Visualising the Logs of Shenandoah Garbage Collection Algorithm

Käesoleva lõputöö eesmärgiks on Red Hati uue mälukoristusalgoritmi Shenandoah logide parseri implementeerimine avatud lähtekoodiga projekti GCViewer raames. Lisaeesmärgiks on anda ülevaade Java mälukoristuse abstraktsioonist.Lõputöö koosneb kahest osast - esimeses osas uuritakse süvendatult prügikoristuse abstraktsiooni Javas ning selle erinevaid implementatsioone, logisüsteemi plaanitavaid muudatusi Java 9 ning teises osas kirjeldatakse parseri implementeerimist ja selle valideerimist.Töö käigus loodi eelmainitud Shenandoah parser, valideeriti see, ning tehti pull request selle GCVieweri projekti lisamiseks.The aim of the current thesis is to implement a Garbage Collection log parser for Red Hat’s Garbage Collection algorithm Shenandoah by extending an open-source project GCViewer. Additional aim is to take a further look into the Garbage Collection in Java. The thesis is split into two main parts. The first part describes the background of Garbage Collection in Java and upcoming changes to the logging system in Java 9. The second part covers the implementation and the validation of the parser.The intended Shenandoah parser was implemented, validated, and a pull request to add it to GCViewer project was created

Empowering society by reusing privately held data for official statistics - A European approach

The High-Level Expert Group on facilitating the use of new data sources for official statistics has been created in the context of the data and digital strategy of the European Commission (EC). The task of the Expert Group is to provide recommendations aimed at enhancing data sharing between businesses and government (B2G) for the purpose of producing official statistics (B2G4S). The Expert Group consists of high-level experts with various backgrounds that are particularly relevant to B2G4S. Businesses generate and use data primarily for business-related purposes. The motivation for B2G4S stems from the high societal value that such privately held data can potentially generate when transformed into reliable, relevant and timely official statistics that are made available to everybody, for free. Transforming data into statistical information requires cooperation between private data holders and statistical authorities. On a voluntary basis there have been many collaborative efforts by businesses and statistical authorities to produce statistics based on privately held data, but for various reasons the use of such data for official statistics is still far below the level required to provide society with the high-quality and timely official statistics it needs in the increasingly data-driven world

Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes

The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201 and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups we disclose lineages that began to radiate similar to 1-3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel

Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF) >= 5% and low-frequency variants (0.5Peer reviewe

Cerebral small vessel disease genomics and its implications across the lifespan

White matter hyperintensities (WMH) are the most common brain-imaging feature of cerebral small vessel disease (SVD), hypertension being the main known risk factor. Here, we identify 27 genome-wide loci for WMH-volume in a cohort of 50,970 older individuals, accounting for modification/confounding by hypertension. Aggregated WMH risk variants were associated with altered white matter integrity (p = 2.5×10-7) in brain images from 1,738 young healthy adults, providing insight into the lifetime impact of SVD genetic risk. Mendelian randomization suggested causal association of increasing WMH-volume with stroke, Alzheimer-type dementia, and of increasing blood pressure (BP) with larger WMH-volume, notably also in persons without clinical hypertension. Transcriptome-wide colocalization analyses showed association of WMH-volume with expression of 39 genes, of which four encode known drug targets. Finally, we provide insight into BP-independent biological pathways underlying SVD and suggest potential for genetic stratification of high-risk individuals and for genetically-informed prioritization of drug targets for prevention trials.Peer reviewe

Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine

Migraine is a debilitating neurological disorder affecting around one in seven people worldwide, but its molecular mechanisms remain poorly understood. There is some debate about whether migraine is a disease of vascular dysfunction or a result of neuronal dysfunction with secondary vascular changes. Genome-wide association (GWA) studies have thus far identified 13 independent loci associated with migraine. To identify new susceptibility loci, we carried out a genetic study of migraine on 59,674 affected subjects and 316,078 controls from 22 GWA studies. We identified 44 independent single-nucleotide polymorphisms (SNPs) significantly associated with migraine risk (P < 5 × 10−8) that mapped to 38 distinct genomic loci, including 28 loci not previously reported and a locus that to our knowledge is the first to be identified on chromosome X. In subsequent computational analyses, the identified loci showed enrichment for genes expressed in vascular and smooth muscle tissues, consistent with a predominant theory of migraine that highlights vascular etiologies

Carta de Leila D. Bram (U.S. Navy) a Ferran Sunyer , 9 maig 1966

Carta de Leila D. Bram (US Navy), on el felicita pel premi que l'IEC li ha concedit. Li demana si, un cop publicat, n'hi pot enviar dos "reprints" i diu que, en cas de retard en la publicació, els agradaria veure'n una còpia per avançat

Coastal grassland wader abundance in relation to breeding habitat characteristics in Matsalu Bay, Estonia

Wader populations have been declining worldwide, providing a fundamental question as to which environmental factors limit population growth. Many studies have focused on the effects of habitat change on wader populations as a result of climate change, agricul-tural intensification or abandonment of arable land. However, there are few studies inves-tigating the relationship between wader distribution/abundance and prey abundance. This study focused on the relationship between breeding wader abundance, habitat character-istics and prey abundance on different types of coastal and floodplain grasslands. The study was carried out in the Matsalu Bay area, Western Estonia between 2001 and 2005. Results showed that most wader species were strongly related to habitat flooding type but not to plant species richness or evenness or mean vegetation coverage. Abundance of epigeic earthworms at a site was positively correlated with wader species diversity and abundance, as well as at the individual species level for abundance of Northern Lapwing Vanellus vanellus, Black-tailed Godwit Limosa limosa and Redshank Tringa totanus

Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations.

Copy-number variations (CNV) are believed to play an important role in a wide range of complex traits, but discovering such associations remains challenging. While whole-genome sequencing (WGS) is the gold-standard approach for CNV detection, there are several orders of magnitude more samples with available genotyping microarray data. Such array data can be exploited for CNV detection using dedicated software (e.g., PennCNV); however, these calls suffer from elevated false-positive and -negative rates. In this study, we developed a CNV quality score that weights PennCNV calls (pCNVs) based on their likelihood of being true positive. First, we established a measure of pCNV reliability by leveraging evidence from multiple omics data (WGS, transcriptomics, and methylomics) obtained from the same samples. Next, we built a predictor of omics-confirmed pCNVs, termed omics-informed quality score (OQS), using only PennCNV software output parameters. Promisingly, OQS assigned to pCNVs detected in close family members was up to 35% higher than the OQS of pCNVs not carried by other relatives (p &lt; 3.0 × 10 &lt;sup&gt;-90&lt;/sup&gt; ), outperforming other scores. Finally, in an association study of four anthropometric traits in 89,516 Estonian Biobank samples, the use of OQS led to a relative increase in the trait variance explained by CNVs of up to 56% compared with published quality filtering methods or scores. Overall, we put forward a flexible framework to improve any CNV detection method leveraging multi-omics evidence, applied it to improve PennCNV calls, and demonstrated its utility by improving the statistical power for downstream association analyses

Põllumajanduslike katseasutiste töötulemusi : lühikokkuvõtteid katseist 1932-1938

Digiteeritud Euroopa Regionaalarengu Fondi rahastusel, projekti "Eesti teadus- ja õppekirjandus" (2014-2020.12.03.21-0848) raames.https://www.ester.ee/record=b1466872*es