Browsing by Subject "MAP"

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  • Vanhatalo, Jarno; Li, Zitong; Sillanpää, Mikko J. (2019)
    Motivation: Recent advances in high dimensional phenotyping bring time as an extra dimension into the phenotypes. This promotes the quantitative trait locus (QTL) studies of function-valued traits such as those related to growth and development. Existing approaches for analyzing functional traits utilize either parametric methods or semi-parametric approaches based on splines and wavelets. However, very limited choices of software tools are currently available for practical implementation of functional QTL mapping and variable selection. Results: We propose a Bayesian Gaussian process (GP) approach for functional QTL mapping. We use GPs to model the continuously varying coefficients which describe how the effects of molecular markers on the quantitative trait are changing over time. We use an efficient gradient based algorithm to estimate the tuning parameters of GPs. Notably, the GP approach is directly applicable to the incomplete datasets having even larger than 50% missing data rate (among phenotypes). We further develop a stepwise algorithm to search through the model space in terms of genetic variants, and use a minimal increase of Bayesian posterior probability as a stopping rule to focus on only a small set of putative QTL. We also discuss the connection between GP and penalized B-splines and wavelets. On two simulated and three real datasets, our GP approach demonstrates great flexibility for modeling different types of phenotypic trajectories with low computational cost. The proposed model selection approach finds the most likely QTL reliably in tested datasets.
  • Mascher, Martin; Muehlbauer, Gary J.; Rokhsar, Daniel S.; Chapman, Jarrod; Schmutz, Jeremy; Barry, Kerrie; Munoz-Amatriain, Maria; Close, Timothy J.; Wise, Roger P.; Schulman, Alan H.; Himmelbach, Axel; Mayer, Klaus F. X.; Scholz, Uwe; Poland, Jesse A.; Stein, Nils; Waugh, Robbie (2013)
  • Kivikoski, Mikko; Rastas, Pasi; Löytynoja, Ari; Merila, Juha (2021)
    We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads, we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.6-Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.
  • Chen, Linxiao; Turunen, Joonas (2020)
    We consider Boltzmann random triangulations coupled to the Ising model on their faces, under Dobrushin boundary conditions and at the critical point of the model. The first part of this paper computes explicitly the partition function of this model by solving its Tutte's equation, extending a previous result by Bernardi and Bousquet-Melou (J Combin Theory Ser B 101(5):315-377, 2011) to the model with Dobrushin boundary conditions. We show that the perimeter exponent of the model is 7/3 in contrast to the exponent 5/2 for uniform triangulations. In the second part, we show that the model has a local limit in distribution when the two components of the Dobrushin boundary tend to infinity one after the other. The local limit is constructed explicitly using the peeling process along an Ising interface. Moreover, we show that the main interface in the local limit touches the (infinite) boundary almost surely only finitely many times, a behavior opposite to that of the Bernoulli percolation on uniform maps. Some scaling limits closely related to the perimeters of finite clusters are also obtained.
  • Hjort, Jan; Karjalainen, Olli; Aalto, Juha Antero; Westermann, Sebastian; Romanovsky, Vladimir; Nelson, Frederick; Etzelmüller, Bernd; Luoto, Miska (2018)
    Degradation of near-surface permafrost can pose a serious threat to the utilization of natural resources, and to the sustainable development of Arctic communities. Here we identify at unprecedentedly high spatial resolution infrastructure hazard areas in the Northern Hemisphere's permafrost regions under projected climatic changes and quantify fundamental engineering structures at risk by 2050. We show that nearly four million people and 70% of current infrastructure in the permafrost domain are in areas with high potential for thaw of near-surface permafrost. Our results demonstrate that one-third of pan-Arctic infrastructure and 45% of the hydrocarbon extraction fields in the Russian Arctic are in regions where thaw-related ground instability can cause severe damage to the built environment. Alarmingly, these figures are not reduced substantially even if the climate change targets of the Paris Agreement are reached.
  • Koort, Joanna; Coenye, Tom; Vandamme, Peter; Sukura, Antti; Björkroth, Johanna (Society for General Microbiology, 2004)
    Isolates 302, 334, 356, 377 and 379, detected in modified atmosphere packaged (MAP) broiler meat, together with LMG 12317T and LMG 13617, detected in dog tonsils, were analysed in a polyphasic taxonomy study including numerical analysis of ribopatterns and whole cell protein patterns, 16S rDNA sequence analysis, DNA-DNA hybridisation and determination of some phenotypic properties. The results indicated that these isolates represent a new species in the genus Enterococcus. The isolates showed classical phenotypic reactions for the genus Enterococcus with the exception of not possessing the Lancefield group D antigen. Isolates 334, LMG 12317T, and LMG 13617 showed the highest 16S rDNA sequence similarity (98.3-99.0%) with the Enterococcus pallens type strain. In the distance matrix tree based on 16S rDNA sequences, the three isolates were located in the Enterococcus avium –group with E. pallens as their closest phylogenic neighbour. Numerical analyses of whole cell protein patterns and HindIII/EcoRI ribotypes placed all seven isolates together in a single cluster separated from the E. avium group reference strains. The DNA-DNA hybridisation level between strains 334 and LMG 12317T was 93.5% confirming that they represent the same species. Low hybridisation levels (12-30%) were, on the other hand, obtained with the E. pallens and Enterococcus raffinosus type strains. The name Enterococcus hermanniensis sp. nov. is proposed, with strain LMG 12317T (=CCUG 48100 T) as the type strain.
  • Björkroth, Johanna; Ristiniemi, Minna; Vandamme, Peter; Korkeala, Hannu (Elsevier, 2005)
    In order to show which of the initial lactic acid bacteria (LAB) contaminants are also causing spoilage of a modified-atmosphere-packaged (MAP), marinated broiler leg product at 6ºC, LAB were enumerated and identified on the 2nd and 17th day following manufacture. A total of 8 fresh and 13 spoiled packages were studied for LAB levels. In addition, aerobic mesophilic bacteria and Enterobacteriaceae were determined. The average CFU/g values in the 8 fresh packages were 1.3 × 103, 9.8 × 103 and 2.6 × 102 on de Man Rogosa Sharpe agar (MRS), Plate Count Agar (PCA) and Violet Red Bile Glucose agar (VRBG), respectively. The commercial shelf life for the product had been set as 12 days and all packages analyzed on the 17th day were deemed unfit for human consumption by the sensory analysis. The corresponding CFU/g averages in the spoiled product were 1.4 × 109, 1.1 × 109 and 3.9 × 107 on MRS, PCA and VRBG agar, respectively. For characterization of LAB population, 104 colonies originating from the fresh and 144 colonies from the spoiled packages were randomly picked, cultured pure and identified to species level using a 16 and 23S rDNA HindIII RFLP (ribotyping) database. The results showed that enterococci (35.7% of the LAB population) were dominating in the fresh product whereas carnobacteria (59.7%) dominated among the spoilage LAB. Enterococcus faecalis, Carnobacterium piscicola and Carnobacterium divergens were the main species detected. In general, when the initial LAB population is compared to the spoilage LAB, a shift from homofermentative cocci towards carnobacteria, Lactobacillus sakei/curvatus and heterofermentative rods is seen in this marinated product.
  • Juntheikki, Joni (Helsingfors universitet, 2014)
    Purpose of this thesis is to estimate the carbon sequestration potential in eucalyptus plantations in Uruguay. This study also aims to show how beneficial these plantations are for carbon sinks. The aim of this research is calculate total carbon balance in eucalyptus plantations and compare the results to degraded lands. This study is first-of-its-kind study in Uruguay, but not unique globally. The objective was to use a modeling approach to formulate the results. The methodology of this study is based to the dynamic growth model (CO2fix V3.1). Model is developed to calculate and estimate forest carbon fluxes and stocks. In this study the model was utilized for estimating how much carbon is sequestered in eucalyptus plantations and soils. In this thesis the model was used to simulate eucalyptus forest plantations that stem from numerous studies and different data. Ad hoc Excel model was generated to form calculated results from the simulated data. A separate sensitivity analysis is also formulated to reveal a possible different outcome. The framework is based on a stand-level inventory data of forestry plantations provided by the Ministry of Uruguay (MGAP) and companies. Also multiple scientific reports and previous studies were used as guidelines for simulations and results. The forest stand, yield, soil and weather data used for this study are from three different departments. There are over 700 000 hectares of different species of eucalyptus plantations in Uruguay. The theoretical framework was tested computationally with eleven simulations. CO2fix was parameterized for fast-growing eucalyptus species used in different parts of Uruguay. The model gave outputs per hectare and then this result was scaled up to the national level. This study will also estimate how much grassland (Pampa) and former pasture land could sequester carbon. Situation prior to plantation is a baseline scenario and it is compared to the expected carbon sequestration of plantations. The model is also used to calculate the effect of changing rotation length on carbon stocks of forest ecosystem (forest vegetation and soil) and wood products. The results of this study show that currently the 707,674 hectares of eucalyptus plantations in Uruguay have the potential to sequester 65 million tonnes of carbon and reduce 238 million tonnes of CO2. The calculated carbon storage is 38 and simulated 25 million tonnes of C, products are deducted from the equation. During 22 years (1990–2012) the annual carbon sequestration benefit (afforestation-baseline) without products is 1 757 847 Mg C. The results suggest that it is reasonable to establish eucalyptus plantations on degraded, grassland (Pampa) and abandoned pasture land. The implications of the results are that eucalyptus plantations in Uruguay actually enhance carbon sequestration, are carbon sinks and store more carbon than grassland and abandoned pasture land. Plantations have a vast sequestration potential and are important in mitigating of CO2 emission and effects of the climate change. The findings endorse the significance of plantations to increase carbon sinks and this role will broaden in the future. The most relevant findings of this study are that afforestation increases the soil carbon in 10-year rotation plantations by 34% (101.1>75.6) and in 12-year rotation 38% (104.4>75.6 Mg Cha-1) in a 60-year simulation. The net (afforestation-baseline) average carbon stock benefit in the soil is 25.5 Mg C ha?1 in a 60-year simulation. The (CO2Fix) model indicate that the total average carbon sequestration for eucalyptus plantations is 92.3 Mg Cha?1. The average total carbon storage ranges from 25.8–138.5 Mg Cha?1 during a 60-year simulation. The simulations show that the net annual carbon storage in the living biomass is 29.1, 25.5 (soil) and 37.6 Mg C (products) on the average scenario. There is some fluctuation in the sequestration results in other 10 simulations. Previous studies have showed that the average carbon stock for eucalyptus plantations varies from 30–60 Mg C ha-1, when soil and products are deducted. The capacity of forest ecosystems to sequester carbon in the long run could be even more strengthened if a rotation length increases. Extending rotation from 10 to 12 years increased the average soil carbon stock from 25.5 to 28.8 Mg C (by 13%) in 60 year simulation. The results also indicate that mean annual precipitation (MAP) alters the carbon sinks of the forest ecosystem. There are some limitations in this study and they are clearly explained and analyzed. Hence, most of the results are estimations. Ministry and companies need to prolong planting of trees and even intensify annual programs in order to achieve carbon sequestration targets. Further research is needed to get an estimate of the total forest ecosystem carbon storages and fluxes.
  • Mpindi, John Patrick; Sara, Henri; Haapa-Paananen, Saija; Kilpinen, Sami; Pisto, Tommi; Bucher, Elmar; Ojala, Kalle; Iljin, Kristiina; Vainio, Paula; Bjorkman, Mari; Gupta, Santosh; Kohonen, Pekka; Nees, Matthias; Kallioniemi, Olli (2011)
    Background Meta-analysis of gene expression microarray datasets presents significant challenges for statistical analysis. We developed and validated a new bioinformatic method for the identification of genes upregulated in subsets of samples of a given tumour type (‘outlier genes’), a hallmark of potential oncogenes. Methodology A new statistical method (the gene tissue index, GTI) was developed by modifying and adapting algorithms originally developed for statistical problems in economics. We compared the potential of the GTI to detect outlier genes in meta-datasets with four previously defined statistical methods, COPA, the OS statistic, the t-test and ORT, using simulated data. We demonstrated that the GTI performed equally well to existing methods in a single study simulation. Next, we evaluated the performance of the GTI in the analysis of combined Affymetrix gene expression data from several published studies covering 392 normal samples of tissue from the central nervous system, 74 astrocytomas, and 353 glioblastomas. According to the results, the GTI was better able than most of the previous methods to identify known oncogenic outlier genes. In addition, the GTI identified 29 novel outlier genes in glioblastomas, including TYMS and CDKN2A. The over-expression of these genes was validated in vivo by immunohistochemical staining data from clinical glioblastoma samples. Immunohistochemical data were available for 65% (19 of 29) of these genes, and 17 of these 19 genes (90%) showed a typical outlier staining pattern. Furthermore, raltitrexed, a specific inhibitor of TYMS used in the therapy of tumour types other than glioblastoma, also effectively blocked cell proliferation in glioblastoma cell lines, thus highlighting this outlier gene candidate as a potential therapeutic target. Conclusions/Significance Taken together, these results support the GTI as a novel approach to identify potential oncogene outliers and drug targets. The algorithm is implemented in an R package (Text S1).
  • Hassan, Shabbeer; Surakka, Ida; Taskinen, Marja-Riitta; Salomaa, Veikko; Palotie, Aarno; Wessman, Maija; Tukiainen, Taru; Pirinen, Matti; Palta, Priit; Ripatti, Samuli (2021)
    Previous research has shown that using population-specific reference panels has a significant effect on downstream population genomic analyses like haplotype phasing, genotype imputation, and association, especially in the context of population isolates. Here, we developed a high-resolution recombination rate mapping at 10 and 50 kb scale using high-coverage (20-30x) whole-genome sequenced data of 55 family trios from Finland and compared it to recombination rates of non-Finnish Europeans (NFE). We tested the downstream effects of the population-specific recombination rates in statistical phasing and genotype imputation in Finns as compared to the same analyses performed by using the NFE-based recombination rates. We found that Finnish recombination rates have a moderately high correlation (Spearman's rho = 0.67-0.79) with NFE, although on average (across all autosomal chromosomes), Finnish rates (2.268 +/- 0.4209 cM/Mb) are 12-14% lower than NFE (2.641 +/- 0.5032 cM/Mb). Finnish recombination map was found to have no significant effect in haplotype phasing accuracy (switch error rates similar to 2%) and average imputation concordance rates (97-98% for common, 92-96% for low frequency and 78-90% for rare variants). Our results suggest that haplotype phasing and genotype imputation mostly depend on population-specific contexts like appropriate reference panels and their sample size, but not on population-specific recombination maps. Even though recombination rate estimates had some differences between the Finnish and NFE populations, haplotyping and imputation had not been noticeably affected by the recombination map used. Therefore, the currently available HapMap recombination maps seem robust for population-specific phasing and imputation pipelines, even in the context of relatively isolated populations like Finland.
  • Huang, Jie; Howie, Bryan; McCarthy, Shane; Memari, Yasin; Walter, Klaudia; Min, Josine L.; Danecek, Petr; Malerba, Giovanni; Trabetti, Elisabetta; Zheng, Hou-Feng; Gambaro, Giovanni; Richards, J. Brent; Durbin, Richard; Timpson, Nicholas J.; Marchini, Jonathan; Soranzo, Nicole; UK10K Consortium; Paunio, Tiina (2015)
    Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants.
  • Susiluoto, Tuija; Korkeala, Hannu; Björkroth, Johanna (Elsevier, 2002)
    Lactic acid bacteria (LAB) in retail, modified-atmosphere-packaged (MAP), marinated broiler meat strips on sell-by day were mainly identified as Leuconostoc gasicomitatum. A total of 32 packages, 3 to 5 packages of 7 differently marinated broiler meat products, were studied at the end of the producer-defined shelf life (at 6ºC, 7 to 9 days depending on the manufacturer). Prior to the microbiological analyses, appearance and smell of the product was checked and pH measured. Bacteria were cultured on MRS and Tomato Juice Agar (TJA), Rogosa SL agar (SLA), Plate Count Agar (PCA) and Streptomycin Thallium Acetate Agar (STAA) for the enumeration of LAB, lactobacilli, total bacterial count and B. thermosphacta, respectively. The average CFU/g of the 32 packages was 2.3 × 108 on PCA. The highest bacterial average, 3.1 × 108, was recovered on TJA, the corresponding CFU/g averages on MRS and SLA being 2.3 × 108 and 1.3 × 108, respectively. Despite the high LAB numbers, radical spoilage changes such as unpleasant odor, slime production and formation of gas were not recognized. B. thermosphacta did not form a significant part of the bacterial population since none of the levels exceeded the spoilage threshold level of 105 CFU/g reported in previous studies. In order to characterize the dominating LAB population, as many as 85, 85 and 88 colonies from MRS, TJA and SLA, respectively, were randomly picked and cultured pure. LAB were identified to species level using a 16 and 23S rDNA HindIII RFLP (ribotyping) database. Fifty-six of the 170 isolates picked from the non-selective LAB media (MRS and TJA) were identified as Leuconostoc gasicomitatum, followed by Carnobacterium divergens (41 isolates), Lactobacillus sakei and Lactobacillus curvatus subsp. melibiosus (31 isolates) and Lactobacillus curvatus subsp. curvatus (20 isolates) species. SLA proved not to be completely selective for lactobacilli because the growth of Leuconostoc spp. was not inhibited, Carnobacterium spp. were the only species not detected on SLA.
  • Planck Collaboration; Akrami, Y.; Keihanen, E.; Kiiveri, K.; Kurki-Suonio, H.; Lindholm, V.; Savelainen, M.; Suur-Uski, A. -S.; Valiviita, J. (2020)
    We present full-sky maps of the cosmic microwave background (CMB) and polarized synchrotron and thermal dust emission, derived from the third set of Planck frequency maps. These products have significantly lower contamination from instrumental systematic effects than previous versions. The methodologies used to derive these maps follow closely those described in earlier papers, adopting four methods (Commander, NILC, SEVEM, and SMICA) to extract the CMB component, as well as three methods (Commander, GNILC, and SMICA) to extract astrophysical components. Our revised CMB temperature maps agree with corresponding products in the Planck 2015 delivery, whereas the polarization maps exhibit significantly lower large-scale power, reflecting the improved data processing described in companion papers; however, the noise properties of the resulting data products are complicated, and the best available end-to-end simulations exhibit relative biases with respect to the data at the few percent level. Using these maps, we are for the first time able to fit the spectral index of thermal dust independently over 3 degrees regions. We derive a conservative estimate of the mean spectral index of polarized thermal dust emission of beta (d)=1.55 +/- 0.05, where the uncertainty marginalizes both over all known systematic uncertainties and different estimation techniques. For polarized synchrotron emission, we find a mean spectral index of beta (s)=-3.1 +/- 0.1, consistent with previously reported measurements. We note that the current data processing does not allow for construction of unbiased single-bolometer maps, and this limits our ability to extract CO emission and correlated components. The foreground results for intensity derived in this paper therefore do not supersede corresponding Planck 2015 products. For polarization the new results supersede the corresponding 2015 products in all respects.
  • Parkkinen, Juuso A.; Kaski, Samuel (2014)
  • Amara, Edward; Heiskanen, Janne; Aynekulu, Ermias; Pellikka, Petri Kauko Emil (2019)
    Global sustainable development goals include reducing greenhouse gas emissions from land-use change and maintaining biodiversity. Many studies have examined carbon stocks and tree species diversity, but few have studied the humid Guinean savanna ecosystem. This study focuses on a humid savanna landscape in northern Sierra Leone, aiming to assess carbon stocks and tree species diversity and compare their relationships in different vegetation types. We surveyed 160 sample plots (0.1 ha) in the field for tree species, aboveground carbon (AGC) and soil organic carbon (SOC). In total, 90 tree species were identified in the field. Gmelina arborea, an exotic tree species common in the foothills of the Kuru Hills Forest Reserve, and Combretum glutinosum, Pterocarpus erinaceous and Terminaria glaucescens, which are typical savanna trees, were the most common species. At landscape level, the mean AGC stock was 29.4 Mg C ha(-1) (SD 21.3) and mean topsoil (0-20 cm depth) SOC stock was 42.2 Mg C ha(-1) (SD 20.6). Mean tree species richness and Shannon index per plot were 7 (SD 4) and 1.6 (SD 0.6), respectively. Forests and woodlands had significantly higher mean AGC and tree species richness than bushland, wooded grassland or cropland (p <0.05). In the forest and bushland, a small number of large diameter trees covered a large portion of the total AGC stocks. Furthermore, a moderate linear correlation was observed between AGC and tree species richness (r = 0.475, p <0.001) and AGC and Shannon index (r = 0.375, p <0.05). The correlation between AGC and SOC was weak (r = 0.17, p <0.05). The results emphasise the role of forests and woodlands and large diameter trees in retaining AGC stocks and tree species diversity in the savanna ecosystem.
  • Koort, Joanna; Coenye, Tom; Vandamme, Peter; Björkroth, Johanna (Elsevier, 2006)
    Lactic acid bacteria (LAB) isolated from marinated or non-marinated, modified atmosphere packaged (MAP) broiler leg products and air samples of a large-scale broiler meat processing plant were identified and analyzed for their phenotypic properties. Previously, these strains had been found to be coccal LAB. However, the use of a 16 and 23S rRNA gene RFLP database had not resulted in species identification because none of the typically meat-associated LAB type strains had clustered together with these strains in the numerical analysis of the RFLP patterns. To establish the taxonomic position of these isolates, 16S rRNA gene sequence analysis, numerical analysis of ribopatterns, and DNA–DNA hybridization experiments were done. The 16S rRNA gene sequences of three isolates possessed the highest similarities (over 99%) with the sequence of S. parauberis type strain. However, in the numerical analysis of HindIII ribopatterns, the type strain did not cluster together with these isolates. Reassociation values between S. parauberis type or reference strain and the strains studied varied from 82 to 97%, confirming that these strains belong to S. parauberis. Unexpectedly, most of the broiler meat-originating strains studied for their phenotypical properties did not utilize lactose at all and the same strains fermented also galactose very weakly, properties considered atypical for S. parauberis. This is, to our knowledge, the first report of lactose negative S. parauberis strains and also the first report associating S. parauberis with broiler slaughter and meat products.
  • Veach, Victoria; Moilanen, Atte; Di Minin, Enrico (2017)
    Including threats in spatial conservation prioritization helps identify areas for conservation actions where biodiversity is at imminent risk of extinction. At the global level, an important limitation when identifying spatial priorities for conservation actions is the lack of information on the spatial distribution of threats. Here, we identify spatial conservation priorities under three prominent threats to biodiversity (residential and commercial development, agricultural expansion, and forest loss), which are primary drivers of habitat loss and threaten the persistence of the highest number of species in the International Union for the Conservation of Nature (IUCN) Red List, and for which spatial data is available. We first explore how global priority areas for the conservation of vertebrate (mammals, birds, and amphibians) species coded in the Red List as vulnerable to each threat differ spatially. We then identify spatial conservation priorities for all species vulnerable to all threats. Finally, we identify the potentially most threatened areas by overlapping the identified priority areas for conservation with maps for each threat. We repeat the same with four other well-known global conservation priority area schemes, namely Key Biodiversity Areas, Biodiversity Hotspots, the global Protected Area Network, and Wilderness Areas. We find that residential and commercial development directly threatens only about 4% of the global top 17% priority areas for species vulnerable under this threat. However, 50% of the high priority areas for species vulnerable to forest loss overlap with areas that have already experienced some forest loss. Agricultural expansion overlapped with similar to 20% of high priority areas. Biodiversity Hotspots had the greatest proportion of their total area under direct threat from all threats, while expansion of low intensity agriculture was found to pose an imminent threat to Wilderness Areas under future agricultural expansion. Our results identify areas where limited resources should be allocated to mitigate risks to vertebrate species from habitat loss.
  • Langner, Andreas; Miettinen, Jukka; Kukkonen, Markus; Vancutsem, Christelle; Simonetti, Dario; Vieilledent, Ghislain; Verhegghen, Astrid; Gallego, Javier; Stibig, Hans-Juergen (2018)
    This study presents an approach to forest canopy disturbance monitoring in evergreen forests in continental Southeast Asia, based on temporal differences of a modified normalized burn ratio (NBR) vegetation index. We generate NBR values from each available Landsat 8 scene of a given period. A step of ' self-referencing' normalizes the NBR values, largely eliminating illumination/topography effects, thus maximizing inter-comparability. We then create yearly composites of these self-referenced NBR (rNBR) values, selecting per pixel the maximum rNBR value over each observation period, which reflects the most open canopy cover condition of that pixel. The ArNBR is generated as the difference between the composites of two reference periods. The methodology produces seamless and consistent maps, highlighting patterns of canopy disturbances (e. g., encroachment, selective logging), and keeping artifacts at minimum level. The monitoring approach was validated within four test sites with an overall accuracy of almost 78% using very high resolution satellite reference imagery. The methodology was implemented in a Google Earth Engine (GEE) script requiring no user interaction. A threshold is applied to the final output dataset in order to separate signal from noise. The approach, capable of detecting sub-pixel disturbance events as small as 0.005 ha, is transparent and reproducible, and can help to increase the credibility of monitoring, reporting and verification (MRV), as required in the context of reducing emissions from deforestation and forest degradation (REDD+).
  • Kian, Yavar; Kurylev, Yaroslav; Lassas, Matti; Oksanen, Lauri (2019)
    We consider a restricted Dirichlet-to-Neumann map Lambda(T)(S, R) associated with the operator partial derivative(2)(t) - Delta(g) + A + q where Delta(g) is the Laplace-Beltrami operator of a Riemannian manifold (M, g), and A and q are a vector field and a function on M. The restriction Lambda(T)(S, R) corresponds to the case where the Dirichlet traces are supported on (0, T) x S and the Neumann traces are restricted on (0, T) x R. Here S and R are open sets, which may be disjoint, on the boundary of M. We show that Lambda(T)(S, R) determines uniquely, up the natural gauge invariance, the lower order terms A and q in a neighborhood of the set R assuming that R is strictly convex and that the wave equation is exactly controllable from S in time T/2. We give also a global result under a convex foliation condition. The main novelty is the recovery of A and q when the sets R and S are disjoint. We allow A and q to be non-self-adjoint, and in particular, the corresponding physical system may have dissipation of energy. Crown Copyright (C) 2019 Published by Elsevier Inc. All rights reserved.