKGROUND: Phage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes...
2016: BMC Genomics
Kai Huang, Bingbing Li, Feng Zhou, Surong Mei, Yikai Zhou, Tao Jing
Ion-imprinted polymers (IIPs) have drawn much attention in the selective determination of heavy metals. In this study, 8-hydroxyquinoline-grafted gelatin with different types of functional groups was first introduced as a biomolecular monomer to enhance the selectivity of imprinted cavities. Based on its swelling and film-forming properties, a simple strategy containing formation of the hydrogel film, swelling/folding followed by cross-linking, was proposed to prepare three-dimensional IIPs with high adsorption capacity (235...
July 5, 2016: Analytical Chemistry
Saket Patel, Meenakshi, Ananda S Hodage, Ajay Verma, Shailendra Agrawal, Abhimanyu Yadav, Sangit Kumar
Monomeric Hg(II) selenolate complexes derived from 2-phenylbenzamide ligands were prepared by oxidative addition of diselenides [{C6H4(CONR2)Se}2, R = Me, Et, iPr] to elemental Hg and reductive cleavage of the Se–N bond of isoselenazolone derivatives [(NO2)C6H3(CONSe)R, (R = allyl, nbutyl)] followed by the treatment with HgCl2. The complexes have been characterized by multinuclear NMR (1H, 13C and 77Se) spectroscopy and mass spectrometry which suggest the monomeric form of these in solution. The molecular structures of diselenides [C6H4(CONR2)Se]2 and mercury selenolates [Hg{(NO2)C6H3(CONH-C3H5) Se}2], [Hg{C6H4(CONiPr2)Se}2] and [Hg{C6H4(CONMe2)Se}2] were established by a single crystal X-ray diffraction study...
March 7, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Howard D Routman, Pierre-Henri Flurin, Thomas W Wright, Joseph D Zuckerman, Matthew A Hamilton, Christopher P Roche
Multiple different reverse total shoulder arthroplasty (rTSA) prosthesis designs are available in the global marketplace for surgeons to perform this growing procedure. Subtle differences in rTSA prosthesis design parameters have been shown to have significant biomechanical impact and clinical consequences. We propose an rTSA prosthesis design classification system to objectively identify and categorize different designs based upon their specific glenoid and humeral prosthetic characteristics for the purpose of standardizing nomenclature that will help the orthopaedic surgeon determine which combination of design configurations best suit a given clinical scenario...
December 2015: Bulletin of the Hospital for Joint Diseases
Kevin Lee, Marie Cherel, Francois Budin, John Gilmore, Kirsten Zaldarriaga Consing, Jerod Rasmussen, Pathik D Wadhwa, Sonja Entringer, Matthew F Glasser, David C Van Essen, Claudia Buss, Martin Styner
PURPOSE: To develop and evaluate a novel processing framework for the relative quantification of myelin content in cerebral white matter (WM) regions from brain MRI data via a computed ratio of T1 to T2 weighted intensity values. DATA: We employed high resolution (1mm(3) isotropic) T1 and T2 weighted MRI from 46 (28 male, 18 female) neonate subjects (typically developing controls) scanned on a Siemens Tim Trio 3T at UC Irvine. METHODS: We developed a novel, yet relatively straightforward image processing framework for WM myelin content estimation based on earlier work by Glasser et al...
2015: Proceedings of SPIE
Ameesha R Shetty, Vidya de Gannes, Chioma C Obi, Susan Lucas, Alla Lapidus, Jan-Fang Cheng, Lynne A Goodwin, Samuel Pitluck, Linda Peters, Natalia Mikhailova, Hazuki Teshima, Cliff Han, Roxanne Tapia, Miriam Land, Loren J Hauser, Nikos Kyrpides, Natalia Ivanova, Ioanna Pagani, Patrick S G Chain, Vincent J Denef, Tanya Woyke, William J Hickey
Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads)...
2015: Standards in Genomic Sciences
Gengqiang Shi, Yi Hu
Seeding cells play an important role in the peripheral nerve damage repair. Seeding cells studied conse- quently in peripheral nerve are Schwann cells, bone marrow mesenchymal stem cells and neural stem cells. Schwann cells, the first seeding cells, are various unique glial cells in the peripheral nervous system, which can form the myelin sheath for insulation and package of the neuron projecting axons in the peripheral nervous system so that the conduction velocity of the nerve signal was accelerated. It can be proved that Schwann cells played an important role in the maintenance of peripheral nerve function and in the regeneration process after peripheral nerve injury...
April 2015: Sheng Wu Yi Xue Gong Cheng Xue za Zhi, Journal of Biomedical Engineering, Shengwu Yixue Gongchengxue Zazhi
Marie Cherel, Francois Budin, Marcel Prastawa, Guido Gerig, Kevin Lee, Claudia Buss, Amanda Lyall, Kirsten Zaldarriaga Consing, Martin Styner
Automatic tissue segmentation of the neonate brain using Magnetic Resonance Images (MRI) is extremely important to study brain development and perform early diagnostics but is challenging due to high variability and inhomogeneity in contrast throughout the image due to incomplete myelination of the white matter tracts. For these reasons, current methods often totally fail or give unsatisfying results. Furthermore, most of the subcortical midbrain structures are misclassified due to a lack of contrast in these regions...
February 21, 2015: Proceedings of SPIE
Monika Ślęzak, Anna Skalniak, Barbara Groszek, Jakub Piątkowsk, Dorota Pach
OBJECTIVE: Carbon monoxide (CO) exposure is still one of the leading causes of unintentional poisonings. Although its neurological sequels have been extensively studied, the knowledge about cytogenetic conse- quences still remains very limited. The aim of this study was to estimate the genotoxic potential of carbon monoxide in the course of acute poisoning. METHODS: The examined group consisted of 73 patients treated because of accidental acute CO poisoning, and 22 healthy control individuals...
2014: Przegla̧d Lekarski
Payam Tabarsi, Amir Yousefzadeh, Katayoun Najafizadeh, Atousa Droudinia, Rouzbeh Bayati, Majid Marjani, Shadi Shafaghi, Banafsheh Farokhzad, Pedram Javanmard, Ali Akbar Velayati
With regard to the significant morbidity and mortality due to tuberculosis in lung transplant recipients, the identification of brain-dead organ donors with latent tuberculosis by use of the QuantiFERON TB Gold (QFT-G) test may be of help to reduce the risk of TB reactivation and mortality in lung recipients. This study was conducted in the National Research Institute of Tuber-culosis and Lung Diseases (NRITLD) in Iran, from January to March 2013. A total of 38 conse-cutive brain-dead donors, not currently infected with active tuberculosis, were recruited...
November 2014: Saudi Journal of Kidney Diseases and Transplantation
Haidar Nadrian, Mohammad Ali Morowatisharifabad, Kaveh Bahmanpour
BACKGROUND: In order to help rheumatoid arthritis (RA) patients in carrying out and at-taining relevant self-care behaviors and adaptation to the physical limitations of this dis-ease and, conse-quently, promoting their level of health status, an education program based on the PRECEDE component of the PRECEDE-PROCEED model targeting patients with RA was developed. This paper describes the planning of a RA Patient Education Program (RAPEP) designed to promote their quality of life. METHODS: The development of the program began with a comprehensive review of the li-terature...
2011: Health Promotion Perspectives
Francisco Calbo Torrecillas
The use of antimicrobials has meant for humanity one of the biggest progresses in our recent History and has enhanced an improvement in living conditions (with different nuances depending on the levels of development). Handling of infectious diseases by curing the patient and limiting the transmissions source has been a very remarkable achievement from Public Health, since the second half of the 20th Century. The antibiotic resistance has been recognized with different levels of attention, but it has been acknowledged from the beginning of the Antibiotics era, with different levels of attention...
2012: Anales de la Real Academia Nacional de Medicina
David Gordon, Phil Green
SUMMARY: The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads...
November 15, 2013: Bioinformatics
Oliver Nolte
Laboratory based diagnosis of infectious diseases usually relies on culture of the disease causing micro-organism, followed by identification and susceptibility testing. Since Borrelia burgdorferi sensu lato, the etiologic agent of Lyme disease or Lyme borreliosis, requires very specific culture conditions (e.g. specific liquid media, long term cul-ture) traditional bacteriology is often not done on a routine basis. Instead, confirmation of the clinical diagnosis needs ei-ther indirect techniques (like serology or measurement of cellular activity in the presence of antigens) or direct but culture independent techniques, like microscopy or nucleic acid amplification techniques (NAT), with polymerase chain reaction (PCR) being the most frequently applied NAT method in routine laboratories...
2012: Open Neurology Journal
Josef Finsterer
BACKGROUND: Though not obvious at a first glance, myopathies may be associated with ischemic stroke. Stroke-like episodes resemble ischemic stroke only to some extent but are a unique feature of certain mitochondrial disorders with a pathogenesis at variance from that of ischemic stroke. Only limited data are available about ischemic stroke in pri-mary myopathies and the management of stroke-like episodes in mitochondrial disorders. This review aims to summarize and discuss current knowledge about stroke in myopathies and to delineate stroke-like episodes from ischemic stroke...
2012: Open Neurology Journal
Jon Gurrea Arroyo, Inigo Gomez Bollain, Conse Pueyo Esquiu
Interdisciplinary, multidisciplinary and comprehensive treatment plans are now part of everyday practice. The interaction between different specialists can provide patients with better, more conservative and more pleasing results. This case report shows the step by step of a multidisciplinary treatment plan and the rationale for each part of a process where conservative dentistry, periodontics, orthodontics, implant dentistry and prosthetics are involved.
2012: European Journal of Esthetic Dentistry: Official Journal of the European Academy of Esthetic Dentistry
Moara Machado, Wagner Cs Magalhães, Allan Sene, Bruno Araújo, Alessandra C Faria-Campos, Stephen J Chanock, Leandro Scott, Guilherme Oliveira, Eduardo Tarazona-Santos, Maira R Rodrigues
BACKGROUND: Targeted re-sequencing is one of the most powerful and widely used strategies for population genetics studies because it allows an unbiased screening for variation that is suitable for a wide variety of organisms. Examples of studies that require re-sequencing data are evolutionary inferences, epidemiological studies designed to capture rare polymorphisms responsible for complex traits and screenings for mutations in families and small populations with high incidences of specific genetic diseases...
2011: Investigative Genetics
A J Taylor, R B Gibson, J P Roberts
Two-photon-absorption coefficients are measured for fused silica, LiF, and the alkali earth halides BaF(2), SrF(2), CaF(2), and MgF(2), using 0.7-psec, 248-nm pulses with intensities in the range (0.5-30) x 10(10) W/cm (2) . The conse-quences of these measurements in the design of high-brightness excimer lasers are discussed.
October 1, 1988: Optics Letters
Kate T Montgomery, Oleg Iartchouck, Li Li, Stephanie Loomis, Vanessa Obourn, Raju Kucherlapati
The ability to search for genetic variants that may be related to human disease is one of the most exciting consequences of the availability of the sequence of the human genome. Large cohorts of individuals exhibiting certain phenotypes can be studied and candidate genes resequenced. However, the challenge of analyzing sequence data from many individuals with accuracy, speed, and economy is great. This unit describes one set of software tools: Phred, Phrap, PolyPhred, and Consed. Coverage includes the advantages and disadvantages of these analysis tools, details for obtaining and using the software, and the results one may expect...
October 2008: Current Protocols in Human Genetics
David Gordon
Consed is a program for viewing and editing assemblies prepared by the Phrap assembly program. This unit presents a general introduction to Consed. It also provides instructions for identifying problem regions and searching in Consed. Additional protocols describe creating tags, picking primers, correcting joins and adding and removing reads. Instructions are also given for the use of Assembly View, predicting the results of a restriction digestion, the use of Consed in conjunction with PolyPhred, and using Autofinish, as well as a procedure for running Phred and Phrap...
August 2003: Current Protocols in Bioinformatics
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