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https://www.readbyqxmd.com/read/28333628/rate-distortion-optimized-graph-based-representation-for-multiview-with-complex-camera-configurations
#1
Xin Su, Thomas Maugey, Christine Guillemot
Graph-Based Representation (GBR) has recently been proposed for describing color and geometry of multiview video content. The graph vertices represent the color information, while the edges represent the geometry information, i.e. the disparity, by connecting corresponding pixels in two camera views. In this paper, we generalize the GBR to multiview images with complex camera configurations. Compared with the existing GBR, the proposed representation can handle not only horizontal displacements of the cameras but also forward/backward translations, rotations, etc...
March 21, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28327996/genome-sequencing-of-the-sweetpotato-whitefly-bemsia-tabaci-med-q
#2
Wen Xie, Chunhai Chen, Zezhong Yang, Litao Guo, Xin Yang, Dan Wang, Ming Chen, Jinqun Huang, Yanan Wen, Yang Zeng, Yating Liu, Jixing Xia, Lixia Tian, Hongying Cui, Qingjun Wu, Shaoli Wang, Baoyun Xu, Xianchun Li, Xinqiu Tan, Murad Ghanim, Baoli Qiu, Huipeng Pan, Dong Chu, Helene Delatte, M N Maruthi, Feng Ge, Xueping Zhou, Xiaowei Wang, Fanghao Wan, Yuzhou Du, Chen Luo, Fengming Yan, Evan L Preisser, Xiaoguo Jiao, Brad S Coates, Jinyang Zhao, Qiang Gao, Jinquan Xia, Ye Yin, Yong Liu, Judith K Brown, Xuguo Joe Zhou, Youjun Zhang
Background: The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. Findings: A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries...
March 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28325684/monitoring-and-visualizing-microrna-dynamics-during-live-cell-differentiation-using-microrna-responsive-non-viral-reporter-vectors
#3
Hideyuki Nakanishi, Kenji Miki, Kaoru R Komatsu, Masayuki Umeda, Megumi Mochizuki, Azusa Inagaki, Yoshinori Yoshida, Hirohide Saito
MicroRNA (miRNA) activity differs with cell type, suggesting it can be used as a cell marker. In this study, we developed novel miRNA-responsive non-viral reporter vectors to continuously monitor and visualize miRNA dynamics during differentiation and to efficiently purify target living cells. Each vector codes miRNA-responsive and reference reporter genes in a single mRNA. These two genes are independent modules but transcribed by a single promoter, which enables us to distinguish miRNA-mediated post-transcriptional repression from transcriptional repression...
March 2, 2017: Biomaterials
https://www.readbyqxmd.com/read/28322997/a-new-hybrid-coding-for-protein-secondary-structure-prediction-based-on-primary-structure-similarity
#4
Zhong Li, Jing Wang, Shunpu Zhang, Qifeng Zhang, Wuming Wu
The coding pattern of protein can greatly affect the prediction accuracy of protein secondary structure. In this paper, a novel hybrid coding method based on the physicochemical properties of amino acids and tendency factors is proposed for the prediction of protein secondary structure. The principal component analysis (PCA) is first applied to the physicochemical properties of amino acids to construct a 3-bit-code, and then the 3 tendency factors of amino acids are calculated to generate another 3-bit-code...
March 16, 2017: Gene
https://www.readbyqxmd.com/read/28321182/sparse-and-specific-coding-during-information-transmission-between-co-cultured-dentate-gyrus-and-ca3-hippocampal-networks
#5
Daniele Poli, Srikanth Thiagarajan, Thomas B DeMarse, Bruce C Wheeler, Gregory J Brewer
To better understand encoding and decoding of stimulus information in two specific hippocampal sub-regions, we isolated and co-cultured rat primary dentate gyrus (DG) and CA3 neurons within a two-chamber device with axonal connectivity via micro-tunnels. We tested the hypothesis that, in these engineered networks, decoding performance of stimulus site information would be more accurate when stimuli and information flow occur in anatomically correct feed-forward DG to CA3 vs. CA3 back to DG. In particular, we characterized the neural code of these sub-regions by measuring sparseness and uniqueness of the responses evoked by specific paired-pulse stimuli...
2017: Frontiers in Neural Circuits
https://www.readbyqxmd.com/read/28320313/retention-of-duplicated-long-wavelength-opsins-in-mosquito-lineages-by-positive-selection-and-differential-expression
#6
Gloria I Giraldo-Calderón, Michael J Zanis, Catherine A Hill
BACKGROUND: Opsins are light sensitive receptors associated with visual processes. Insects typically possess opsins that are stimulated by ultraviolet, short and long wavelength (LW) radiation. Six putative LW-sensitive opsins predicted in the yellow fever mosquito, Aedes aegypti and malaria mosquito, Anopheles gambiae, and eight in the southern house mosquito, Culex quinquefasciatus, suggest gene expansion in the Family Culicidae (mosquitoes) relative to other insects. Here we report the first detailed molecular and evolutionary analyses of LW opsins in three mosquito vectors, with a goal to understanding the molecular basis of opsin-mediated visual processes that could be exploited for mosquito control...
March 21, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28320084/lncrna-meg3-inhibited-osteogenic-differentiation-of-bone-marrow-mesenchymal-stem-cells-from-postmenopausal-osteoporosis-by-targeting-mir-133a-3p
#7
Qiujun Wang, Ying Li, Yuanxia Zhang, Lan Ma, Lin Lin, Jia Meng, Lihong Jiang, Liping Wang, Ping Zhou, Yina Zhang
BACKGROUND AND AIMS: Long non-coding RNA (lncRNA) MEG3 has proven to be an important regulator involved in the pathogenesis and development of various human diseases. However, the functional involvement of MEG3 in postmenopausal osteoporosis (PMOP) and its mechanism is still unclear. METHODS: Bone marrow mesenchymal stem cells (BMSCs) were isolated and cultured from mouse pathologic models and patients with PMOP, respectively. The expression of MEG3 and miR-133a-3p in BMSCs was detected using qRT-PCR...
March 14, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28317264/a-collection-of-enhancer-trap-insertional-mutants-for-functional-genomics-in-tomato
#8
Fernando Pérez-Martín, Fernando J Yuste-Lisbona, Benito Pineda, María Pilar Angarita-Díaz, Begoña García-Sogo, Teresa Antón, Sibilla Sánchez, Estela Giménez, Alejandro Atarés, Antonia Fernández-Lozano, Ana Ortíz-Atienza, Manuel García-Alcázar, Laura Castañeda, Rocío Fonseca, Carmen Capel, Geraldine Goergen, Jorge Sánchez, Jorge L Quispe, Juan Capel, Trinidad Angosto, Vicente Moreno, Rafael Lozano
With the completion of genome sequencing projects, the next challenge is to close the gap between gene annotation and gene functional assignment. Genomic tools to identify gene functions are based on the analysis of phenotypic variations between a wild-type and its mutant; hence, mutant collections are a valuable resource. In this sense, T-DNA collections allow for an easy and straightforward identification of the tagged gene, serving as the basis of both forward and reverse genetic strategies. This study reports on the phenotypic and molecular characterization of an enhancer trap T-DNA collection in tomato (Solanum lycopersicum L...
March 19, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28317235/astrocyte-specific-insulin-like-growth-factor-1-gene-transfer-in-aging-female-rats-improves-stroke-outcomes
#9
Andre K Okoreeh, Shameena Bake, Farida Sohrabji
Middle aged female rats sustain larger stroke infarction and disability than younger female rats. This older group also shows age-related reduction of insulin like growth factor (IGF)-1 in serum and in astrocytes, a cell type necessary for poststroke recovery. To determine the impact of astrocytic IGF-1 for ischemic stroke, these studies tested the hypothesis that gene transfer of IGF-1 to astrocytes will improve stroke outcomes in middle aged female rats. Middle aged (10-12 month old), acyclic female rats were injected with recombinant adeno-associated virus serotype 5 (AAV5) packaged with the coding sequence of the human (h)IGF-1 gene downstream of an astrocyte-specific promoter glial fibrillary acidic protein (GFAP) (AAV5-GFP-hIGF-1) into the striatum and cortex...
March 20, 2017: Glia
https://www.readbyqxmd.com/read/28315290/uca1-regulates-the-growth-and-metastasis-of-pancreatic-cancer-by-sponging-mir-135a
#10
Xiaobo Zhang, Feng Gao, Lei Zhou, Huaitao Wang, Gang Shi, Xiaodong Tan
Pancreatic cancer (PC) is a devastating malignant disease with poor prognosis. This study is aimed to investigate the role of urothelial carcinoma associated 1(UCA1) in the progression of PC. Our results revealed that long non-coding RNAs (lncRNAs)-UCA1 was overexpressed in PC tissues compared with adjacent histologically normal tissues. Down-regulated level of UCA1 was also detected in five human pancreatic cancer cell lines (SW1990,BxPC-3, MiaPaCa-2, PANC-1, CAPAN-1) compared with normal pancreatic duct epithelial HPDE cells...
March 7, 2017: Oncology Research
https://www.readbyqxmd.com/read/28303602/agreement-between-an-in-house-replication-competent-and-a-reference-replication-defective-recombinant-virus-assay-for-measuring-phenotypic-resistance-to-hiv-1-protease-reverse-transcriptase-and-integrase-inhibitors
#11
Francesco Saladini, Alessia Giannini, Adele Boccuto, Ilaria Vicenti, Maurizio Zazzi
BACKGROUND: Although clinical management of drug resistance is routinely based on genotypic methods, phenotypic assays remain necessary for the characterization of novel HIV-1 inhibitors, particularly against common drug-resistant variants. We describe the development and assessment of the performance of a recombinant virus assay for measuring HIV-1 susceptibility to protease (PR), reverse transcriptase (RT), and integrase (IN) inhibitors. METHODS: The system is based on the creation of replication-competent chimeric viruses through homologous recombination between patient or laboratory virus-derived PCR fragments and the corresponding NL4-3 vector where the whole Gag-PR, RT-RNaseH or IN coding regions has been deleted through inverse PCR...
March 17, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28302529/gene-expression-modulation-of-abc-transporter-genes-in-response-to-permethrin-in-adults-of-the-mosquito-malaria-vector-anopheles-stephensi
#12
Valentina Mastrantonio, Marco Ferrari, Sara Epis, Agata Negri, Giulia Scuccimarra, Matteo Montagna, Guido Favia, Daniele Porretta, Sandra Urbanelli, Claudio Bandi
Living organisms have evolved an array of genes coding for detoxifying enzymes and efflux protein pumps, to cope with endogenous and xenobiotic toxic compounds. The study of the genes activated during toxic exposure is relevant to the area of arthropod vector control, since these genes are one of the targets upon which natural selection acts for the evolution of insecticide resistance. ATP-binding cassette (ABC) transporters participate to insecticide detoxification acting as efflux pumps, that reduce the intracellular concentration of toxic compounds, or of their metabolic derivatives...
March 13, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28296173/snail-acetylation-by-histone-acetyltransferase-p300-in-lung-cancer
#13
Rui Chang, Yinjie Zhang, Peng Zhang, Qinghua Zhou
BACKGROUND: Epithelial to mesenchymal transition (EMT) is a complex and dynamic molecular event in lung cancer metastasis that has not yet been thoroughly investigated. EMT transcriptional factors, such as Snail, play a central role in regulation of the EMT process. In this study, we sought to identify an association between p300 and Snail in lung cancer, as well as the engagement of p300 in Snail acetylation. METHODS: We transfected p300 small interfering RNA into lung cancer cells to detect Snail and E-cadherin expression levels by real time-PCR...
March 13, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/28295550/lncrna-malat-1-elevates-hmgb1-to-promote-autophagy-resulting-in-inhibition-of-tumor-cell-apoptosis-in-multiple-myeloma
#14
Da Gao, Zhen Xiao, Hui-Ping Li, Dong-Hai Han, Ya-Peng Zhang
BACKGROUND: Long non-coding RNAs (lncRNAs) can participate in the pathological process of multiple myeloma (MM) via regulation of specific gene expression and function. This research aimed to study the role of MALAT-1 and the underlying mechanism in MM. METHODS: In this study, the expression of MALAT-1 and HMGB1 protein in the bone marrow mononuclear cells from MM patients at different stages and in MM cell lines was determined by qRT-PCR and western blot, respectively...
March 11, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28293255/sparse-codebook-model-of-local-structures-for-retrieval-of-focal-liver-lesions-using-multiphase-medical-images
#15
Jian Wang, Xian-Hua Han, Yingying Xu, Lanfen Lin, Hongjie Hu, Chongwu Jin, Yen-Wei Chen
Characterization and individual trait analysis of the focal liver lesions (FLL) is a challenging task in medical image processing and clinical site. The character analysis of a unconfirmed FLL case would be expected to benefit greatly from the accumulated FLL cases with experts' analysis, which can be achieved by content-based medical image retrieval (CBMIR). CBMIR mainly includes discriminated feature extraction and similarity calculation procedures. Bag-of-Visual-Words (BoVW) (codebook-based model) has been proven to be effective for different classification and retrieval tasks...
2017: International Journal of Biomedical Imaging
https://www.readbyqxmd.com/read/28292251/prediction-of-lysine-malonylation-sites-based-on-pseudo-amino-acid-compositions
#16
Qilin Xiang, Kaiyan Feng, Bo Liao, Yuewu Liu, Guohua Huang
Protein malonylation is a newly discovered post-translational modification. Due to the limitations of experimental techniques, it is a great challenge to fast and accurately identify malonylation sites. We proposed a computational method to address the problem by extracting protein segments so that the lysine is at the center of each segment, which were further coded by the pseudo amino acid compositions. Then a support vector machine classifier trained by a training dataset was built to distinguish malonylation sites from non-malonylation ones...
March 14, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28291518/a-novel-expression-system-for-lytic-polysaccharide-monooxygenases
#17
Gaston Courtade, Simone Balzer Le, Gerd Inger Sætrom, Trygve Brautaset, Finn L Aachmann
Lytic polysaccharide monooxygenases (LPMOs) are key enzymatic players of lignocellulosic biomass degradation processes. As such, they have been introduced in cellulolytic cocktails for more efficient and less expensive lignocellulose saccharification. The recombinant production of LPMOs in bacteria for scientific investigations using vectors typically based on the T7 and lacUV5 promoters has been hampered by low yields. Reasons for this have been catabolite repression when producing the proteins in defined media with glucose as the sole carbon source, as well as the lack of an inducible expression system that allows controlled production of LPMOs that are correctly processed during translocation to the periplasmic space...
February 14, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28289423/automated-method-to-determine-two-critical-growth-stages-of-wheat-heading-and-flowering
#18
Pouria Sadeghi-Tehran, Kasra Sabermanesh, Nicolas Virlet, Malcolm J Hawkesford
Recording growth stage information is an important aspect of precision agriculture, crop breeding and phenotyping. In practice, crop growth stage is still primarily monitored by-eye, which is not only laborious and time-consuming, but also subjective and error-prone. The application of computer vision on digital images offers a high-throughput and non-invasive alternative to manual observations and its use in agriculture and high-throughput phenotyping is increasing. This paper presents an automated method to detect wheat heading and flowering stages, which uses the application of computer vision on digital images...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28288679/muscovy-duck-reovirus-%C3%AF-ns-protein-triggers-autophagy-enhancing-virus-replication
#19
Yijian Wu, Longping Cui, Erpeng Zhu, Wuduo Zhou, Quanxi Wang, Xiaoping Wu, Baocheng Wu, Yifan Huang, Hung-Jen Liu
BACKGROUND: Muscovy duck reovirus (MDRV) causes high morbidity and mortality in Muscovy ducklings at 10 days old and can persist in an infected flock until the ducklings of 6 weeks old. It shares common physicochemical properties with avian reovirus (ARV) and differs in coding assignment and pathogenicity. The ARV p17 protein has been shown to trigger autophagy via activation multiple signaling pathways, which benefits virus replication. Since MDRV lacks the p17 protein, whether and how MDRV induces autophagy remains unknown...
March 14, 2017: Virology Journal
https://www.readbyqxmd.com/read/28288625/functional-differentiation-of-3-ketosteroid-%C3%AE-1-dehydrogenase-isozymes-in-rhodococcus-ruber-strain-chol-4
#20
Govinda Guevara, Laura Fernández de Las Heras, Julián Perera, Juana María Navarro Llorens
BACKGROUND: The Rhodococcus ruber strain Chol-4 genome contains at least three putative 3-ketosteroid Δ(1)-dehydrogenase ORFs (kstD1, kstD2 and kstD3) that code for flavoenzymes involved in the steroid ring degradation. The aim of this work is the functional characterization of these enzymes prior to the developing of different biotechnological applications. RESULTS: The three R. ruber KstD enzymes have different substrate profiles. KstD1 shows preference for 9OHAD and testosterone, followed by progesterone, deoxy corticosterone AD and, finally, 4-BNC, corticosterone and 19OHAD...
March 14, 2017: Microbial Cell Factories
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