Point Source Extraction with MOPEX

MOPEX (MOsaicking and Point source EXtraction) is a package developed at the Spitzer Science Center for astronomical image processing. We report on the point source extraction capabilities of MOPEX. Point source extraction is implemented as a two step process: point source detection and profile fitting. Non-linear matched filtering of input images can be performed optionally to increase the signal-to-noise ratio and improve detection of faint point sources. Point Response Function (PRF) fitting of point sources produces the final point source list which includes the fluxes and improved positions of the point sources, along with other parameters characterizing the fit. Passive and active deblending allows for successful fitting of confused point sources. Aperture photometry can also be computed for every extracted point source for an unlimited number of aperture sizes. PRF is estimated directly from the input images. Implementation of efficient methods of background and noise estimation, and modified Simplex algorithm contribute to the computational efficiency of MOPEX. The package is implemented as a loosely connected set of perl scripts, where each script runs a number of modules written in C/C++. Input parameter setting is done through namelists, ASCII configuration files. We present applications of point source extraction to the mosaic images taken at 24 and 70 micron with the Multiband Imaging Photometer (MIPS) as part of the Spitzer extragalactic First Look Survey and to a Digital Sky Survey image. Completeness and reliability of point source extraction is computed using simulated data.Comment: 20 pages, 13 Postscript figures, accepted for publication in PAS

Keinot edistää sää- ja ilmastoriskien hallintaa

ELASTINEN-tutkimushankkeessa selvitettiin sää- ja ilmastoriskien hallinnan tilaa Suomessa ja arvioitiin riskienhallintakeinoja sekä eri toimijoiden roolia. Lisäksi tarkasteltiin, miten riskienhallinnan kustannuksia ja hyötyjä arvioidaan sekä miten riskienhallinta voidaan kääntää liiketoiminnaksi. Yhteiskunnan toimivuuden ja turvallisuuden ylläpitäminen edellyttää aktiivista varautumista sään ääriilmiöihin. Hankkeen tulosten mukaan suomalaiset organisaatiot eivät usein arvioi sää- ja ilmastoriskejä systemaattisesti. Varautumisessa tulee ottaa huomioon, että ilmastonmuutos voi muuttaa sään ääri-ilmiöitä, niiden esiintymistiheyttä ja voimakkuutta. Näin varautuminen sään ääri ilmiöihin on myös osa sopeutumista ilmastonmuutokseen. ELASTINEN-hanke esittää kolme suositusta, joilla sää- ja ilmastoriskien hallintaa voitaisiin parantaa ja sopeutumistyötä tukea: 1) monipuolistetaan tiedon tuottoa ja käyttöä, 2) vahvistetaan yhteistyötä ja kehitetään toimintatapoja sekä 3) kehitetään palveluita ja liiketoimintamahdollisuuksia. Suositusten toteuttamiseksi esitetään toimenpide-ehdotuksia, minkä lisäksi on tunnistettu toimien toteuttajatahoja. Nykyistä monipuolisempi ja helpommin saatavilla oleva tieto parantaisi mahdollisuuksia arvioida ja hallita sää- ja ilmastoriskejä sekä kykyä sopeutua ilmastonmuutoksen vaikutuksiin. Suomessa tulisi myös arvioida säännöllisesti Suomen ulkopuolella tapahtuvia ilmastonmuutoksen vaikutuksia, jotka voivat heijastua Suomeen. Sää- ja ilmastoriskien hallintatoimia tulisi valita ja arvioida myös taloudellisen tehokkuuden näkökulmasta

Membrane-Dependent Binding and Entry Mechanism of Dopamine into Its Receptor

Synaptic neurotransmission has recently been proposed to function via either a membrane-independent or a membrane-dependent mechanism, depending on the neurotransmitter type. In the membrane-dependent mechanism, amphipathic neurotransmitters first partition to the lipid headgroup region and then diffuse along the membrane plane to their membrane-buried receptors. However, to date, this mechanism has not been demonstrated for any neurotransmitter-receptor complex. Here, we combined isothermal calorimetry measurements with a diverse set of molecular dynamics simulation methods to investigate the partitioning of an amphipathic neurotransmitter (dopamine) and the mechanism of its entry into the ligand-binding site. Our results show that the binding of dopamine to its receptor is consistent with the membrane-dependent binding and entry mechanism. Both experimental and simulation results showed that dopamine favors binding to lipid membranes especially in the headgroup region. Moreover, our simulations revealed a ligand-entry pathway from the membrane to the binding site. This pathway passes through a lateral gate between transmembrane alpha-helices 5 and 6 on the membrane-facing side of the protein. All in all, our results demonstrate that dopamine binds to its receptor by a membrane-dependent mechanism, and this is complemented by the more traditional binding mechanism directly through the aqueous phase. The results suggest that the membrane-dependent mechanism is common in other synaptic receptors, too

Adaptation to climate change in Finland : Current state and future prospects

The KOKOSOPU project has aimed at a comprehensive evaluation of the national adaptation policy with particular emphasis on the National Adaptation Plan and international policy development. In addition, future challenges related to societal development have been taken into account. Projections of climate change, Finland’s Climate Act and the strengthened adaptation policy in the EU emphasise the importance of the national adaptation policy. A key objective of the National Adaptation Plan 2014–2022 was to strengthen the adaptive capacity of Finnish society. This objective is still relevant. The conditions for reaching the objective have, however, partly changed. First, cross border consequences of climate change are increasingly emphasised. Second, issues of justice and fairness with respect to the consequences of climate change and adaptation actions are being identified as central. Third, greater weight is given to the overall sustainability of adaptation and climate action. The changing conditions for climate change adaptation should be reflected in the allocation of resources, in improved coordination within the administration and in co-operation between the public and private sector. In addition, knowledge and education should be enhanced, and resources provided for RDI, and for monitoring and evaluation that supports continued improvement of adaptation activities

Adaptation to climate change in Finland : Current state and future prospects

The KOKOSOPU project has aimed at a comprehensive evaluation of the national adaptation policy with particular emphasis on the National Adaptation Plan and international policy development. In addition, future challenges related to societal development have been taken into account. Projections of climate change, Finland’s Climate Act and the strengthened adaptation policy in the EU emphasise the importance of the national adaptation policy. A key objective of the National Adaptation Plan 2014–2022 was to strengthen the adaptive capacity of Finnish society. This objective is still relevant. The conditions for reaching the objective have, however, partly changed. First, cross border consequences of climate change are increasingly emphasised. Second, issues of justice and fairness with respect to the consequences of climate change and adaptation actions are being identified as central. Third, greater weight is given to the overall sustainability of adaptation and climate action. The changing conditions for climate change adaptation should be reflected in the allocation of resources, in improved coordination within the administration and in co-operation between the public and private sector. In addition, knowledge and education should be enhanced, and resources provided for RDI, and for monitoring and evaluation that supports continued improvement of adaptation activities

Using a game to engage stakeholders in extreme event attribution science

The impacts of weather and climate-related disasters are increasing, and climate change can exacerbate many disasters. Effectively communicating climate risk and integrating science into policy requires scientists and stakeholders to work together. But dialogue between scientists and policymakers can be challenging given the inherently multidimensional nature of the issues at stake when managing climate risks. Building on the growing use of serious games to create dialogue between stakeholders, we present a new game for policymakers called Climate Attribution Under Loss and Damage: Risking, Observing,co-Negotiating (CAULDRON). CAULDRON aims to communicate understanding of the science attributing extreme events to climate change in a memorable and compelling way, and create space for dialogue around policy decisions addressing changing risks and loss and damage from climate change. We describe the process of developing CAULDRON, and draw on observations of players and their feedback to demonstrate its potential to facilitate the interpretation of probabilistic climate information and the understanding of its relevance to informing policy. Scientists looking to engage with stakeholders can learn valuable lessons in adopting similar innovative approaches. The suitability of games depends on the policy context but, if used appropriately, experiential learning can drive co-produced understanding and meaningful dialogue

Pan-Eurasian Experiment (PEEX): Towards a holistic understanding of the feedbacks and interactions in the land-Atmosphere-ocean-society continuum in the northern Eurasian region

The northern Eurasian regions and Arctic Ocean will very likely undergo substantial changes during the next decades. The Arctic-boreal natural environments play a crucial role in the global climate via albedo change, carbon sources and sinks as well as atmospheric aerosol production from biogenic volatile organic compounds. Furthermore, it is expected that global trade activities, demographic movement, and use of natural resources will be increasing in the Arctic regions. There is a need for a novel research approach, which not only identifies and tackles the relevant multi-disciplinary research questions, but also is able to make a holistic system analysis of the expected feedbacks. In this paper, we introduce the research agenda of the Pan-Eurasian Experiment (PEEX), a multi-scale, multi-disciplinary and international program started in 2012 (https://www.atm.helsinki.fi/peex/). PEEX sets a research approach by which large-scale research topics are investigated from a system perspective and which aims to fill the key gaps in our understanding of the feedbacks and interactions between the land-Atmosphere-Aquatic-society continuum in the northern Eurasian region. We introduce here the state of the art for the key topics in the PEEX research agenda and present the future prospects of the research, which we see relevant in this context

Identifying and tracking key climate adaptation actors in the UK

To understand how climate adaptation planning and decision-making will progress, a better understanding is needed as to which organisations are expected to take on key responsibilities. Methodological challenges have impeded efforts to identify and track adaptation actors beyond the coarse scale of nation states. Yet, for effective adaptation to succeed, who do national governments need to engage, support and encourage? Using the UK as a case study, we conducted a systematic review of official government documents on climate adaptation, between 2006 and 2015, to understand which organisations are identified as key to future adaptation efforts and tracked the extent to which these organisations changed over time. Our unique longitudinal dataset found a very large number of organisations (n = 568). These organisations varied in size (small-medium enterprises to large multinationals), type (public, private and not-for-profit), sector (e.g. water, energy, transport and health), scale (local, national and international), and roles and responsibilities (policymaking, decision-making, knowledge production, retail). Importantly, our findings reveal a mismatch between official government policies that repeatedly call on private organisations to drive adaptation, on the one hand, and a clear dominance of the public sector on the other hand. Yet, the capacity of organisations to fulfil the roles and responsibilities assigned to them, particularly in the public sector, is diminishing. Unless addressed, climate adaptation actions could be assigned to those either unable, or unwilling, to implement them

Overview: Recent advances in the understanding of the northern Eurasian environments and of the urban air quality in China – a Pan-Eurasian Experiment (PEEX) programme perspective

The Pan-Eurasian Experiment (PEEX) Science Plan, released in 2015, addressed a need for a holistic system understanding and outlined the most urgent research needs for the rapidly changing Arctic-boreal region. Air quality in China, together with the long-range transport of atmospheric pollutants, was also indicated as one of the most crucial topics of the research agenda. These two geographical regions, the northern Eurasian Arctic-boreal region and China, especially the megacities in China, were identified as a “PEEX region”. It is also important to recognize that the PEEX geographical region is an area where science-based policy actions would have significant impacts on the global climate. This paper summarizes results obtained during the last 5 years in the northern Eurasian region, together with recent observations of the air quality in the urban environments in China, in the context of the PEEX programme. The main regions of interest are the Russian Arctic, northern Eurasian boreal forests (Siberia) and peatlands, and the megacities in China. We frame our analysis against research themes introduced in the PEEX Science Plan in 2015. We summarize recent progress towards an enhanced holistic understanding of the land–atmosphere–ocean systems feedbacks. We conclude that although the scientific knowledge in these regions has increased, the new results are in many cases insufficient, and there are still gaps in our understanding of large-scale climate–Earth surface interactions and feedbacks. This arises from limitations in research infrastructures, especially the lack of coordinated, continuous and comprehensive in situ observations of the study region as well as integrative data analyses, hindering a comprehensive system analysis. The fast-changing environment and ecosystem changes driven by climate change, socio-economic activities like the China Silk Road Initiative, and the global trends like urbanization further complicate such analyses. We recognize new topics with an increasing importance in the near future, especially “the enhancing biological sequestration capacity of greenhouse gases into forests and soils to mitigate climate change” and the “socio-economic development to tackle air quality issues”

Gene expression signatures for colorectal cancer microsatellite status and HNPCC

The majority of microsatellite instable (MSI) colorectal cancers are sporadic, but a subset belongs to the syndrome hereditary nonpolyposis colorectal cancer (HNPCC). Microsatellite instability is caused by dysfunction of the mismatch repair (MMR) system that leads to a mutator phenotype, and MSI is correlated to prognosis and response to chemotherapy. Gene expression signatures as predictive markers are being developed for many cancers, and the identification of a signature for MMR deficiency would be of interest both clinically and biologically. To address this issue, we profiled the gene expression of 101 stage II and III colorectal cancers (34 MSI, 67 microsatellite stable (MSS)) using high-density oligonucleotide microarrays. From these data, we constructed a nine-gene signature capable of separating the mismatch repair proficient and deficient tumours. Subsequently, we demonstrated the robustness of the signature by transferring it to a real-time RT-PCR platform. Using this platform, the signature was validated on an independent test set consisting of 47 tumours (10 MSI, 37 MSS), of which 45 were correctly classified. In a second step, we constructed a signature capable of separating MMR-deficient tumours into sporadic MSI and HNPCC cases, and validated this by a mathematical cross-validation approach. The demonstration that this two-step classification approach can identify MSI as well as HNPCC cases merits further gene expression studies to identify prognostic signatures