A proposed decision support tool for wood procurement planning based on stereo-matching of aerial images

In Sweden the cap portion of the harvested stem volume derives from Non-Industrial Private Forest (NIPF) owners. In the current study a Decision Support Tool (DST) for wood procurement planning based on stereo-matching of aerial images is presented. Two stages are described, namely (1) automatic segmentation using a Mean Shift algorithm; (2) wall-to-wall mapping of the stands using Semi-Global Matching (SGM) in combination with a high-resolution Digital Elevation Model (DEM). The study was conducted in a coniferous boreal forest area in northern Sweden. 365 sample plots (8 m radius) were measured in the field where HGV (dm) ranged between 49.0 - 246.0 dm (mean 139.3 dm), DGV 67.0 - 400.0 mm (mean 196.8 mm), VOL 7.0 - 665.0 m3/ha (mean 151.1 m3/ha) and BA 20.0 - 635.0 dm2/ha (mean 204.9 dm2/ha). Point clouds were extracted from the aerial images with 60% forward overlap. A canopy cover metric was used to improve the VOL and BA estimations. Plot level accuracies were calculated using leave-one-stand-out-cross-validation resulting in a Root Mean Square Error (in percent of surveyed mean) for: HGV 11.2%, DGV 15.2%, VOL (m3/ha) 33.5% and BA 30.3%. Each stand was given an average of the estimated forest variables enabling ranking between the stands based on their estimated values. The results indicated that the proposed DST can be used as a support in wood procurement planning. Aerial images are an appropriate data source in the proposed DST, mainly because of the readily availability and low cost

Identification of conflict stands by means of laser scanning

The interest in harvesting wood fuel in conflict stands has grown in recent years as a consequence of the increased demand for biofuel. Conflict stands are young forests that have not been cleaned and have a large number of stems ha-1with a great height and diameter distribution. This means that traditional field measurements in conflict stands are difficult and very time consuming. Therefore, the forestry sector is in need of new, more efficient inventory methods. In this study, the Lidar data from Lantmäteriet’s (the Swedish mapping, cadastral and land registration authorities) new national height model was used in combination with plots from the Swedish national forest inventory from 2009 to create functions for; height, volume, diameter and number of stems. The functions were used to create rasters corresponding to the estimated variables. The basis for the identification of the conflict stands in the rasters was the criteria for: height, volume and diameter. In the study 112 plots was used to estimate the basal area weighted mean height. In the estimation of diameter in breast height, volume and stem numbers 33 sample plots were used after the stratification based on the average height (<12 m). The results show that the function for basal area weighted mean height had an adjusted determination degree (R2-adj) of 92,0 % and a standard deviation (SD) of 1.4 m. Volume and diameter had anR2-adj of 88.2 % and 75,6 %, SD of 11.5 m3sk ha-1 and 15,3 mm. The high accuracy of the estimates indicates that conflict stands can be identified by means of laser scanning. The study also shows that it is difficult to estimate the stem numbers ha-1, the function had an R2-adj of 10.7 % and a SD of 7352 stems ha-1.Intresset för skörd av skogsbränsle i så kallade konfliktbestånd har ökat under de senaste åren som en konsekvens av det ökade behovet av biobränsle. Konfliktbestånd är ungskogar som inte har röjts och har därför många träd ha-1 med en stor höjd- och diameterspridning. Det gör att traditionella fältmätningar i konfliktbestånd är svåra och väldigt tidskrävande. Därför är skogsbruket i behov av nya effektivare inventeringsmetoder. I den här studien användes Lidar-data från Lantmäteriets nya nationella höjdmodell (NNH) i kombination med provytor från Riksskogstaxeringen år 2009 för att skapa funktioner för höjd, volym, diameter och stamantal. Dessa användes sedan för att skapa raster som motsvarade de skattade variablerna. Genom att använda kriterier för höjd, volym och diameter låg dessa raster till grund för identifieringen av konfliktbestånd. I studien användes 112 provytor för att skatta grundytevägd medelhöjd (Hgv). Vid skattningen för volym, brösthöjdsdiameter (Dbh) och stamantal användes efter stratifiering baserad på Hgv (<12 m) 33 provytor. Resultaten visar att funktionen för Hgv hade en korrigerad förklaringsgrad (R2-adj) på 92 % och en standardavvikelse (SD) på 1,4 m. Volym och Dbh hade en R2-adj på 88,2 % respektive 75,6% samt en SD på 11,5 m3sk ha-1 och 15,3 mm. Studien visade även att det är svårt att skatta stamantal, funktionen hade en R2-adj på 10,7 % och en SD på 7352 stammar ha-1. Den höga noggrannheten i skattningarna indikerar att konfliktbestånd kan identifieras med hjälp av laserskanning

Models for estimating the vertical distribution of the biomass on small diameter trees in early thinnings

I samband med nya mål för energiförbrukningen har behovet av förnyelsebara energislag ökat. Ett sätt att möta detta ökade behov i Sverige är ett ökat uttag av skogsbränsle. Denna ökning skulle till stor del kunna bestå av ökat bränsleuttag i skog med hög stamtäthet och klena träd. För att på ett mer rationellt sätt kunna göra åtgärder i skog av detta slag är det av stor vikt att på förhand kunna uppskatta hur mycket man ska ta ut och hur mycket man ska lämna kvar som näring åt kvarvarande bestånd. Syftet med detta arbete var att skapa funktioner med vilka man ska kunna skatta biomassafördelningen i vertikal ledd för klena träd. Framtagandet av funktionerna har gjorts genom regressionsanalyser. Funktionerna bygger på data från Kristina Ulvcronas avhandling Effects of Silvicultural Treatments in Young Scots pine-dominated Stands on the Potential for Early Biofuel Harvests. Vid regressionsanalyserna användes höjd samt kvadrering och kubering av höjd som förklarande variabler till den vertikala fördelningen av biomassa för tall, gran och björk. Även funktioner för fördelningen av stamved, stambark och grenar inkl. barr togs fram. Resultaten visar att med hjälp av våra funktioner kan man se att en stor del av biomassa finns långt ner i träden. Denna andel varierar dock mellan de olika trädslagen. För tall finner man att vid 75 % av trädhöjden finns 86 % av den totala biomassan med en förklaringsgrad på 99,8 %. För både gran och björk finns 93 % av biomassan vid 75 % av höjden. Dessa funktioner har förklaringsgrad (R2= 99,9 %). Dock är vissa konstanter icke signifikanta på signifikansnivån 0,05. Funktionerna i detta arbete skulle kunna integreras i en skördardator som ett hjälpmedel för optimal aptering. Dock krävs det att funktionerna vidareutvecklas med ett bredare dataunderlag då våra funktioner endast bygger på data från tre bestånd inom samma region (Västerbottens inland).In connection with the new targets for energy consumption, the need for renewable energy sources currently increase. One way to meet this increasing demand in Sweden is to increase the extraction of forest fuel. This increase could consist of a greater fuel extraction in forests with high stem density and small diameter trees, thus early thinnings. For a more rational way to make actions in forests of this kind it is of great importance to be able to estimate how much of the biomass to extract and how much to leave as nourish to the remaining stand. The aim of this work was to create functions with which you should be able to estimate the biomass distribution in the vertical direction of small diameter trees. When creating the functions regression analysis was used. The functions are based on data from Kristina Ulvcronas thesis Effects of Silvicultural Treatments in Young Scots pine- dominated Stands on the Potential for Early Biofuel Harvest. In the regression analysis height and squared and incubated height has been used as explanatory variables for the vertical distribution of biomass for pine, spruce and birch. Also functions for the distribution of wood, stem bark and branches and needles were developed. The results show that a large proportion of biomass is found far down in the trees. This proportion varies between the different tree species. For pine we found that at 75% of the height is 86% of the total biomass with a coefficient of determination of 99.8 %. For spruce and birch are 93% respectively 93% of the biomass at 75% of the height. These functions have the degree of explanation (R2=99.9%). However, certain constants are not significant at the 0.05 significance level. The functions in this work can be integrated into a harvester computer as a tool for the bucking to be done in an optimal way. However, it is required that the functions are developed with a broader data set as base, this because the functions are based only on data from three populations within the same region (the inland of Västerbotten)

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

Zaremba-Niedzwiedzka K, Viklund J, Zhao W, et al. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome biology. 2013;14(11): R130.BACKGROUND: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt- and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. RESULTS: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. CONCLUSIONS: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host

Изучение байесовского подхода к анализу медико-биологических данных в курсе медицинской и биологической физики

Background: The clinical behaviour of colon cancer is heterogeneous. Five-year overall survival is 50-65% with all stages included. Recurring somatic chromosomal alterations have been identified and some have shown potential as markers for dissemination of the tumour, which is responsible for most colon cancer deaths. We investigated 115 selected stage II-IV primary colon cancers for associations between chromosomal alterations and tumour dissemination. Methods: Follow-up was at least 5 years for stage II-III patients without distant recurrence. Affymetrix SNP 6.0 microarrays and allele-specific copy number analysis were used to identify chromosomal alterations. Fisher's exact test was used to associate alterations with tumour dissemination, detected at diagnosis (stage IV) or later as recurrent disease (stage II-III). Results: Loss of 1p36.11-21 was associated with tumour dissemination in microsatellite stable tumours of stage II-IV (odds ratio = 5.5). It was enriched to a similar extent in tumours with distant recurrence within stage II and stage III subgroups, and may therefore be used as a prognostic marker at diagnosis. Loss of 1p36.11-21 relative to average copy number of the genome showed similar prognostic value compared to absolute loss of copies. Therefore, the use of relative loss as a prognostic marker would benefit more patients by applying also to hyperploid cancer genomes. The association with tumour dissemination was supported by independent data from the The Cancer Genome Atlas. Conclusion: Deletions on 1p36 may be used to guide adjuvant treatment decisions in microsatellite stable colon cancer of stages II and III

A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade

BACKGROUND: According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria. METHODOLOGY/PRINCIPAL FINDINGS: We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade. CONCLUSIONS/SIGNIFICANCE: Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria

Phylogenomics of Oceanic Bacteria

The focus of this thesis has been the phylogenomics and evolution of the Alphaproteobacteria. This is a very diverse group which encompasses bacteria from intraceullar parasites, such as the Rickettsiales, to freeliving bacteria such as the most abundant bacteria on earth, the SAR11. The genome sizes of the Alphaproteobacteria range between 1 Mb and 10 Mb. This group is also connected to the origin of the mitochondria. Several studies have placed the SAR11 clade together with the Rickettsiales and mitochon- dria. Here I have shown that this placement is an artifact of compositional heterogeneity. When choosing genes or sites less affected by heterogeneity we find that the SAR11-clade instead groups with free-living alphaproteobacteria. Gene-content analysis showed that SAR11 was missing several genes for recombination and DNA-repair. The relationships within the SAR11- clade has also been examined and questioned. Specifically, we found no support for placing the taxon referred to as HIMB59 within the SAR11. Ocean metagenomes have been investigated to determine whether the SAR11-clade is a potential relative of the mitochondria. No such relationship was found. Further I have shown how important it is to take the phylogenetic relationships into account when doing statistical analyzes of genomes. The evolution of LD12, the freshwater representative of SAR11, was investigated. Phyloge- nies and synonymous substitution frequencies showed the presence of three distinct subclades within LD12. The recombination to mutation rate was found to be extremely low. This is re- markable in light of the very high rate in the oceanic SAR11. This is may be due to adaptation to a more specialized niche. Finally we have compared structure-based and sequence-based methods for orthology pre- diction. A high fraction of the orfan proteins were predicted to code for intrinsically disordered proteins. Many phylogenetic methods are sensitive to heterogeneity and this needs to be taken into ac- count when doing phylogenies. There have been at least three independent genome reductions in the Alphaproteobacteria. The frequency of recombination differ greatly between freshwater and oceanic SAR11. Forces affecting the size of bacterial genomes and mechanisms of evolu- tionary change depend on the environmental context.

Atmospheric Attenuation for Lidar Systems in Adverse Weather Conditions

In this study, the weather impact on lidar signals has been researched. A lidar system was placed with a target at approximately 90 m and has together with a weather station collected data for about a year before this study. By using the raw detector data from the lidar, the full waveform can be obtained and the amplitude of the return pulse can be calculated. Atmospheric attenuation of lidar signals is often modeled using the lidar equation, which predicts an exponential decrease in energy over the distance. The factor in the exponent is referred to as the extinction coefficient and it is the main property studied in this thesis. By utilizing models for the extinction coefficient under different weather conditions, it is possible to simulate the performance of the lidar.  The extinction coefficient was calculated using different empirical models. The empirical models investigated in this thesis are the Kim and Kruse models for known visibility, the Al Naboulsi model for different types of fog with known visibility, the Carbonneau model for known precipitation amount in rainy conditions, and a similar model for snowy conditions. For the case of rain, a physical model was also used, which is derived through Mie theory. The physical model requires a particle size distribution, which is the number of particles of a certain radius per unit volume. A particle size distribution for rain was generated using the Ulbrich raindrop size distribution, using the precipitation amount recorded by the weather station. Particle size distributions for radiation and advection fog were also simulated.  The measured attenuation in lidar signals was compared to the predicted attenuation that was calculated using different models for the extinction coefficient in the lidar equation. Generally, the models tend to underestimate the amplitude of the return pulse. This can partially be explained by the assumptions used to derive the lidar equation, which neglects all augmentation of the beam. The visibility models gave more accurate results compared to the precipitation models. This was expected, since visibility is defined as a measure of attenuation and precipitation amount is not.  When a lidar signal is emitted, the light will be reflected from optical surfaces within the lidar and cause a pulse to be detected. This pulse is referred to as the zeropulse. In the first couple of meters of the transmission, we expect to see some backscattered light from adverse weather, since the detector has a larger solid angle at shorter distances. This returned light will be combined with the zeropulse and cause it to expand in width. By examining the zeropulse, it was possible to observe a difference between the average zeropulse under some different weather conditions. This leads to the conclusion that it may be possible to extract some information about current weather conditions from the zeropulse data, given that there is little ambient light and snowy weather conditions.  By integrating the zeropulse, variations in the shape of the zeropulse could be described by a single value. Then by separating the data into low and high visibility populations, the zeropulse integral could be used to predict the visibility. The conclusion was that the zeropulse integral can accurately predict whether visibility is above or below a threshold value, given that there is little ambient light and the visibility is known to be below 19950 m

Heroes and models : a study of the adventurer and his sources of inspiration

The purpose of this essay is to examine how the adventure is accomplished as a project, and how this is vindicated, through science or by other means. The scientists of today are not seen as adventurers or heroes, at least not as they used to, but this image lives on as a sort of role or social institution, that can be used by anyone and in any purpose. These roles could be seen as a type of rules for the modern adventurer, and act both as a limit or a possibility. This essay compares two North Pole travelers, Ola Skinnarmo and Salomon August Andrée.Denna uppsats syfte är att undersöka hur man genomför äventyret som ett projekt och hur detta legitimeras, genom vetenskap eller på annat sätt. Vetenskapsmännen ses idag inte som äventyrare eller hjältar, i alla fall inte på samma sätt som förr, men den bilden lever kvar i form av en "rollbeskrivning" eller en sorts "social institution" som kan användas av vem som helst och i alla möjliga syften. Dessa"rollbeskrivningar"skulle kunna ses som en sorts "spelregler" för dagens moderna äventyrare och verka både begränsande och möjliggörande. I uppsatsen jämförs två polarfarare, Ola Skinnarmo och Salomon August Andrée, och deras respektive expeditioner