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  • 1
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    Acid Rock Drainage and Rock Weathering in Antarctica: Important Sources for Iron Cycling in the Southern Ocean (2013)
    American Chemical Society (ACS)
    Details
    Publication Date: 2013-06-07
    Description: Environmental Science & Technology DOI: 10.1021/es305141b
    Print ISSN: 0013-936X
    Electronic ISSN: 1520-5851
    Topics: Chemistry and Pharmacology , Energy, Environment Protection, Nuclear Power Engineering
    Published by American Chemical Society (ACS)
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  • 2
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    Sustainability, Vol. 11, Pages 2471: The Role of Cultural Landscapes in the Delivery of Provisioning Ecosystem Services in Protected Areas (2019)
    MDPI
    Details
    Publication Date: 2019
    Description: The aim of this paper is to assess and highlight the significance of cultural landscapes in protected areas, considering both biodiversity and the delivery of provisioning ecosystem services. In order to do that, we analyzed 26 protected areas in Andalusia (Spain), all of them Natural or National Parks, regarding some of their ecosystem services (agriculture, livestock grazing, microclimate regulation, environmental education and tourism) and diversity of the four terrestrial vertebrate classes: amphibians, reptiles, mammals, and birds. A cluster analysis was also run in order to group the 26 protected areas according to their dominant landscape. The results show that protected areas dominated by dehesa (a heterogeneous system containing different states of ecological maturity), or having strong presence of olive groves, present a larger area of delivery of provisioning ecosystem services, on average. These cultural landscapes play an essential role not only for biodiversity conservation but also as providers of provisioning ecosystem services.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI
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  • 3
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    Unravelling spatiotemporal tree-ring signals in Mediterranean oaks: a variance-covariance modelling approach of carbon and oxygen isotope ratios (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-04
    Description: Identifying how physiological responses are structured across environmental gradients is critical to understanding in what manner ecological factors determine tree performance. Here, we investigated the spatiotemporal patterns of signal strength of carbon isotope discrimination ( 13 C) and oxygen isotope composition ( 18 O) for three deciduous oaks ( Quercus faginea (Lam.), Q. humilis Mill. and Q. petraea (Matt.) Liebl.) and one evergreen oak ( Q. ilex L.) co-occurring in Mediterranean forests along an aridity gradient. We hypothesized that contrasting strategies in response to drought would lead to differential climate sensitivities between functional groups. Such differential sensitivities could result in a contrasting imprint on stable isotopes, depending on whether the spatial or temporal organization of tree-ring signals was analysed. To test these hypotheses, we proposed a mixed modelling framework to group isotopic records into potentially homogeneous subsets according to taxonomic or geographical criteria. To this end, carbon and oxygen isotopes were modelled through different variance–covariance structures for the variability among years (at the temporal level) or sites (at the spatial level). Signal-strength parameters were estimated from the outcome of selected models. We found striking differences between deciduous and evergreen oaks in the organization of their temporal and spatial signals. Therefore, the relationships with climate were examined independently for each functional group. While Q. ilex exhibited a large spatial dependence of isotopic signals on the temperature regime, deciduous oaks showed a greater dependence on precipitation, confirming their higher susceptibility to drought. Such contrasting responses to drought among oak types were also observed at the temporal level (interannual variability), with stronger associations with growing-season water availability in deciduous oaks. Thus, our results indicate that Mediterranean deciduous and evergreen oaks constitute two clearly differentiated functional groups in terms of their carbon and water economies, despite co-existing in a wide range of environments. In contrast, deciduous oaks form a rather homogeneous group in terms of climate sensitivity.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 4
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    CDK targets Sae2 to control DNA-end resection and homologous recombination (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-08-22
    Description: DNA double-strand breaks (DSBs) are repaired by two principal mechanisms: non-homologous end-joining (NHEJ) and homologous recombination (HR). HR is the most accurate DSB repair mechanism but is generally restricted to the S and G2 phases of the cell cycle, when DNA has been replicated and a sister chromatid is available as a repair template. By contrast, NHEJ operates throughout the cell cycle but assumes most importance in G1 (refs 4, 6). The choice between repair pathways is governed by cyclin-dependent protein kinases (CDKs), with a major site of control being at the level of DSB resection, an event that is necessary for HR but not NHEJ, and which takes place most effectively in S and G2 (refs 2, 5). Here we establish that cell-cycle control of DSB resection in Saccharomyces cerevisiae results from the phosphorylation by CDK of an evolutionarily conserved motif in the Sae2 protein. We show that mutating Ser 267 of Sae2 to a non-phosphorylatable residue causes phenotypes comparable to those of a sae2Delta null mutant, including hypersensitivity to camptothecin, defective sporulation, reduced hairpin-induced recombination, severely impaired DNA-end processing and faulty assembly and disassembly of HR factors. Furthermore, a Sae2 mutation that mimics constitutive Ser 267 phosphorylation complements these phenotypes and overcomes the necessity of CDK activity for DSB resection. The Sae2 mutations also cause cell-cycle-stage specific hypersensitivity to DNA damage and affect the balance between HR and NHEJ. These findings therefore provide a mechanistic basis for cell-cycle control of DSB repair and highlight the importance of regulating DSB resection.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2635538/" 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/PMC2635538/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huertas, Pablo -- Cortes-Ledesma, Felipe -- Sartori, Alessandro A -- Aguilera, Andres -- Jackson, Stephen P -- A5290/Cancer Research UK/United Kingdom -- LSHG-CT-2005-512113/Cancer Research UK/United Kingdom -- England -- Nature. 2008 Oct 2;455(7213):689-92. doi: 10.1038/nature07215. Epub 2008 Aug 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18716619" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; CDC28 Protein Kinase, S cerevisiae/*metabolism ; Cell Cycle ; Cell Line ; Cell Survival ; Conserved Sequence ; *DNA Breaks, Double-Stranded ; *DNA Repair ; Endodeoxyribonucleases/metabolism ; Endonucleases ; Exodeoxyribonucleases/metabolism ; Humans ; Mutation ; Phosphorylation ; Phosphoserine/metabolism ; Rad52 DNA Repair and Recombination Protein/metabolism ; *Recombination, Genetic ; Saccharomyces cerevisiae/enzymology/*genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2 (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-06-05
    Description: Genome instability is central to ageing, cancer and other diseases. It is not only proteins involved in DNA replication or the DNA damage response (DDR) that are important for maintaining genome integrity: from yeast to higher eukaryotes, mutations in genes involved in pre-mRNA splicing and in the biogenesis and export of messenger ribonucleoprotein (mRNP) also induce DNA damage and genome instability. This instability is frequently mediated by R-loops formed by DNA-RNA hybrids and a displaced single-stranded DNA. Here we show that the human TREX-2 complex, which is involved in mRNP biogenesis and export, prevents genome instability as determined by the accumulation of gamma-H2AX (Ser-139 phosphorylated histone H2AX) and 53BP1 foci and single-cell electrophoresis in cells depleted of the TREX-2 subunits PCID2, GANP and DSS1. We show that the BRCA2 repair factor, which binds to DSS1, also associates with PCID2 in the cell. The use of an enhanced green fluorescent protein-tagged hybrid-binding domain of RNase H1 and the S9.6 antibody did not detect R-loops in TREX-2-depleted cells, but did detect the accumulation of R-loops in BRCA2-depleted cells. The results indicate that R-loops are frequently formed in cells and that BRCA2 is required for their processing. This link between BRCA2 and RNA-mediated genome instability indicates that R-loops may be a chief source of replication stress and cancer-associated instability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhatia, Vaibhav -- Barroso, Sonia I -- Garcia-Rubio, Maria L -- Tumini, Emanuela -- Herrera-Moyano, Emilia -- Aguilera, Andres -- England -- Nature. 2014 Jul 17;511(7509):362-5. doi: 10.1038/nature13374. Epub 2014 Jun 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centro Andaluz de Biologia Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Avenida Americo Vespucio s/n, 41092 Seville, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24896180" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyltransferases/metabolism ; BRCA2 Protein/deficiency/genetics/*metabolism ; DNA Damage ; DNA Replication ; DNA, Single-Stranded/chemistry/*metabolism ; Exodeoxyribonucleases/chemistry/deficiency/*metabolism ; *Genomic Instability ; Histones/chemistry/metabolism ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Nuclear Proteins/*metabolism ; Nucleic Acid Conformation ; Phosphoproteins/chemistry/deficiency/*metabolism ; Proteasome Endopeptidase Complex/metabolism ; Protein Binding ; RNA/chemistry/*metabolism ; *RNA Transport ; Ribonuclease H/chemistry ; Ribonucleoproteins/biosynthesis/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Sustainability, Vol. 10, Pages 4312: A Comparison of Machine-Learning Methods to Select Socioeconomic Indicators in Cultural Landscapes (2018)
    MDPI
    Details
    Publication Date: 2018
    Description: Cultural landscapes are regarded to be complex socioecological systems that originated as a result of the interaction between humanity and nature across time. Cultural landscapes present complex-system properties, including nonlinear dynamics among their components. There is a close relationship between socioeconomy and landscape in cultural landscapes, so that changes in the socioeconomic dynamic have an effect on the structure and functionality of the landscape. Several numerical analyses have been carried out to study this relationship, with linear regression models being widely used. However, cultural landscapes comprise a considerable amount of elements and processes, whose interactions might not be properly captured by a linear model. In recent years, machine-learning techniques have increasingly been applied to the field of ecology to solve regression tasks. These techniques provide sound methods and algorithms for dealing with complex systems under uncertainty. The term ‘machine learning’ includes a wide variety of methods to learn models from data. In this paper, we study the relationship between socioeconomy and cultural landscape (in Andalusia, Spain) at two different spatial scales aiming at comparing different regression models from a predictive-accuracy point of view, including model trees and neural or Bayesian networks.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI
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  • 7
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    Sensors, Vol. 18, Pages 3545: Design and Modeling of a MEMS Dual-Backplate Capacitive Microphone with Spring-Supported Diaphragm for Mobile Device Applications (2018)
    MDPI
    In: Sensors
    Details
    Publication Date: 2018
    Description: New mobile devices need microphones with a small size, low noise level, reduced cost and high stability respect to variations of temperature and humidity. These characteristics can be obtained using Microelectromechanical Systems (MEMS) microphones, which are substituting for conventional electret condenser microphones (ECM). We present the design and modeling of a capacitive dual-backplate MEMS microphone with a novel circular diaphragm (600 µm diameter and 2.25 µm thickness) supported by fifteen polysilicon springs (2.25 µm thickness). These springs increase the effective area (86.85% of the total area), the linearity and sensitivity of the diaphragm. This design is based on the SUMMiT V fabrication process from Sandia National Laboratories. A lumped element model is obtained to predict the electrical and mechanical behavior of the microphone as a function of the diaphragm dimensions. In addition, models of the finite element method (FEM) are implemented to estimate the resonance frequencies, deflections, and stresses of the diaphragm. The results of the analytical models agree well with those of the FEM models. Applying a bias voltage of 3 V, the designed microphone has a bandwidth from 31 Hz to 27 kHz with 3 dB sensitivity variation, a sensitivity of 34.4 mV/Pa, a pull-in voltage of 6.17 V and a signal to noise ratio of 62 dBA. The results of the proposed microphone performance are suitable for mobile device applications.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Published by MDPI
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  • 8
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    Sensors, Vol. 18, Pages 3644: Melamine Faced Panels Defect Classification beyond the Visible Spectrum (2018)
    MDPI
    In: Sensors
    Details
    Publication Date: 2018
    Description: In this work, we explore the use of images from different spectral bands to classify defects in melamine faced panels, which could appear through the production process. Through experimental evaluation, we evaluate the use of images from the visible (VS), near-infrared (NIR), and long wavelength infrared (LWIR), to classify the defects using a feature descriptor learning approach together with a support vector machine classifier. Two descriptors were evaluated, Extended Local Binary Patterns (E-LBP) and SURF using a Bag of Words (BoW) representation. The evaluation was carried on with an image set obtained during this work, which contained five different defect categories that currently occurs in the industry. Results show that using images from beyond the visual spectrum helps to improve classification performance in contrast with a single visible spectrum solution.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Published by MDPI
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  • 9
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    Coordinated control of replication and transcription by a SAPK protects genomic integrity (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-11-28
    Description: Upon environmental changes or extracellular signals, cells are subjected to marked changes in gene expression. Dealing with high levels of transcription during replication is critical to prevent collisions between the transcription and replication pathways and avoid recombination events. In response to osmostress, hundreds of stress-responsive genes are rapidly induced by the stress-activated protein kinase (SAPK) Hog1 (ref. 6), even during S phase. Here we show in Saccharomyces cerevisae that a single signalling molecule, Hog1, coordinates both replication and transcription upon osmostress. Hog1 interacts with and phosphorylates Mrc1, a component of the replication complex. Phosphorylation occurs at different sites to those targeted by Mec1 upon DNA damage. Mrc1 phosphorylation by Hog1 delays early and late origin firing by preventing Cdc45 loading, as well as slowing down replication-complex progression. Regulation of Mrc1 by Hog1 is completely independent of Mec1 and Rad53. Cells carrying a non-phosphorylatable allele of MRC1 (mrc1(3A)) do not delay replication upon stress and show a marked increase in transcription-associated recombination, genomic instability and Rad52 foci. In contrast, mrc1(3A) induces Rad53 and survival in the presence of hydroxyurea or methyl methanesulphonate. Therefore, Hog1 and Mrc1 define a novel S-phase checkpoint independent of the DNA-damage checkpoint that permits eukaryotic cells to prevent conflicts between DNA replication and transcription, which would otherwise lead to genomic instability when both phenomena are temporally coincident.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duch, Alba -- Felipe-Abrio, Irene -- Barroso, Sonia -- Yaakov, Gilad -- Garcia-Rubio, Maria -- Aguilera, Andres -- de Nadal, Eulalia -- Posas, Francesc -- England -- Nature. 2013 Jan 3;493(7430):116-9. doi: 10.1038/nature11675. Epub 2012 Nov 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell Signaling Unit, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona E-08003, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23178807" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Cell Cycle Checkpoints ; Cell Cycle Proteins/chemistry/genetics/metabolism ; DNA Damage ; *DNA Replication ; DNA-Binding Proteins/metabolism ; *Gene Expression Regulation, Fungal ; Genome, Fungal/*genetics ; Genomic Instability/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Mitogen-Activated Protein Kinases/*metabolism ; Nuclear Proteins/metabolism ; Osmotic Pressure ; Phosphorylation ; Protein-Serine-Threonine Kinases/genetics/metabolism ; Recombination, Genetic ; Replication Origin/genetics ; S Phase ; Saccharomyces cerevisiae/cytology/*genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Stress, Physiological ; Substrate Specificity ; Time Factors ; *Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 10
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    Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-05-09
    Description: Visibly fluorescent proteins (FPs) from jellyfish and corals have revolutionized many areas of molecular and cell biology, but the use of FPs in intact animals, such as mice, has been handicapped by poor penetration of excitation light. We now show that a bacteriophytochrome from Deinococcus radiodurans, incorporating biliverdin as the chromophore, can be engineered into monomeric, infrared-fluorescent proteins (IFPs), with excitation and emission maxima of 684 and 708 nm, respectively; extinction coefficient 〉90,000 M(-1) cm(-1); and quantum yield of 0.07. IFPs express well in mammalian cells and mice and spontaneously incorporate biliverdin, which is ubiquitous as the initial intermediate in heme catabolism but has negligible fluorescence by itself. Because their wavelengths penetrate tissue well, IFPs are suitable for whole-body imaging. The IFPs developed here provide a scaffold for further engineering.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763207/" 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/PMC2763207/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shu, Xiaokun -- Royant, Antoine -- Lin, Michael Z -- Aguilera, Todd A -- Lev-Ram, Varda -- Steinbach, Paul A -- Tsien, Roger Y -- R01 CA158448/CA/NCI NIH HHS/ -- R01 GM086197/GM/NIGMS NIH HHS/ -- R01 GM086197-01/GM/NIGMS NIH HHS/ -- R01 NS027177/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 May 8;324(5928):804-7. doi: 10.1126/science.1168683.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0647, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19423828" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/genetics ; Amino Acid Sequence ; Animals ; *Biliverdine/chemistry/metabolism ; Cell Line ; Deinococcus/*chemistry ; Diagnostic Imaging ; Fluorescence ; Humans ; Liver/anatomy & histology ; *Luminescent Proteins/chemistry/metabolism ; Mice ; Molecular Sequence Data ; *Phytochrome/chemistry/genetics/metabolism ; *Protein Engineering ; Recombinant Fusion Proteins/chemistry/metabolism ; Spectrophotometry, Infrared ; Whole Body Imaging
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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