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  • 1
    Publication Date: 2018-11-07
    Description: Identifying genetic basis of domestication and improvement in livestock contributes to our understanding of the role of artificial selection in shaping the genome. Here we used whole-genome sequencing and the genotyping by sequencing approach to detect artificial selection signatures and identify the associated SNPs of two economic traits in Duroc pigs. A total of 38 candidate selection regions were detected by combining the fixation index and the Composite Likelihood Ratio methods. Further genome-wide association study revealed seven associated SNPs that were related with intramuscular fat content and feed conversion ratio traits, respectively. Enrichment analysis suggested that the artificial selection regions harbored genes, such as MSTN , SOD2 , MC5R and CD83 , which are responsible for economic traits including lean muscle mass, fertility and immunization. Overall, this study found a series of candidate genes putatively associated with the breeding improvement of Duroc pigs and the polygenic basis of adaptive evolution, which can provide important references and fundamental information for future breeding programs.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 2
    Publication Date: 2018-10-05
    Description: Biodiversity experiments have shown that species loss reduces ecosystem functioning in grassland. To test whether this result can be extrapolated to forests, the main contributors to terrestrial primary productivity, requires large-scale experiments. We manipulated tree species richness by planting more than 150,000 trees in plots with 1 to 16 species. Simulating multiple extinction scenarios, we found that richness strongly increased stand-level productivity. After 8 years, 16-species mixtures had accumulated over twice the amount of carbon found in average monocultures and similar amounts as those of two commercial monocultures. Species richness effects were strongly associated with functional and phylogenetic diversity. A shrub addition treatment reduced tree productivity, but this reduction was smaller at high shrub species richness. Our results encourage multispecies afforestation strategies to restore biodiversity and mitigate climate change.
    Keywords: Ecology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2018-06-23
    Description: Spin Hall angle ( SH ) and spin diffusion length ( sd ) are the key parameters in describing the spin-charge conversion, which is an integral part of spintronics. Despite their importance and much effort devoted to quantifying them, significant inconsistencies in the reported values for the same given material exist. We report a self-consistent method to quantify both SH and sd of nonmagnetic materials by spin pumping with various ferromagnetic (FM) pumping sources. We characterize the spin-charge conversion for Pt and Pd with various FM combinations using (i) effective spin-mixing conductance, (ii) microwave photoresistance, and (iii) inverse spin Hall effect measurements and find that the pumped spin current suffers an interfacial spin loss (ISL), whose magnitude varies for different interfaces. By properly treating the ISL effect, we obtained consistent values of SH and sd for both Pt and Pd regardless of the ferromagnet used.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 4
    Publication Date: 2018-03-27
    Description: Tunable emergent heterostructures in a prototypical correlated metal Tunable emergent heterostructures in a prototypical correlated metal, Published online: 26 March 2018; doi:10.1038/s41567-018-0060-9 By means of a sensitive neutron spectroscopy approach the magnetic excitations in the heavy fermion superconductor CeRhIn5 are probed, revealing a uniaxial anisotropy that can be tuned with an external magnetic field.
    Print ISSN: 1745-2473
    Electronic ISSN: 1745-2481
    Topics: Physics
    Published by Springer Nature
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  • 5
    Abstract: As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to approximately 100 x shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.
    Type of Publication: Journal article published
    PubMed ID: 26647970
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  • 6
    Publication Date: 2018-12-19
    Description: Plasma pyridoxic acid (PDA) and homovanillic acid (HVA) were recently identified as novel endogenous biomarkers of organic anion transporter (OAT) 1/3 function in monkeys. Consequently, this clinical study assessed the dynamic changes and utility of plasma PDA and HVA as an initial evaluation of OAT1/3 inhibition in early-phase drug development. The study was designed as a single-dose randomized, three-phase, crossover study; 14 Indian healthy volunteers received probenecid (PROB) (1000 mg orally) alone, furosemide (FSM) (40 mg orally) alone, or FSM 1 hour after receiving PROB (40 and 1000 mg orally) on days 1, 8, and 15, respectively. PDA and HVA plasma concentrations remained stable over time in the prestudy and FSM groups. Administration of PROB significantly increased the area under the plasma concentration-time curve (AUC) of PDA by 3.1-fold (dosed alone; P 〈 0.05), and 3.2-fold (coadministered with FSM; P 〈 0.01), compared with the prestudy and FSM groups, respectively. The corresponding increase in HVA AUC was 1.8-fold ( P 〉 0.05) and 2.1-fold ( P 〈 0.05), respectively. The increases in PDA AUC are similar to those in FSM AUC, whereas those of HVA are smaller (3.1–3.2 and 1.8–2.1 vs. 3.3, respectively). PDA and HVA renal clearance ( CL R ) values were decreased by PROB to smaller extents compared with FSM (0.35–0.37 and 0.67–0.73 vs. 0.23, respectively). These data demonstrate that plasma PDA is a promising endogenous biomarker for OAT1/3 function and that its plasma exposure responds in a similar fashion to FSM upon OAT1/3 inhibition by PROB. The magnitude and variability of response in PDA AUC and CL R values between subjects is more favorable relative to HVA.
    Print ISSN: 0022-3565
    Electronic ISSN: 1521-0103
    Topics: Medicine
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  • 7
    Publication Date: 2012-08-11
    Description: Inhibitory interneurons are essential components of the neural circuits underlying various brain functions. In the neocortex, a large diversity of GABA (gamma-aminobutyric acid) interneurons has been identified on the basis of their morphology, molecular markers, biophysical properties and innervation pattern. However, how the activity of each subtype of interneurons contributes to sensory processing remains unclear. Here we show that optogenetic activation of parvalbumin-positive (PV+) interneurons in the mouse primary visual cortex (V1) sharpens neuronal feature selectivity and improves perceptual discrimination. Using multichannel recording with silicon probes and channelrhodopsin-2 (ChR2)-mediated optical activation, we found that increased spiking of PV+ interneurons markedly sharpened orientation tuning and enhanced direction selectivity of nearby neurons. These effects were caused by the activation of inhibitory neurons rather than a decreased spiking of excitatory neurons, as archaerhodopsin-3 (Arch)-mediated optical silencing of calcium/calmodulin-dependent protein kinase IIalpha (CAMKIIalpha)-positive excitatory neurons caused no significant change in V1 stimulus selectivity. Moreover, the improved selectivity specifically required PV+ neuron activation, as activating somatostatin or vasointestinal peptide interneurons had no significant effect. Notably, PV+ neuron activation in awake mice caused a significant improvement in their orientation discrimination, mirroring the sharpened V1 orientation tuning. Together, these results provide the first demonstration that visual coding and perception can be improved by increased spiking of a specific subtype of cortical inhibitory interneurons.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422431/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422431/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Seung-Hee -- Kwan, Alex C -- Zhang, Siyu -- Phoumthipphavong, Victoria -- Flannery, John G -- Masmanidis, Sotiris C -- Taniguchi, Hiroki -- Huang, Z Josh -- Zhang, Feng -- Boyden, Edward S -- Deisseroth, Karl -- Dan, Yang -- PN2 EY018241/EY/NEI NIH HHS/ -- R01 EY018861/EY/NEI NIH HHS/ -- R01 NS067199/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Aug 16;488(7411):379-83. doi: 10.1038/nature11312.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22878719" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/deficiency/genetics/metabolism ; Discrimination Learning ; Interneurons/*physiology ; Mice ; Models, Neurological ; Neural Inhibition/physiology ; Parvalbumins/metabolism ; Rhodopsin/metabolism ; Rhodopsins, Microbial/metabolism ; Visual Cortex/*cytology/*physiology ; Visual Perception/*physiology ; Wakefulness/physiology ; gamma-Aminobutyric Acid/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2012-09-21
    Description: The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Guofan -- Fang, Xiaodong -- Guo, Ximing -- Li, Li -- Luo, Ruibang -- Xu, Fei -- Yang, Pengcheng -- Zhang, Linlin -- Wang, Xiaotong -- Qi, Haigang -- Xiong, Zhiqiang -- Que, Huayong -- Xie, Yinlong -- Holland, Peter W H -- Paps, Jordi -- Zhu, Yabing -- Wu, Fucun -- Chen, Yuanxin -- Wang, Jiafeng -- Peng, Chunfang -- Meng, Jie -- Yang, Lan -- Liu, Jun -- Wen, Bo -- Zhang, Na -- Huang, Zhiyong -- Zhu, Qihui -- Feng, Yue -- Mount, Andrew -- Hedgecock, Dennis -- Xu, Zhe -- Liu, Yunjie -- Domazet-Loso, Tomislav -- Du, Yishuai -- Sun, Xiaoqing -- Zhang, Shoudu -- Liu, Binghang -- Cheng, Peizhou -- Jiang, Xuanting -- Li, Juan -- Fan, Dingding -- Wang, Wei -- Fu, Wenjing -- Wang, Tong -- Wang, Bo -- Zhang, Jibiao -- Peng, Zhiyu -- Li, Yingxiang -- Li, Na -- Wang, Jinpeng -- Chen, Maoshan -- He, Yan -- Tan, Fengji -- Song, Xiaorui -- Zheng, Qiumei -- Huang, Ronglian -- Yang, Hailong -- Du, Xuedi -- Chen, Li -- Yang, Mei -- Gaffney, Patrick M -- Wang, Shan -- Luo, Longhai -- She, Zhicai -- Ming, Yao -- Huang, Wen -- Zhang, Shu -- Huang, Baoyu -- Zhang, Yong -- Qu, Tao -- Ni, Peixiang -- Miao, Guoying -- Wang, Junyi -- Wang, Qiang -- Steinberg, Christian E W -- Wang, Haiyan -- Li, Ning -- Qian, Lumin -- Zhang, Guojie -- Li, Yingrui -- Yang, Huanming -- Liu, Xiao -- Wang, Jian -- Yin, Ye -- Wang, Jun -- 268513/European Research Council/International -- England -- Nature. 2012 Oct 4;490(7418):49-54. doi: 10.1038/nature11413. Epub 2012 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22992520" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Animal Shells/chemistry/*growth & development ; Animals ; Apoptosis Regulatory Proteins/genetics ; Crassostrea/*genetics ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Female ; Gene Expression Regulation, Developmental/genetics ; Genes, Homeobox/genetics ; Genome/*genetics ; Genomics ; HSP70 Heat-Shock Proteins/genetics ; Humans ; Larva/genetics/growth & development ; Mass Spectrometry ; Molecular Sequence Annotation ; Molecular Sequence Data ; Polymorphism, Genetic/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; Stress, Physiological/genetics/*physiology ; Transcriptome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2013-08-30
    Description: Artificial spin ice is a class of lithographically created arrays of interacting ferromagnetic nanometre-scale islands. It was introduced to investigate many-body phenomena related to frustration and disorder in a material that could be tailored to precise specifications and imaged directly. Because of the large magnetic energy scales of these nanoscale islands, it has so far been impossible to thermally anneal artificial spin ice into desired thermodynamic ensembles; nearly all studies of artificial spin ice have either treated it as a granular material activated by alternating fields or focused on the as-grown state of the arrays. This limitation has prevented experimental investigation of novel phases that can emerge from the nominal ground states of frustrated lattices. For example, artificial kagome spin ice, in which the islands are arranged on the edges of a hexagonal net, is predicted to support states with monopolar charge order at entropies below that of the previously observed pseudo-ice manifold. Here we demonstrate a method for thermalizing artificial spin ices with square and kagome lattices by heating above the Curie temperature of the constituent material. In this manner, artificial square spin ice achieves unprecedented thermal ordering of the moments. In artificial kagome spin ice, we observe incipient crystallization of the magnetic charges embedded in pseudo-ice, with crystallites of magnetic charges whose size can be controlled by tuning the lattice constant. We find excellent agreement between experimental data and Monte Carlo simulations of emergent charge-charge interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Sheng -- Gilbert, Ian -- Nisoli, Cristiano -- Chern, Gia-Wei -- Erickson, Michael J -- O'Brien, Liam -- Leighton, Chris -- Lammert, Paul E -- Crespi, Vincent H -- Schiffer, Peter -- England -- Nature. 2013 Aug 29;500(7464):553-7. doi: 10.1038/nature12399.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23985872" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
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    Nature Publishing Group (NPG)
    Publication Date: 2014-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Shuwei -- England -- Nature. 2014 Oct 9;514(7521):168. doi: 10.1038/514168b.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Draworld Environment Research Center, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25297422" target="_blank"〉PubMed〈/a〉
    Keywords: *Economics ; Renewable Energy/*economics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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