Testing the performance of a commercial active network measurement platform

Diplomityössä testataan ja mitataan yhden kaupallisen aktiivimittausalustan suorituskyky ja tarkkuus. Myös alustan kyky havaita tiettyjä tapahtumia tietoverkoissa testataan. Testeissä on mukana kaksi erityyppistä alustaan kuuluvaa mittalaitetta: alhaisen suorituskyvyn Brix 100 Verifier ja tehokkaampi Brix 1000 Verifier. Testauksen tuloksena voidaan sanoa, että molemmat mittalaitetyypit soveltuvat hyvin kiertoaikaviiveen mittaamiseen. Yhdensuuntaisen viiveen mittaukseen Brix 100 ei sovellu etenkään mitattaessa alhaisia viivetasoja (∼1ms). Ulkoista synkronisointilähdettä, kuten GPS-kelloa, käytettäessä Brix 1000 -mittalaitetta voidaan käyttää myös yhdensuuntaisen viiveen mittaamiseen. Mittausalusta havaitsee verkossa tapahtuvat kuormitustilanteet ja reititinviat, mutta se ei kykene havaitsemaan lyhyitä alle sekunnin mittaisia katkoja. Työn teoriaosassa esitellään joitain tunnettuja aktiivimittausmekasimeja ja -metodeja sekä pureudutaan aktiivimittauksiin ja niiden ongelmakohtiin yleisellä tasolla. Lisäksi työssä esitellään tunnettuja akateemisia aktiivimittaukseen liittyviä projekteja.In this thesis, a commercial active network measurement platform is tested for performance and accuracy. The platform is also tested for ability to detect certain events in networks. Two types of measurement probes are tested: the low performance Brix 100 Verifier and the high performance Brix 1000 Verifier. It is found that both platform's measurement probe types are accurate when measuring round-trip delay, but do not perform nearly as well when measuring one-way delay. External synchronization, such as GPS, helps the Brix 1000 Verifier to reach sub-millisecond measurement accuracy. As Brix 100 Verifiers do not support external synchronization, their accuracy is suitable only for measuring one-way delays larger than a few milliseconds. The platform is able to detect sudden high load levels and router failures in a network, but fails to detect short (sub-second) link breaks. In the theory part of this thesis, some well known active measurement methods and mechanisms are presented. Also, challenges related to active measurement are discussed and some of the recent major academic active measurement projects are introduced

Standardized spider (Arachnida, Araneae) inventory of Hankoniemi, Finland

Background During a field course on spider taxonomy and ecology at the University of Helsinki, the authors had the opportunity to sample four plots with a dual objective of both teaching on field methods, spider identification and behaviour and uncovering the spider diversity patterns found in the southern coastal forests of Hankoniemi, Finland. As an ultimate goal, this field course intended to contribute to a global project that intends to uncover spider diversity patterns worldwide. With that purpose, a set of standardised methods and procedures was followed that allow the comparability of obtained data with numerous other projects being conducted across all continents. New information A total of 104 species and 1997 adults was collected. Of these, 41 species (39%) were Linyphiidae and 13 (12%) Theridiidae. All other families had 6 or less species represented. Linyphiidae were also dominant in terms of adult individuals captured, with 1015 (51%), followed by 428 (21%) Lycosidae, 158 (8%) Tetragnathidae and 145 (7%) Theridiidae. All other families had less than 100 individuals. The most abundant species were Neriene peltata, Alopecosa taeniata, Piratula hygrophila and Dismodicus elevatus, all with more than 100 individuals. All sites had between 56 and 62 species and between 445 and 569 individuals.Peer reviewe

Developing a spatially explicit modelling and evaluation framework for integrated carbon sequestration and biodiversity conservation: application in southern Finland

The challenges posed by climate change and biodiversity loss are deeply interconnected. Successful co-managing of these tangled drivers requires innovative methods that can prioritize and target management actions against multiple criteria, while also enabling cost-effective land use planning and impact scenario assessment. This paper synthesises the development and application of an integrated multidisciplinary modelling and evaluation framework for carbon and biodiversity in forest systems. By analysing and spatio-temporally modelling carbon processes and biodiversity elements, we determine an optimal solution for their co-management in the study landscape. We also describe how advanced Earth Observation measurements can be used to enhance mapping and monitoring of biodiversity and ecosystem processes. The scenarios used for the dynamic models were based on official Finnish policy goals for forest management and climate change mitigation. The development and testing of the system were executed in a large region in southern Finland (Kokemäenjoki basin, 27 024 km2) containing highly instrumented LTER (Long-Term Ecosystem Research) stations; these LTER data sources were complemented by fieldwork, remote sensing and national data bases. In the study area, estimated total net emissions were currently 4.2 TgCO2eq a-1, but modelling of forestry measures and anthropogenic emission reductions demonstrated that it would be possible to achieve the stated policy goal of carbon neutrality by low forest harvest intensity. We show how this policy-relevant information can be further utilised for optimal allocation of set-aside forest areas for nature conservation, which would significantly contribute to preserving both biodiversity and carbon values in the region. Biodiversity gain in the area could be increased without a loss of carbon-related benefits.The challenges posed by climate change and biodiversity loss are deeply interconnected. Successful co-managing of these tangled drivers requires innovative methods that can prioritize and target management actions against multiple criteria, while also enabling cost-effective land use planning and impact scenario assessment. This paper synthesises the development and application of an integrated multidisciplinary modelling and evaluation framework for carbon and biodiversity in forest systems. By analysing and spatio-temporally modelling carbon processes and biodiversity elements, we determine an optimal solution for their co-management in the study landscape. We also describe how advanced Earth Observation measurements can be used to enhance mapping and monitoring of biodiversity and ecosystem processes. The scenarios used for the dynamic models were based on official Finnish policy goals for forest management and climate change mitigation. The development and testing of the system were executed in a large region in southern Finland (Kokemäenjoki basin, 27,024 km2) containing highly instrumented LTER (Long-Term Ecosystem Research) stations; these LTER data sources were complemented by fieldwork, remote sensing and national data bases. In the study area, estimated total net emissions were currently 4.2 TgCO2eq a−1, but modelling of forestry measures and anthropogenic emission reductions demonstrated that it would be possible to achieve the stated policy goal of carbon neutrality by low forest harvest intensity. We show how this policy-relevant information can be further utilized for optimal allocation of set-aside forest areas for nature conservation, which would significantly contribute to preserving both biodiversity and carbon values in the region. Biodiversity gain in the area could be increased without a loss of carbon-related benefits.Peer reviewe

Quantification and valuation of ecosystem services to optimize sustainable re-use for low-productive drained peatlands

LIFEPeatLandUse (LIFE12 ENV/FI/000150) 2013 – 2018, LAYMAN’S REPORT201

Common Inflammation-Related Candidate Gene Variants and Acute Kidney Injury in 2647 Critically Ill Finnish Patients

Acute kidney injury (AKI) is a syndrome with high incidence among the critically ill. Because the clinical variables and currently used biomarkers have failed to predict the individual susceptibility to AKI, candidate gene variants for the trait have been studied. Studies about genetic predisposition to AKI have been mainly underpowered and of moderate quality. We report the association study of 27 genetic variants in a cohort of Finnish critically ill patients, focusing on the replication of associations detected with variants in genes related to inflammation, cell survival, or circulation. In this prospective, observational Finnish Acute Kidney Injury (FINNAKI) study, 2647 patients without chronic kidney disease were genotyped. We defined AKI according to Kidney Disease: Improving Global Outcomes (KDIGO) criteria. We compared severe AKI (Stages 2 and 3, n = 625) to controls (Stage 0, n = 1582). For genotyping we used iPLEX(TM) Assay (Agena Bioscience). We performed the association analyses with PLINK software, using an additive genetic model in logistic regression. Despite the numerous, although contradictory, studies about association between polymorphisms rs1800629 in TNFA and rs1800896 in IL10 and AKI, we found no association (odds ratios 1.06 (95% CI 0.89-1.28, p = 0.51) and 0.92 (95% CI 0.80-1.05, p = 0.20), respectively). Adjusting for confounders did not change the results. To conclude, we could not confirm the associations reported in previous studies in a cohort of critically ill patients.Peer reviewe

Multi-ancestry genome-wide association study accounting for gene-psychosocial factor interactions identifies novel loci for blood pressure traits

Psychological and social factors are known to influence blood pressure (BP) and risk of hypertension and associated cardiovascular diseases. To identify novel BP loci, we carried out genome-wide association meta-analyses of systolic, diastolic, pulse, and mean arterial BP, taking into account the interaction effects of genetic variants with three psychosocial factors: depressive symptoms, anxiety symptoms, and social support. Analyses were performed using a two-stage design in a sample of up to 128,894 adults from five ancestry groups. In the combined meta-analyses of stages 1 and 2, we identified 59 loci (p value < 5e−8), including nine novel BP loci. The novel associations were observed mostly with pulse pressure, with fewer observed with mean arterial pressure. Five novel loci were identified in African ancestry, and all but one showed patterns of interaction with at least one psychosocial factor. Functional annotation of the novel loci supports a major role for genes implicated in the immune response (PLCL2), synaptic function and neurotransmission (LIN7A and PFIA2), as well as genes previously implicated in neuropsychiatric or stress-related disorders (FSTL5 and CHODL). These findings underscore the importance of considering psychological and social factors in gene discovery for BP, especially in non-European populations

Multi-ancestry sleep-by-SNP interaction analysis in 126,926 individuals reveals lipid loci stratified by sleep duration.

Both short and long sleep are associated with an adverse lipid profile, likely through different biological pathways. To elucidate the biology of sleep-associated adverse lipid profile, we conduct multi-ancestry genome-wide sleep-SNP interaction analyses on three lipid traits (HDL-c, LDL-c and triglycerides). In the total study sample (discovery + replication) of 126,926 individuals from 5 different ancestry groups, when considering either long or short total sleep time interactions in joint analyses, we identify 49 previously unreported lipid loci, and 10 additional previously unreported lipid loci in a restricted sample of European-ancestry cohorts. In addition, we identify new gene-sleep interactions for known lipid loci such as LPL and PCSK9. The previously unreported lipid loci have a modest explained variance in lipid levels: most notable, gene-short-sleep interactions explain 4.25% of the variance in triglyceride level. Collectively, these findings contribute to our understanding of the biological mechanisms involved in sleep-associated adverse lipid profiles

Heme oxygenase-1 repeat polymorphism in septic acute kidney injury

Acute kidney injury (AKI) is a syndrome that frequently affects the critically ill. Recently, an increased number of dinucleotide repeats in the HMOX1 gene were reported to associate with development of AKI in cardiac surgery. We aimed to test the replicability of this finding in a Finnish cohort of critically ill septic patients. This multicenter study was part of the national FINNAKI study. We genotyped 300 patients with severe AKI (KDIGO 2 or 3) and 353 controls without AKI (KDIGO 0) for the guanine-thymine (GTn) repeat in the promoter region of the HMOX1 gene. The allele calling was based on the number of repeats, the cut off being 27 repeats in the S-L (short to long) classification, and 27 and 34 repeats for the S-M-L2 (short to medium to very long) classification. The plasma concentrations of heme oxygenase-1 (HO-1) enzyme were measured on admission. The allele distribution in our patients was similar to that published previously, with peaks at 23 and 30 repeats. The S-allele increases AKI risk. An adjusted OR was 1.30 for each S-allele in an additive genetic model (95% CI 1.01-1.66; p = 0.041). Alleles with a repeat number greater than 34 were significantly associated with lower HO-1 concentration (p<0.001). In septic patients, we report an association between a short repeat in HMOX1 and AKI risk