Enhanced processing of SPOT multispectral satellite imagery for environmental monitoring and modelling

The Taita Hills in southeastern Kenya form the northernmost part of Africa’s Eastern Arc Mountains, which have been identified by Conservation International as one of the top ten biodiversity hotspots on Earth. As with many areas of the developing world, over recent decades the Taita Hills have experienced significant population growth leading to associated major changes in land use and land cover (LULC), as well as escalating land degradation, particularly soil erosion. Multi-temporal medium resolution multispectral optical satellite data, such as imagery from the SPOT HRV, HRVIR, and HRG sensors, provides a valuable source of information for environmental monitoring and modelling at a landscape level at local and regional scales. However, utilization of multi-temporal SPOT data in quantitative remote sensing studies requires the removal of atmospheric effects and the derivation of surface reflectance factor. Furthermore, for areas of rugged terrain, such as the Taita Hills, topographic correction is necessary to derive comparable reflectance throughout a SPOT scene. Reliable monitoring of LULC change over time and modelling of land degradation and human population distribution and abundance are of crucial importance to sustainable development, natural resource management, biodiversity conservation, and understanding and mitigating climate change and its impacts. The main purpose of this thesis was to develop and validate enhanced processing of SPOT satellite imagery for use in environmental monitoring and modelling at a landscape level, in regions of the developing world with limited ancillary data availability. The Taita Hills formed the application study site, whilst the Helsinki metropolitan region was used as a control site for validation and assessment of the applied atmospheric correction techniques, where multiangular reflectance field measurements were taken and where horizontal visibility meteorological data concurrent with image acquisition were available. The proposed historical empirical line method (HELM) for absolute atmospheric correction was found to be the only applied technique that could derive surface reflectance factor within an RMSE of < 0.02 ps in the SPOT visible and near-infrared bands; an accuracy level identified as a benchmark for successful atmospheric correction. A multi-scale segmentation/object relationship modelling (MSS/ORM) approach was applied to map LULC in the Taita Hills from the multi-temporal SPOT imagery. This object-based procedure was shown to derive significant improvements over a uni-scale maximum-likelihood technique. The derived LULC data was used in combination with low cost GIS geospatial layers describing elevation, rainfall and soil type, to model degradation in the Taita Hills in the form of potential soil loss, utilizing the simple universal soil loss equation (USLE). Furthermore, human population distribution and abundance were modelled with satisfactory results using only SPOT and GIS derived data and non-Gaussian predictive modelling techniques. The SPOT derived LULC data was found to be unnecessary as a predictor because the first and second order image texture measurements had greater power to explain variation in dwelling unit occurrence and abundance. The ability of the procedures to be implemented locally in the developing world using low-cost or freely available data and software was considered. The techniques discussed in this thesis are considered equally applicable to other medium- and high-resolution optical satellite imagery, as well the utilized SPOT data.Taitavuoret sijaitsevat Kaakkois-Keniassa ja muodostavat pohjoisimman osan Itäisistä Kaarivuorista. Conservation International -järjestön mukaan Itäisten Kaarivuorten alue kuuluu luonnon monimuotoisuuden (biodiversiteetin) kannalta kymmenen tärkeimmän joukkoon maailmassa. Taitavuorilla, kuten monilla muilla kehittyvien maiden alueilla, viime vuosikymmenten aikana väestönkasvu on johtanut merkittäviin maankäytön muutoksiin kuten esimerkiksi kiihtyvään maan heikkenemiseen, erityisesti maaperäeroosion muodossa. Moniaikaiset optisen alueen SPOT-satelliittikuvat tarjoavat arvokasta tietoa ympäristön tilan seurantaan ja ympäristömallinnukseen paikallisella ja alueellisella tasolla. SPOT-satelliittikuva-aineiston hyödyntäminen kvantitatiivisessa kaukokartoituksessa vaatii kuitenkin ilmakehän vaikutuksen poistamista sekä maanpinnan heijastussuhteen määrittämistä. Lisäksi alueilla, joilla maasto on epätasaista, kuten Taitavuorilla, satelliittikuvalle on tehtävä topografinen korjaus, jotta maanpinnan heijastusarvot olisivat vertailukelpoisia koko satelliittikuvan alueella. Maankäytön muutosten monitorointi ja maaperän huononemisen sekä väestön levinneisyyden ja runsauden mallintaminen ovat ratkaisevan tärkeitä kestävälle kehitykselle, luonnonvarojen hallinnalle, biologisen monimuotoisuuden suojelulle ja ilmastonmuutoksen hillitsemiselle ja sen vaikutusten vähentämiselle. Tämän tutkimuksen tarkoituksena oli kehittää ja arvioida tehostettuja prosessointimenetelmiä SPOT-satelliittikuville. Tutkimuksessa kehitettyjä menetelmiä voidaan hyödyntää ympäristön tilan seurannassa ja mallintamisessa kehittyvissä maissa alueilla, joilla täydentävä tutkimusaineisto on puutteellista. Tässä tutkimuksessa Taitavuoret oli varsinainen tutkimusalue, jossa sovellukset kehitettiin ja Helsinki toimi kontrollialueena validoinnissa ja ilmakehäkorjausten hyvyyden arvioinnissa. Tutkimuksessa esitetty ilmakehäkorjaus menetelmä, ns. historical empirical line method (HELM), osoittautui ainoaksi menetelmäksi, jolla maanpinnan heijastussuhteen arvion keskivirhe (RMSE) oli < 0.02 ja suhteellinen tarkkuus < 10%. Yllä mainittu tarkkuustaso on yleisesti hyväksytty vertailuarvo osoittamaan ilmakehäkorjauksen onnistumisen. Monitasoista kuvasegmentointia ja objekti-orientoitunutta mallintamista (MSS/ORM) hyödynnettiin Taitavuorten maankäytön kartoittamisessa SPOT-satelliittikuvalta. Objekti-orientoitunut menetelmä onnistui parantamaan huomattavasti yksi-tasoista maximum-likelihood -luokitusta. Kuvasegmentoinnilla tuotettua Taitavuorten maankäyttöaineistoa käytettiin maaperän huonontumisen mallintamisessa yhdessä alhaisen kustannuksen geospatiaalisten karttatasojen kanssa, jotka kuvaavat mm. Taitavuorten topografiaa, sadantaa ja maaperää. Mallintamisessa arvioitiin potentiaalista maa-aineksen häviämistä ns. USLE-eroosiomallin avulla. Lisäksi Taitavuorten väestön leviämistä ja väestön määrää mallinnettiin SPOT-satelliittikuvalta ja paikkatieto-aineistoista saaduilla geospatiaalisilla muuttujilla. Ennustemallit kalibroitiin käyttäen epälineaarista regressiota. Mallinnuksessa pyrkimyksenä oli sen toistettavuus myös kehittyvissä maissa. Täten mallinnuksessa pyrittiin hyödyntämään alhaisen kustannuksen tai vapaasti saatavilla olevia aineistoja ja ohjelmistoja

“I'm Worth More than That”: Trait Positivity Predicts Increased Rejection of Unfair Financial Offers

Humans react strongly to unfairness, sometimes rejecting inequitable proposals even if this sacrifices personal financial gain. Here we explored whether emotional dispositions - trait tendencies to experience positive or negative feelings – shape the rejection of unfair financial offers. Participants played an Ultimatum Game, where the division of a sum of money is proposed and the player can accept or reject this offer. Individuals high in trait positivity and low in trait negativity rejected more unfair offers. These relationships could not be explained by existing accounts which argue that rejection behaviour results from a failure to regulate negative emotions, or serves to arbitrate social relationships and identity. Instead, the relationship between dispositional affect and rejection behaviour may be underpinned by perceived self worth, with those of a positive disposition believing that they are “worth more than that” and those of a negative disposition resigning themselves to “taking the crumbs from under the table”

A predictive modelling technique for human population distribution and abundance estimation using remote sensing and geospatial data in a rural mountainous area in Kenya

Peer reviewe

Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults

BACKGROUND: Heterocellular hereditary persistence of fetal hemoglobin (HPFH) is a common multifactorial trait characterized by a modest increase of fetal hemoglobin levels in adults. We previously localized a Quantitative Trait Locus for HPFH in an extensive Asian-Indian kindred to chromosome 6q23. As part of the strategy of positional cloning and a means towards identification of the specific genetic alteration in this family, a thorough annotation of the candidate interval based on a strategy of in silico / wet biology approach with comparative genomics was conducted. RESULTS: The ~1.5 Mb candidate region was shown to contain five protein-coding genes. We discovered a very large uncharacterized gene containing WD40 and SH3 domains (AHI1), and extended the annotation of four previously characterized genes (MYB, ALDH8A1, HBS1L and PDE7B). We also identified several genes that do not appear to be protein coding, and generated 17 kb of novel transcript sequence data from re-sequencing 97 EST clones. CONCLUSION: Detailed and thorough annotation of this 1.5 Mb interval in 6q confirms a high level of aberrant transcripts in testicular tissue. The candidate interval was shown to exhibit an extraordinary level of alternate splicing – 19 transcripts were identified for the 5 protein coding genes, but it appears that a significant portion (14/19) of these alternate transcripts did not have an open reading frame, hence their functional role is questionable. These transcripts may result from aberrant rather than regulated splicing

Monte Carlo simulation and remote sensing applied to agricultural survey sampling strategy in Taita Hills, Kenya

Peer reviewe

Is there a renoprotective value to leukodepletion during heart valve surgery? A randomized controlled trial (ROLO)

Background: Acute Kidney Injury (AKI) adversely affects outcomes after cardiac surgery. A major mediator of AKI is the activation of leukocytes through exposure to the cardiopulmonary bypass circuit. We evaluate the use of leukodepletion filters throughout bypass to protect against post-operative AKI by removing activated leukocytes during cardiac surgery. Methods: This is a single-centre, double-blind, randomized controlled trial comparing the use of leukodepletion versus a standard arterial filter throughout bypass. Elective adult patients undergoing heart valve surgery with or without concomitant procedures were investigated. The primary clinical outcome measured was the development of AKI according to the KDIGO criteria. Secondary measures included biomarkers of renal tubular damage (urinary Retinol Binding Protein and Kidney Injury Molecule-1), glomerular kidney injury (urinary Micro Albumin and serum Cystatin C) and urinary Neutrophil Gelatinase Associated Lipocalin, as well as the length of hospital stay and quality of life measures through EQ-5D-5L questionnaires. Results: The ROLO trial randomized 64 participants with a rate of recruitment higher than anticipated (57% achieved, 40% anticipated). The incidence of AKI was greater in the leukodepletion filter group (44% versus 23%, risk difference 21, 95% CI − 2 to 44%). This clinical finding was supported by biomarker levels especially by a tendency toward glomerular insult at 48 h, demonstrated by a raised serum Cystatin C (mean difference 0.11, 95% CI 0.00 to 0.23, p = 0.068) in the leukodepleted group. There was however no clear association between the incidence or severity of AKI and length of hospital stay. On average, health related quality of life returned to pre-operative levels in both groups within 3 months of surgery. Conclusions: Leukocyte depletion during cardiopulmonary bypass does not significantly reduce the incidence of AKI after valvular heart surgery. Other methods to ameliorate renal dysfunction after cardiac surgery need to be investigated. Trial registration: The trial was registered by the International Standard Randomized Controlled Trial Number Registry ISRCTN42121335. Registered on the 18 February 2014. The trial was run by the Bristol Clinical Trials and Evaluation Unit. This trial was financially supported by the National Institute of Health Research (Research for Patient Benefit), award ID: PB-PG-0711-25,090

Agricultural Expansion and Its Consequences in the Taita Hills, Kenya

The indigenous cloud forests in the Taita Hills have suffered substantial degradation for several centuries due to agricultural expansion. Additionally, climate change imposes an imminent threat for local economy and environmental sustainability. In such circumstances, elaborating tools to conciliate socioeconomic growth and natural resources conservation is an enormous challenge. This chapter describes applications of remote sensing and geographic information systems for assessing land-cover changes in the Taita Hills and its surrounding lowlands. Furthermore, it provides an overall assessment on the consequences of land-cover changes to water resources, biodiversity and livelihoods. The analyses presented in this study were undertaken at multiple spatial scales, using field data, airborne digital images and satellite imagery. Furthermore, a modelling framework was designed to delineate agricultural expansion projections and evaluate the future impacts of agriculture on soil erosion and irrigation water demand.Peer reviewe

The commodification and exploitation of fresh water: Property, human rights and green criminology

In recent years, both developing and industrialised societies have experienced riots and civil unrest over the corporate exploitation of fresh water. Water conflicts increase as water scarcity rises and the unsustainable use of fresh water will continue to have profound implications for sustainable development and the realisation of human rights. Rather than states adopting more costly water conservation strategies or implementing efficient water technologies, corporations are exploiting natural resources in what has been described as the “privatization of water”. By using legal doctrines, states and corporations construct fresh water sources as something that can be owned or leased. For some regions, the privatization of water has enabled corporations and corrupt states to exploit a fundamental human right. Arguing that such matters are of relevance to criminology, which should be concerned with fundamental environmental and human rights, this article adopts a green criminological perspective and draws upon Treadmill of Production theory

TLR9 expression in chronic lymphocytic leukemia identifies a promigratory subpopulation and novel therapeutic target

Chronic lymphocytic leukemia (CLL) remains incurable despite B-cell receptor–targeted inhibitors revolutionizing treatment. This suggests that other signaling molecules are involved in disease escape mechanisms and resistance. Toll-like receptor 9 (TLR9) is a promising candidate that is activated by unmethylated cytosine guanine dinucleotide–DNA. Here, we show that plasma from patients with CLL contains significantly more unmethylated DNA than plasma from healthy control subjects (P < .0001) and that cell-free DNA levels correlate with the prognostic markers CD38, β(2)-microglobulin, and lymphocyte doubling time. Furthermore, elevated cell-free DNA was associated with shorter time to first treatment (hazard ratio, 4.0; P = .003). We also show that TLR9 expression was associated with in vitro CLL cell migration (P < .001), and intracellular endosomal TLR9 strongly correlated with aberrant surface expression (sTLR9; r = 0.9). In addition, lymph node–derived CLL cells exhibited increased sTLR9 (P = .016), and RNA-sequencing of paired sTLR9(hi) and sTLR9(lo) CLL cells revealed differential transcription of genes involved in TLR signaling, adhesion, motility, and inflammation in sTLR9(hi) cells. Mechanistically, a TLR9 agonist, ODN2006, promoted CLL cell migration (P < .001) that was mediated by p65 NF-κB and STAT3 transcription factor activation. Importantly, autologous plasma induced the same effects, which were reversed by a TLR9 antagonist. Furthermore, high TLR9 expression promoted engraftment and rapid disease progression in a NOD/Shi-scid/IL-2Rγ(null) mouse xenograft model. Finally, we showed that dual targeting of TLR9 and Bruton’s tyrosine kinase (BTK) was strongly synergistic (median combination index, 0.2 at half maximal effective dose), which highlights the distinct role for TLR9 signaling in CLL and the potential for combined targeting of TLR9 and BTK as a more effective treatment strategy in this incurable disease

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases