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  • 1
    Publication Date: 2015-10-20
    Description: We present an improved procedure of generating initial conditions (ICs) for climate model hindcast experiments with specified sea surface temperature and sea ice. The motivation is to minimize errors in the ICs and lead to a better evaluation of atmospheric parameterizations' performance in the hindcast mode. We apply state variables (horizontal velocities, temperature and specific humidity) from the operational analysis/reanalysis for the atmospheric initial states. Without a data assimilation system, we apply a two-step process to obtain other necessary variables to initialize both the atmospheric (e.g., aerosols and clouds) and land models (e.g., soil moisture). First, we nudge only the model horizontal velocities towards operational analysis/reanalysis values, given a 6-hour relaxation time scale, to obtain all necessary variables. Compared to the original strategy in which horizontal velocities, temperature and specific humidity are nudged, the revised approach produces a better representation of initial aerosols and cloud fields which are more consistent and closer to observations and model's preferred climatology. Second, we obtain land ICs from an offline land model simulation forced with observed precipitation, winds, and surface fluxes. This approach produces more realistic soil moisture in the land ICs. With this refined procedure, the simulated precipitation, clouds, radiation, and surface air temperature over land are improved in the Day 2 mean hindcasts. Following this procedure, we propose a “Core” integration suite which provides an easily repeatable test allowing model developers to rapidly assess the impacts of various parameterization changes on the fidelity of modelled cloud-associated processes relative to observations. This article is protected by copyright. All rights reserved.
    Electronic ISSN: 1942-2466
    Topics: Geography , Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
    Publication Date: 2015-10-30
    Description: We present a new method capable of measuring iron isotope ratios of igneous materials to high precision by multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS) using a 57 Fe- 58 Fe double spike. After sample purification, near-baseline signal levels of nickel are still present in the sample solution, acting as an isobaric interference on 58 amu. To correct for the interference, the minor 60 Ni isotope is monitored and used to subtract a proportional 58 Ni signal from the total 58 amu beam. The 60 Ni signal is difficult to precisely measure on the Faraday detector due to Johnson noise occurring at similar magnitude. This noise-dominated signal is subtracted from the total 58 amu beam, and its error amplified during the double spike correction. Placing the 60 Ni beam on an ion counter produces a more precise measurement, resulting in a near-threefold improvement in δ 56 Fe reproducibility, from ±0.145‰ when measured on Faraday to 0.052‰. Faraday detectors quantify the 60 Ni signal poorly, and fail to discern the transient 20 Ne 40 Ar interference visible on the ion counter, which is likely responsible for poor reproducibility. Another consideration is instrumental stability (defined herein as drift in peak center mass), which affects high resolution analyses. Analyses experiencing large drift relative to bracketing standards often yield non-replicating data. Based on this, we present a quantitative outlier detection method capable of detecting drift-affected data. After outlier rejection, long-term precision on individual runs of our secondary standard improves to ±0.046‰. Averaging 3-4 analyses further improves precision to 0.019‰, allowing distinction between ultramafic minerals. This article is protected by copyright. All rights reserved.
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
    Publication Date: 2011-07-29
    Description: The formation and decomposition of methane+methylcyclohexane (MCH) hydrate in a static batch reactor, which was also designed as a high-pressure microwave reactor, were investigated. The addition of 300 ppm sodium dodecyl sulfate (SDS) provides continuous formation of CH 4 +MCH hydrate under static conditions. Increasing the initial pressure within the narrow range of 2.7 to 4.6 MPa at 274 K enhances the formation rate by even several times. The gas storage capacity can be largely improved with partial coexisting of sI CH 4 hydrate. Unlike a stirred formation, an increase of nonaqueous MCH inhibits the static formation of sH hydrate. The following regasification by 2.45 GHz microwave heating indicates that the dissociation is rate-controlled by the parallel connection of efficient internal heating and conventional external heating. The multiphase convection characterized by osmotic dehydration and driven by intensified regasification is considered as the dominant mechanism affecting the quiescent dissociation. Enhanced quiescent production and regasification of sH gas hydrate are key aspects for industrial applications of gas hydrate storage and transportation. The decisive factors influencing the static formation and regasification of methane +methyl- cyclohexane hydrate using sodium dodecyl sulfate and 2.45 GHz microwave heating were evaluated. Multiphase convection is considered as the dominant mechanism affecting the quiescent dissociation.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 4
    Publication Date: 2001-06-08
    Description: Heterologous prime/boost regimens have the potential for raising high levels of immune responses. Here we report that DNA priming followed by a recombinant modified vaccinia Ankara (rMVA) booster controlled a highly pathogenic immunodeficiency virus challenge in a rhesus macaque model. Both the DNA and rMVA components of the vaccine expressed multiple immunodeficiency virus proteins. Two DNA inoculations at 0 and 8 weeks and a single rMVA booster at 24 weeks effectively controlled an intrarectal challenge administered 7 months after the booster. These findings provide hope that a relatively simple multiprotein DNA/MVA vaccine can help to control the acquired immune deficiency syndrome epidemic.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amara, R R -- Villinger, F -- Altman, J D -- Lydy, S L -- O'Neil, S P -- Staprans, S I -- Montefiori, D C -- Xu, Y -- Herndon, J G -- Wyatt, L S -- Candido, M A -- Kozyr, N L -- Earl, P L -- Smith, J M -- Ma, H L -- Grimm, B D -- Hulsey, M L -- Miller, J -- McClure, H M -- McNicholl, J M -- Moss, B -- Robinson, H L -- P01 AI 43045/AI/NIAID NIH HHS/ -- P30 DA 12121/DA/NIDA NIH HHS/ -- P51 RR000165/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2001 Apr 6;292(5514):69-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center and Yerkes Regional Primate Research Center, Emory University, Atlanta, GA 30329, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11393868" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/administration & dosage/*immunology ; Acquired Immunodeficiency Syndrome/immunology/*prevention & control/virology ; Animals ; Antibodies, Viral/blood/immunology ; CD4-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/immunology ; Germinal Center/immunology ; HIV Antibodies/blood/immunology ; HIV-1/genetics/immunology/physiology ; Immunity, Mucosal ; Immunization, Secondary ; Immunologic Memory ; Interferon-gamma/biosynthesis ; Lymph Nodes/immunology ; Macaca mulatta ; SAIDS Vaccines/administration & dosage/immunology ; Simian Acquired Immunodeficiency Syndrome/immunology/prevention & ; control/virology ; Simian Immunodeficiency Virus/genetics/immunology/physiology ; T-Lymphocytes/immunology ; Vaccines, DNA/administration & dosage/*immunology ; Vaccines, Synthetic/administration & dosage/immunology ; Vaccinia virus/immunology ; Viral Load
    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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  • 5
    Publication Date: 2008-04-26
    Description: The mammalian vomeronasal organ detects complex chemical signals that convey information about gender, strain, and the social and reproductive status of an individual. How these signals are encoded is poorly understood. We developed transgenic mice expressing the calcium indicator G-CaMP2 and analyzed population responses of vomeronasal neurons to urine from individual animals. A substantial portion of cells was activated by either male or female urine, but only a small population of cells responded exclusively to gender-specific cues shared across strains and individuals. Female cues activated more cells and were subject to more complex hormonal regulations than male cues. In contrast to gender, strain and individual information was encoded by the combinatorial activation of neurons such that urine from different individuals activated distinctive cell populations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602951/" 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/PMC2602951/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Jie -- Ma, Limei -- Kim, Sangseong -- Nakai, Junichi -- Yu, C Ron -- NIDCD 008003/PHS HHS/ -- R01 DC008003/DC/NIDCD NIH HHS/ -- R01 DC008003-03/DC/NIDCD NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 25;320(5875):535-8. doi: 10.1126/science.1154476.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18436787" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Behavior, Animal ; Calcium/metabolism ; Cluster Analysis ; Cues ; Female ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred CBA ; Neurons, Afferent/*physiology ; *Pheromones ; Principal Component Analysis ; Receptors, Pheromone/physiology ; Sex Characteristics ; *Urine/chemistry ; Vomeronasal Organ/cytology/*physiology
    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: 2009-08-22
    Description: We recently reported the chemical synthesis, assembly, and cloning of a bacterial genome in yeast. To produce a synthetic cell, the genome must be transferred from yeast to a receptive cytoplasm. Here we describe methods to accomplish this. We cloned a Mycoplasma mycoides genome as a yeast centromeric plasmid and then transplanted it into Mycoplasma capricolum to produce a viable M. mycoides cell. While in yeast, the genome was altered by using yeast genetic systems and then transplanted to produce a new strain of M. mycoides. These methods allow the construction of strains that could not be produced with genetic tools available for this bacterium.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lartigue, Carole -- Vashee, Sanjay -- Algire, Mikkel A -- Chuang, Ray-Yuan -- Benders, Gwynedd A -- Ma, Li -- Noskov, Vladimir N -- Denisova, Evgeniya A -- Gibson, Daniel G -- Assad-Garcia, Nacyra -- Alperovich, Nina -- Thomas, David W -- Merryman, Chuck -- Hutchison, Clyde A 3rd -- Smith, Hamilton O -- Venter, J Craig -- Glass, John I -- New York, N.Y. -- Science. 2009 Sep 25;325(5948):1693-6. doi: 10.1126/science.1173759. Epub 2009 Aug 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19696314" target="_blank"〉PubMed〈/a〉
    Keywords: Centromere ; *Cloning, Molecular ; DNA Methylation ; DNA Restriction Enzymes/genetics/metabolism ; Deoxyribonucleases, Type III Site-Specific/genetics ; *Gene Transfer Techniques ; *Genetic Engineering ; *Genome, Bacterial ; Mycoplasma capricolum/*genetics ; Mycoplasma mycoides/*genetics/growth & development/isolation & purification ; Plasmids ; Saccharomyces cerevisiae/*genetics ; Sequence Analysis, DNA ; Sequence Deletion ; Transformation, Bacterial
    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: 2012-11-10
    Description: Phosphine is a small redox-active gas that is used to protect global grain reserves, which are threatened by the emergence of phosphine resistance in pest insects. We find that polymorphisms responsible for genetic resistance cluster around the redox-active catalytic disulfide or the dimerization interface of dihydrolipoamide dehydrogenase (DLD) in insects (Rhyzopertha dominica and Tribolium castaneum) and nematodes (Caenorhabditis elegans). DLD is a core metabolic enzyme representing a new class of resistance factor for a redox-active metabolic toxin. It participates in four key steps of core metabolism, and metabolite profiles indicate that phosphine exposure in mutant and wild-type animals affects these steps differently. Mutation of DLD in C. elegans increases arsenite sensitivity. This specific vulnerability may be exploited to control phosphine-resistant insects and safeguard food security.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schlipalius, David I -- Valmas, Nicholas -- Tuck, Andrew G -- Jagadeesan, Rajeswaran -- Ma, Li -- Kaur, Ramandeep -- Goldinger, Anita -- Anderson, Cameron -- Kuang, Jujiao -- Zuryn, Steven -- Mau, Yosep S -- Cheng, Qiang -- Collins, Patrick J -- Nayak, Manoj K -- Schirra, Horst Joachim -- Hilliard, Massimo A -- Ebert, Paul R -- R01NS060129/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 9;338(6108):807-10. doi: 10.1126/science.1224951.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Agri-Science Queensland, Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Brisbane, QLD 4001, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23139334" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arsenicals/pharmacology ; Arsenites/pharmacology ; Beetles/drug effects/*enzymology/genetics/metabolism ; Caenorhabditis elegans/drug effects/*enzymology/genetics/metabolism ; Caenorhabditis elegans Proteins/chemistry/genetics/metabolism ; Catalytic Domain ; Dihydrolipoamide Dehydrogenase/chemistry/*genetics/metabolism ; Insect Proteins/chemistry/genetics/metabolism ; Insecticide Resistance/*genetics ; *Insecticides/pharmacology ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Mutation ; Oxidation-Reduction ; Pesticides ; *Phosphines/pharmacology ; Polymorphism, Genetic ; Protein Multimerization ; Tribolium/drug effects/*enzymology/genetics/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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  • 8
    Publication Date: 2012-08-21
    Description: Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins drive membrane fusion by assembling into a four-helix bundle in a zippering process. Here, we used optical tweezers to observe in a cell-free reconstitution experiment in real time a long-sought SNARE assembly intermediate in which only the membrane-distal amino-terminal half of the bundle is assembled. Our findings support the zippering hypothesis, but suggest that zippering proceeds through three sequential binary switches, not continuously, in the amino- and carboxyl-terminal halves of the bundle and the linker domain. The half-zippered intermediate was stabilized by externally applied force that mimicked the repulsion between apposed membranes being forced to fuse. This intermediate then rapidly and forcefully zippered, delivering free energy of 36 k(B)T (where k(B) is Boltzmann's constant and T is temperature) to mediate fusion.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677750/" 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/PMC3677750/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gao, Ying -- Zorman, Sylvain -- Gundersen, Gregory -- Xi, Zhiqun -- Ma, Lu -- Sirinakis, George -- Rothman, James E -- Zhang, Yongli -- DK027044/DK/NIDDK NIH HHS/ -- GM093341/GM/NIGMS NIH HHS/ -- R01 GM093341/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 14;337(6100):1340-3. doi: 10.1126/science.1224492. Epub 2012 Aug 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22903523" target="_blank"〉PubMed〈/a〉
    Keywords: Cell-Free System ; DNA/chemistry/metabolism ; Entropy ; Neurons/metabolism ; *Optical Tweezers ; Qa-SNARE Proteins/chemistry ; SNARE Proteins/*chemistry ; Vesicle-Associated Membrane Protein 2/chemistry
    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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  • 9
    Publication Date: 2014-06-07
    Description: How sleep helps learning and memory remains unknown. We report in mouse motor cortex that sleep after motor learning promotes the formation of postsynaptic dendritic spines on a subset of branches of individual layer V pyramidal neurons. New spines are formed on different sets of dendritic branches in response to different learning tasks and are protected from being eliminated when multiple tasks are learned. Neurons activated during learning of a motor task are reactivated during subsequent non-rapid eye movement sleep, and disrupting this neuronal reactivation prevents branch-specific spine formation. These findings indicate that sleep has a key role in promoting learning-dependent synapse formation and maintenance on selected dendritic branches, which contribute to memory storage.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447313/" 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/PMC4447313/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Guang -- Lai, Cora Sau Wan -- Cichon, Joseph -- Ma, Lei -- Li, Wei -- Gan, Wen-Biao -- P01 NS074972/NS/NINDS NIH HHS/ -- R01 NS047325/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2014 Jun 6;344(6188):1173-8. doi: 10.1126/science.1249098.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Skirball Institute, Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY 10016, USA. Department of Anesthesiology, New York University School of Medicine, New York, NY 10016, USA. ; Skirball Institute, Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY 10016, USA. ; Skirball Institute, Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY 10016, USA. Drug Discovery Center, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China. ; Drug Discovery Center, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China. ; Skirball Institute, Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY 10016, USA. gan@saturn.med.nyu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24904169" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Dendritic Spines/*physiology ; Female ; Learning/*physiology ; Male ; Mice ; Mice, Mutant Strains ; Motor Cortex/*physiology ; Sleep, REM/*physiology
    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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  • 10
    Publication Date: 2007-03-10
    Description: The plant hormone abscisic acid (ABA) regulates many physiological and developmental processes in plants. The mechanism of ABA perception at the cell surface is not understood. Here, we report that a G protein-coupled receptor genetically and physically interacts with the G protein alpha subunit GPA1 to mediate all known ABA responses in Arabidopsis. Overexpressing this receptor results in an ABA-hypersensitive phenotype. This receptor binds ABA with high affinity at physiological concentration with expected kinetics and stereospecificity. The binding of ABA to the receptor leads to the dissociation of the receptor-GPA1 complex in yeast. Our results demonstrate that this G protein-coupled receptor is a plasma membrane ABA receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Xigang -- Yue, Yanling -- Li, Bin -- Nie, Yanli -- Li, Wei -- Wu, Wei-Hua -- Ma, Ligeng -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1712-6. Epub 2007 Mar 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17347412" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/*metabolism/pharmacology ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; GTP-Binding Protein alpha Subunits/metabolism ; Gene Expression Profiling ; Genes, Reporter ; Germination ; Models, Biological ; Mutation ; Plant Growth Regulators/*metabolism ; Plant Leaves/cytology/physiology ; Plants, Genetically Modified ; Potassium Channels/metabolism ; Protein Binding ; Receptors, G-Protein-Coupled/chemistry/genetics/*metabolism ; Recombinant Proteins/metabolism ; Seeds/growth & development ; *Signal Transduction
    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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