Browsing by Subject "STEM"

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  • Pyorala, Jiri; Kankare, Ville; Liang, Xinlian; Saarinen, Ninni; Rikala, Juha; Kivinen, Veli-Pekka; Sipi, Marketta; Holopainen, Markus; Hyyppa, Juha; Vastaranta, Mikko (2019)
    Wood procurement in sawmills could be improved by resolving detailed three-dimensional stem geometry references from standing timber. This could be achieved, using the increasingly available terrestrial point clouds from various sources. Here, we collected terrestrial laser-scanning (TLS) data from 52 Scots pines (Pinus sylvestris L.) with the purpose of evaluating the accuracy of the log geometry and analysing its relationship with wood quality. For reference, the log-specific top-end diameter, volume, tapering, sweep, basic density and knottiness were measured in a sawmill. We produced stem models from the TLS data and bucked them into logs similar to those measured in the sawmill. In comparison to the sawmill data, the log-specific TLS-based top-end diameter, volume, taper and sweep estimates showed relative mean differences of 1.6, -2.4, -3.0 and 78 per cent, respectively. The correlation coefficients between increasing taper and decreasing wood density and whorl-to-whorl distances were 0.49 and -0.51, respectively. Although the stem-model geometry was resolved from the point clouds with similar accuracy to that at the sawmills, the remaining uncertainty in defining the sweep and linking the wood quality with stem geometry may currently limit the method's feasibilities. Instead of static TLS, mobile platforms would likely be more suitable for operational point cloud data acquisition.
  • Pyörälä, Jiri; Kankare, Ville; Vastaranta, Mikko; Rikala, Juha; Holopainen, Markus; Sipi, Marketta; Hyyppä, Juha; Uusitalo, Jori (2018)
    While X-ray scanning is increasingly used to measure the interior quality of logs, terrestrial laser scanning (TLS) could be used to collect information on external tree characteristics. As branches are one key indicator of wood quality, we compared TLS and X-ray scanning data in deriving whorl locations and each whorl's maximum branch and knot diameters for 162 Scots pine (Pinus sylvestris L.) log sections. The mean number of identified whorls per tree was 37.25 and 22.93 using X-ray and TLS data, respectively. The lowest TLS-derived whorl in each sample tree was an average 5.56 m higher than that of the X-ray data. Whorl-to-whorl mean distances and the means of the maximum branch and knot diameters in a whorl measured for each sample tree using TLS and X-ray data had mean differences of -0.12 m and -6.5 mm, respectively. One of the most utilized wood quality indicators, tree-specific maximum knot diameter measured by X-ray, had no statistically significant difference to the tree-specific maximum branch diameter measured from the TLS point cloud. It appears challenging to directly derive comparative branch structure information using TLS and X-ray. However, some features that are extractable from TLS point clouds are potential wood quality indicators.
  • Yrttimaa, Tuomas; Saarinen, Ninni; Luoma, Ville; Tanhuanpaa, Topi; Kankare, Ville; Liang, Xinlian; Hyyppa, Juha; Holopainen, Markus; Vastaranta, Mikko (2019)
    Dead wood is a key forest structural component for maintaining biodiversity and storing carbon. Despite its important role in a forest ecosystem, quantifying dead wood alongside standing trees has often neglected when investigating the feasibility of terrestrial laser scanning (TLS) in forest inventories. The objective of this study was therefore to develop an automatic method for detecting and characterizing downed dead wood with a diameter exceeding 5 cm using multi-scan TLS data. The developed four-stage algorithm included (1) RANSAC-cylinder filtering, (2) point cloud rasterization, (3) raster image segmentation, and (4) dead wood trunk positioning. For each detected trunk, geometry-related quality attributes such as dimensions and volume were automatically determined from the point cloud. For method development and validation, reference data were collected from 20 sample plots representing diverse southern boreal forest conditions. Using the developed method, the downed dead wood trunks were detected with an overall completeness of 33% and correctness of 76%. Up to 92% of the downed dead wood volume were detected at plot level with mean value of 68%. We were able to improve the detection accuracy of individual trunks with visual interpretation of the point cloud, in which case the overall completeness was increased to 72% with mean proportion of detected dead wood volume of 83%. Downed dead wood volume was automatically estimated with an RMSE of 15.0 m(3)/ha (59.3%), which was reduced to 6.4 m(3)/ha (25.3%) as visual interpretation was utilized to aid the trunk detection. The reliability of TLS-based dead wood mapping was found to increase as the dimensions of dead wood trunks increased. Dense vegetation caused occlusion and reduced the trunk detection accuracy. Therefore, when collecting the data, attention must be paid to the point cloud quality. Nevertheless, the results of this study strengthen the feasibility of TLS-based approaches in mapping biodiversity indicators by demonstrating an improved performance in quantifying ecologically most valuable downed dead wood in diverse forest conditions.
  • Liang, Xinlian; Hyyppä, Juha; Kaartinen, Harri; Lehtomäki, Matti; Pyörälä, Jiri; Pfeifer, Norbert; Holopainen, Markus; Brolly, Gábor; Francesco, Pirotti; Hackenberg, Jan; Huang, Huabing; Jo, Hyun-Woo; Katoh, Masato; Liu, Luxia; Mokroš, Martin; Morel, Jules; Olofsson, Kenneth; Poveda-Lopez, Jose; Trochta, Jan; Wang, Di; Wang, Jinhu; Xi, Zhouxi; Yang, Bisheng; Zheng, Guang; Kankare, Ville; Luoma, Ville; Yu, Xiaowei; Chen, Liang; Vastaranta, Mikko; Saarinen, Ninni; Wang, Yunsheng (2018)
    The last two decades have witnessed increasing awareness of the potential of terrestrial laser scanning (TLS) in forest applications in both public and commercial sectors, along with tremendous research efforts and progress. It is time to inspect the achievements of and the remaining barriers to TLS-based forest investigations, so further research and application are clearly orientated in operational uses of TLS. In such context, the international TLS benchmarking project was launched in 2014 by the European Spatial Data Research Organization and coordinated by the Finnish Geospatial Research Institute. The main objectives of this benchmarking study are to evaluate the potential of applying TLS in characterizing forests, to clarify the strengths and the weaknesses of TLS as a measure of forest digitization, and to reveal the capability of recent algorithms for tree-attribute extraction. The project is designed to benchmark the TLS algorithms by processing identical TLS datasets for a standardized set of forest attribute criteria and by evaluating the results through a common procedure respecting reliable references. Benchmarking results reflect large variances in estimating accuracies, which were unveiled through the 18 compared algorithms and through the evaluation framework, i.e., forest complexity categories, TLS data acquisition approaches, tree attributes and evaluation procedures. The evaluation framework includes three new criteria proposed in this benchmarking and the algorithm performances are investigated through combining two or more criteria (e.g., the accuracy of the individual tree attributes are inspected in conjunction with plot-level completeness) in order to reveal algorithms’ overall performance. The results also reveal some best available forest attribute estimates at this time, which clarify the status quo of TLS-based forest investigations. Some results are well expected, while some are new, e.g., the variances of estimating accuracies between single-/multi-scan, the principle of the algorithm designs and the possibility of a computer outperforming human operation. With single-scan data, i.e., one hemispherical scan per plot, most of the recent algorithms are capable of achieving stem detection with approximately 75% completeness and 90% correctness in the easy forest stands (easy plots: 600 stems/ha, 20 cm mean DBH). The detection rate decreases when the stem density increases and the average DBH decreases, i.e., 60% completeness with 90% correctness (medium plots: 1000 stem/ha, 15 cm mean DBH) and 30% completeness with 90% correctness (difficult plots: 2000 stems/ha, 10 cm mean DBH). The application of the multi-scan approach, i.e., five scans per plot at the center and four quadrant angles, is more effective in complex stands, increasing the completeness to approximately 90% for medium plots and to approximately 70% for difficult plots, with almost 100% correctness. The results of this benchmarking also show that the TLS-based approaches can provide the estimates of the DBH and the stem curve at a 1–2 cm accuracy that are close to what is required in practical applications, e.g., national forest inventories (NFIs). In terms of algorithm development, a high level of automation is a commonly shared standard, but a bottleneck occurs at stem detection and tree height estimation, especially in multilayer and dense forest stands. The greatest challenge is that even with the multi-scan approach, it is still hard to completely and accurately record stems of all trees in a plot due to the occlusion effects of the trees and bushes in forests. Future development must address the redundant yet incomplete point clouds of forest sample plots and recognize trees more accurately and efficiently. It is worth noting that TLS currently provides the best quality terrestrial point clouds in comparison with all other technologies, meaning that all the benchmarks labeled in this paper can also serve as a reference for other terrestrial point clouds sources.
  • Guo, Jiesi; Wang, Ming-Te; Ketonen, Elina E.; Eccles, Jacquelynne Sue; Salmela-Aro, Katariina (2018)
    This study used variable- and pattern-centered approaches to better capture the impact of adolescents’ joint developmental trajectories of subjective task values (STVs) in three domains (Finnish, math and science, and social subject) from grades 9 to 11 on science, technology, engineering, and mathematics (STEM) aspirations at four years postsecondary school and STEM participation at six years postsecondary school (N = 849 Finnish youth; 52.1% female; 99% native Finnish). Results showed that while adolescents’ average STVs in different domains remained stable, three differential joint STV trajectories emerged across domains. Individual changes of STVs in one domain shaped STVs in other domains to form unique relative STV hierarchies within subgroups that impacted long-term STEM aspirations and participation. Gender differences in STV trajectory profile distributions partially explained the overall underrepresentation of women in STEM fields. This study is among the first to incorporate multiple domains and explore how STVs fluctuate over time in both homogeneous and heterogeneous fashions. These findings underscore the importance of examining heterogeneity in motivational trajectories across domains.
  • Awad, Shady Adnan; Kankainen, Matti; Ojala, Teija; Koskenvesa, Perttu; Eldfors, Samuli; Ghimire, Bishwa; Kumar, Ashwini; Kytölä, Soili; Kamel, Mahmoud M.; Heckman, Caroline A.; Porkka, Kimmo; Mustjoki, Satu (2020)
    Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm accounting for similar to 15% of all leukemia. Progress of the disease from an indolent chronic phase to the more aggressive accelerated phase or blast phase (BP) occurs in a minority of cases and is associated with an accumulation of somatic mutations. We performed genetic profiling of 85 samples and transcriptome profiling of 12 samples from 59 CML patients. We identified recurrent somatic mutations in ABL1 (37%), ASXL1 (26%), RUNX1 (16%), and BCOR (16%) in the BP and observed that mutation signatures in the BP resembled those of acute myeloid leukemia (AML). We found that mutation load differed between the indolent and aggressive phases and that nonoptimal responders had more nonsilent mutations than did optimal responders at the time of diagnosis, as well as in follow-up. Using RNA sequencing, we identified other than BCR-ABL1 cancer-associated hybrid genes in 6 of the 7 BP samples. Uncovered expression alterations were in turn associated with mechanisms and pathways that could be targeted in CML management and by which somatic alterations may emerge in CML. Last, we showed the value of genetic data in CML management in a personalized medicine setting.
  • Aksela, Maija; Haatainen, Outi (Queensland University of Technology, 2019)
  • Davies, Sarah W.; Putnam, Hollie M.; Ainsworth, Tracy D.; Baum, Julia K.; Bove, Colleen B.; Crosby, Sarah C.; Côté, Isabelle M.; Duplouy, Anne; Fulweiler, Robinson W.; Griffin, Alyssa; Hanley, Torrance C.; Hill, Tessa M.; Humanes, Adriana; Mangubhai, Sangeeta; Metaxas, Anna; Parker, Laura; Rivera, Hanny E.; Silbiger, Nyssa J.; Smith, Nicola S.; Spalding, Ana; Traylor-Knowles, Nikki; Weigel, Brooke L.; Wright, Rachel M.; Bates, Amanda E. (2021)
    Success and impact metrics in science are based on a system that perpetuates sexist and racist “rewards” by prioritizing citations and impact factors. These metrics are flawed and biased against already marginalized groups and fail to accurately capture the breadth of individuals’ meaningful scientific impacts. We advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion. We outline pathways for a paradigm shift in scientific values based on multidimensional mentorship and promoting mentee well-being. These actions will require collective efforts supported by academic leaders and administrators to drive essential systemic change.
  • Pyörälä, Jiri; Liang, Xinlian; Vastaranta, Mikko; Saarinen, Ninni; Kankare, Ville; Wang, Yunsheng; Holopainen, Markus; Hyyppä, Juha (2018)
    State-of-the-art technology available at sawmills enables measurements of whorl numbers and the maximum branch diameter for individual logs, but such information is currently unavailable at the wood procurement planning phase. The first step toward more detailed evaluation of standing timber is to introduce a method that produces similar wood quality indicators in standing forests as those currently used in sawmills. Our aim was to develop a quantitative method to detect and model branches from terrestrial laser scanning (TLS) point clouds data of trees in a forest environment. The test data were obtained from 158 Scots pines (Pinus sylvestris L.) in six mature forest stands. The method was evaluated for the accuracy of the following branch parameters: Number of whorls per tree and for every whorl, the maximum branch diameter and the branch insertion angle associated with it. The analysis concentrated on log-sections (stem diameter > 15 cm) where the branches most affect wood's value added. The quantitative whorl detection method had an accuracy of 69.9% and a 1.9% false positive rate. The estimates of the maximum branch diameters and the corresponding insertion angles for each whorl were underestimated by 0.34 cm (11.1%) and 0.67 degrees (1.0%), with a root-mean-squared error of 1.42 cm (46.0%) and 17.2 degrees (26.3%), respectively. Distance from the scanner, occlusion, and wind were the main external factors that affect the method's functionality. Thus, the completeness and point density of the data should be addressed when applying TLS point cloud based tree models to assess branch parameters.
  • Fellman, Aslak (Helsingin yliopisto, 2021)
    The plasma-facing materials of future fusion reactors are exposed to high doses of radiation. The characterization of the radiation damage is an essential part in the study of fusion relevant materi- als. Electron microscopy is one of the most important tools used for characterization of radiation damage, as it provides direct observations of the microstructure of materials. However, the char- acterization of defects from electron microscope images remains difficult. Simulated images can be used to bridge the gap between experimental results and models. In this thesis, scanning transmission electron microscope (STEM) images of radiation damage were simulated. Molecular dynamics simulations were employed in order to create defects in tungsten. STEM images were simulated based on the created systems using the multislice method. A data- base of images of h001i dislocation loops and defects produced from collision cascade simulations was generated. The simulated images provide insight into the observed contrast of the defect structures. Differences in the image contrast between vacancy and interstitial h001i dislocation loops were reported. In addition to this, the results were compared against experimental images and used in identification of a dislocation loop. The simulated images demonstrate that it is feasible to simulate STEM images of radiation damage produced from collision cascade simulations.
  • Liang, Xinlian; Kankare, Ville; Hyyppä, Juha; Wang, Yunsheng; Kukko, Antero; Haggren, Henrik; Yu, Xiaowei; Kaartinen, Harri; Jaakkola, Anttoni; Guan, Fengying; Holopainen, Markus; Vastaranta, Mikko (2016)
    Decision making on forest resources relies on the precise information that is collected using inventory. There are many different kinds of forest inventory techniques that can be applied depending on the goal, scale, resources and the required accuracy. Most of the forest inventories are based on field sample. Therefore, the accuracy of the forest inventories depends on the quality and quantity of the field sample. Conventionally, field sample has been measured using simple tools. When map is required, remote sensing materials are needed. Terrestrial laser scanning (TLS) provides a measurement technique that can acquire millimeter-level of detail from the surrounding area, which allows rapid, automatic and periodical estimates of many important forest inventory attributes. It is expected that TLS will be operationally used in forest inventories as soon as the appropriate software becomes available, best practices become known and general knowledge of these findings becomes more wide spread. Meanwhile, mobile laser scanning, personal laser scanning, and image-based point clouds became capable of capturing similar terrestrial point cloud data as TLS. This paper reviews the advances of applying TLS in forest inventories, discusses its properties with reference to other related techniques and discusses the future prospects of this technique. (C) 2016 The Authors. Published by Elsevier B.V. on behalf of International Society for Photogrammetry and Remote Sensing, Inc. (ISPRS). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licensesiby-nc-nd/11.0/).
  • Branchetti, Laura; Cutler, Marianne; Laherto, Antti; Levrini, Olivia; Palmgren, Kirsi Elina; Tasquier, Giulia; Wilson, Caitlin (2018)
    In the world where young people feel that the future is no longer a promise but a threat, and science and technology are sources of fears and global problems, a challenging task for education is to support students in imagining a future for the world and for themselves. The aim of the EU-funded project “I SEE” is to create an approach in science education that addresses the problems posed by global unsustainability, the uncertainty of the future, social liquidity and the irrelevance of STEM education for young people. This way, we believe, STEM education can support young people in projecting themselves into the future as agents and active persons, citizens and professionals, and open their minds to future possibilities. In this paper we propose a teaching and learning approach for futurizing science education, and describe how that approach was used to develop the first I SEE module implemented in summer school in June 2017 with students from three countries. In sum, the I SEE teaching and learning approach consists of three stages and learning outcomes connected to each of them: encountering the focal issue; engaging with the interaction between science ideas and future dimensions, and synthesizing the ideas and putting them into practice. The middle stage of the model is the main part, involving future-oriented practices that turn knowledge into future- scaffolding skills. We describe four kinds of such future-oriented practices: a) activities to flesh out the future-oriented structure of scientific discourse, language and concepts; b) activities inspired by futures studies or by the working life and societal matters; c) exposure activities to enlarge the imagination about possible future STEM careers; and d) action competence activities. We conclude the paper by reflecting on our experiences of the implementation of the climate change module with upper secondary school students.
  • Janssen, Thomas A. J.; Hölttä, Teemu; Fleischer, Katrin; Naudts, Kim; Dolman, Han (2020)
    Functional relationships between wood density and measures of xylem hydraulic safety and efficiency are ambiguous, especially in wet tropical forests. In this meta-analysis, we move beyond wood density per se and identify relationships between xylem allocated to fibers, parenchyma, and vessels and measures of hydraulic safety and efficiency. We analyzed published data of xylem traits, hydraulic properties and measures of drought resistance from neotropical tree species retrieved from 346 sources. We found that xylem volume allocation to fiber walls increases embolism resistance, but at the expense of specific conductivity and sapwood capacitance. Xylem volume investment in fiber lumen increases capacitance, while investment in axial parenchyma is associated with higher specific conductivity. Dominant tree taxa from wet forests prioritize xylem allocation to axial parenchyma at the expense of fiber walls, resulting in a low embolism resistance for a given wood density and a high vulnerability to drought-induced mortality. We conclude that strong trade-offs between xylem allocation to fiber walls, fiber lumen, and axial parenchyma drive drought resistance in neotropical trees. Moreover, the benefits of xylem allocation to axial parenchyma in wet tropical trees might not outweigh the consequential low embolism resistance under more frequent and severe droughts in a changing climate.