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https://www.readbyqxmd.com/read/28091699/musculoskeletal-mri-findings-of-juvenile-localized-scleroderma
#1
Eric P Eutsler, Daniel B Horton, Monica Epelman, Terri Finkel, Lauren W Averill
BACKGROUND: Juvenile localized scleroderma comprises a group of autoimmune conditions often characterized clinically by an area of skin hardening. In addition to superficial changes in the skin and subcutaneous tissues, juvenile localized scleroderma may involve the deep soft tissues, bones and joints, possibly resulting in functional impairment and pain in addition to cosmetic changes. OBJECTIVE: There is literature documenting the spectrum of findings for deep involvement of localized scleroderma (fascia, muscles, tendons, bones and joints) in adults, but there is limited literature for the condition in children...
January 14, 2017: Pediatric Radiology
https://www.readbyqxmd.com/read/28090632/identification-of-highly-selective-mmp-14-inhibitory-fabs-by-deep-sequencing
#2
Tyler Lopez, Dong Hyun Nam, Evan Kaihara, Zahid Mustafa, Xin Ge
Matrix metalloproteinase (MMP)-14 is an important target for cancer treatment due to its critical roles in tumor invasion and metastasis. Previous failures of all compound-based broad-spectrum MMP inhibitors in clinical trials suggest that selectivity is the key for a successful therapy. With inherent high specificity, monoclonal antibodies (mAbs) therefore arise as attractive inhibitors able to target the particular MMP of interest. As a routine screening method, enzyme-linked immunosorbent assays (ELISA) have been applied to panned phage libraries for the isolation of mAbs inhibiting MMP-14...
January 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28089895/effects-of-fulvic-acid-on-growth-performance-and-intestinal-health-of-juvenile-loach-paramisgurnus-dabryanus-sauvage
#3
Yang Gao, Jie He, Zhuliu He, Zhiwei Li, Bo Zhao, Yi Mu, Jeong-Yeol Lee, Zhangjie Chu
A 60-day feeding trial was conducted to determine the effect of dietary fulvic acid supplements on intestinal digestive activity (enzymatic analysis), antioxidant activity, immune enzyme activity and microflora composition of juvenile loach (initial weight of 6.2 ± 0.1 g) reared in experimental aquaria. Five test diets containing 0, 0.5, 1.0, 1.5, and 2% fulvic acid were randomly assigned to three aquaria, respectively. Elevated growth performance including final weight, weight gain (WG), specific growth rate (SGR) and feed conversion ratio (FCR) was observed in loaches that were fed fulvic acid...
January 9, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28089793/eggshell-palaeogenomics-palaeognath-evolutionary-history-revealed-through-ancient-nuclear-and-mitochondrial-dna-from-madagascan-elephant-bird-aepyornis-sp-eggshell
#4
Alicia Grealy, Matthew Phillips, Gifford Miller, M Thomas P Gilbert, Jean-Marie Rouillard, David Lambert, Michael Bunce, James Haile
Palaeognaths, the sister group of all other living birds (neognaths), were once considered to be vicariant relics from the breakup of the Gondwanan supercontinent. However, recent molecular studies instead argue for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing their evolutionary relationships and dating their divergences, which often relies on phylogenetic information from extinct relatives and nuclear genomes. Mitogenomes from the extinct elephant birds of Madagascar have helped inform the palaeognath phylogeny; however, nuclear information has remained unavailable...
January 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28088902/brain-tumor-segmentation-using-deep-belief-networks-and-pathological-knowledge
#5
Tianming Zhan, Yi Chen, Xunning Hong, Zhenyu Lu, Yunjie Chen
In this paper, we propose an automatic brain tumor segmentation method based on Deep Belief Networks (DBNs) and pathological knowledge. The proposed method is targeted against gliomas (both low and high grade) obtained in multi-sequence magnetic resonance images (MRIs). Firstly, a novel deep architecture is proposed to combine the multi-sequences intensities feature extraction with classification to get the classification probabilities of each voxel. Then, graph cut based optimization is executed on the classification probabilities to strengthen the spatial relationships of voxels...
January 12, 2017: CNS & Neurological Disorders Drug Targets
https://www.readbyqxmd.com/read/28087666/dysregulation-of-b-cell-repertoire-formation-in-myasthenia-gravis-patients-revealed-through-deep-sequencing
#6
Jason A Vander Heiden, Panos Stathopoulos, Julian Q Zhou, Luan Chen, Tamara J Gilbert, Christopher R Bolen, Richard J Barohn, Mazen M Dimachkie, Emma Ciafaloni, Teresa J Broering, Francois Vigneault, Richard J Nowak, Steven H Kleinstein, Kevin C O'Connor
Myasthenia gravis (MG) is a prototypical B cell-mediated autoimmune disease affecting 20-50 people per 100,000. The majority of patients fall into two clinically distinguishable types based on whether they produce autoantibodies targeting the acetylcholine receptor (AChR-MG) or muscle specific kinase (MuSK-MG). The autoantibodies are pathogenic, but whether their generation is associated with broader defects in the B cell repertoire is unknown. To address this question, we performed deep sequencing of the BCR repertoire of AChR-MG, MuSK-MG, and healthy subjects to generate ∼518,000 unique VH and VL sequences from sorted naive and memory B cell populations...
January 13, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28081260/comparative-genome-sequencing-reveals-within-host-genetic-changes-in-neisseria-meningitidis-during-invasive-disease
#7
Johanna Klughammer, Marcus Dittrich, Jochen Blom, Vera Mitesser, Ulrich Vogel, Matthias Frosch, Alexander Goesmann, Tobias Müller, Christoph Schoen
Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation...
2017: PloS One
https://www.readbyqxmd.com/read/28081125/the-neural-representation-of-prospective-choice-during-spatial-planning-and-decisions
#8
Raphael Kaplan, John King, Raphael Koster, William D Penny, Neil Burgess, Karl J Friston
We are remarkably adept at inferring the consequences of our actions, yet the neuronal mechanisms that allow us to plan a sequence of novel choices remain unclear. We used functional magnetic resonance imaging (fMRI) to investigate how the human brain plans the shortest path to a goal in novel mazes with one (shallow maze) or two (deep maze) choice points. We observed two distinct anterior prefrontal responses to demanding choices at the second choice point: one in rostrodorsal medial prefrontal cortex (rd-mPFC)/superior frontal gyrus (SFG) that was also sensitive to (deactivated by) demanding initial choices and another in lateral frontopolar cortex (lFPC), which was only engaged by demanding choices at the second choice point...
January 2017: PLoS Biology
https://www.readbyqxmd.com/read/28080920/phaeohyphomycosis-associated-with-ossification-of-the-skull-and-cervical-vertebrae-in-a-swell-shark-cephaloscyllium-ventriosum
#9
Claire D Erlacher-Reid, Hendrik H Nollens, Todd L Schmitt, Judy St Leger, Sarena Sunico
A female, captive bred, juvenile swell shark ( Cephaloscyllium ventriosum ) was observed swimming in tight circles and rolling. Radiographs and computed tomography of this individual revealed extensive cartilage mineralization of the skull and cranial cervical vertebrae compared with diagnostic images of clinically healthy conspecifics. Gross necropsy and histopathologic examination revealed ossification and fibrosis of the cartilaginous matrix of the skull and cervical vertebrae with deep invasion by a pigmented hyphal fungus...
December 2016: Journal of Zoo and Wildlife Medicine: Official Publication of the American Association of Zoo Veterinarians
https://www.readbyqxmd.com/read/28079877/genome-wide-transposon-screening-and-quantitative-insertion-site-sequencing-for-cancer-gene-discovery-in-mice
#10
Mathias J Friedrich, Lena Rad, Iraad F Bronner, Alexander Strong, Wei Wang, Julia Weber, Matthew Mayho, Hannes Ponstingl, Thomas Engleitner, Carolyn Grove, Anja Pfaus, Dieter Saur, Juan Cadiñanos, Michael A Quail, George S Vassiliou, Pentao Liu, Allan Bradley, Roland Rad
Transposon-mediated forward genetics screening in mice has emerged as a powerful tool for cancer gene discovery. It pinpoints cancer drivers that are difficult to find with other approaches, thus complementing the sequencing-based census of human cancer genes. We describe here a large series of mouse lines for insertional mutagenesis that are compatible with two transposon systems, PiggyBac and Sleeping Beauty, and give guidance on the use of different engineered transposon variants for constitutive or tissue-specific cancer gene discovery screening...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28079269/ledipasvir-plus-sofosbuvir-as-salvage-therapy-for-hcv-genotype-1-failures-to-prior-ns5a-inhibitors-regimens
#11
Norio Akuta, Hitomi Sezaki, Fumitaka Suzuki, Shunichiro Fujiyama, Yusuke Kawamura, Tetsuya Hosaka, Masahiro Kobayashi, Mariko Kobayashi, Satoshi Saitoh, Yoshiyuki Suzuki, Yasuji Arase, Kenji Ikeda, Hiromitsu Kumada
There is little information on retreatment efficacy and predictors of the combination of ledipasvir and sofosbuvir (ledipasvir/sofosbuvir) for patients who fail to respond to NS5A inhibitors. NS5A resistance variants are known to persist for long periods after such treatment. Here, we evaluated 54 patients with chronic HCV genotype 1b infection, free of decompensated cirrhosis and hepatocellular carcinoma, for sustained virological response after 12 weeks (SVR12) of once-daily treatment with 90 mg ledipasvir and 400 mg sofosbuvir...
January 12, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28078489/identification-and-profiling-of-conserved-and-novel-micrornas-involved-in-oil-and-oleic-acid-production-during-embryogenesis-in-carya-cathayensis-sarg
#12
Zhengjia Wang, Ruiming Huang, Zhichao Sun, Tong Zhang, Jianqin Huang
MicroRNAs (miRNAs) are important regulators of plant development and fruit formation. Mature embryos of hickory (Carya cathayensis Sarg.) nuts contain more than 70% oil (comprising 90% unsaturated fatty acids), along with a substantial amount of oleic acid. To understand the roles of miRNAs involved in oil and oleic acid production during hickory embryogenesis, three small RNA libraries from different stages of embryogenesis were constructed. Deep sequencing of these three libraries identified 95 conserved miRNAs with 19 miRNA*s, 7 novel miRNAs (as well as their corresponding miRNA*s), and 26 potentially novel miRNAs...
January 11, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28078050/complete-genome-sequence-of-lutibacter-profundi-lp1-t-isolated-from-an-arctic-deep-sea-hydrothermal-vent-system
#13
Juliane Wissuwa, Sven Le Moine Bauer, Ida Helene Steen, Runar Stokke
Lutibacter profundi LP1(T) within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki's Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1(T) is the first genome to be published within the genus Lutibacter. L. profundi LP1(T) consists of a single 2,966,978 bp circular chromosome with a GC content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains genes for all central carbohydrate metabolic pathways...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28077653/characterizing-hiv-1-splicing-using-next-generation-sequencing
#14
Ann Emery, Shuntai Zhou, Elizabeth Pollom, Ronald Swanstrom
: Full-length HIV-1 RNA serves as the genome or as an mRNA, or this RNA undergoes splicing using four donors and ten acceptors to create over 50 physiologically relevant transcripts in two size classes (1.8 kb and 4 kb). We developed an assay using Primer ID-tagged deep sequencing to quantify HIV-1 splicing. Using the NL4-3 lab strain we found that A5 (env/nef) is the most commonly used acceptor (about 50%) with A3 (tat) the least used (about 3%). Two small exons are made when a splice to acceptor A1 or A2 is followed by activation of donor D2 or D3, and the high-level use of D2 and D3 dramatically reduces the amount of vif and vpr transcripts...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077647/sensitive-next-generation-sequencing-method-reveals-deep-genetic-diversity-of-hiv-1-in-the-democratic-republic-of-the-congo
#15
M A Rodgers, E Wilkerson, A Vallari, C McArthur, L Sthreshley, C A Brennan, G Cloherty, T de Oliveira
: As the epidemiological epicentre of the human immunodeficiency virus (HIV) pandemic, the Democratic Republic of the Congo (DRC) is a reservoir of circulating HIV strains exhibiting high levels of diversity and recombination. In this study, we characterized HIV specimens collected in two rural areas of the DRC between 2001 and 2003 to identify rare strains of HIV. The env gp41 region was sequenced and characterized for 172 HIV-positive specimens. The env sequences were predominantly subtype A (43...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28076812/spermine-condenses-dna-but-not-rna-duplexes
#16
Andrea M Katz, Igor S Tolokh, Suzette A Pabit, Nathan Baker, Alexey V Onufriev, Lois Pollack
Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predictions of molecular-dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence containing a mixture of 14 GC pairs and 11 AU pairs resists condensation relative to DNA of an equivalent sequence or to 25 bp poly(rA):poly(rU) RNA...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28074898/the-curved-lead-pathway-method-to-enable-a-single-lead-to-reach-any-two-intracranial-targets
#17
Chen-Yu Ding, Liang-Hong Yu, Yuan-Xiang Lin, Fan Chen, Zhang-Ya Lin, De-Zhi Kang
Deep brain stimulation is an effective way to treat movement disorders, and a powerful research tool for exploring brain functions. This report proposes a "curved lead pathway" method for lead implantation, such that a single lead can reach in sequence to any two intracranial targets. A new type of stereotaxic system for implanting a curved lead to the brain of human/primates was designed, the auxiliary device needed for this method to be used in rat/mouse was fabricated and verified in rat, and the Excel algorithm used for automatically calculating the necessary parameters was implemented...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28074246/draft-genome-of-scalindua-rubra-obtained-from-the-interface-above-the-discovery-deep-brine-in-the-red-sea-sheds-light-on-potential-salt-adaptation-strategies-in-anammox-bacteria
#18
Daan R Speth, Ilias Lagkouvardos, Yong Wang, Pei-Yuan Qian, Bas E Dutilh, Mike S M Jetten
Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua...
January 10, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28074121/complete-genome-sequence-and-whole-genome-phylogeny-of-kosmotoga-pacifica-type-strain-slhlj1-t-from-an-east-pacific-hydrothermal-sediment
#19
Lijing Jiang, Stéphane L'Haridon, Mohamed Jebbar, Hongxiu Xu, Karine Alain, Zongze Shao
Kosmotoga pacifica strain SLHLJ1(T) is a thermophilic chemoorganoheterotrophic bacterium isolated from a deep-sea hydrothermal sediment. It belongs to the physiologically homogeneous Thermotogaceae family. Here, we describe the phenotypic features of K. pacifica together with its genome sequence and annotation. The chromosome has 2,169,170 bp, organized in one contig. A total of 1897 candidate protein-encoding genes and 177 RNA genes were identified. The 16S rRNA gene sequence of this strain is distantly related to sequences of some relatives classified in the same genus (K...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28073746/mirdis-a-web-tool-for-endogenous-and-exogenous-microrna-discovery-based-on-deep-sequencing-data-analysis
#20
Hanyuan Zhang, Bruno Vieira Resende E Silva, Juan Cui
Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes...
January 10, 2017: Briefings in Bioinformatics
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