Sex-specific familial aggregation of cancers in Finland

Despite the fact that the effect of sex on the occurrence of cancers has been studied extensively, it remains unclear whether sex modifies familial aggregation of cancers. We explored sex-specific familial aggregation of cancers in a large population-based historical cohort study. We combined cancer and population registry data, inferring familial relationships from birth municipality-surname-sex (MNS) combinations. Our data consisted of 391,529 incident primary cancers in 377,210 individuals with 319,872 different MNS combinations. Cumulative sex-specific numbers of cancers were compared to expected cumulative incidence. Familial cancer risks were similar between the sexes in our population-wide analysis. Families with concordant cancer in both sexes exhibited similar sex-specific cancer risks. However, some families had exceptionally high sex-specific cumulative cancer incidence. We identified six families with exceptionally strong aggregation in males: three families with thyroid cancer (ratio between observed and expected incidence 184.6; 95% credible interval (95% CI) 33.1-1012.7, 173.4 (95% CI 65.4-374.3), and 161.4 (95% CI 29.6-785.7), one with stomach (ratio 14.4 (95% CI 6.9-37.2)), colon (ratio 15.5 (95% CI 5.7-56.3)) cancers and one with chronic lymphocytic leukaemia (ratio 33.5 (95% CI 17.2-207.6)). Our results imply that familial aggregation of cancers shows no sex-specific preference. However, the atypical sex-specific aggregation of stomach cancer, colon cancer, thyroid cancer and chronic lymphocytic leukaemia in certain families is difficult to fully explain with present knowledge of possible causes, and could yield useful knowledge if explored further.Peer reviewe

Cultivating resilience by empirically revealing response diversity

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The effect of rainfall amount and timing on annual transpiration in a grazed savanna grassland

The role of precipitation (P) variability with respect to evapotranspiration (ET) and its two components, transpiration (T) and evaporation (E), from savannas continues to draw significant research interest given its relevance to a number of ecohydrological applications. Our study reports on 6 years of measured ET and estimated T and E from a grazed savanna grassland at Welgegund, South Africa. Annual P varied significantly with respect to amount (508 to 672 mm yr(-1)), with dry years characterized by infrequent early-season rainfall. T was determined using annual water-use efficiency and gross primary production estimates derived from eddy-covariance measurements of latent heat flux and net ecosystem CO2 exchange rates. The computed annual T for the 4 wet years with frequent early wet-season rainfall was nearly constant, 326 +/- 19 mm yr(-1) (T/ET=0.51), but was lower and more variable between the 2 dry years (255 and 154 mm yr(-1), respectively). Annual T and T/ET were linearly related to the early wet-season storm frequency. The constancy of annual T during wet years is explained by the moderate water stress of C4 grasses as well as trees' ability to use water from deeper layers. During extreme drought, grasses respond to water availability with a dieback-regrowth pattern, reducing leaf area and transpiration and, thus, increasing the proportion of transpiration contributed by trees. The works suggest that the early-season P distribution explains the interannual variability in T, which should be considered when managing grazing and fodder production in these grasslands.Peer reviewe

Typpitaselaskurin käyttöohje

Typpitaselaskuri on tarkoitettu työkaluksi, jolla viljelijät ja neuvojat voivat laskea ja tulkita peltolohkojen typpitaseita sekä soveltaa tietoa viljelyn kehittämiseksi ympäristöä ja taloudellista tulosta silmällä pitäen. Peltolohkon typpitase eli lannoitteissa annetun ja sadon mukana poistuneen typen erotus vaihtelee riippuen mm. viljelykasvista, typpilannoituksen määrästä, maaperän laadusta ja kasvukauden säästä. Korkeaan ja ympäristön kannalta haitallisen suureen typpitaseeseen voidaan päätyä sekä liian suuren typpilannoituksen että heikoksi jääneen satotason vuoksi. Tämän vuoksi on tärkeää ymmärtää, mitä erisuuruiset typpitaseet merkitsevät erityyppisissä olosuhteissa ympäristön tai viljelyn onnistumisen kannalta. Typpitaselaskuri kehitettiin, jotta typpitaseita voitaisiin vertailla aiempaa paremmin ja taseisiin sisältyvää informaatiota päästäisiin hyödyntämään peltoviljelyssä. Typpitaselaskurilla saa laskettua peltolohkojen typpitaseet ja laskuri antaa niille tulkinnan. Laskuri toimii seuraavilla viljelykasveilla: kaura, ohra, kevätvehnä, syysvehnä, syysruis, tärkkelysperuna, sokerijuurikas, kevätrypsi ja säilörehunurmi. Typpitaseiden tulkintaan sisältyy 1) tieto siitä, miten suuri typpitase on suhteessa viiteryhmäänsä, ts. samanlaisissa oloissa samalla kasvilajilla toteutuneisiin taseisiin, 2) arvio taseen aiheuttamasta ympäristöriskistä ja 3) ehdotuksia typpitaseesta aiheutuvan ympäristöriskin pienentämiseksi. Toimenpide-ehdotukset on sovitettu kuhunkin tilanteeseen ja niissä on huomioitu sekä typpitaseesta aiheutuva ympäristöriski että vertailu viiteryhmään. Typpitaselaskurin avulla voi myös suunnitella kevätviljoille (kaura, kevätvehnä, ohra) taloudellisesti optimaalista typpilannoitusta kivennäismailla. Laskuri huomioi optimoinnissa peltolohkon satotason ilman typpilannoitusta ja antaa siitä tarvittaessa arvion viljelijän syöttämien tietojen avulla. Viljelijä voi myös antaa laskuriin edeltävän viljelyn (esikasvi, lannan käyttö, typpitase) tuoman typpilisän, joka vaikuttaa peltolohkon typpilannoitustarpeeseen. Optimoinnissa huomioidaan pellon aikaisempi satotaso ja käytetty lannoitus, lasketaan taloudellisesti optimaalinen typpilannoitus ja sitä vastaava typpitase sekä ilmoitetaan sadon valkuaispitoisuus. Taloudellisesti optimaalisella typpilannoituksella peltolohkolla viljeltävälle kasville saadaan suurin mahdollinen hehtaarituotto eli kasvin myyntituottojen ja lannoituskustannusten erotus. Laskurin toiminta ja sen tekemät tulkinnat perustuvat laajaan tietovarantoon suomalaisilla peltolohkoilla vuosina 1988–2018 toteutuneista typpitaseista, typpilannoituskokeissa havaittuihin typpilannoitusvasteisiin ja viljelijöiden pelloilta vuosina 2016−2019 mitattuihin lannoittamattomien alueiden satotasoihin. Laskuri on vapaasti käytettävissä Luonnonvarakeskuksen Maatalousinfo-verkkopalvelun kautta.202

Nudging service providers and assessing service trade-offs to reduce the social inefficiencies of payments for ecosystem services schemes

Socially inefficient payment for ecosystem services (PES) schemes result when adverse shifts in the provisioning of other ecosystem services (ES) or overpayment to service providers occur. To address these inefficiencies, a holistic evaluation of trade-offs between services should be conducted in parallel with determining land owners' service provisioning preferences. Recent evidence also suggests that nudging stakeholders' preferences could be a useful policy design tool to address global change challenges. Forest owners' landscape management preferences were nudged to determine the impact on the social efficiency of PES schemes for biodiversity conservation and climate change mitigation in Finland. ES indicators for biodiversity conservation, carbon storage, and the albedo effect were included with traditional provisioning services (i.e. timber) and bioenergy to assess the consequent intra-service trade-offs. Synergies in provisioning of regulating services were identified, but were found to be more efficient when the management objective is for biodiversity conservation rather than climate change regulation. Nudging led to marginal gains in service provisioning above the baseline management and above neutral owner preferences, and increased aggregate service provisioning. This demonstrates the importance of considering intra-service trade-offs and that nudging could be an important tool for designing efficient PES schemes. (C) 2015 Elsevier Ltd. All rights reserved.Peer reviewe

Sampling Rate Effects on Resting State fMRI Metrics

Low image sampling rates used in resting state functional magnetic resonance imaging (rs-fMRI) may cause aliasing of the cardiorespiratory pulsations over the very low frequency (VLF) BOLD signal fluctuations which reflects to functional connectivity (FC). In this study, we examine the effect of sampling rate on currently used rs-fMRI FC metrics. Ultra-fast fMRI magnetic resonance encephalography (MREG) data, sampled with TR 0.1 s, was downsampled to different subsampled repetition times (sTR, range 0.3–3 s) for comparisons. Echo planar k-space sampling (TR 2.15 s) and interleaved slice collection schemes were also compared against the 3D single shot trajectory at 2.2 s sTR. The quantified connectivity metrics included stationary spatial, time, and frequency domains, as well as dynamic analyses. Time domain methods included analyses of seed-based functional connectivity, regional homogeneity (ReHo), coefficient of variation, and spatial domain group level probabilistic independent component analysis (ICA). In frequency domain analyses, we examined fractional and amplitude of low frequency fluctuations. Aliasing effects were spatially and spectrally analyzed by comparing VLF (0.01–0.1 Hz), respiratory (0.12–0.35 Hz) and cardiac power (0.9–1.3 Hz) FFT maps at different sTRs. Quasi-periodic pattern (QPP) of VLF events were analyzed for effects on dynamic FC methods. The results in conventional time and spatial domain analyses remained virtually unchanged by the different sampling rates. In frequency domain, the aliasing occurred mainly in higher sTR (1–2 s) where cardiac power aliases over respiratory power. The VLF power maps suffered minimally from increasing sTRs. Interleaved data reconstruction induced lower ReHo compared to 3D sampling (p < 0.001). Gradient recalled echo-planar imaging (EPI BOLD) data produced both better and worse metrics. In QPP analyses, the repeatability of the VLF pulse detection becomes linearly reduced with increasing sTR. In conclusion, the conventional resting state metrics (e.g., FC, ICA) were not markedly affected by different TRs (0.1–3 s). However, cardiorespiratory signals showed strongest aliasing in central brain regions in sTR 1–2 s. Pulsatile QPP and other dynamic analyses benefit linearly from short TR scanning

Root‐zone soil moisture variability across African savannas : from pulsed rainfall to land‐cover switches

The main source of soil moisture variability in savanna ecosystems is pulsed rainfall. Rainfall pulsing impacts water‐stress durations, soil moisture switching between wet‐to‐dry and dry‐to‐wet states, and soil moisture spectra as well as derived measures from it such as soil moisture memory. Rainfall pulsing is also responsible for rapid changes in grassland leaf area and concomitant changes in evapotranspirational (ET) losses, which then impact soil moisture variability. With the use of a hierarchy of models and soil moisture measurements, temporal variability in root‐zone soil moisture and water‐stress periods are analysed at four African sites ranging from grass to miombo savannas. The normalized difference vegetation index (NDVI) and potential ET (PET)‐adjusted ET model predict memory timescale and dry persistence in agreement with measurements. The model comparisons demonstrate that dry persistence and mean annual dry periods must account for seasonal and interannual changes in maximum ET represented by NDVI and to a lesser extent PET. Interestingly, the precipitation intensity and soil moisture memory were linearly related across three savannas with ET/infiltration ∼ 1.0. This relation and the variability of length and timing of dry periods are also discussed.National Science Foundation; European Commission; Bundesministerium für Bildung und Forschung; Academy of Finland.http://wileyonlinelibrary.com/journal/ecohj2020Geography, Geoinformatics and Meteorolog

Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease–Associated Colorectal Cancer

doi: 10.1053/j.gastro.2021.04.042Background & Aims Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs. Methods Whole-genome sequencing, single nucleotide polymorphism arrays, RNA sequencing, genome-wide methylation analysis, and immunohistochemistry were performed using fresh-frozen and formalin-fixed tissue samples of tumor and corresponding normal tissues from 31 patients with IBD-CRC. Results Transcriptome-based tumor subtyping revealed the complete absence of canonical epithelial tumor subtype associated with WNT signaling in IBD-CRCs, dominated instead by mesenchymal stroma-rich subtype. Negative WNT regulators AXIN2 and RNF43 were strongly down-regulated in IBD-CRCs and chromosomal gains at HNF4A, a negative regulator of WNT-induced epithelial–mesenchymal transition (EMT), were less frequent compared to sCRCs. Enrichment of hypomethylation at HNF4α binding sites was detected solely in sCRC genomes. PIGR and OSMR involved in mucosal immunity were dysregulated via epigenetic modifications in IBD-CRCs. Genome-wide analysis showed significant enrichment of noncoding mutations to 5′untranslated region of TP53 in IBD-CRCs. As reported previously, somatic mutations in APC and KRAS were less frequent in IBD-CRCs compared to sCRCs. Conclusions Distinct mechanisms of WNT pathway dysregulation skew IBD-CRCs toward mesenchymal tumor subtype, which may affect prognosis and treatment options. Increased OSMR signaling may favor the establishment of mesenchymal tumors in patients with IBD.BACKGROUND & AIMS: Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs. METHODS: Whole-genome sequencing, single nucleotide polymorphism arrays, RNA sequencing, genome-wide methylation analysis, and immunohistochemistry were performed using fresh-frozen and formalin-fixed tissue samples of tumor and corresponding normal tissues from 31 patients with IBD-CRC. RESULTS: Transcriptome-based tumor subtyping revealed the complete absence of canonical epithelial tumor subtype associated with WNT signaling in IBD-CRCs, dominated instead by mesenchymal stroma-rich subtype. Negative WNT regulators AXIN2 and RNF43 were strongly down-regulated in IBD-CRCs and chromosomal gains at HNF4A, a negative regulator of WNTinduced epithelial-mesenchymal transition (EMT), were less frequent compared to sCRCs. Enrichment of hypomethylation at HNF4 alpha binding sites was detected solely in sCRC genomes. PIGR and OSMR involved in mucosal immunity were dysregulated via epigenetic modifications in IBD-CRCs. Genome-wide analysis showed significant enrichment of noncoding mutations to 50 untranslated region of TP53 in IBD-CRCs. As reported previously, somatic mutations in APC and KRAS were less frequent in IBD-CRCs compared to sCRCs. CONCLUSIONS: Distinct mechanisms of WNT pathway dysregulation skew IBD-CRCs toward mesenchymal tumor subtype, which may affect prognosis and treatment options. Increased OSMR signaling may favor the establishment of mesenchymal tumors in patients with IBD.Peer reviewe

A molecular-based identification resource for the arthropods of Finland

Publisher Copyright: © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.Peer reviewe

Molecular understanding of the suppression of new-particle formation by isoprene

Nucleation of atmospheric vapours produces more than half of global cloud condensation nuclei and so has an important influence on climate. Recent studies show that monoterpene (C10H16) oxidation yields highly oxygenated products that can nucleate with or without sulfuric acid. Monoterpenes are emitted mainly by trees, frequently together with isoprene (C5H8), which has the highest global emission of all organic vapours. Previous studies have shown that isoprene suppresses new-particle formation from monoterpenes, but the cause of this suppression is under debate. Here, in experiments performed under atmospheric conditions in the CERN CLOUD chamber, we show that isoprene reduces the yield of highly oxygenated dimers with 19 or 20 carbon atoms - which drive particle nucleation and early growth - while increasing the production of dimers with 14 or 15 carbon atoms. The dimers (termed C-20 and C-15, respectively) are produced by termination reactions between pairs of peroxy radicals (RO2 center dot) arising from monoterpenes or isoprene. Compared with pure monoterpene conditions, isoprene reduces nucleation rates at 1.7 nm (depending on the isoprene = monoterpene ratio) and approximately halves particle growth rates between 1.3 and 3.2 nm. However, above 3.2 nm, C-15 dimers contribute to secondary organic aerosol, and the growth rates are unaffected by isoprene. We further show that increased hydroxyl radical (OH center dot) reduces particle formation in our chemical system rather than enhances it as previously proposed, since it increases isoprene-derived RO2 center dot radicals that reduce C-20 formation. RO2 center dot termination emerges as the critical step that determines the highly oxygenated organic molecule (HOM) distribution and the corresponding nucleation capability. Species that reduce the C-20 yield, such as NO, HO2 and as we show isoprene, can thus effectively reduce biogenic nucleation and early growth. Therefore the formation rate of organic aerosol in a particular region of the atmosphere under study will vary according to the precise ambient conditions.Peer reviewe