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3.
  • Buckland, Philip I., 1973-, et al. (författare)
  • BugsCEP, an entomological database twenty-five years on
  • 2014
  • Ingår i: Antenna (Journal of the Royal Entomological Society). - London : Royal Entomological Society of London. - 0140-1890. ; 38:1, s. 21-28
  • Tidskriftsartikel (refereegranskat)
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4.
  • Buckland, Philip I., 1973-, et al. (författare)
  • The Strategic Environmental Archaeology Database : a resource for international, multiproxy and transdisciplinary studies of environmental and climatic change
  • 2015
  • Konferensbidrag (refereegranskat)abstract
    • Climate and environmental change are global challenges which require global data and infrastructure to investigate. These challenges also require a multi-proxy approach, integrating evidence from Quaternary science and archaeology with information from studies on modern ecology and physical processes among other disciplines. The Strategic Environmental Archaeology Database (SEAD http://www.sead.se) is a Swedish based international research e-infrastructure for storing, managing, analysing and disseminating palaeoenvironmental data from an almost unlimited number of analysis methods. The system currently makes available raw data from over 1500 sites (>5300 datasets) and the analysis of Quaternary fossil insects, plant macrofossils, pollen, geochemistry and sediment physical properties, dendrochronology and wood anatomy, ceramic geochemistry and bones, along with numerous dating methods. This capacity will be expanded in the near future to include isotopes, multi-spectral and archaeo-metalurgical data. SEAD also includes expandable climate and environment calibration datasets, a complete bibliography and extensive metadata and services for linking these data to other resources. All data is available as Open Access through http://qsead.sead.se and downloadable software. SEAD is maintained and managed at the Environmental Archaeology Lab and HUMlab at Umea University, Sweden. Development and data ingestion is progressing in cooperation with The Laboratory for Ceramic Research and the National Laboratory for Wood Anatomy and Dendrochronology at Lund University, Sweden, the Archaeological Research Laboratory, Stockholm University, the Geoarchaeological Laboratory, Swedish National Historical Museums Agency and several international partners and research projects. Current plans include expanding its capacity to serve as a data source for any system and integration with the Swedish National Heritage Board's information systems. SEAD is partnered with the Neotoma palaeoecology database (http://www.neotomadb.org) and a new initiative for building cyberinfrastructure for transdisciplinary research and visualization of the long-term human ecodynamics of the North Atlantic funded by the National Science Foundation (NSF).
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5.
  • Freire, Rafael V.M., et al. (författare)
  • Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles : combining in silico tools and experimental methods
  • 2021
  • Ingår i: Journal of Colloid and Interface Science. - : Elsevier. - 0021-9797 .- 1095-7103. ; 596, s. 352-363
  • Tidskriftsartikel (refereegranskat)abstract
    • With the growing challenges of bacteria becoming resistant to conventional antibiotics, antimicrobial peptides (AMPs) may offer a potential alternative. One of the most studied AMPs, the human cathelicidin derived AMP LL-37 is notable for its antimicrobial activity even though its mechanism of action is not fully understood yet. This work investigates the interaction of LL-37 with 1-Palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-(1-glycerol) (POPG) vesicles, which were employed as a bacterial membrane model given the common presence of this phospholipid in the bacterial membrane. Experimental techniques including small angle X-ray scattering, transmission electron microscopy and dynamic light scattering were used to characterize the interactions among LL-37 and POPG. Molecular dynamics simulations complement the experimental studies with molecular-level insights into the process. LL-37 was discovered to actively and critically interact with the POPG vesicles, modifying the membrane curvature that eventually leads to structural transformations from vesicles to mixed micelles. The results shed light on the mechanisms underlying the interactions among LL-37 and bacteria mimetic vesicles and can guide the further development of AMP based antimicrobial materials and therapies.
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6.
  • Buckland, Philip I., 1973- (författare)
  • The Bugs Coleopteran Ecology Package (BugsCEP) database : 1000 sites and half a million fossils later
  • 2014
  • Ingår i: Quaternary International. - : Elsevier. - 1040-6182 .- 1873-4553. ; 341, s. 272-282
  • Tidskriftsartikel (refereegranskat)abstract
    • The Bugs database project started in the late 1980s as what would now be considered a relatively simple system, albeit advanced for its time, linking fossil beetle species lists to modern habitat and distribution information. Since then, Bugs has grown into a complex database of fossils records, habitat and distribution data, dating and climate reference data wrapped into an advanced software analysis package. At the time of writing, the database contains raw data and metadata for 1124 sites, and Russell Coope directly contributed to the analysis of over 154 (14%) of them, some 98790 identifications published in 231 publications. Such quantifications are infeasible without databases, and the analytical power of combining a database of modern and fossil insects with analysis tools is potentially immense for numerous areas of science ranging from conservation to Quaternary geology.BugsCEP, The Bugs Coleopteran Ecology Package, is the latest incarnation of the Bugs database project. Released in 2007, the database is continually added too and is available for free download from http://www.bugscep.com. The software tools include quantitative habitat reconstruction and visualisation, correlation matrices, MCR climate reconstruction, searching by habitat and retrieving, among other things, a list of taxa known from the selected habitat types. It also provides a system for entering, storing and managing palaeoentomological data as well as a number of expert system like reporting facilities.Work is underway to create an online version of BugsCEP, implemented through the Strategic Environmental Archaeology Database (SEAD) project (http://www.sead.se). The aim is to provide more direct access to the latest data, a community orientated updating system, and integration with other proxy data. Eventually, the tools available in the offline BugsCEP will be duplicated and Bugs will be entirely in the web.This paper summarises aspects of the current scope, capabilities and applications of the BugsCEP database and software, with special reference to and quantifications of the contributions of Russell Coope to the field of palaeoentomology as represented in the database. The paper also serves to illustrate the potential for the use of BugsCEP in biographical studies, and discusses some of the issues relating to the use of large scale sources of quantitative data.All datasets used in this article are available through the current version of BugsCEP available at http://www.bugscep.com.
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7.
  • Rocha, Luis E C, 1981- (författare)
  • Exploring patterns of empirical networks
  • 2011
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • We are constantly struggling to understand how nature works, trying to identify recurrent events and looking for analogies and relations between objects or individuals. Knowing patterns of behavior is powerful and fundamental for survival of any species. In this thesis, datasets of diverse systems related to transportation, economics, sexual and social contacts, are characterized by using the formalisms of time series and network theory. Part of the results consists on the collection and analyzes of original network data, the rest focuses on the simulation of dynamical processes on these networks and to study how they are affected by the particular structures. The majority of the thesis is about temporal networks, i.e. networks whose structure changes in time. The new temporal dimension reveals structural dynamical properties that help to understand the feedback mechanisms responsible to make the network structure to adapt and to understand the emergence and inhibition of diverse phenomena in dynamic systems, as epidemics in sexual and contact networks.
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8.
  • Linder, Cedric, et al. (författare)
  • The overlooked challenge of learning to extrapolate three-dimensionality
  • 2013
  • Ingår i: Book of Abstracts. - : Charles University.
  • Konferensbidrag (refereegranskat)abstract
    • Learning astronomy has many learning challenges due to the highly diverse, conceptual, and theoretical thinking used in the discipline. One taken for granted challenge is the learning to extrapolate three-dimensionality. Although we have the ability to see our surroundings in threedimensional terms, beyond a distance of about 200m this ability quickly becomes very limited. So, when looking up at the night sky, learning to discern critical features that are embedded in dimensionality does not come easily. There have been several articles addressing how fruitful 3D simulations are for astronomy education, but they do not address what students discern, nor the nature of that discernment. Taking the concept of discernment to be about noticing something and assigning meaning to it, our research question is: In terms of dimensionality, what do astronomy/physics students and professors discern when engaging with a simulated video flythrough of our Galaxy and beyond?A web-based questionnaire was designed using links to video clips drawn from a well-regarded simulation-video of travel through our galaxy and beyond. 137 physics and astronomy university students and teaching professors, who were drawn from nine countries, completed the questionnaire. The descriptions provided by them were used to formulate six categories of discernment in relation to multidimensionality. These results are used to make the case that astronomy learning that aims at developing the ability to extrapolate three-dimensionality needs to be grounded in the creation of meaningful motion parallax experiences. Teaching and learning implications are discussed.
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9.
  • Brandt, S. Anders, 1970-, et al. (författare)
  • A harmonized GIS course curriculum for Swedish universities
  • 2007
  • Ingår i: EUC'07 HERODOT Proceedings. ; , s. 10 s.-
  • Konferensbidrag (övrigt vetenskapligt)abstract
    • With the implementation of the Bologna declaration, European and other universities must change or adjust courses and programmes so they fit into the Bologna model. In Sweden this will take place during 2007. The intention with the declaration, for example, is that a basic course in one subject at one university should be treated as equivalent to the same type of course at another university. Once a year, the recently formed section for education of the Swedish Cartographic Society gathers university lecturers and others for an education conference to discuss matters concerning higher education in geomatics, geoinformatics, geography, etc. Last year’s conference identified the need for a harmonized course curriculum in basic GIS. One of the advantages of such a course is easier transfer of study records for inclusion of course credits in study programmes at other universities. Therefore, an attempt has been made to write a harmonized course curriculum for basic GIS. The course will contain about 50% common content and about 50% of content decided by the individual university. The common content will be described as learning outcomes, and then it is up to the universities to place the learning outcomes into a context. Thanks to this common core, the course can be given for such diverse programmes as archaeology, land surveying, or economy, and still be able to include the required knowledge for students to continue on more advanced courses at other universities.
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10.
  • Aronsson, Christopher (författare)
  • Tunable and modular assembly of polypeptides and polypeptide-hybrid biomaterials
  • 2016
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • Biomaterials are materials that are specifically designed to be in contact with biological systems and have for a long time been used in medicine. Examples of biomaterials range from sophisticated prostheses used for replacing outworn body parts to ordinary contact lenses. Currently it is possible to create biomaterials that can e.g. specifically interact with cells or respond to certain stimuli. Peptides, the shorter version of proteins, are excellent molecules for fabrication of such biomaterials. By following and developing design rules it is possible to obtain peptides that can self-assemble into well-defined nanostructures and biomaterials.The aim of this thesis is to create ”smart” and tunable biomaterials by molecular self-assembly using dimerizing –helical polypeptides. Two different, but structurally related, polypeptide-systems have been used in this thesis. The EKIV-polypeptide system was developed in this thesis and consists of four 28-residue polypeptides that can be mixed-and-matched to self-assemble into four different coiled coil heterodimers. The dissociation constant of the different heterodimers range from μM to < nM. Due to the large difference in affinities, the polypeptides are prone to thermodynamic social self-sorting. The JR-polypeptide system, on the other hand, consists of several 42-residue de novo designed helix-loop-helix polypeptides that can dimerize into four-helix bundles. In this work, primarily the glutamic acid-rich polypeptide JR2E has been explored as a component in supramolecular materials. Dimerization was induced by exposing the polypeptide to either Zn2+, acidic conditions or the complementary polypeptide JR2K.By conjugating JR2E to hyaluronic acid and the EKIV-polypeptides to star-shaped poly(ethylene glycol), respectively, highly tunable hydrogels that can be self-assembled in a modular fashion have been created. In addition, self-assembly of spherical superstructures has been investigated and were obtained by linking two thiol-modified JR2E polypeptides via a disulfide bridge in the loop region. ŒThe thesis also demonstrates that the polypeptides and the polypeptide-hybrids can be used for encapsulation and release of molecules and nanoparticles. In addition, some of the hydrogels have been explored for 3D cell culture. By using supramolecular interactions combined with bio-orthogonal covalent crosslinking reactions, hydrogels were obtained that enabled facile encapsulation of cells that retained high viability.The results of the work presented in this thesis show that dimerizing α–helical polypeptides can be used to create modular biomaterials with properties that can be tuned by specific molecular interactions. The modularity and the tunable properties of these smart biomaterials are conceptually very interesting andmake them useful in many emerging biomedical applications, such as 3D cell culture, cell therapy, and drug delivery.
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