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https://www.readbyqxmd.com/read/29774597/assessment-of-the-generalization-of-learned-image-reconstruction-and-the-potential-for-transfer-learning
#1
Florian Knoll, Kerstin Hammernik, Erich Kobler, Thomas Pock, Michael P Recht, Daniel K Sodickson
PURPOSE: Although deep learning has shown great promise for MR image reconstruction, an open question regarding the success of this approach is the robustness in the case of deviations between training and test data. The goal of this study is to assess the influence of image contrast, SNR, and image content on the generalization of learned image reconstruction, and to demonstrate the potential for transfer learning. METHODS: Reconstructions were trained from undersampled data using data sets with varying SNR, sampling pattern, image contrast, and synthetic data generated from a public image database...
May 17, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/29774020/high-diversity-of-myocyanophage-in-various-aquatic-environments-revealed-by-high-throughput-sequencing-of-major-capsid-protein-gene-with-a-new-set-of-primers
#2
Weiguo Hou, Shang Wang, Brandon R Briggs, Gaoyuan Li, Wei Xie, Hailiang Dong
Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29773674/deep-sequencing-of-complex-proteoglycans-a-novel-strategy-for-high-coverage-and-site-specific-identification-of-glycosaminoglycan-linked-peptides
#3
Joshua A Klein, Le Meng, Joseph Zaia
Proteoglycans are distributed in all animal tissues and play critical, multifaceted, physiological roles.  Expressed in a spatially- and temporally-regulated manner, these molecules regulate interactions among growth factors and cell surface receptors and play key roles in basement membranes and other extracellular matrices.  Due to the high degree of glycosylation by glycosaminoglycan (GAG), N-glycan and mucin-type O-glycan classes, the peptide sequence coverage of complex proteoglycans is revealed poorly by standard mass spectrometry-based proteomics methods...
May 17, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29773618/draft-genome-sequence-of-mariprofundus-micogutta-strain-et2
#4
Hiroko Makita, Shinro Nishi, Yoshihiro Takaki, Emiko Tanaka, Takuro Nunoura, Satoshi Mitsunobu, Ken Takai
Mariprofundus micogutta strain ET2 was isolated in 2014 from a deep-sea hydrothermal field on the Bayonnaise Knoll of the Izu-Ogasawara arc. Here, we report its draft genome, which comprises 2,497,805 bp and contains 2,417 predicted coding sequences.
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29773613/draft-genome-sequences-of-two-chemosynthetic-arcobacter-strains-isolated-from-hydraulically-fractured-wells-in-marcellus-and-utica-shales
#5
Jenny Panescu, Rebecca A Daly, Kelly C Wrighton, Paula J Mouser
Genome sequences were obtained for two isolates of the genus Arcobacter from saline fluids produced from hydraulically fractured shale gas wells in the Marcellus and Utica formations. These genomes provide insight into microbial sulfur cycles occurring in a high-salt deep terrestrial shale environment.
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29772794/amid-accurate-magnetic-indoor-localization-using-deep-learning
#6
Namkyoung Lee, Sumin Ahn, Dongsoo Han
Geomagnetic-based indoor positioning has drawn a great attention from academia and industry due to its advantage of being operable without infrastructure support and its reliable signal characteristics. However, it must overcome the problems of ambiguity that originate with the nature of geomagnetic data. Most studies manage this problem by incorporating particle filters along with inertial sensors. However, they cannot yield reliable positioning results because the inertial sensors in smartphones cannot precisely predict the movement of users...
May 17, 2018: Sensors
https://www.readbyqxmd.com/read/29772263/comparative-analysis-of-microrna-expression-in-dog-lungs-infected-with-the-h3n2-and-h5n1-canine-influenza-viruses
#7
Yun Zheng, Xinliang Fu, Lifang Wang, Wenyan Zhang, Pei Zhou, Xin Zhang, Weijie Zeng, Jidang Chen, Zongxi Cao, Kun Jia, Shoujun Li
MicroRNAs, a class of noncoding RNAs 18 to 23 nucleotides (nt) in length, play critical roles in a wide variety of biological processes. The objective of this study was to examine differences in microRNA expression profiles derived from the lungs of beagle dogs infected with the avian-origin H3N2 canine influenza virus (CIV) or the highly pathogenic avian influenza (HPAI) H5N1 virus (canine-origin isolation strain). After dogs were infected with H3N2 or H5N1, microRNA expression in the lungs was assessed using a deep-sequencing approach...
May 14, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29771676/extreme-trust-region-policy-optimization-for-active-object-recognition
#8
Huaping Liu, Yupei Wu, Fuchun Sun
In this brief, we develop a deep reinforcement learning method to actively recognize objects by choosing a sequence of actions for an active camera that helps to discriminate between the objects. The method is realized using trust region policy optimization, in which the policy is realized by an extreme learning machine and, therefore, leads to efficient optimization algorithm. The experimental results on the publicly available data set show the advantages of the developed extreme trust region optimization method...
June 2018: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/29771675/action-driven-visual-object-tracking-with-deep-reinforcement-learning
#9
Sangdoo Yun, Jongwon Choi, Youngjoon Yoo, Kimin Yun, Jin Young Choi
In this paper, we propose an efficient visual tracker, which directly captures a bounding box containing the target object in a video by means of sequential actions learned using deep neural networks. The proposed deep neural network to control tracking actions is pretrained using various training video sequences and fine-tuned during actual tracking for online adaptation to a change of target and background. The pretraining is done by utilizing deep reinforcement learning (RL) as well as supervised learning...
June 2018: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/29769615/indoor-wet-cells-as-a-habitat-for-melanized-fungi-opportunistic-pathogens-on-humans-and-other-vertebrates
#10
Xiaofang Wang, Wenying Cai, A H G Gerrits van den Ende, Junmin Zhang, Ting Xie, Liyan Xi, Xiqing Li, Jiufeng Sun, Sybren de Hoog
Indoor wet cells serve as an environmental reservoir for a wide diversity of melanized fungi. A total of 313 melanized fungi were isolated at five locations in Guangzhou, China. Internal transcribed spacer (rDNA ITS) sequencing showed a preponderance of 27 species belonging to 10 genera; 64.22% (n = 201) were known as human opportunists in the orders Chaetothyriales and Venturiales, potentially causing cutaneous and sometimes deep infections. Knufia epidermidis was the most frequently encountered species in bathrooms (n = 26), while in kitchens Ochroconis musae (n = 14), Phialophora oxyspora (n = 12) and P...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769555/cattle-with-a-precise-zygote-mediated-deletion-safely-eliminate-the-major-milk-allergen-beta-lactoglobulin
#11
Jingwei Wei, Stefan Wagner, Paul Maclean, Brigid Brophy, Sally Cole, Grant Smolenski, Dan F Carlson, Scott C Fahrenkrug, David N Wells, Götz Laible
We applied precise  zygote-mediated genome editing to eliminate beta-lactoglobulin (BLG), a major allergen in cows' milk. To efficiently generate LGB knockout cows, biopsied embryos were screened to transfer only appropriately modified embryos. Transfer of 13 pre-selected embryos into surrogate cows resulted in the birth of three calves, one dying shortly after birth. Deep sequencing results confirmed conversion of the genotype from wild type to the edited nine bp deletion by more than 97% in the two male calves...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769051/knee-dgemric-at-7-t-comparison-against-1-5-t-and-evaluation-of-t-1-mapping-methods
#12
Pernilla Peterson, Carl Johan Tiderius, Emma Olsson, Björn Lundin, Lars E Olsson, Jonas Svensson
BACKGROUND: dGEMRIC (delayed Gadolinium Enhanced Magnetic Resonance Image of Cartilage) is a well-established technique for cartilage quality assessment in osteoarthritis at clinical field strengths. The method is robust, but requires injection of contrast agent and a cumbersome examination procedure. New non-contrast-agent-based techniques for cartilage quality assessment are currently being developed at 7 T. However, dGEMRIC remains an important reference technique during this development...
May 16, 2018: BMC Musculoskeletal Disorders
https://www.readbyqxmd.com/read/29768482/sequencing-of-complete-mitochondrial-genomes-confirms-synonymization-of-hyalomma-asiaticum-asiaticum-and-kozlovi-and-advances-phylogenetic-hypotheses-for-the-ixodidae
#13
Zhi-Qiang Liu, Yan-Feng Liu, Nuer Kuermanali, Deng-Feng Wang, Shi-Jun Chen, Hui-Ling Guo, Li Zhao, Jun-Wei Wang, Tao Han, Yuan-Zhi Wang, Jie Wang, Chen-Feng Shen, Zhuang-Zhi Zhang, Chuang-Fu Chen
Phylogeny of hard ticks (Ixodidae) remains unresolved. Mitochondrial genomes (mitogenomes) are increasingly used to resolve phylogenetic controversies, but remain unavailable for the entire large Hyalomma genus. Hyalomma asiaticum is a parasitic tick distributed throughout the Asia. As a result of great morphological variability, two subspecies have been recognised historically; until a morphological data-based synonymization was proposed. However, this hypothesis was never tested using molecular data. Therefore, objectives of this study were to: 1...
2018: PloS One
https://www.readbyqxmd.com/read/29768361/a-novel-kiaa0196-mutation-in-a-chinese-patient-with-spastic-paraplegia-8-a-case-report
#14
Limin Ma, Yingying Shi, Zhongcan Chen, Shujian Li, Weiwei Qin, Jiewen Zhang
RATIONALE: We report a case of Spastic paraplegia 8 (SPG8) with a novel mutation of KIAA0196 gene. PATIENTS CONCERNS: A 12-year-old boy presented as ankle sprained, lower limb stiffness, abnormal gait since he was 5 years old. DIAGNOSES: The next generation sequence showed a novel c.1128delG (p.L376fs) mutation in KIAA0196 gene, the electromyography showed the pyramidal tract conduction dysfunction and deep sensory conduction abnormalities of lower limbs without motor neuron damage...
May 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29767361/making-and-sequencing-heavily-multiplexed-high-throughput-16s-ribosomal-rna-gene-amplicon-libraries-using-a-flexible-two-stage-pcr-protocol
#15
Ankur Naqib, Silvana Poggi, Weihua Wang, Marieta Hyde, Kevin Kunstman, Stefan J Green
Deep sequencing of polymerase chain reaction (PCR)-amplified small subunit (16S or 18S) ribosomal RNA (rRNA) genes fragments is commonly employed to characterize the composition and structure of microbial communities. Preparing genomic DNA for sequencing of such gene fragments on Illumina sequencers can be performed in a straightforward, two-stage PCR method, described herein. The protocol described allows for up to 384 samples to be sequenced simultaneously, and provides great flexibility in choice of primers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29765588/dna-barcoding-a-taxonomically-complex-hemiparasitic-genus-reveals-deep-divergence-between-ploidy-levels-but-lack-of-species-level-resolution
#16
Xumei Wang, Galina Gussarova, Markus Ruhsam, Natasha de Vere, Chris Metherell, Peter M Hollingsworth, Alex D Twyford
DNA barcoding is emerging as a useful tool not only for species identification but also for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode data sets can provide insights into the mechanisms underlying the generation of species diversity. Here, we study evolutionary processes in taxonomically complex British Euphrasia (Orobanchaceae), a group with multiple ploidy levels, frequent self-fertilization, young species divergence and widespread hybridization...
June 2018: AoB Plants
https://www.readbyqxmd.com/read/29765142/targeted-deep-sequencing-of-gastric-marginal-zone-lymphoma-identified-alterations-of-traf3-and-tnfaip3-that-were-mutually-exclusive-for-malt1-rearrangement
#17
Jiyeon Hyeon, Boram Lee, So-Hyun Shin, Hae Yong Yoo, Seok Jin Kim, Won Seog Kim, Woong-Yang Park, Young-Hyeh Ko
Gastric extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue is a distinct entity in that Helicobacter pylori infection plays the most important causative role in the development of the disease. To investigate the genomic alteration in gastric marginal zone lymphoma that was resistant to the H. pylori eradication therapy, we analyzed 19 cases of the gastric marginal zone lymphoma using fluorescence in situ hybridization for MALT1, BCL10 rearrangement, and targeted sequencing using an Illumina platform...
May 15, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29764943/microscopic-and-molecular-evidence-of-the-first-elasmobranch-adomavirus-the-cause-of-skin-disease-in-a-giant-guitarfish-rhynchobatus-djiddensis
#18
Jennifer A Dill, Alvin C Camus, John H Leary, Terry Fei Fan Ng
Only eight families of double-stranded DNA (dsDNA) viruses are known to infect vertebrate animals. During an investigation of papillomatous skin disease in an elasmobranch species, the giant guitarfish ( Rhynchobatus djiddensis ), a novel virus, distinct from all known viral families in regard to particle size, morphology, genome organization, and helicase phylogeny was discovered. Large inclusion bodies containing 75-nm icosahedral viral particles were present within epithelial cell nuclei in the proliferative skin lesions...
May 15, 2018: MBio
https://www.readbyqxmd.com/read/29764472/high-species-diversity-of-trichostrongyle-parasite-communities-within-and-between-western-canadian-commercial-and-conservation-bison-herds-revealed-by-nemabiome-metabarcoding
#19
Russell W Avramenko, Ana Bras, Elizabeth M Redman, Murray R Woodbury, Brent Wagner, Todd Shury, Stefano Liccioli, M Claire Windeyer, John S Gilleard
BACKGROUND: Many trichostrongylid nematode species are reported to infect bison, some of which are major causes of disase and production loss in North American bison herds. However, there is little information on the species distribution and relative abundance of these parasites in either commercial or conservation herds. This is largely because trichostrongylid nematode species cannot be distinguished by visual microscopic examination of eggs present in feces. Consequently, we have applied ITS2 rDNA nemabiome metabarcoding to describe the trichostrongyle parasite species diversity in 58 bison production groups derived from 38 commercial North American plains bison (Bison bison bison) herds from across western Canada, and two bison conservation herds located in Elk Island National Park (EINP) [plains bison and wood bison (Bison bison athabascae)] and one in Grasslands National Park (GNP) (plains bison)...
May 15, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29764394/comprehensive-analysis-of-coding-lncrna-gene-co-expression-network-uncovers-conserved-functional-lncrnas-in-zebrafish
#20
Wen Chen, Xuan Zhang, Jing Li, Shulan Huang, Shuanglin Xiang, Xiang Hu, Changning Liu
BACKGROUND: Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing. RESULTS: We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures...
May 9, 2018: BMC Genomics
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