bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of extreme weather conditions on European crop production in 2018
Authors: Beillouin Damien , Schauberger Bernhard , Bastos Ana , Ciais Phillipe , Makowski David 
Published: September 2020

Extreme weather increases the risk of large-scale crop failure. The mechanisms involved are complex and intertwined, hence undermining the identification of simple adaptation levers to help improve the resilience of agricultural production. Based on more than 82 000 yield data reported at the regional level in 17 European countries, we assess how climate affected the yields of nine crop species. Using machine learning models, we analyzed historical yield data since 1901 and then focus on 2018, which has experienced a multiplicity and a diversity of atypical extreme climatic conditions. Machine learning models explain up to 65% of historical yield anomalies. We find that both extremes in temperature and precipitation are associated with negative yield anomalies, but with varying impacts in different parts of Europe. In 2018, Northern and Eastern Europe experienced multiple and simultaneous crop failures—among the highest observed in recent decades. These yield losses were associated with extremely low rainfalls in combination with high temperatures between March and August 2018. However, the higher than usual yields recorded in Southern Europe—caused by favourable spring rainfall conditions—nearly offset the large decrease in Northern European crop production. Our results outline the importance of considering single and compound climate extremes to analyse the causes of yield losses in Europe. We found no clear upward or downward trend in the frequency of extreme yield losses for any of the considered crops between 1990 and 2018.This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.
Analysis of floodplain forest sensitivity to drought
Authors: Kowalska Natalia , Šigut Ladislav , Stojanović Marko , Fischer Milan , Kyselova Ina , Pavelka Marian 
Published: September 2020

Floodplain forests are very complex, productive ecosystems, capable of storing huge amounts of soil carbon. With the increasing occurrence of extreme events, they are today among the most threatened ecosystems. Our study's main goal was to assess the productivity of a floodplain forest located at Lanžhot in the Czech Republic from two perspectives: carbon uptake (using an eddy covariance method) and stem radius variations (using dendrometers). We aimed to determine which conditions allow for high ecosystem production and what role drought plays in reducing such production potential. Additionally, we were interested to determine the relative soil water content threshold indicating the onset and duration of this event. We hypothesized that summer drought in 2018 had the most significant negative effects on the overall annual carbon and water budgets. In contrast with our original hypothesis, we found that an exceptionally warm spring in 2018 caused a positive gross primary production (GPP) and evapotranspiration (ET) anomaly that consequently led in 2018 to the highest seasonal total GPP and ET from all of the investigated years (2015–2018). The results showed ring-porous species to be the most drought resistant. Relative soil water content threshold of approximately 0.45 was determined as indicating the onset of drought stress.
This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Physiological response of Swiss ecosystems to 2018 drought across plant types and elevation
Authors: Gharun Mana , Hörtnagl Lukas , Paul-Limoges Eugénie , Ghiasi Shiva , Feigenwinter Iris , Burri Susanne , Marquardt Kristiina , Etzold Sophia , Zweifel Roman , Eugster Werner , Buchmann Nina 
Published: September 2020

Using five eddy covariance flux sites (two forests and three grasslands), we investigated ecosystem physiological responses to the 2018 drought across elevational gradients in Switzerland. Flux measurements showed that at lower elevation sites (below 1000 m.a.s.l.; grassland and mixed forest) annual ecosystem productivity (GPP) declined by approximately 20% compared to the previous 2 years (2016 and 2017), which led to a reduced annual net ecosystem productivity (NEP). At the high elevation sites, however, GPP increased by approximately 14% and as a result NEP increased in the alpine and montane grasslands, but not in the subalpine coniferous forest. There, increased ecosystem respiration led to a reduced annual NEP, despite increased GPP and lengthening of the growing period. Among all ecosystems, the coniferous forest showed the most pronounced negative stomatal response to atmospheric dryness (i.e. vapour pressure deficit, VPD) that resulted in a decline in surface conductance and an increased water-use efficiency during drought. While increased temperature enhanced the water-use efficiency of both forests, de-coupling of GPP from evapotranspiration at the low-elevation grassland site negatively affected water-use efficiency due to non-stomatal reductions in photosynthesis. Our results show that hot droughts (such as in 2018) lead to different responses across plants types, and thus ecosystems. Particularly grasslands at lower elevations are the most vulnerable ecosystems to negative impacts of future drought in Switzerland.
This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Sensitivity of gross primary productivity to climatic drivers during the summer drought of 2018 in Europe
Authors: Fu Zheng , Ciais Philippe , Bastos Ana , Stoy Paul C. , Yang Hui , Green Julia K. , Wang Bingxue , Yu Kailiang , Huang Yuanyuan , Knohl Alexander , Šigut Ladislav , Gharun Mana , Cuntz Matthias , Arriga Nicola , Roland Marilyn , Peichl Matthias , Migliavacca Mirco , Cremonese Edoardo , Varlagin Andrej , Brümmer Christian , Gourlez de la Motte Louis , Fares Silvano , Buchmann Nina , El-Madany Tarek S. , Pitacco Andrea , Vendrame Nadia , Li Zhaolei , Vincke Caroline , Magliulo Enzo , Koebsch Franziska 
Published: September 2020

In summer 2018, Europe experienced a record drought, but it remains unknown how the drought affected ecosystem carbon dynamics. Using observations from 34 eddy covariance sites in different biomes across Europe, we studied the sensitivity of gross primary productivity (GPP) to environmental drivers during the summer drought of 2018 versus the reference summer of 2016. We found a greater drought-induced decline of summer GPP in grasslands (−38%) than in forests (−10%), which coincided with reduced evapotranspiration and soil water content (SWC). As compared to the ‘normal year’ of 2016, GPP in different ecosystems exhibited more negative sensitivity to summer air temperature (Ta) but stronger positive sensitivity to SWC during summer drought in 2018, that is, a stronger reduction of GPP with soil moisture deficit. We found larger negative effects of Ta and vapour pressure deficit (VPD) but a lower positive effect of photosynthetic photon flux density on GPP in 2018 compared to 2016, which contributed to reduced summer GPP in 2018. Our results demonstrate that high temperature-induced increases in VPD and decreases in SWC aggravated drought impacts on GPP.
This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Morphological stasis masks ecologically divergent coral species on tropical reefs
Authors: Bongaerts P , Cooke IR , Ying H , Wels D , Haan den S , Hernandez-Agreda A , Brunner CA , Dove S , Englebert N , Eyal G , Forêt S , Grinblat M , Hay KB , Harii S , Hayward DC , Lin Y , Mihaljević M , Moya A , Muir P , Sinniger F , Smallhorn-West P , Torda G , Ragan MA , van Oppen MJH , Hoegh-Guldberg O 
Published: September 2020

ABSTRACTCoral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa), and uncover through a comprehensive genomic and phenotypic assessment that it comprises morphologically indistinguishable, but ecologically divergent cryptic lineages. Demographic modelling based on whole-genome resequencing disproved that morphological crypsis was due to recent divergence, and instead indicated ancient morphological stasis. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid diagnostic assay revealed differentiation of their ecological distributions. Leveraging “common garden” conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate how ecologically and phenotypically divergent coral species can evolve despite morphological stasis, and provide new leads into the potential mechanisms facilitating such divergence in sympatry. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.
Mutational landscapes of normal breast during age and pregnancy determine cancer risk
Authors: Cereser Biancastella , Tabassum Neha , Belluz Lisa Del Bel , Yiu Angela , Zagorac Sladjana , Miere Cristian , Werner Benjamin , Moderau Nina , Jeffries-Jones Alicia Rose , Stebbing Justin 
Published: September 2020

ABSTRACTThe accumulation of somatic mutations in the healthy breast throughout life and pregnancy is poorly understood1–10. Similarly, the mutational landscape of both epithelial and stromal components of the mammary gland has not been investigated. Both are relevant for breast cancer (BC), as the interplay between age, pregnancy, and cancer risk has not been fully characterized11. We describe whole genome sequencing analysis of epithelial and stromal compartments from the normal breast. We show that, in a similar way to other normal organs, the mutational burden of the mammary nulliparous epithelium significantly increases with age. In a nulliparous status, mutated clones are maintained at a consistently small size throughout the life of the individual; however, at parity, pre-existent clones significantly increase in size with age. Both epithelial and stromal compartments of the healthy breast contain pre-existing known cancer mutations, albeit at low rate, indicative of subsequent positive selection for mutations in tissue-specific driver genes. In line with this, both compartments also present gene enrichment in preferentially mutated cancer pathways. Our results show that mutational landscapes differ between the parous and nulliparous epithelium and suggest an explanation for both differential breast cancer risk and development of pregnancy-associated BC (PABC).
Mosaic evolution of molecular pathways for sex pheromone communication in a butterfly
Authors: Nieberding Caroline M. , Beldade Patrícia , Baumlé Véronique , Martin Gilles San , Arun Alok , Lognay Georges , Montagné Nicolas , Bastin-Héline Lucie , Jacquin-Joly Emmanuelle , Noirot Céline , Klopp Christophe , Visser Bertanne 
Published: September 2020

AbstractUnraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved, ancestral traits, and newly evolved, derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~98 million years ago. In moths, females typically emit pheromones to attract male mates, but in butterflies pheromones and used by females for mate choice. The molecular bases of sex pheromone communication are well understood in moths, but have remained virtually unexplored in butterflies. We used a combination of transcriptomics, real time qPCR, and phylogenetics, to identify genes involved in different steps of sex pheromone communication in the butterflyBicyclus anynana. Our results show that the biosynthesis and reception of sex pheromones relies both on moth-specific gene families (reductases) and on more ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly,B. anynanafurther appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulation of sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale analysis of the genetic pathways underlying sex pheromone communication in a butterfly.
3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk
Authors: Liu Ning , Sadlon Timothy , Wong Ying Ying , Pederson Stephen , Breen James , Barry Simon C 
Published: September 2020

AbstractBackgroundGenome-wide association and fine-mapping studies have enabled the discovery of single nucleotide polymorphisms (SNPs) and other variants that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the SNPs lie in non-coding regions, limiting the identification of mechanisms that contribute to autoimmune disease progression.MethodsAutoimmunity results from a failure of immune tolerance, suggesting that regulatory T cells (Treg) are likely a significant point of impact for this genetic risk, as Treg are critical for immune tolerance. Focusing on T1D as a model of defective function of Treg in autoimmunity, we designed a SNPs filtering workflow called 3 Dimensional Functional Annotation of Accessible Cell Type Specific SNPs (3DFAACTS-SNP) that utilises overlapping profiles of Treg-specific epigenomic data (ATAC-seq, Hi-C and FOXP3-ChIP) to identify regulatory elements potentially driving the effect of variants associated with T1D, and the gene(s) that they control.ResultsUsing 3DFAACTS-SNP we identified 36 SNPs with plausible Treg-specific mechanisms of action contributing to T1D from 1,228 T1D fine-mapped variants, identifying 119 novel interacting regions resulting in the identification of 51 candidate target genes. We further demonstrated the utility of the workflow by applying it to three other fine-mapped/meta-analysed SNP autoimmune datasets, identifying 17 Treg-centric candidate variants and 35 interacting genes. Finally, we demonstrate the broad utility of 3DFAACTS-SNP for functional annotation of any genetic variation using all common (>10% allele frequency) variants from the Genome Aggregation Database (gnomAD). We identified 7,900 candidate variants and 3,245 candidate target genes, generating a list of potential sites for future T1D or autoimmune research.ConclusionsWe demonstrate that it is possible to further prioritise variants that contribute to T1D based on regulatory function and illustrate the power of using cell type specific multi-omics datasets to determine disease mechanisms. The 3DFAACTS-SNP workflow can be customised to any cell type for which the individual datasets for functional annotation have been generated, giving broad applicability and utility.
Frontotemporal dementia mutant tau (P301L) locks Fyn in an open, active conformation conducive to nanoclustering
Authors: Small Christopher , Martínez-Mármol Ramón , Wallis Tristan P. , Gormal Rachel S. , Götz Jürgen , Meunier Frédéric A. 
Published: September 2020

AbstractFyn is a Src kinase that controls critical signalling cascades and its postsynaptic enrichment underpins synaptotoxicity in Alzheimer’s disease (AD) and frontotemporal dementia (FTLD-tau). Previously, we found that pathogenic FTLD tau mutant (P301L) expression promotes aberrant trapping of Fyn in nanoclusters within hippocampal dendrites via an unknown mechanism (Padmanabhan et al., 2019). Here, we imaged Fyn-mEos2 using single particle tracking photoactivated localization microscopy (sptPALM) to demonstrate that nanoclustering of Fyn in hippocampal dendrites is promoted by Fyn’s open, primed conformation. Disrupting the auto-inhibitory, closed conformation of Fyn through phospho-inhibition, and perturbation of Fyn’s SH3 domain increases, Fyn’s nanoscale trapping. However, inhibition of Fyn’s catalytic domain has no impact on its mobility. Tau-P301L promotes Fyn lateral trapping via Fyn opening and ensuing increased catalytic activation. Pathogenic tau may therefore drive synaptotoxicity by locking Fyn in an open, catalytically active conformation, leading to postsynaptic entrapment and aberrant signalling cascades.
Impact of chronic transcranial Random-Noise Stimulation (tRNS) on prefrontal cortex excitation-inhibition balance in juvenile mice
Authors: Sánchez-León Carlos A. , Sánchez-López Álvaro , Gómez-Climent María A. , Cordones Isabel , Kadosh Roi Cohen , Márquez-Ruiz Javier 
Published: September 2020

AbstractTranscranial random noise stimulation (tRNS), a non-invasive neuromodulatory technique capable of altering cortical activity, has been proposed to improve the signal-to-noise ratio at the neuronal level and the sensitivity of the neurons following an inverted U-function. The aim of this study was to examine the effects of tRNS on vGLUT1 and GAD 65-67 and its safety in terms of pathological changes. For that, juvenile mice were randomly distributed in three different groups: “tRNS 1x” receiving tRNS at the density current used in humans (0.3 A/m2, 20 min), “tRNS 100x” receiving tRNS at two orders of magnitude higher (30.0 A/m2, 20 min) and “sham” (0.3 A/m2, 15 s). Nine tRNS sessions during five weeks were administered to the prefrontal cortex of alert animals. No detectable tissue macroscopic lesions were observed after tRNS sessions. Post-stimulation immunohistochemical analysis of GAD 65-67 and vGLUT1 immunoreactivity showed a reduced GAD 65-67 immunoreactivity levels in the region directly beneath the electrode for tRNS 1x group with no significant effects in the tRNS 100x nor sham group. The observed results points to an excitatory effect associated with a decrease in GABA levels in absence of major histopathological alterations providing a novel mechanistic explanation for tRNS effects.
The Pleistocene species pump past its prime: evidence from European butterfly sister species
Authors: Ebdon Sam , Laetsch Dominik R. , Dapporto Leonardo , Hayward Alexander , Ritchie Michael G. , Dincă Vlad , Vila Roger , Lohse Konrad 
Published: September 2020

AbstractThe Pleistocene glacial cycles had a profound impact on the ranges and genetic make-up of organisms. Whilst it is clear that the contact zones that have been described for many sister taxa are secondary and have formed during the last interglacial, it is unclear when the taxa involved began to diverge. Previous estimates based on small numbers of loci are unreliable given the stochasticity of genetic drift and the contrasting effects of incomplete lineage sorting and gene flow on gene divergence. Here we use genome-wide transcriptome data to estimate divergence for 18 sister species pairs of European butterflies showing either sympatric or contact zone distributions. We find that in most cases species divergence predates the mid-Pleistocene transition or even the entire Pleistocene period. We also show that although post divergence gene flow is restricted to contact zone pairs, they are not systematically younger than sympatric pairs. This suggests that contact zones are not limited to the embryonic stages of the speciation process, but can involve notably old taxa. Finally, we show that mitochondrial and nuclear divergence are only weakly correlated and mitochondrial divergence is higher for contact-zone pairs. This suggests a possible role of selective sweeps affecting mitochondrial variation in maintaining contact zones.Impact SummaryThe influence of the Pleistocene glacial cycles on structuring species and genetic diversity in temperate taxa has permeated biogeographic and phylogeographic thinking for decades. Although phylogeographic studies have repeatedly claimed that the Pleistocene acted as a species pump, systematic tests of this idea based on robust estimates of species divergence are lacking. Here we estimate divergence times for all sister species pairs of European butterfly using genome-wide transcriptome data. We find that most species pairs are substantially older than the onset of Pleistocene glacial cycling. We also show that post divergence gene flow is restricted to pairs that form contact-zones. However, in contrast to expectations under a null model of allopatric speciation contract zone pairs are not necessarily younger than sympatric pairs.
The effect of response biases on resolution thresholds of Sloan letters in central and paracentral vision
Authors: Barhoom Hatem , Joshi Mahesh R , Schmidtmann Gunnar 
Published: September 2020

AbstractPurposeLetter resolution depends on three factors: perceivability, response bias, and similarity. The aim of the present study was to investigate the effect of response bias (the sensory-independent factor) on resolution thresholds of Sloan letters in central and paracentral vision.MethodsNine subjects with normal ocular health were recruited for this study. Using the method of constant stimuli, individual Sloan letters resolution thresholds were measured at 0° (central) and at ±3° eccentricity along the vertical meridian of the visual field. Response biases and letter similarities were computed using Luce’s choice model.ResultsResults showed that the differences in resolution thresholds of individual Sloan letters were significant at the central (F (9, 80) =5.02,p<.001), the upper (χ2 (9) = 50.38,p<.05) and the lower (χ2 (9) = 56.32,p<.05) visual field locations. Unlike letter similarity measures, response biases showed significant correlations to the differences in thresholds at the central (r = −0.83,p<.05), the upper (r = - 0.73,p<.05) and the lower (r = −0.70,p<.05) visual field locations.ConclusionsOur findings suggest that response biases have a significant effect on resolution of Sloan letters that could result in overestimating resolution acuity in central and paracentral visual field locations.