Agent Based Modeling in Land-Use and Land-Cover Change Studies

Agent based models (ABM) for land use and cover change (LUCC) holds the promise to provide new insight into the processes and patterns of the human and biophysical interactions in ways that have never been explored. Advances in computer technology make it possible to run almost infinite numbers of simulations with multiple heterogeneously shaped actors that reciprocally interact via vertical and horizontal power lines on various levels. Based upon an extensive literature review the basic components for such exercises are explored and discussed. This resulted in a systematic representation of these components consisting of: (1) Spatial static input data, (2) Actor and Actor-group static input data, (3) Spatial dynamic input, (4) Actor and Actor-group dynamic input data, (5) the model with the rules describing the rules, (6) Spatial static output, (7) Actor and Actor-group static output, (8) Dynamic output of Actor behaviour changes, (9) Dynamic output of actor-group behavioural changes, (10) Dynamic output of spatial patterns, (11) Dynamic output of temporal patterns. This representation proves to be epistemologically useful in the analysis of the relationships between the ABM LUCC components. In this paper, this representation is also used to enumerate the strengths and limitations of agent based modelling in LUCC

SolRgene: an online database to explore disease resistance genes in tuber-bearing Solanum species

Background The cultivated potato (Solanum tuberosum L.) is an important food crop, but highly susceptible to many pathogens. The major threat to potato production is the Irish famine pathogen Phytophthora infestans, which causes the devastating late blight disease. Potato breeding makes use of germplasm from wild relatives (wild germplasm) to introduce resistances into cultivated potato. The Solanum section Petota comprises tuber-bearing species that are potential donors of new disease resistance genes. The aim of this study was to explore Solanum section Petota for resistance genes and generate a widely accessible resource that is useful for studying and implementing disease resistance in potato. Description The SolRgene database contains data on resistance to P. infestans and presence of R genes and R gene homologues in Solanum section Petota. We have explored Solanum section Petota for resistance to late blight in high throughput disease tests under various laboratory conditions and in field trials. From resistant wild germplasm, segregating populations were generated and assessed for the presence of resistance genes. All these data have been entered into the SolRgene database. To facilitate genetic and resistance gene evolution studies, phylogenetic data of the entire SolRgene collection are included, as well as a tool for generating phylogenetic trees of selected groups of germplasm. Data from resistance gene allele-mining studies are incorporated, which enables detection of R gene homologs in related germplasm. Using these resources, various resistance genes have been detected and some of these have been cloned, whereas others are in the cloning pipeline. All this information is stored in the online SolRgene database, which allows users to query resistance data, sequences, passport data of the accessions, and phylogenic classifications. Conclusion Solanum section Petota forms the basis of the SolRgene database, which contains a collection of resistance data of an unprecedented size and precision. Complemented with R gene sequence data and phylogenetic tools, SolRgene can be considered the primary resource for information on R genes from potato and wild tuber-bearing relatives

Identification of a novel resistance (E40F) and compensatory (K43E) substitution in HIV-1 reverse transcriptase

<p>Abstract</p> <p>Background</p> <p>HIV-1 nucleoside reverse transcriptase inhibitors (NRTIs) have been used in the clinic for over twenty years. Interestingly, the complete resistance pattern to this class has not been fully elucidated. Novel mutations in RT appearing during treatment failure are still being identified. To unravel the role of two of these newly identified changes, E40F and K43E, we investigated their effect on viral drug susceptibility and replicative capacity.</p> <p>Results</p> <p>A large database (Quest Diagnostics database) was analysed to determine the associations of the E40F and K43E changes with known resistance mutations. Both amino acid changes are strongly associated with the well known NRTI-resistance mutations M41L, L210W and T215Y. In addition, a strong positive association between these changes themselves was observed. A panel of recombinant viruses was generated by site-directed mutagenesis and phenotypically analysed. To determine the effect on replication capacity, competition and <it>in vitro </it>evolution experiments were performed. Introduction of E40F results in an increase in Zidovudine resistance ranging from nine to fourteen fold depending on the RT background and at the same time confers a decrease in viral replication capacity. The K43E change does not decrease the susceptibility to Zidovudine but increases viral replication capacity, when combined with E40F, demonstrating a compensatory role for this codon change.</p> <p>Conclusion</p> <p>In conclusion, we have identified a novel resistance (E40F) and compensatory (K43E) change in HIV-1 RT. Further research is indicated to analyse the clinical importance of these changes.</p

Photometric Variability in the CSTAR Field: Results From the 2008 Data Set

The Chinese Small Telescope ARray (CSTAR) is the first telescope facility built at Dome A, Antarctica. During the 2008 observing season, the installation provided long-baseline and high-cadence photometric observations in the i-band for 18,145 targets within 20 deg2 CSTAR field around the South Celestial Pole for the purpose of monitoring the astronomical observing quality of Dome A and detecting various types of photometric variability. Using sensitive and robust detection methods, we discover 274 potential variables from this data set, 83 of which are new discoveries. We characterize most of them, providing the periods, amplitudes and classes of variability. The catalog of all these variables is presented along with the discussion of their statistical properties.Comment: 38 pages, 11 figures, 4 tables; Accepted for publication in ApJ

Gattini 2010: Cutting Edge Science at the Bottom of the World

The high altitude Antarctic sites of Dome A and the South Pole offer intriguing locations for future large scale optical astronomical Observatories. The Gattini project was created to measure the optical sky brightness, large area cloud cover and aurora of the winter-time sky above such high altitude Antarctic sites. The Gattini-DomeA camera was installed on the PLATO instrument module as part of the Chinese-led traverse to the highest point on the Antarctic plateau in January 2008. This single automated wide field camera contains a suite of Bessel photometric filters (B, V, R) and a long-pass red filter for the detection and monitoring of OH emission. We have in hand one complete winter-time dataset (2009) from the camera that was recently returned in April 2010. The Gattini-South Pole UV camera is a wide-field optical camera that in 2011 will measure for the first time the UV properties of the winter-time sky above the South Pole dark sector. This unique dataset will consist of frequent images taken in both broadband U and B filters in addition to high resolution (R similar to 5000) long slit spectroscopy over a narrow bandwidth of the central field. The camera is a proof of concept for the 2m-class Antarctic Cosmic Web Imager telescope, a dedicated experiment to directly detect and map the redshifted lyman alpha fluorescence or Cosmic Web emission we believe possible due to the unique geographical qualities of the site. We present the current status of both projects

Simultaneous quasi-periodic optical and HF radar signatures observed in the postnoon sector

Zhongshan Station in Antarctica is located close to the polar cusp/cleft latitude. The field of view of the Syowa East HF radar also covers Zhongshan Station. Simultaneous quasi-periodic phenomena of optical aurora, HF radar backscatter power and Doppler velocity, and ground based magnetograms were observed in the magnetic postnoon sector (～330 MLT to 1510 MLT) on 3 August 1997. The characteristics of the quasi-periodic event are summarized in the following; 1) East-west aligned band/arc type discrete aurora showed quasi-periodic luminosity variations with period of -6-10 min, 2) Quasi-periodic variations of the optical aurora had one to one correspondence with the variations of HF radar backscatter powers and magnetic pulsations, 3) The HF backscatter region was located at the lower latitude of the quasi-periodic optical aurora, 4) Quasi-periodic variations of line-of-site Doppler velocity detected by HF radar showed very close relation to the magnetic pulsations observed at Zhongshan in Antarctica and the IMAGE magnetometer array in the northern hemisphere, 5) The IMAGE data revealed that the region of quasi-periodic HF radar backscatter (irregularities) corresponds to the region of intensity maximum of magnetic pulsations

Do I-Pass for FAIR?:A self-assessment tool to measure the FAIR-ness of an organization

The 15 FAIR data principles are intended to be applied to a dataset, but the acronym FAIR is also used as an adjective for other (digital) matters, such as FAIR data stewardship, FAIR data infrastructure and FAIR data services. Moreover, in the context of Open Science and scientific integrity, more and more Dutch universities and research organizations discuss a FAIR organization as an important goal, thus implementing RDM practices and support with the FAIR principles as a main driver. Triggered by this use of the acronym FAIR for organizations, an LCRDM (National Coordination Point Research Data Management) task group explored the definition, characteristics and principles of a so-called ‘FAIR enabling organization’. The task group delivered two products: (1) a definition for a FAIR enabling organization and (2) a self-assessment tool to evaluate the FAIR-ness of a research organization (research institute, university or university of applied sciences). This self-assessment tool is a simple instrument, presented in an editable PDF form. By answering the questions and evaluating the level (beginner, intermediate, or advanced) at which you assess the performance of your organization, you will be able to define the actual FAIR-ness. In addition you can define a Road Map to become a FAIR Enabling Research Organization using the information in de more advances level(s)

The First Release of the CSTAR Point Source Catalog from Dome A, Antarctica

In 2008 January the 24th Chinese expedition team successfully deployed the Chinese Small Telescope ARray (CSTAR) to DomeA, the highest point on the Antarctic plateau. CSTAR consists of four 14.5cm optical telescopes, each with a different filter (g, r, i and open) and has a 4.5degree x 4.5degree field of view (FOV). It operates robotically as part of the Plateau Observatory, PLATO, with each telescope taking an image every 30 seconds throughout the year whenever it is dark. During 2008, CSTAR #1 performed almost flawlessly, acquiring more than 0.3 million i-band images for a total integration time of 1728 hours during 158 days of observations. For each image taken under good sky conditions, more than 10,000 sources down to 16 mag could be detected. We performed aperture photometry on all the sources in the field to create the catalog described herein. Since CSTAR has a fixed pointing centered on the South Celestial Pole (Dec =-90 degree), all the sources within the FOV of CSTAR were monitored continuously for several months. The photometric catalog can be used for studying any variability in these sources, and for the discovery of transient sources such as supernovae, gamma-ray bursts and minor planets.Comment: 1 latex file and 9 figures The paper is accepted by PAS

The sky brightness and transparency in i-band at Dome A, Antarctica

The i-band observing conditions at Dome A on the Antarctic plateau have been investigated using data acquired during 2008 with the Chinese Small Telescope ARray. The sky brightness, variations in atmospheric transparency, cloud cover, and the presence of aurorae are obtained from these images. The median sky brightness of moonless clear nights is 20.5 mag arcsec^{-2} in the SDSS $i$ band at the South Celestial Pole (which includes a contribution of about 0.06 mag from diffuse Galactic light). The median over all Moon phases in the Antarctic winter is about 19.8 mag arcsec^{-2}. There were no thick clouds in 2008. We model contributions of the Sun and the Moon to the sky background to obtain the relationship between the sky brightness and transparency. Aurorae are identified by comparing the observed sky brightness to the sky brightness expected from this model. About 2% of the images are affected by relatively strong aurorae.Comment: There are 1 Latex file and 14 figures accepted by A