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  • 1
    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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  • 2
    Publication Date: 2015-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Zhenwu -- Huang, Qifei -- Yang, Yufei -- England -- Nature. 2015 Sep 24;525(7570):455. doi: 10.1038/525455d.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉North China Electric Power University, Beijing, China. ; Chinese Research Academy of Environmental Sciences, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26399819" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Explosions/legislation & jurisprudence/prevention & control ; *Government Regulation ; *Hazardous Substances/chemistry ; Humans ; Safety/*legislation & jurisprudence
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2015-02-18
    Description: Enhancers regulate spatiotemporal gene expression and impart cell-specific transcriptional outputs that drive cell identity. Super-enhancers (SEs), also known as stretch-enhancers, are a subset of enhancers especially important for genes associated with cell identity and genetic risk of disease. CD4(+) T cells are critical for host defence and autoimmunity. Here we analysed maps of mouse T-cell SEs as a non-biased means of identifying key regulatory nodes involved in cell specification. We found that cytokines and cytokine receptors were the dominant class of genes exhibiting SE architecture in T cells. Nonetheless, the locus encoding Bach2, a key negative regulator of effector differentiation, emerged as the most prominent T-cell SE, revealing a network in which SE-associated genes critical for T-cell biology are repressed by BACH2. Disease-associated single-nucleotide polymorphisms for immune-mediated disorders, including rheumatoid arthritis, were highly enriched for T-cell SEs versus typical enhancers or SEs in other cell lineages. Intriguingly, treatment of T cells with the Janus kinase (JAK) inhibitor tofacitinib disproportionately altered the expression of rheumatoid arthritis risk genes with SE structures. Together, these results indicate that genes with SE architecture in T cells encompass a variety of cytokines and cytokine receptors but are controlled by a 'guardian' transcription factor, itself endowed with an SE. Thus, enumeration of SEs allows the unbiased determination of key regulatory nodes in T cells, which are preferentially modulated by pharmacological intervention.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409450/" 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/PMC4409450/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vahedi, Golnaz -- Kanno, Yuka -- Furumoto, Yasuko -- Jiang, Kan -- Parker, Stephen C J -- Erdos, Michael R -- Davis, Sean R -- Roychoudhuri, Rahul -- Restifo, Nicholas P -- Gadina, Massimo -- Tang, Zhonghui -- Ruan, Yijun -- Collins, Francis S -- Sartorelli, Vittorio -- O'Shea, John J -- 105663/Z/14/Z/Wellcome Trust/United Kingdom -- R01 CA186714/CA/NCI NIH HHS/ -- ZIA AR041159-07/Intramural NIH HHS/ -- England -- Nature. 2015 Apr 23;520(7548):558-62. doi: 10.1038/nature14154. Epub 2015 Feb 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lymphocyte Cell Biology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA. ; Translational Immunology Section, NIAMS, NIH, Bethesda, Maryland 20892, USA. ; Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA. ; Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA. ; The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, Connecticut 06030, USA. ; Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, NIH, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25686607" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthritis, Rheumatoid/*genetics/immunology/pathology ; Basic-Leucine Zipper Transcription Factors/metabolism ; Cell Differentiation/genetics ; Cell Lineage/genetics ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation/genetics ; Genetic Predisposition to Disease/genetics ; Janus Kinase 3/antagonists & inhibitors ; Mice ; Mice, Inbred C57BL ; Piperidines/pharmacology ; Pyrimidines/pharmacology ; Pyrroles/pharmacology ; RNA, Untranslated/genetics ; T-Lymphocytes, Helper-Inducer/immunology/*metabolism/*pathology ; Transcription, Genetic/genetics ; p300-CBP Transcription Factors/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2018-07-14
    Description: Van der Waals (vdW) assembly of layered materials is a promising paradigm for creating electronic and optoelectronic devices with novel properties. Ferroelectricity in vdW layered materials could enable nonvolatile memory and low-power electronic and optoelectronic switches, but to date, few vdW ferroelectrics have been reported, and few in-plane vdW ferroelectrics are known. We report the discovery of in-plane ferroelectricity in a widely investigated vdW layered material, β'-In 2 Se 3 . The in-plane ferroelectricity is strongly tied to the formation of one-dimensional superstructures aligning along one of the threefold rotational symmetric directions of the hexagonal lattice in the c plane. Surprisingly, the superstructures and ferroelectricity are stable to 200°C in both bulk and thin exfoliated layers of In 2 Se 3 . Because of the in-plane nature of ferroelectricity, the domains exhibit a strong linear dichroism, enabling novel polarization-dependent optical properties.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 5
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2016-01-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Zhenwu -- Huang, Qifei -- Nie, Zhiqiang -- Yang, Yufei -- New York, N.Y. -- Science. 2015 Dec 4;350(6265):1176-7. doi: 10.1126/science.350.6265.1176-c.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Research Academy, North China Electric Power University, Beijing, 102206, China. ; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China. huangqf@craes.org.cn. ; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26785469" target="_blank"〉PubMed〈/a〉
    Keywords: *Animal Migration ; Animals ; *Birds
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2015-12-15
    Description: Release of promoter-proximal paused RNA polymerase II (Pol II) during early elongation is a critical step in transcriptional regulation in metazoan cells. Paused Pol II release is thought to require the kinase activity of cyclin-dependent kinase 9 (CDK9) for the phosphorylation of DRB sensitivity-inducing factor, negative elongation factor, and C-terminal domain (CTD) serine-2 of Pol II. We found that Pol II-associated factor 1 (PAF1) is a critical regulator of paused Pol II release, that positive transcription elongation factor b (P-TEFb) directly regulates the initial recruitment of PAF1 complex (PAF1C) to genes, and that the subsequent recruitment of CDK12 is dependent on PAF1C. These findings reveal cooperativity among P-TEFb, PAF1C, and CDK12 in pausing release and Pol II CTD phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Ming -- Yang, Wenjing -- Ni, Ting -- Tang, Zhanyun -- Nakadai, Tomoyoshi -- Zhu, Jun -- Roeder, Robert G -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2015 Dec 11;350(6266):1383-6. doi: 10.1126/science.aad2338.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA. ; Systems Biology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA. ; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China. ; Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA. roeder@rockefeller.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26659056" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor ; Cyclin-Dependent Kinase 9/metabolism ; Cyclin-Dependent Kinases/metabolism ; *Gene Expression Regulation ; Humans ; Nuclear Proteins/genetics/*metabolism ; Phosphorylation ; Positive Transcriptional Elongation Factor B/metabolism ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; RNA Polymerase II/chemistry/genetics/*metabolism ; *Transcription Elongation, Genetic ; Transcription Factors/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2018-08-16
    Description: Graphene nanosheets (GNSs) were grown on a Si nanoporous pillar array (Si-NPA) via chemical vapour deposition, using a thin layer of pre-deposited Ni nanocrystallites as catalyst. GNSs were determined to be of high quality and good dispersivity, with a typical diameter size of 15 x 8 nm. Light absorption measurements showed that GNSs had an absorption band edge at 3.3 eV. They also showed sharp and regular excitonic emitting peaks in the ultraviolet and visible region (2.06–3.6 eV). Moreover, phonon replicas with long-term stability appeared with the excitonic peaks at room temperature. Temperature-dependent photoluminescence from the GNSs revealed that the excitonic emission derived from free and bound excitonic recombination. A physical model based on band energy theory was constructed to analyse the carrier transport of GNSs. The Ni nanocrystallites on Si-NPA, which acted as a metal-enhanced fluorescence substrate, were supposed to accelerate the excitonic recombination of GNSs and enhanced the measured emission intensity. Results of this study would be valuable in determining the luminescence mechanism of GNSs and could be applied in real-world optoelectronic devices.
    Keywords: nanotechnology, solid-state physics, chemical physics
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 8
    Publication Date: 2018-08-09
    Description: The study reported was intended to improve the leaching rate of boron-bearing tailings, using a method of sodium roasting that uses boron-bearing tailings as the raw material and Na 2 CO 3 as the sodium agent. The effects of the roasting temperature and Na 2 CO 3 amount on the leaching rate of boron-bearing tailings are mainly evaluated. The morphology and composition of the samples after sodium roasting are analysed by scanning electron microscopy and X-ray diffraction. The results show that sodium roasting can significantly improve the leaching rate of boron-bearing tailings. Under the optimal conditions where roasting temperature is 950°C, Na 2 CO 3 amount is five times the theoretical amount and roasting time is 2 h, the leaching rate of boron-bearing tailings is up to 86.78%. Based on the analysis of the characterization results and the mechanism analysis of the sodium roasting process, the main reason for the increase of leaching rate is the reaction between Na 2 O produced by the decomposition of Na 2 CO 3 and the boron in boron-bearing tailings resulting in soluble sodium borate. The results provide a scientific basis for the efficient comprehensive use of boron-bearing tailings.
    Keywords: materials science
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 9
    Publication Date: 2018-03-14
    Description: Motivation Large-scale molecular data have been increasingly used as an important resource for prognostic prediction of diseases and detection of associated genes. However, standard approaches for omics data analysis ignore the group structure among genes encoded in functional relationships or pathway information. Results We propose new Bayesian hierarchical generalized linear models, called group spike-and-slab lasso GLMs, for predicting disease outcomes and detecting associated genes by incorporating large-scale molecular data and group structures. The proposed model employs a mixture double-exponential prior for coefficients that induces self-adaptive shrinkage amount on different coefficients. The group information is incorporated into the model by setting group-specific parameters. We have developed a fast and stable deterministic algorithm to fit the proposed hierarchal GLMs, which can perform variable selection within groups. We assess the performance of the proposed method on several simulated scenarios, by varying the overlap among groups, group size, number of non-null groups, and the correlation within group. Compared with existing methods, the proposed method provides not only more accurate estimates of the parameters but also better prediction. We further demonstrate the application of the proposed procedure on three cancer datasets by utilizing pathway structures of genes. Our results show that the proposed method generates powerful models for predicting disease outcomes and detecting associated genes. Availability and implementation The methods have been implemented in a freely available R package BhGLM ( http://www.ssg.uab.edu/bhglm/ ). Contact nyi@uab.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 10
    Publication Date: 2018-05-02
    Description: Purpose: The survival of patients with hepatocellular carcinoma (HCC) recurrence after curative resection is usually poor. We sought to evaluate the safety and efficacy of adjuvant transarterial chemoembolization (TACE) in HBV-related HCC patients with an intermediate (a single tumor larger than 5 cm without microvascular invasion) or high risk (a single tumor with microvascular invasion, or two or three tumors) of recurrence. Experimental Design: In this randomized phase 3 trial, 280 eligible patients were assigned to adjuvant TACE ( n = 140) or no adjuvant treatment (control; n = 140) groups. The primary endpoint was recurrence-free survival (RFS); secondary endpoints included overall survival (OS) and safety. Multivariable Cox-proportional hazards model was used to determine the independent impact of TACE on patients' outcomes. Results: Patients who received adjuvant TACE had a significantly longer RFS than those in the control group [56.0% vs. 42.1%, P = 0.01; HR, 0.68; 95% confidence interval (CI), 0.49–0.93]. Patients in the adjuvant TACE group had 7.8% higher 3-year OS rate than the control group (85.2% vs. 77.4%; P = 0.04; HR, 0.59; 95% CI, 0.36–0.97). The impact of adjuvant TACE on RFS and OS remained significant after controlling for other known prognostic factors (HR, 0.67; P = 0.01 for RFS; and HR, 0.59; P = 0.04 for OS). There was no grade 3 or 4 toxicity after adjuvant TACE. Conclusions: For patients with HBV-related HCC who had an intermediate or high risk of recurrence after curative hepatectomy, our study showed adjuvant TACE significantly reduced tumor recurrence, improved RFS and OS, and the procedure was well tolerated. Clin Cancer Res; 24(9); 2074–81. ©2018 AACR .
    Print ISSN: 1078-0432
    Electronic ISSN: 1557-3265
    Topics: Medicine
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