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Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming,and long non-coding RNAs

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Science Bulletin 2015年第20期60卷 1722-1733页

作者： Andrew paul Hutchins Duanqing Pei Key Laboratory of Regenerative Biology South China Institute for Stem Cell Biology and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine South China Institute for Stem Cell Biology and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangzhou Branch of the Supercomputing Center of Chinese Academy of Sciences South China Institute for Stem Cell Biology and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences

Transposable elements(TEs) are mobile genomic sequences of DNA capable of autonomous and nonautonomous duplication. TEs have been highly successful,and nearly half of the human genome now consists of various families of TEs. Originally thought to be non-functional,these elements have been co-opted by animal genomes to perform a variety of physiological functions ranging from TE-derived proteins acting directly in normal biological functions, to innovations in transcription factor logic and influence on epigenetic control of gene expression. During embryonic development, when the genome is epigenetically reprogrammed and DNA-demethylated, TEs are released from repression and show embryonic stage-specific expression, and in human and mouse embryos, intact TEderived endogenous viral particles can even be detected. Asimilar process occurs during the reprogramming of somatic cells to pluripotent cells: When the somatic DNA is demethylated, TEs are released from repression. In embryonic stem cells(ESCs), where DNA is hypomethylated, an elaborate system of epigenetic control is employed to suppress TEs, a system that often overlaps with normal epigenetic control of ESC gene expression. Finally, many long non-coding RNAs(lnc RNAs) involved in normal ESC function and those assisting or impairing reprogramming contain multiple TEs in their RNA. These TEs may act as regulatory units to recruit RNA-binding proteins and epigenetic modifiers. This review covers how TEs are interlinked with the epigenetic machinery and lnc RNAs, and how these links influence each other to modulate aspects of ESCs,embryogenesis, and somatic cell reprogramming.

关键词： Transposable elements Endogenousretroviruses Embryonic stem cells lncRNA Reprogramming Pluripotency

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Effect of stocking density on performances of juvenile turbot (Scophthalmus maximus) in recirculating aquaculture systems

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Chinese Journal of Oceanology and Limnology 2013年第3期31卷 514-522页

作者：李贤刘鹰 Jean-paul BLANCHETON Key Laboratory of Marine Biotechnology Institute of OceanologyChinese Academy of Sciences Graduate University of Chinese Academy of Sciences IFREMER UMR Ecosym USTL

Limited information has been available about the influence of loading density on the performances of Scophthalmus maximus, especially in recirculating aquaculture systems （RAS）. In this study, turbot （13.84±2.74 g; average weigh±SD） were reared at four different initial densities （low 0.66, medium 1.26, sub-high 2.56, high 4.00 kg/m^2） for 10 weeks in RAS at 23±1℃ Final densities were 4.67, 7.25, 14.16, and 17.47 kg/m^2, respectively, which translate to 82, 108, 214, and 282 percent coverage of the tank bottom. Density had both negative and independent impacts on growth. The final mean weight, specific growth rate （SGR）, and voluntary feed intake significantly decreased and the coefficient of variation （CV） of final body weight increased with increase in stocking density. The medium and sub-high density groups did not differ significantly in SGR, mean weight, CV, food conversion rate （FCR）, feed intake, blood parameters, and digestive enzymes. The protease activities of the digestive tract at pH 7, 8.5, 9, and 10 were significantly higher for the highest density group, but tended to be lower （not significantly） at pH 4 and 8.5 for the lowest density group. The intensity of protease activity was inversely related to feed intake at the different densities. Catalase activity was higher （but not significantly） at the highest density, perhaps because high density started to induce an oxidative effect in turbot. In conclusion, turbot can be cultured in RAS at a density of less than 17.47 kg/m^2. With good water quality and no feed limitation, initial density between 1.26 and 2.56 kg/m^2 （final： 7.25 and 14.16 kg/m^2） would not negatively affect the turbot cultured in RAS. For culture at higher density, multi-level feeding devices are suggested to ease feeding competition.

关键词： turbot stocking density growth protease activity

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Personal Information Self-Management:A Survey of Technologies Supporting Administrative Services

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Journal of Computer Science & Technology 2021年第3期36卷 664-692页

作者： paul Marillonnet Maryline Laurent Mikaël Ates Entr'ouvert Paris 75014France SAMOVAR Télécom SudParisInstitut Polytechnique de ParisEvry 91000France

This paper presents a survey of technologies for personal data self-management interfacing with administrative and territorial public service *** classifies a selection of scientific technologies into four categories of solutions:Personal Data Store(PDS),Identity Manager(IdM),Anonymous Certificate System and Access Control Delegation *** category,along with its technological approach,is analyzed thanks to 18 identified functional criteria that encompass architectural and communication aspects,as well as user data lifecycle *** originality of the survey is ***,as far as we know,there is no such thorough survey covering such a panel of a dozen of existing ***,it is the first survey addressing Personally Identifiable Information(PII)management for both administrative and private service ***,this paper achieves a functional comparison of solutions of very different technical *** outcome of this paper is the clear identification of functional gaps of each *** a result,this paper establishes the research directions to follow in order to fill these functional gaps.

关键词： personal information management privacy enforcement user-centric solution technological survey

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Neutrophil chemoattractant receptors in health and disease: double-edged swords

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Cellular & Molecular Immunology 2020年第5期17卷 433-450页

作者： Mieke Metzemaekers Mieke Gouwy paul Proost Laboratory of Molecular Immunology Rega InstituteKU LeuvenHerestraat 49 bus 1042B-3000 LeuvenBelgium

Neutrophils are frontline cells of the innate immune *** effector leukocytes are equipped with intriguing antimicrobial machinery and consequently display high cytotoxic *** neutrophil recruitment is essential to combat microbes and to restore homeostasis,for inflammation modulation and resolution,wound healing and tissue *** fulfilling the appropriate effector functions,however,dampening neutrophil activation and infiltration is crucial to prevent damage to the *** humans,chemoattractant molecules can be categorized into four biochemical families,i.e.,chemotactic lipids,formyl peptides,complement anaphylatoxins and *** are critically involved in the tight regulation of neutrophil bone marrow storage and egress and in spatial and temporal neutrophil trafficking between *** function by activating dedicated heptahelical G protein-coupled receptors(GPCRs).In addition,emerging evidence suggests an important role for atypical chemoattractant receptors(ACKRs)that do not couple to G proteins in fine-tuning neutrophil migratory and functional *** expression levels of chemoattractant receptors are dependent on the level of neutrophil maturation and state of activation,with a pivotal modulatory role for the(inflammatory)***,we provide an overview of chemoattractant receptors expressed by neutrophils in health and *** on the(patho)physiological context,specific chemoattractant receptors may be up-or downregulated on distinct neutrophil subsets with beneficial or detrimental consequences,thus opening new windows for the identification of disease biomarkers and potential drug targets.

关键词： Neutrophils chemoattractant G protein-coupled receptors chemokine leukocyte migration

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Influences of Biochar and Biochar-Mineral Complex on Mycorrhizal Colonisation and Nutrition of Wheat and Sorghum

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Pedosphere 2015年第5期25卷 686-695页

作者： paul BLACKWELL Stephen JOSEPH paul MUNROE Hossain M.ANAWAR paul STORER Robert J.GILKES Zakaria M.SOLAIMAN Department of Agriculture and Food Western Australia Geraldton Regional Office School of Materials Science and Engineering University of New South WalesSydney Discipline of Chemistry University of Newcastle University of Wollongong School of Earth and Environment and UWA Institute of Agriculture The University of Western Australia Australian Mineral Fertilisers Pty Ltd. Soil Biology and Molecular Ecology Group School of Earth and Environment and UWA Institute of AgricultureThe University of Western Australia

The high price of synthetic fertilisers and the price barrier for biochar as a soil amendment have encouraged the exploration of using biochar in fertiliser replacement formulations. Biochars coupled with fertilisers can be applied at lower application rates to achieve benefits in plant growth and nutrition, as well as soil biological fertility. It is necessary to evaluate the use of biochar as a fertiliser substitute. Therefore, this study investigated the comparative influences of biochars, including Acacia saligna （AS）, Simcoa jarrah （S J） and Wundowie jarrah （W J）, mineral fertiliser with microbes （MF ＋ M）, biochar-mineral complex （BMC） and their combination on mycorrhizal colonisation, growth and nutrition of wheat in a glasshouse experiment and sorghum in field conditions. BMC ＋ MF ＋ M treatment produced higher mycorrhizal colonisation than MF ＋ M alone, indicating that BMC had a significant role in increasing mycorrhizal colonisation. SJ （treated with acetic acid） and MF ＋ M treatments, as well as AS ＋ MF ＋ M application, showed similar effects on mycorrhizal colonisation, but lower colonisation than the BMC ＋ MF ＋ M treatment. Ovcrall~ the BMC ＋ MF ＋ M treatment supported the maximum shoot, root and total plant dry weight followed by AS ＋ MF ＋ M and WJ ＋ MF ＋ M. The MF ＋ M treatment had the maximum shoot N and K concentrations, while BMC ＋ MF ＋ M application had the maximum shoot P concentration. AS ＋ MF -4- M and WJ ＋ MF ＋ M treatments supported the maximum N uptake by wheat shoots, while BMC ＋ MF ＋ M supported the maximum P uptake. The results showed that biochars and BMCs could increase mycorrhizal colonisation, plant growth and nutrient uptake of wheat, particularly N, P, K, S and Zn. The field experiment confirmed that BMC application at a rate of 300 kg ha-1 could increase the yield of irrigated sorghum on a loam soil and provide better applied P use efficiency compared to a water-soluble fertiliser alone. These results indicated that biochar-based fer

关键词： carbon sequestration nutrient uptake P use efficiency soil biological fertility wheat production

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An emerging market for groundwater remediation in China： Policies, statistics, and future outlook

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Frontiers of Environmental Science & Engineering 2018年第1期12卷 1-3页

作者： Deyi Hou Guanghe Li paul Nathanai School of Environment Tsinghua University Beijing 100084 China School of Geography University of Nottingham Nottingham NG7 2RD UK

There is a rapidly emerging and potentially huge market for the remediation of contaminated ground- water in China. The Chinese government published a Water Action Plan in April 2015, a Soil Action Plan in May 2016, and a draft Soil Pollution Prevention and Control Law in June 2017. All of these new policies and regulations put pressures on local governments and contaminated site owners, obliging them to conduct site investigation and to cleanup contaminated groundwater. The Chinese population in northern regions heavily depend on groundwater, with nearly 70% of water supply coming from aquifer sources in the Beijing-Tianjin-Hebei region. However, poor groundwater quality due to natural geochemical background and anthropogeic pollution is a serious concern, with poor or very poor quality water observed in nearly 80% of groundwater monitoring wells in 17 northern provinces. Shallow groundwater in many areas has been contaminated by toxic pollutants such as heavy metals and chlorinated organic compounds. There is an urgent need to better understand the situation and to conduct groundwater remediation at contaminated sites. The Chinese government is investing heavily in the research and development for groundwater remediation, which is expected to greatly add to the quality and quantity of groundwater remediation projects in the near future.

关键词： Groundwater pollution Contaminated land,Groundwater remediation Emerging market

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Rock mechanical investigation of strata loading characteristics to assess caving and requirement of support resistance in a mechanized powered support longwall face

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International Journal of Mining Science and Technology 2016年第6期26卷 1081-1087页

作者： Aveek Mangal P.S.paul Department of Mining Engineering Indian Institute of Technology(Indian School of Mines)Dhanbad826004JharkhandIndia

Longwall mining is one of the most acclaimed and widely used in underground method for coal extraction. The interaction of powered supports with the roof is the key issue in strata mechanics of longwall mining. Controlled caving of rock mass is a prerequisite pro thriving exploitation of coal deposits by longwall retreat with caving technique and support resistance has evolved as the most promising and effective scientific tool to predict various aspects related to strata mechanics of such workings. Load density,height of caving block, distance of fractured zone ahead of the face, overhang of goaf and mechanical strength of the debris above and below the support base have been found to influence the magnitude of load on supports. Designing powered support has been attempted at the different countries in different methods. This paper reviews the mechanism of roof caving and the conventional approaches of caving behaviour and support resistance requirement in the context of major strata control experiences gained worldwide. The theoretical explanation of the mechanism of roof caving is still continuing with consistently improved understanding through growing field experiences in the larger domain of geo-mining conditions and state-of-art strata mechanics analysis and monitoring techniques.

关键词： Longwall mining Geo-mechanics Caving behaviour Support resistance

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A review of modern treeline migration, the factors controlling it and the implications for carbon storage

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Journal of Mountain Science 2021年第2期18卷 291-306页

作者： HANSSON Amanda DARGUSCH paul SHULMEISTER Jamie School of Earth and Environmental Science University of QueenslandBrisbane QLD 4072Australia School of Earth and Environment University of CanterburyChristchurch 8140New Zealand

Numerous studies have reported that treelines are moving to higher elevations and higher *** treelines are temperature limited and warmer climate expands the area in which trees are capable of ***,climate change has been assumed to be the main driver behind this treeline *** latest review of treeline studies was published in 2009 by Harsch et *** then,a plethora of papers have been published studying local treeline *** we bring together this knowledge through a review of 142 treeline related publications,including 477 study *** summarize the information known about factors limiting tree-growth at and near *** migration is not only dependent on favorable growing conditions but also requires seedling establishment and survival above the current *** conditions appear to have become favorable at many locations,particularly so in recent *** review revealed that at 66%of these treeline sites forest cover had increased in elevational or latitudinal *** physical form of treelines influences how likely they are to migrate and can be used as an indicator when predicting future treeline *** analysis also revealed that while a greater percentage of elevational treelines are moving,the latitudinal treelines are capable of moving at greater horizontal *** can potentially have substantial impacts on ecosystem carbon *** conclude the review,we present the three main hypotheses as to whether ecosystem carbon budgets will be reduced,increased or remain the same due to treeline *** the answer still remains under debate,we believe that all three hypotheses are likely to apply depending on the encroached ***,evidence is emerging on how treeline migration may turn tundra landscapes from net sinks to net sources of carbon dioxide in the future.

关键词： Treeline advance Treeline migration Forest dynamics Alpine forests Ecosystem carbon storage Carbon sequestration Global meta-analysis

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Rhyolites in continental mafic Large Igneous Provinces: Petrology,geochemistry and petrogenesis

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Geoscience Frontiers 2021年第1期12卷 53-80页

作者： Mahesh Halder Debajyoti paul Sarajit Sensarma Department of Earth Sciences Indian Institute of Technology KanpurKanpur 208016India Centre of Advanced Study in Geology University of LucknowLucknow 226007India

We present a detailed review of the petrological and geochemical aspects of rhyolite and associated silicic volcanic rocks(up to 20 vol%of all rocks)reported to date from twelve well known Phanerozoic continental mafic Large Igneous Provinces(LIPs).These typically spread over900℃.Rhyolites formed by significant crustal contribution are characterized by strong negative Nb-Ta anomalies,absence of clinopyroxene phenocrysts,and are likely to have a magma temperature<900℃.Geochemical signatures suggest rhyolite melt generation in the plagioclase stability field with a minor fraction originating from lower crustal depths.A large part of the compositional variability in rhyolites,particularly the SrNd-Pb-O isotope ratios,suggests a significant role of continental crust(upper crustal melting or AFC)in the evolution of these silicic rocks in the continental mafic LIPs.

关键词： Large Igneous Province Silicic rock Rhyolite Geochemistry Petrogenesis AFC

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Utilization of Pyrrolic Compounds as Indicators of Secondary Migration for Woodford Oils in the Anadarko Basin,Oklahoma,USA

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Journal of Earth Science 2024年第5期35卷 1499-1512页

作者： Mu Liu R.paul Philp Key Laboratory of Cenozoic Geology and Environment Institute of Geology and GeophysicsChinese Academy of SciencesBeijing 100029China School of Geosciences University of OklahomaNorman 73109United States

Migration pathways and distances of the oils in reservoir are thought to affect the distribution of pyrrolic compounds such as carbazole,its alkyl derivatives(alkylated carbazoles)and benzocarbazoles,although other factors,including maturity and depositional environments may also affect the distribution of these organic nitrogen *** this study,14 oil samples produced from conventional reservoirs in pauls Valley,south Oklahoma were investigated using organic geochemical *** sterane and hopane fingerprints suggest that most of the oils were sourced from the Devonian Woodford *** parameters consistently indicate that the maturity level of the studied samples are all of similar maturity(Rc=~0.7%),suggesting the distribution of the organic nitrogen organic compounds is possibly reflecting variations in relative migration *** distribution of alkylcarbazoles revealed a preferential enrichment during migration,with the nitrogen-shielded alkylcarbazole tending to be enriched relative to the nitrogen-semi-shielded alkylcarbozoles particularly in oils produced close to the Arbuckle uplift to the ***,another family of pyrrolic compounds,benzocarbazoles,whose distributions also indicated that the pauls Valley Woodford oils came from deeper part of the Anadarko Basin as the benzo-[a]/([a]+[c])-carbazole ratios decrease *** more specific migration systems,although the pyrrolic compound indicators are potentially disturbed by the structural complexes,the general migration directions suggest that the studied oils in pauls Valley Hunton uplift were sourced from the deep basin area,and migrate upwards in porous sediments due to the *** study investigates the feasibility of using pyrrolic compounds to estimate relative migration distances and will aid in the interpretation of migration history by using the distribution of carbazole,alkylated carbazoles,benzocarbazoles isomers in the Anadarko and Ardmore Basin

关键词： carbazole migration oil Oklahoma biomarker organic geochemistry

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