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Sjöstedt de Luna, Sara
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Publications (10 of 40) Show all publications
Abramowicz, K., Schelin, L., Sjöstedt de Luna, S. & Strandberg, J. (2019). Multiresolution clustering of dependent functional data with application to climate reconstruction. Stat, 8(1), Article ID e240.
Open this publication in new window or tab >>Multiresolution clustering of dependent functional data with application to climate reconstruction
2019 (English)In: Stat, E-ISSN 2049-1573, Vol. 8, no 1, article id e240Article in journal (Refereed) Published
Abstract [en]

We propose a new nonparametric clustering method for dependent functional data, the double clustering bagging Voronoi method. It consists of two levels of clustering. Given a spatial lattice of points, a function is observed at each grid point. In the first‐level clustering, features of the functional data are clustered. The second‐level clustering takes dependence into account, by grouping local representatives, built from the resulting first‐level clusters, using a bagging Voronoi strategy. Depending on the distance measure used, features of the functions may be included in the second‐step clustering, making the method flexible and general. Combined with the clustering method, a multiresolution approach is proposed that searches for stable clusters at different spatial scales, aiming to capture latent structures. This provides a powerful and computationally efficient tool to cluster dependent functional data at different spatial scales, here illustrated by a simulation study. The introduced methodology is applied to varved lake sediment data, aiming to reconstruct winter climate regimes in northern Sweden at different time resolutions over the past 6,000 years.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
Keywords
bagging Voronoi strategy, climate reconstruction, clustering, dependency, functional data
National Category
Probability Theory and Statistics
Identifiers
urn:nbn:se:umu:diva-164004 (URN)10.1002/sta4.240 (DOI)
Funder
Swedish Research Council, 340-2013-5203Swedish Research Council, 2016-02763
Available from: 2019-10-11 Created: 2019-10-11 Last updated: 2019-10-14Bibliographically approved
Abramowicz, K., Häger, C., Pini, A., Schelin, L., Sjöstedt de Luna, S. & Vantini, S. (2018). Nonparametric inference for functional-on-scalar linear models applied to knee kinematic hop data after injury of the anterior cruciate ligament. Scandinavian Journal of Statistics, 45(4), 1036-1061
Open this publication in new window or tab >>Nonparametric inference for functional-on-scalar linear models applied to knee kinematic hop data after injury of the anterior cruciate ligament
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2018 (English)In: Scandinavian Journal of Statistics, Vol. 45, no 4, p. 1036-1061Article in journal (Refereed) Published
Abstract [en]

Motivated by the analysis of the dependence of knee movement patterns during functional tasks on subject-specific covariates, we introduce a distribution-free procedure for testing a functional-on-scalar linear model with fixed effects. The procedure does not only test the global hypothesis on the entire domain but also selects the intervals where statistically significant effects are detected. We prove that the proposed tests are provided with an asymptotic control of the intervalwise error rate, that is, the probability of falsely rejecting any interval of true null hypotheses. The procedure is applied to one-leg hop data from a study on anterior cruciate ligament injury. We compare knee kinematics of three groups of individuals (two injured groups with different treatments and one group of healthy controls), taking individual-specific covariates into account.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
Keywords
analysis of covariance, functional data, human movement, intervalwise testing, permutation test
National Category
Probability Theory and Statistics
Identifiers
urn:nbn:se:umu:diva-150935 (URN)10.1111/sjos.12333 (DOI)000450039100010 ()
Funder
Swedish Research Council, K2014-99X-21876-04-4Swedish Research Council, 340-2013-5203Swedish Research Council, 2016-02763Västerbotten County Council, ALF VLL548501Västerbotten County Council, VLL-358901Västerbotten County Council, 7002795
Available from: 2018-08-20 Created: 2018-08-20 Last updated: 2019-01-07Bibliographically approved
Abramowizc, K., Arnqvist, P., Secchi, P., Sjöstedt de Luna, S., Vantini, S. & Vitelli, V. (2017). Clustering misaligned dependent curves applied to varved lake sediment for climate reconstruction. Stochastic environmental research and risk assessment (Print), 31(1), 71-85
Open this publication in new window or tab >>Clustering misaligned dependent curves applied to varved lake sediment for climate reconstruction
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2017 (English)In: Stochastic environmental research and risk assessment (Print), ISSN 1436-3240, E-ISSN 1436-3259, Vol. 31, no 1, p. 71-85Article in journal (Refereed) Published
Abstract [en]

In this paper we introduce a novel functional clustering method, the Bagging Voronoi K-Medoid Aligment (BVKMA) algorithm, which simultaneously clusters and aligns spatially dependent curves. It is a nonparametric statistical method that does not rely on distributional or dependency structure assumptions. The method is motivated by and applied to varved (annually laminated) sediment data from lake Kassjön in northern Sweden, aiming to infer on past environmental and climate changes. The resulting clusters and their time dynamics show great potential for seasonal climate interpretation, in particular for winter climate changes.

Place, publisher, year, edition, pages
Springer, 2017
Keywords
Functional data, Clustering, Dependence, Misalignment, Sediment data
National Category
Probability Theory and Statistics
Research subject
Mathematical Statistics
Identifiers
urn:nbn:se:umu:diva-130727 (URN)10.1007/s00477-016-1287-6 (DOI)000394278600006 ()
Available from: 2017-01-30 Created: 2017-01-30 Last updated: 2018-06-09Bibliographically approved
Nanos, N. & Sjöstedt de Luna, S. (2017). Fitting diameter distribution models to data from forest inventories with concentric plot design. Forest Systems, 26(2), Article ID UNSP e01S.
Open this publication in new window or tab >>Fitting diameter distribution models to data from forest inventories with concentric plot design
2017 (English)In: Forest Systems, ISSN 2171-5068, E-ISSN 2171-9845, Vol. 26, no 2, article id UNSP e01SArticle in journal (Refereed) Published
Abstract [en]

Aim: Several national forest inventories use a complex plot design based on multiple concentric subplots where smaller diameter trees are inventoried when lying in the smaller-radius subplots and ignored otherwise. Data from these plots are truncated with threshold (truncation) diameters varying according to the distance from the plot centre. In this paper we designed a maximum likelihood method to fit the Weibull diameter distribution to data from concentric plots. Material and methods: Our method (M1) was based on multiple truncated probability density functions to build the likelihood. In addition, we used an alternative method (M2) presented recently. We used methods M1 and M2 as well as two other reference methods to estimate the Weibull parameters in 40000 simulated plots. The spatial tree pattern of the simulated plots was generated using four models of spatial point patterns. Two error indices were used to assess the relative performance of M1 and M2 in estimating relevant stand-level variables. In addition, we estimated the Quadratic Mean plot Diameter (QMD) using Expansion Factors (EFs). Main results: Methods M1 and M2 produced comparable estimation errors in random and cluster tree spatial patterns. Method M2 produced biased parameter estimates in plots with inhomogeneous Poisson patterns. Estimation of QMD using EFs produced biased results in plots within inhomogeneous intensity Poisson patterns. Research highlights: We designed a new method to fit the Weibull distribution to forest inventory data from concentric plots that achieves high accuracy and precision in parameter estimates regardless of the within-plot spatial tree pattern.

Place, publisher, year, edition, pages
INIA, 2017
Keywords
expansion factors, forest growth and yield, National Forest Inventory, spatial point pattern, Weibull
National Category
Probability Theory and Statistics Forest Science
Identifiers
urn:nbn:se:umu:diva-131311 (URN)10.5424/fs/2017262-10486 (DOI)000413335800012 ()
Available from: 2017-02-10 Created: 2017-02-10 Last updated: 2018-06-09Bibliographically approved
Sedaghat, M., Wadbro, E., Wilkes, J., Sjöstedt de Luna, S., Seleznjev, O. & Elmroth, E. (2016). DieHard: Reliable Scheduling to Survive Correlated failures in Cloud Data Centers. In: 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid): . Paper presented at 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), Cartagena, Colombia, May 16-19, 2016. IEEE
Open this publication in new window or tab >>DieHard: Reliable Scheduling to Survive Correlated failures in Cloud Data Centers
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2016 (English)In: 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), IEEE, 2016Conference paper, Published paper (Refereed)
Abstract [en]

In large scale data centers, a single fault can lead to correlated failures of several physical machines and the tasks running on them, simultaneously. Such correlated failures can severely damage the reliability of a service or a job running on the failed hardware. This paper models the impact of stochastic and correlated failures on job reliability in a data center. We focus on correlated failures caused by power outages or failures of network components, on jobs running multiple replicas of identical tasks. We present a statistical reliability model and an approximation technique for computing a job’s reliability in the presence of correlated failures. In addition, we address the problem of scheduling a job with reliability constraints.We formulate the scheduling problem as an optimization problem, with the aim being to maintain the desired reliability with the minimum number of extra tasks to resist failures.We present a scheduling algorithm that approximates the minimum number of required tasks and a placement to achieve a desired job reliability. We study the efficiency of our algorithm using an analytical approach and by simulating a cluster with different failure sources and reliabilities. The results show that the algorithm can effectively approximate the minimum number of extra tasks required to achieve the job’s reliability.

Place, publisher, year, edition, pages
IEEE, 2016
Keywords
Cloud computing, Scheduling; Reliability, Fault tolerance, Correlated failures
National Category
Computer Sciences
Research subject
Computer Science
Identifiers
urn:nbn:se:umu:diva-116791 (URN)10.1109/CCGrid.2016.11 (DOI)
Conference
16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), Cartagena, Colombia, May 16-19, 2016
Note

Originally published in manuscript form.

Available from: 2016-02-11 Created: 2016-02-11 Last updated: 2019-06-14Bibliographically approved
Arnqvist, P., Bigler, C., Renberg, I. & Sjöstedt de Luna, S. (2016). Functional clustering of varved lake sediment to reconstruct past seasonal climate. Environmental and Ecological Statistics, 23(4), 513-529
Open this publication in new window or tab >>Functional clustering of varved lake sediment to reconstruct past seasonal climate
2016 (English)In: Environmental and Ecological Statistics, ISSN 1352-8505, E-ISSN 1573-3009, Vol. 23, no 4, p. 513-529Article in journal (Refereed) Published
Abstract [en]

Annually laminated (varved) lake sediments constitutes excellent environmental archives, and have the potential to play an important role for understanding past seasonal climate with their inherent annual time resolution and within-year seasonal patterns. We propose to use functional data analysis methods to extract the relevant information with respect to climate reconstruction from the rich but complex information in the varves, including the shapes of the seasonal patterns, the varying varve thickness, and the non-linear sediment accumulation rates. In particular we analyze varved sediment from lake Kassjon in northern Sweden, covering the past 6400 years. The properties of each varve reflect to a large extent weather conditions and internal biological processes in the lake the year that the varve was deposited. Functional clustering is used to group the seasonal patterns into different types, that can be associated with different weather conditions. The seasonal patterns were described by penalized splines and clustered by the k-means algorithm, after alignment. The observed (within-year) variability in the data was used to determine the degree of smoothing for the penalized spline approximations. The resulting clusters and their time dynamics show great potential for seasonal climate interpretation, in particular for winter climate changes.

Place, publisher, year, edition, pages
Springer, 2016
Keywords
Climate, Clustering, Curve registration, Functional data analysis, Penalized least squares, Varved lake diment
National Category
Probability Theory and Statistics Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-130095 (URN)10.1007/s10651-016-0351-1 (DOI)000387424200002 ()
Available from: 2017-01-13 Created: 2017-01-11 Last updated: 2018-06-09Bibliographically approved
Chen, Z.-Q., Abramowicz, K., Raczkowski, R., Ganea, S., Wu, H. X., Lundqvist, S.-O., . . . Mellerowicz, E. J. (2016). Method for accurate fiber length determination from increment cores for large-scale population analyses in Norway spruce. Holzforschung, 70(9), 829-838
Open this publication in new window or tab >>Method for accurate fiber length determination from increment cores for large-scale population analyses in Norway spruce
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2016 (English)In: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 70, no 9, p. 829-838Article in journal (Refereed) Published
Abstract [en]

Fiber (tracheid) length is an important trait targeted for genetic and silvicultural improvement. Such studies require large-scale non-destructive sampling, and accurate length determination. The standard procedure for non-destructive sampling is to collect increment cores, singularize their cells by maceration, measure them with optical analyzer and apply various corrections to suppress influence of non-fiber particles and cut fibers, as fibers are cut by the corer. The recently developed expectation-maximization method (EM) not only addresses the problem of non-fibers and cut fibers, but also corrects for the sampling bias. Here, the performance of the EM method has been evaluated by comparing it with length-weighing and squared length-weighing, both implemented in fiber analyzers, and with microscopy data for intact fibers, corrected for sampling bias, as the reference. This was done for 12-mm increment cores from 16 Norway spruce (Picea abies (L.) Karst) trees on fibers from rings 8-11 (counted from pith), representing juvenile wood of interest in breeding programs. The EM-estimates provided mean-fiber-lengths with bias of only +2.7% and low scatter. Length-weighing and length2-weighing gave biases of -7.3% and +9.3%, respectively, and larger scatter. The suggested EM approach constitutes a more accurate non-destructive method for fiber length (FL) determination, expected to be applicable also to other conifers.

Place, publisher, year, edition, pages
Walter de Gruyter, 2016
Keywords
expectation-maximization, fiber length, increment core, optical fiber analyzer, Picea abies, tracheid length
National Category
Wood Science Paper, Pulp and Fiber Technology
Identifiers
urn:nbn:se:umu:diva-127630 (URN)10.1515/hf-2015-0138 (DOI)000385808000004 ()
Projects
Bio4Energy
Available from: 2016-11-30 Created: 2016-11-16 Last updated: 2019-09-06Bibliographically approved
Mathisen, P., Thelaus, J., Sjöstedt de Luna, S. & Andersson, A. (2016). Rapid adaptation of predation resistance in bacteria isolated from a seawater microcosm. Aquatic Microbial Ecology, 78(2), 81-92
Open this publication in new window or tab >>Rapid adaptation of predation resistance in bacteria isolated from a seawater microcosm
2016 (English)In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 78, no 2, p. 81-92Article in journal (Refereed) Published
Abstract [en]

Bacterial defense against protozoan grazing has been shown to occur in many different bacteria. Predation resistance traits may however be plastic, making bacterial com munities resilient or resistant to predation perturbations. We studied the adaptation of pre dation resistance traits in bacteria isolated from a microcosm experiment. In the initial microcosm ex periment the predation pressure on bacteria varied markedly, while changes in the bacterial community composition could not be verified. Seven bacteria were isolated from the microcosm (Micrococcus sp., Rhodobacter sp., Paracoccus sp., Shewanella sp., Rhizobium sp. and 2 un identified species) and these were repeatedly exposed to high predation by the ciliate Tetrahymena pyriformis. High variations in edibility and rate of adaptation of predation resistance traits were observed among the strains. The initial mortality rate of the different bacterial taxa and the change over time varied by a factor of 7 and 24, respectively. Rhodobacter sp. was already predation resistant at the start of the experiment and did not change much over time, while Micrococcus sp., Paracoccus sp. and Shewanella sp. initially were relatively edible and later developed predation resistance. In conclusion, we show that rapid adaptation of predation resistance traits is common among bacteria in an aquatic microbial community, and that a single test of a bacterium’s edibility will in many cases not be enough to fully understand its ecological role, as it will not reveal the potential adaptive response. The results suggest the potential of rapid changes of predation resistance as a mechanism for bacterial communities to be resilient to variations in predation disturbances.

Keywords
Bacterial isolates, Predation pressure, Predation resistance, Inedible, Adaptation, Tetrahymena
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-131263 (URN)10.3354/ame01802 (DOI)000394504400002 ()
Available from: 2017-02-10 Created: 2017-02-10 Last updated: 2018-06-09Bibliographically approved
Haemig, P. D., Sjöstedt de Luna, S., Blank, H. & Lundqvist, H. (2015). Ecology and phylogeny of birds foraging at outdoor restaurants in Sweden. Biodiversity Data Journal, 3, Article ID e6360.
Open this publication in new window or tab >>Ecology and phylogeny of birds foraging at outdoor restaurants in Sweden
2015 (English)In: Biodiversity Data Journal, ISSN 1314-2836, E-ISSN 1314-2828, Vol. 3, article id e6360Article in journal (Refereed) Published
Abstract [en]

Background: Birds frequently visit the outdoor serving areas of restaurants to feed on scraps of food and leftovers. Although this feeding association between humans and birds is widespread and could have significant effects, both positive and negative, for all taxa involved, the authors know of no published studies that have investigated restaurant bird communities. To lay the foundation for future research, the authors conducted a basic study of birds at 80 outdoor restaurants in Sweden, identifying which species and taxonomic clades of birds visited the restaurants and comparing restaurant birds in urban and rural environments. New information: Thirteen species of birds visited the outdoor restaurants. Eight of these species were predominant, i.e. accounting for 51% or more of bird presence (sum of minutes of all individual birds) at one or more restaurants. Every restaurant studied had a predominant species, but species often differed from each other in frequency of predominance in different landscapes. No endangered species were seen visiting restaurants. However, three farmland bird species (House Sparrow Passer domesticus, White Wagtail Motacilla alba, Eurasian Tree Sparrow Passer montanus), whose numbers are reported to be declining in the countryside, were predominant at the majority of restaurants in rural areas, suggesting that rural restaurants might be able to contribute to the conservation of these species. The thirteen species of restaurant-visiting birds belonged to five monophyletic clades. Ninety percent of all restaurants had, as their predominant species, birds from either Clade A (Passeridae, Motacillidae, Fringillidae) or Clade C (Corvidae). Statistical testing revealed that Clade A and Clade C were distributed differently in environments along the urban-rural gradient. At all spatial scales measured, birds of Clade C were predominant at the majority of restaurants in urban areas, while birds of Clade A were the predominant clade at the majority of restaurants in rural areas. The authors use this evidence, and observations of birds foraging in association with other primates, to hypothesize that the outdoor serving areas of modern restaurants may be helping to preserve and nurture ancient human-bird symbioses that have been part of human ecology since antiquity.

Place, publisher, year, edition, pages
Pensoft Publishers, 2015
Keywords
Birds, cafés, conservation, ecology, ecophylogenetics, feeding associations, foraging associations, landscapes, restaurants, rural environments, urban environments
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-116915 (URN)10.3897/BDJ.3.e6360 (DOI)
Available from: 2016-02-15 Created: 2016-02-15 Last updated: 2018-06-07Bibliographically approved
Rocklöv, J., Edvinsson, S., Arnqvist, P., Sjöstedt de Luna, S. & Schumann, B. (2014). Association of seasonal climate variability and age-specific mortality in northern Sweden before the onset of industrialization. Paper presented at ISEE, ISES and ISIAQ Conference 2013. International Journal of Environmental Research and Public Health, 11(7), 6940-6954
Open this publication in new window or tab >>Association of seasonal climate variability and age-specific mortality in northern Sweden before the onset of industrialization
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2014 (English)In: International Journal of Environmental Research and Public Health, ISSN 1661-7827, E-ISSN 1660-4601, Vol. 11, no 7, p. 6940-6954Article in journal (Refereed) Published
Abstract [en]

BACKGROUND AND AIMS: Little is known about health impacts of climate in pre-industrial societies. We used historical data to investigate the association of temperature and precipitation with total and age-specific mortality in Skellefteå, northern Sweden, between 1749 and 1859.

METHODS: We retrieved digitized aggregated population data of the Skellefteå parish, and monthly temperature and precipitation measures. A generalized linear model was established for year to year variability in deaths by annual and seasonal average temperature and cumulative precipitation using a negative binomial function, accounting for long-term trends in population size. The final full model included temperature and precipitation of all four seasons simultaneously. Relative risks (RR) with 95% confidence intervals (CI) were calculated for total, sex- and age-specific mortality.

RESULTS: In the full model, only autumn precipitation proved statistically significant (RR 1.02; CI 1.00-1.03, per 1cm increase of autumn precipitation), while winter temperature (RR 0.98; CI 0.95-1.00, per 1 °C increase in temperature) and spring precipitation (RR 0.98; CI 0.97-1.00 per 1 cm increase in precipitation) approached significance. Similar effects were observed for men and women. The impact of climate variability on mortality was strongest in children aged 3-9, and partly also in older children. Infants, on the other hand, appeared to be less affected by unfavourable climate conditions.

CONCLUSIONS: In this pre-industrial rural region in northern Sweden, higher levels of rain during the autumn increased the annual number of deaths. Harvest quality might be one critical factor in the causal pathway, affecting nutritional status and susceptibility to infectious diseases. Autumn rain probably also contributed to the spread of air-borne diseases in crowded living conditions. Children beyond infancy appeared most vulnerable to climate impacts.

Place, publisher, year, edition, pages
Basel, Switzerland: MDPI AG, 2014
Keywords
climate variability, seasonal climate variability, mortality, age-specific mortality, pre-industrial societies, Sweden
National Category
Mathematics
Identifiers
urn:nbn:se:umu:diva-91936 (URN)10.3390/ijerph110706940 (DOI)000339989500022 ()25003551 (PubMedID)
Conference
ISEE, ISES and ISIAQ Conference 2013
Note

This article belongs to the Special Issue Environment and Health - Bridging South, North, East and West: Proceedings from the ISEE, ISES and ISIAQ Conference 2013

Available from: 2014-08-18 Created: 2014-08-18 Last updated: 2018-06-07Bibliographically approved
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