Novel storage architectures and pointer-free search trees for database systems

Database systems research is an old and well-established field in computer science. Many of the key concepts appeared as early as the 60s, while the core of relational databases, which have dominated the database world for a while now, was solidified during the 80s. However, the underlying hardware has not displayed such stability in the same period, which means that a lot of assumptions that were made about the hardware by early database systems are not necessarily true for modern computer architectures. In particular, over the last few decades there have been two notable consistent trends in the evolution of computer hardware. The first is that the memory hierarchy of mainstream computer systems has been getting deeper, with its different levels moving away from each other, and new levels being added in between as a result, in particular cache memories. The second is that, when it comes to data transfers between any two adjacent levels of the memory hierarchy, access latencies have not been keeping up with transfer rates. The challenge is therefore to adapt database index structures so that they become immune to these two trends. The latter is addressed by gradually increasing the size of the data transfer unit; the former, by organizing the data so that it exhibits good locality for memory transfers across multiple memory boundaries.We have developed novel structures that facilitate both of these strategies. We started our investigation with the venerable B+-tree, which is the cornerstone order-preserving index of any database system, and we have developed a novel pointer-free tree structure for its pages that optimizes its cache performance and makes it immune to the page size. We then adapted our approach to the R-tree and the GiST, making it applicable to multi-dimensional data indexes as well as generalized indexes for any abstract data type. Finally, we have investigated our structure in the context of main memory alone, and have demonstrated its superiority over the established approaches in that setting too. While our research has its roots in data structures and algorithms theory, we have conducted it with a strong experimental focus, as the complex interactions within the memory hierarchy of a modern computer system can be quite challenging to model and theorize about effectively. Our findings are therefore backed by solid experimental results that verify our hypotheses and prove the superiority of our structures over competing approaches

Fungal Communities Vectored by Ips sexdentatus in Declining Pinus sylvestris in Ukraine: Focus on Occurrence and Pathogenicity of Ophiostomatoid Species

Drought-induced stress and attacks by bark beetle Ips sexdentatus currently result in a massive dieback of Pinus sylvestris in eastern Ukraine. Limited and fragmented knowledge is available on fungi vectored by the beetle and their roles in tree dieback. The aim was to investigate the fungal community vectored by I. sexdentatus and to test the pathogenicity of potentially aggressive species to P. sylvestris. Analysis of the fungal community was accomplished by combining different methods using insect, plant, and fungal material. The material consisted of 576 beetles and 96 infested wood samples collected from six sample plots within a 300 km radius in eastern Ukraine and subjected to fungal isolations and (beetles only) direct sequencing of ITS rDNA. Pathogenicity tests were undertaken by artificially inoculating three-to-four-year-old pine saplings with fungi. For the vector test, pine logs were exposed to pre-inoculated beetles. In all, 56 fungal taxa were detected, 8 exclusively by isolation, and 13 exclusively by direct sequencing. Those included nine ophiostomatoids, five of which are newly reported as I. sexdentatus associates. Two ophiostomatoid fungi, which exhibited the highest pathogenicity, causing 100% dieback and mortality, represented genera Graphium and Leptographium. Exposure of logs to beetles resulted in ophiostomatoid infections. In conclusion, the study revealed numerous I. sexdentatus-vectored fungi, several of which include aggressive tree pathogens

Long-term pathological consequences of resin tapping wounds on stems of Scots pine (Pinus sylvestris L.)

Key message After 5-6 decades since inflicting resin tapping wounds, overmature (> 120 years old) Pinus sylvestris stems remain undecayed and vigorous. Overmature trees of Pinus sylvestris bearing large wounds made by resin tapping decades ago are still present in woodlands of south-eastern Baltic Sea region. The aim of the present study was to investigate health condition of those trees focusing on fungal infections and to estimate impact of the injury on radial stem growth. The study was conducted in Latvia in three overmature stands of P. sylvestris, resin-tapped in 1950-1970 s. On the studied ninety 120-167-year-old trees, exposed sapwood constituted from 1140 to 7755 cm(2) per individual stem. Of the 127 wounds sampled, 52 (41%) showed wood discoloration. The discoloration in its extent was limited, expanding beyond wound margins approx. 1 (max 3) cm in radial, and 6-7 cm in longitudinal directions. Of the 127 wood samples/wounds subjected to fungal isolations, 96% resulted in fungal growth, yielding 236 fungal isolates that represented 47 fungal taxa. The most common among macro-fungi was basidiomycete Porodaedalea pini, which was isolated from 9% of stems. The fungus is currently classed not as a tree pathogen, but instead as an indicator species for woodland sites to be considered for nature conservation. Data from tree ring widths have revealed that tree reacted to the resin tapping injury by increasing radial increment of the un-affected part of the circumference of the stem. Current study demonstrated that even on the long term, resin tapping has little influence on health condition and vitality of P. sylvestris, even at the very old age. This should be considered as a supporting message in case resin taping practices in the region are to be revived

Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses

Peer reviewedPublisher PD

Infestation by Ips amitinus (Eichhoff, 1872), Its Associated Fungi, and Butt Rots in Stands of Pinus sibirica in South-Western Siberia

: In 2019, the bark beetle Ips amitinus (native to central Europe) was identified in southwestern Siberia at a distance exceeding 2500 km east of its previously known easternmost location in the European part of Russia. In Siberia, its invasive populations are characterised by high abundance and harmfulness. Here, I. amitinus accomplishes primary attacks on standing vital trees of Pinus sibirica with a lethal outcome. This invasion has already resulted in massive dieback in stands of pine over a large geographic territory. By, 2021, the invaded area was estimated to cover at least 31,200 km2 . The objectives of this study were to investigate fungi associated with/vectored by I. amitinus in its invasive area in south-western Siberia and wood decay fungi that cause root and butt rots to P. sibirica. This led to the following conclusions: (i) DNA analysis of sixty adult beetles of Ips amitinus collected from P. sibirica in south-west Siberia revealed the presence of 143 fungal taxa; (ii) species richness was significantly higher in beetles collected from dead branches than from (more recently infested) dying branches; (iii) fungal communities were >90% dominated by yeasts, among which the most common were Nakazawaea holstii, Kuraishia molischiana, and N. ambrosiae; (iv) entomopathogenic Beauveria bassiana s.l. was the most common fungus isolated from dead/mycosed beetles of I. amitinus, followed by Lophium arboricola and four Ophiostoma spp.; and (v) Heterobasidion parviporum was the most common decay fungus detected, which was causing heart rot in stems of P. sibirica

Identifying Fraxinus excelsior tolerant to ash dieback: Visual field monitoring versus a molecular marker

Ash dieback (ADB) caused by the pathogen Hymenoscyphus fraxineus is the cause of massive mortality of Fraxinus spp. in Europe. The aim of this work was to check for the presence of the molecular marker for ADB tolerance in mapped healthy-looking F. excelsior trees, and to compare its occurrence in trees exhibiting severe ADB symptoms. Monitoring of 135 healthy-looking F. excelsior on the island of Gotland, Sweden, showed that after 3-4 years 99.3% of these trees had 0%-10% crown damage, thus remaining in a similar health condition as when first mapped. After 5-6 years, 94.7% of these trees had 0%-10% crown damage. Molecular analysis of leaf tissues from 40 of those showed the presence of the molecular marker in 34 (85.0%) trees, while it was absent in 6 (15.0%) trees. Analysis of leaf tissues from 40 severely ADB-diseased trees showed the presence of the molecular marker in 17 (42.5%) trees, but its absence in 23 (57.5%) trees (p < .0001). The results demonstrated that monitoring of healthy-looking F. excelsior is a simple and straightforward approach for the selection of presumably ADB-tolerant ash for future breeding. The cDNA-based molecular marker revealed moderate capacity on its own to discriminate between presumably ADB-tolerant and susceptible F. excelsior genotypes

Fungi associated with Ips acuminatus (Coleoptera: Curculionidae) in Ukraine with a special emphasis on pathogenicity of ophiostomatoid species

Conifer bark beetles are well known to be associated with fungal complexes, which consist of pathogenic ophiostomatoid fungi as well as obligate saprotroph species. However, there is little information on fungi associated with Ips acuminatus in central and eastern Europe. The aim of the study was to investigate the composition of the fungal communities associated with the pine engraver beetle, I. acuminatus, in the forest-steppe zone in Ukraine and to evaluate the pathogenicity of six associated ophiostomatoid species by inoculating three-year-old Scots pine seedlings with these fungi. In total, 384 adult beetles were collected from under the bark of declining and dead Scots pine trees at two different sites. Fungal culturing from 192 beetles resulted in 447 cultures and direct sequencing of ITS rRNA from 192 beetles in 496 high-quality sequences. Identification of the above revealed that the overall fungal community was composed of 60 species. Among these, the most common were Entomocorticium sp. (24.5%), Diplodia pinea (24.0%), Ophiostoma ips (16.7%), Sydowia polyspora (15.1%), Graphilbum cf rectangulosporium (15.1%), Ophiostoma minus (13.8%) and Cladosporium pini-ponderosae (13.0%). Pathogenicity tests were done using six species of ophiostomatoid fungi, which were inoculated into Scots pine seedlings. All ophiostomatoid fungi tested successfully infected seedlings of Scots pine with varying degrees of virulence. Ophiostoma minus was the only fungus that caused dieback in inoculated seedlings. It is concluded that I. acuminatus vectors a species-rich fungal community including pathogens such as D. pinea and O. minus. The fungal community reported in the present study is different from that reported in other regions of Europe. Pathogenicity tests showed that O. minus was the most virulent causing dieback in seedlings of Scots pine, while other fungi tested appeared to be only slightly pathogenic or completely non-pathogenic

Invasive Populations of the Emerald Ash Borer Agrilus planipennis Fairmaire, 1888 (Coleoptera: Buprestidae) in Saint Petersburg, Russia: A Hitchhiker?

Simple Summary The emerald ash borer (EAB) is an invasive beetle of Asian origin that has killed millions of ash trees in North America and Russia, with a devastating economic and ecological impact. In September 2020, EAB was detected for the first time in Saint Petersburg, Russia, notably killing ash trees. The invasion came from the eastern direction (Moscow) and became a significantly notable event for Saint Petersburg, famous for its historical parks. Moreover, Saint Petersburg is 120-130 km from the eastern EU borders of Estonia and Finland, with railway, motorway, and ferry connections. Currently, EAB is one of the most serious quarantine insect pests in the EU. There is a risk that the eventual EAB invasion could potentially extirpate European populations of ash. Currently, 95% are devastated by the invasive fungal disease ash dieback. Here, we investigated the development of EAB populations in Saint Petersburg, from its initial invasion (estimated year 2015), until 2021. We found that climatic conditions of north Russia do not favor the natural aerial spread of EAB. The two isolated populations were located, respectively, close to a motorway, and the Neva River (used for cargo shipping), implying that the insect spreads by transport vehicles, or "hitchhiking". This could potentially lead to the eventual invasion of the EU by this serious, tree-killing beetle. The emerald ash borer (EAB), Agrilus planipennis, is an invasive beetle of East Asian origin that has killed millions of ash trees (Fraxinus spp.) in North America and Russia. In September 2020, EAB was detected in Saint Petersburg, a notable event for the metropolitan city. The aim of the present study was to investigate the occurrence and ecology of EAB in Saint Petersburg. The presence of two distinct enclave populations of EAB was revealed, each of which has, most likely, been established through separate events of "hitchhiking" via transport vehicles. Following the invasion, the further spread of EAB in Saint Petersburg was slow and locally restricted, most likely due to climatic factors. This spread by "hitchhiking" suggests that the possibility of the further long-distance geographic spread of EAB in the Baltic Sea region (the EU) is high, both by ground transport (120-130 km distance from EU borders) and ferries that transport cars across the Baltic Sea. In certain cases, the development of EAB on Fraxinus excelsior, based on the stem portion colonized, larval densities, number of galleries, exit holes, viable larvae, and emerged adult beetles, was more successful than in Fraxinus pennsylvanica trees. The observed relatively high sensitivity of F. excelsior to EAB, therefore, casts doubt on the efficacy and benefits of the currently ongoing selection and breeding projects against ash dieback (ADB) disease, which is caused by the fungus Hymenoscyphus fraxineus. Inventory, mapping, and monitoring of surviving F. excelsior trees infested by both ADB and EAB are necessary to acquire genetic resources for work on the strategic long-term restoration of F. excelsior, tackling the probable invasion of EAB to the EU

Lymphoid organisation in labial salivary gland biopsies is a possible predictor for the development of malignant lymphoma in primary Sjögren's syndrome

Objective The development of non-Hodgkin's lymphoma (NHL) confers a high risk of mortality in primary Sjogren's syndrome (pSS) patients, but the sensitivity and specificity of proposed lymphoma predictors are insufficient for practical use. The performance of lymphoid organisation in the form of germinal centre (GC)-like lesions was evaluated in labial salivary gland biopsies taken at pSS diagnosis as a potential lymphoma-predicting biomarker. Methods Labial salivary gland tissue biopsies available from two Swedish pSS research cohorts (n = 175) were re-evaluated by light microscopy in a blind study in order to identify GC-like structures as a sign of ectopic lymphoid tissue formation and organisation. A linkage study was performed with the Swedish Cancer Registry for lymphoma identification. The risk of developing NHL in GC-positive patients in comparison with GC-negative patients was evaluated using Kaplan-Meier statistics and log-rank test. Associations between GC-like structures and clinical and/or laboratory disease markers were also determined using. 2 or Fisher's exact tests. Results At diagnosis, 25% of pSS patients had GC-like structures in their salivary glands. Seven of the 175 patients studied (14% GC+ and 0.8% GC-) developed NHL during 1855 patient-years at risk, with a median onset of 7 years following the initial diagnostic salivary gland biopsy. Six of the seven patients had GC-like structures at diagnosis; the remaining patient was GC negative at the time of diagnosis (p=0.001). Conclusions The detection of GC-like structures by light microscopy in pSS diagnostic salivary biopsies is proposed as a highly predictive and easy-to-obtain marker for NHL development. This allows for risk stratification of patients and the possibility to initiate preventive B-cell-directed therapy

North-Westward Expansion of the Invasive Range of Emerald Ash Borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae) towards the EU: From Moscow to Saint Petersburg

Agrilus planipennis is a devastating invasive pest of ash trees in European Russia, Ukraine, and North America. To monitor the north-western limit of its European invasive range, in June 2018 we established 10 study plots along the federal highway M10 (Russia) that runs between Moscow and Saint Petersburg through Tver' City (approx. 180 km from Moscow), and lined with ash trees. On each plot, 2-4 Fraxinus pennsylvanica trees with heights ranging 6.1-17.0 m and diameters ranging 7.0-18.0 cm were girdled, i.e., 50 cm of their bark were removed. The study plots were visited and girdled trees were examined in September and November, 2018, and in October, 2019. Observations revealed that the current continuous north-western limit of A. planipennis range in European Russia coincides with the north-western border of Tver' City and this range limit has not distinctly shifted north-westward during 2015-2019. In spite of the rich food supply (due to abundant F. pennsylvanica and F. excelsior plantings) in Tver' City and along roads going to and from, the population density of A. planipennis in the area is currently low. Recent (September 2020) sudden detection of a spatially isolated A. planipennis outbreak approx. 520 km far north-westward from Tver' (in Saint Petersburg) suggested that A. planipennis most likely had arrived at Saint Petersburg not by gradual stepwise (flying tree-to-tree) expansion of its continuous invasive range in Tver' City, but as a result of its accidental introduction by means of, e.g., "insect-hitchhiked" vehicles, transported plants for planting, and/or other commodities. The proximity of the reported A. planipennis outbreak to the borders of the EU (approx. 130 km to Estonia and Finland) requires urgent measures for its containment and control, and constant monitoring