bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for a multicellular symplasmic water pumping mechanism across vascular plant roots
Authors: Couvreur Valentin , Heymans Adrien , Lobet Guillaume , Draye Xavier 
Published: April 2021

AbstractWith global warming, climate zones are projected to shift poleward, and the frequency and intensity of droughts to increase, driving threats to crop production and ecosystems. Plant hydraulic traits play major roles in coping with such droughts, and process-based plant hydraulics (water flowing alongdecreasing pressure Ψpor total water potential Ψtotgradients) has newly been implemented in land surface models.An enigma reported for the past 35 years is the observation of water flowing alongincreasing water potential gradientsacross roots. By combining the most advanced modelling tool from the emerging field of plant micro-hydrology with pioneering cell solute mapping data, we found thatthe current paradigm of water flow across roots ofall vascular plantsis incomplete: it lacks the impact of solute concentration (and thus negative osmotic potential Ψo) gradients acrosslivingcells. This gradient acts as a water pump as it reduces water tension without loading solutes in plant vasculature (xylem). Importantly, water tension adjustments in roots may have large impacts in leaves due to the tension-cavitation feedback along stems.Here, we mathematically demonstrate the water pumping mechanism by solving water flow equations analytically on a triple-cell system. Then we show that the simplistic upscaled equations hold in 2- and 3-D maize, grapevine and Arabidopsis complex hydraulic anatomies, and that water may flow “uphill” of water potential gradients toward xylem as observed experimentally.Besides its contribution to the fundamental understanding of plant water relations, this study lays new foundations for future multidisciplinary research encompassing plant physiology and ecohydrology, and has the ambition to mathematically capture a keystone process for the accurate forecasting of plant water status in crop models and LSMs.Graphical AbstractHighlights-We provide a scale-consistent solution of water flow equations across root tissues-Symplasmic osmotic potential gradients are missing in the current theory of root water uptake-The model solves the empirical enigma of root water uptake uphill of water potential gradients
Real-Time EEG Neurofeedback as a Tool to Improve Neural Entrainment to Speech
Authors: Carrera Arias Francisco Javier , Molinaro Nicola , Lizarazu Mikel 
Published: April 2021

AbstractNeurofeedback represents a particular type of biofeedback whose aim is to teach self-control of brain function by measuring brain activity and presenting a feedback signal in real-time. Traditionally, neurofeedback has been used to complement interventions for various neuropsychological disorders through techniques like frequency training, which attempts to change the power ratio of certain EEG frequency bands. However, to date, there are no neurofeedback approaches that look directly into modulating the neural entrainment to speech. Speech-brain entrainment, which stands for the alignment of the neural activity to the envelope of the speech input, has been shown to be key to speech comprehension. In fact, atypical neural entrainment to speech seems to be consistently found in language development disorders such as dyslexia. Thus, making speech entrainment neurofeedback a promising technique to obtain behavioral improvements. In this work, we present the first open-source brain-computer interface system that can be reliably used to provide speech entrainment neurofeedback while still being flexible enough to deliver more traditional coherence-based neurofeedback. In addition, it has the potential of being an open-source alternative to deliver other types of neurofeedback if configured to do so.
Refining the evolutionary time machine: an assessment of whole genome amplification using single historicalDaphniaeggs
Authors: O’Grady Christopher James , Dhandapani Vignesh , Colbourne John K. , Frisch Dagmar 
Published: April 2021

AbstractWhole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivoreDaphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in singleDaphniadormant eggs, we developed an optimised workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently producedDaphnia magnadormant eggs from laboratory cultures, and to historical dormant eggs ofDaphnia pulicariacollected from Arctic lake sediment between 10y and 300y old. Resulting genome coverage breadth in most samples was ~70%, including those from >100y old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with SNPs in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300y). The mtDNA provides an additional source for evolutionary studies of these populations. We provide an optimised workflow for WGA followed by whole genome sequencing including steps to minimise exogenous DNA.
Deformation of membrane vesicles due to chiral surface proteins
Authors: Behera Arabinda , Kumar Gaurav , Akram Sk Ashif , Sain Anirban 
Published: April 2021

Chiral, rod-like molecules can self-assemble into cylindrical membrane tubules and helical ribbons. They have been successfully modeled using the theory of chiral nematics. Models have also predicted the role of chiral lipids in forming nanometer-sized membrane buds in the cell. However, in most theoretical studies, the membrane shapes are considered fixed (cylinder, sphere, saddle, etc.), and their optimum radius of curvatures are found variationally by minimizing the energy of the composite system consisting of membrane and chiral nematics. Numerical simulations have only recently started to consider membrane deformation and chiral orientation simultaneously. Here we examine how deformable, closed membrane vesicles and chiral nematic rods mutually influence each other’s shape and orientation, respectively, using Monte-Carlo (MC) simulation on a closed triangulated surface. For this, we adopt a discrete form of chiral interaction between rods, originally proposed by Van der Meer et al. (1976) for off-lattice simulations. In our simulation, both conical and short cylindrical tubules emerge, depending on the strength of the chiral interaction and the intrinsic chirality of the molecules. We show that the Helfrich-Prost term, which couple nematic tilt with local membrane curvature in continuum models, can account for most of the observations in the simulation. At higher chirality, our theory also predicts chiral tweed phase on cones, with varying bandwidths.PACS numbers: PACS : 87.16.-b, 87.15.Aa, 81.40.Jj, 87.15.Rn
Enhanced longitudinal differential expression detection in proteomics with robust reproducibility optimization regression
Authors: Välikangas Tommi , Suomi Tomi , Chandler Courtney E. , Scott Alison J , Tran Bao Q. , Ernst Robert K. , Goodlett David R. , Elo Laura L. 
Published: April 2021

AbstractQuantitative proteomics has matured into an established tool and longitudinal proteomic experiments have begun to emerge. However, no effective, simple-to-use differential expression method for longitudinal proteomics data has been released. Typically, such data is noisy, contains missing values, has only few time points and biological replicates. To address this need, we provide a comprehensive evaluation of several existing differential expression methods for high-throughput longitudinal omics data and introduce a new method, Robust longitudinal Differential Expression (RolDE). The methods were evaluated using nearly 2000 semi-simulated spike-in proteomic datasets and a large experimental dataset. The RolDE method performed overall best; it was most tolerant to missing values, displayed good reproducibility and was the top method in ranking the results in a biologically meaningful way. Furthermore, contrary to many approaches, the open source RolDE does not require prior knowledge concerning the types of differences searched, but can easily be applied even by non-experienced users.
Prostaglandin E2directly inhibits the conversion of inducible regulatory T cells through EP2 and EP4 receptors via antagonizing TGF-β signalling
Authors: Goepp Marie , Crittenden Siobhan , Zhou You , Rossi Adriano G , Narumiya Shuh , Yao Chengcan 
Published: April 2021

AbstractBackground and PurposeRegulatory T (Treg) cells are essential for control of inflammatory processes by suppressing Th1 and Th17 cells. The bioactive lipid mediator prostaglandin E2(PGE2) promotes inflammatory Th1 and Th17 cells and exacerbates T cell-mediated autoimmune diseases. However, the actions of PGE2on the development and function of Treg cells, particularly under inflammatory conditions, are debated. In this study, we examined whether PGE2had a direct action on T cells to modulatede novodifferentiation of Treg cells.Experimental ApproachWe employed anin vitroT cell culture system of TGF-β-dependent Treg induction from naïve T cells. PGE2and selective agonists for its receptors, and other small molecular inhibitors were used. Mice with specific lack of EP4 receptors in T cells were used to assess Treg cell differentiationin vivo. Human peripheral blood T cells from healthy individuals were used to induce differentiation of inducible Treg cells.Key ResultsTGF-β-induced Foxp3 expression and Treg cell differentiationin vitrowas markedly inhibited by PGE2, which was due to interrupting TGF-β signalling. EP2 or EP4 agonism mimicked suppression of Foxp3 expression in WT T cells, but not in T cells deficient in EP2 or EP4, respectively. Moreover, deficiency of EP4 in T cells impaired iTreg cell differentiationin vivo. PGE2also appeared to inhibit the conversion of human iTreg cells.Conclusion and ImplicationsOur results show a direct, negative regulation of iTreg cell differentiation by PGE2, highlighting the potential for selectively targeting the PGE2-EP2/EP4 pathway to control T cell-mediated inflammation.What is already knownPGE2promotes inflammatory Th1 and Th17 cells and facilitates T cell-mediated immune inflammation, but the action of PGE2on Treg cells is debated.What does this study addPGE2directly acts on T cells to inhibit inducible Treg cell differentiationin vitroandin vivothrough its receptors EP2 and EP4 and by antagonising TGF-β signalling.What is the clinical significanceTherapeutically blocking the EP4 receptor may be beneficial for management of T cell-mediated autoimmune inflammation.
Independent information from PET, CSF and plasma biomarkers of tau pathology in Alzheimer’s disease
Authors: Ossenkoppele Rik , Reimand Juhan , Smith Ruben , Leuzy Antoine , Strandberg Olof , Palmqvist Sebastian , Stomrud Erik , Zetterberg Henrik ,   the Alzheimer’s Disease Neuroimaging Initiative, Scheltens Philip , Dage Jeffrey L. , Bouwman Femke , Blennow Kaj , Mattsson-Carlgren Niklas , Janelidze Shorena , Hansson Oskar 
Published: April 2021

ABSTRACTPET, CSF and plasma biomarkers of tau pathology may be differentially associated with Alzheimer’s disease (AD) related demographic, cognitive, genetic and neuroimaging markers. We examined 771 participants with normal cognition, mild cognitive impairment or dementia from BioFINDER-2 (n=400) and ADNI (n=371). All had tau-PET ([18F]RO948 in BioFINDER-2, [18F]flortaucipir in ADNI) and CSF p-tau181 biomarkers available. Plasma p-tau181 and plasma/CSF p-tau217 were available in BioFINDER-2 only. Concordance between PET, CSF and plasma tau biomarkers ranged between 66% and 95%. Across the whole group, ridge regression models showed that increased CSF and plasma p-tau181 and p-tau217 levels were independently of tau PET associated with higher age, andAPOEε4-carriership and Aβ-positivity, while increased tau-PET signal in the temporal cortex was associated with worse cognitive performance and reduced cortical thickness. We conclude that biofluid and neuroimaging markers of tau pathology convey partly independent information, with CSF and plasma p-tau181 and p-tau217 levels being more tightly linked with early markers of AD (especially Aβ pathology), while tau-PET shows the strongest associations with cognitive and neurodegenerative markers of disease progression.
Individualized VDJ recombination predisposes the available Ig sequence space
Authors: Slabodkin Andrei , Chernigovskaya Maria , Mikocziova Ivana , Akbar Rahmad , Scheffer Lonneke , Pavlović Milena , Bashour Habib , Snapkov Igor , Mehta Brij Bhushan , Weber Cédric R. , Gutierrez-Marcos Jose , Sollid Ludvig M. , Haff Ingrid Hobæk , Sandve Geir Kjetil , Robert Philippe A. , Greiff Victor 
Published: April 2021

AbstractThe process of recombination between variable (V), diversity (D), and joining (J) immunoglobulin (Ig) gene segments determines an individual’s naïve Ig repertoire, and consequently (auto)antigen recognition. VDJ recombination follows probabilistic rules that can be modeled statistically. So far, it remains unknown whether VDJ recombination rules differ between individuals. If these rules differed, identical (auto)antigen-specific Ig sequences would be generated with individual-specific probabilities, signifying that the available Ig sequence space is individual-specific. We devised a sensitivity-tested distance measure that enables inter-individual comparison of VDJ recombination models. We discovered, accounting for several sources of noise as well as allelic variation in Ig sequencing data, that not only unrelated individuals but also human monozygotic twins and even inbred mice possess statistically distinguishable immunoglobulin recombination models. This suggests that, in addition to genetic, there is also non-genetic modulation of VDJ recombination. We demonstrate that population-wide individualized VDJ recombination can result in orders of magnitude of difference in the probability to generate (auto)antigen-specific Ig sequences. Our findings have implications for immune receptor-based individualized medicine approaches relevant to vaccination, infection, and autoimmunity.
Scalable Batch Fabrication of Ultrathin Flexible Neural Probes using Bioresorbable Silk Layer
Authors: Cointe Clement , Laborde Adrian , Nowak Lionel G , Bourrier David , Bergaud Christian , Maziz Ali 
Published: April 2021

ABSTRACTFlexible deep brain probes have been the focus of many research works and aims at achieving better compliance with the surrounding brain tissue while maintaining minimal rejection. Strategies have been explored to find the best way to implant a flexible probe in the brain, while maintaining its flexibility once positioned in the cortex. Here, we present a novel and versatile scalable batch fabrication approach to deliver ultra-thin and flexible penetrating neural probe consisting of a silk-parylene bilayer. The biodegradable silk layer provides a temporary and programmable stiffener to ensure ease of insertion of the ultrathin parylene-based flexible devices. The innovative and yet robust batch fabrication technology allows complete design freedom of the neural probe in terms of materials, size, shape and thickness. These results provide a novel technological solution for implanting ultra-flexible and ultrathin devices, which possesses great potential for brain research.
Nuclear retention of pre-mRNA involving Cajal bodies during meiotic prophase in plants
Authors: Rudzka Magda , Hyjek-Składanowska Malwina , Wróblewska-Ankiewicz Patrycja , Majewska Karolina , Gołębiewski Marcin , Sikora Marcin , Smoliński Dariusz Jan , Kołowerzo-Lubnau Agnieszka 
Published: April 2021

SummaryGene regulation ensures that the appropriate genes are expressed at the proper times. Nuclear retention of incompletely spliced or mature mRNAs emerges as a novel, previously underappreciated layer of post-transcriptional gene regulation. Studies on this phenomenon indicated that it exerted significant impact on the regulation of gene expression by regulating export and translation delay, which allows synthesis of specific proteins in response to a stimulus, e.g. under stress conditions or at strictly controlled time points, e.g. during cell differentiation or development. Here, we found that transcription in microsporocytes, during prophase of the first meiotic division, occurs in pulsatile manner. After each pulse, the transcriptional activity is silenced, but the transcripts synthesized at this time are not exported immediately to the cytoplasm, but are retained in the nucleoplasm and Cajal bodies (CBs). In contrast to nucleoplasm, mature transcripts were not found in CBs. Only non-fully-spliced transcripts with retained introns were stored in the CBs. Retained introns are spliced at precisely defined times, and fully mature mRNAs are released into the cytoplasm, where the proteins are produced. These proteins are necessary for further cell development during meiotic prophase. Our findings provide new insight into the regulatory mechanisms of gene expression based on mRNA retention in the nucleus during the development of generative cells in plants. Similar processes were observed during spermatogenesis in animals. This indicates the existence of an evolutionarily conserved mechanism of gene expression regulation during generative cells development in Eukaryota.
The forest avifauna of Arabuko Sokoke Forest and adjacent modified habitats
Authors: Chiawo David O. , Kombe Wellington N. , Craig Adrian J.F.K. 
Published: April 2021

AbstractArabuko Sokoke Forest (ASF) is the largest area of coastal forest remaining in East Africa and a major Important Bird Area in mainland Kenya. The study analysed data from point count surveys over 15 months in three land use types; primary forest (PF), plantation forest (PL), and farmlands (FM), and compared these to the first comprehensive bird checklist for the forest, as well as recent surveys from other studies. Avifaunal diversity and abundance were compared using multivariate analysis to determine bird responses to different land use characteristics. The primary forest held a distinctive bird community, while the bird communities of farmlands and plantation forest were more similar to each other. Land use had a significant effect on overall avian diversity and abundance. The current forest avifauna was divided into forest specialists (16 species), forest generalists (26 species) and forest visitors (30 species). Seven species of forest specialist and generalists recorded prior to 1980 may no longer occur in the forest. Of 38 specialists and generalists recorded in our point counts, 19 were also recorded on farmland and 28 in plantations. One forest specialist, the Green Barbet, was most encountered outside the forest. Future research should focus on habitat use by these bird species, and the extent of movement by forest birds between the remaining patches of coastal forest. Patterns of habitat use by birds in the area suggest that vegetation heterogeneity and habitat complexity are especially significant in sustaining diverse and abundant bird populations. The management of plantations and farmland will be critical for the conservation of forest generalists and forest visitors.
Chromatin profiling reveals genome stability heterogeneity in clinical isolates of the human pathogenAspergillus fumigatus
Authors: Colabardini Ana Cristina , Wang Fang , Miao Zhengqiang , Pardeshi Lakhansing , Valero Clara , de Castro Patrícia Alves , Akiyama Daniel Yuri , Tan Kaeling , Nora Luisa Czamanski , Silva-Rocha Rafael , Marcet-Houben Marina , Gabaldón Toni , Fill Taicia , Wong Koon Ho , Goldman Gustavo H. 
Published: April 2021

AbstractInvasive Pulmonary aspergillosis is a life-threatening infection in immunosuppressed patients caused by the filamentous fungusAspergillus fumigatus. Chromatin structure regulation is important for genome stability maintenance and has the potential to lead to genome rearrangements driving differences in virulence and pathogenesis of differentA. fumigatusisolates. Here, we compared the chromatin activities of the most investigated clinical isolates Af293 and CEA17 and uncovered striking differences in the number, locations and expression of transposable elements. We found evidence for higher genome instability in Af293 as compared to CEA17 and identified a spontaneous Af293 variant that exhibits gross chromosomal alterations including the loss of a 320 kb long segment in chromosome VIII and the amplification of a biosynthetic gene cluster. As a consequence of these re-arrangements, the variant shows increased secondary metabolites production, growth and virulence. Our work emphasizes genome stability heterogeneity as an evolutionary driver ofA. fumigatusfitness and virulence.
MRI-derived brain age as a biomarker of ageing in rats: validation using a healthy lifestyle intervention
Authors: Brusini Irene , MacNicol Eilidh , Kim Eugene , Smedby Örjan , Wang Chunliang , Westman Eric , Veronese Mattia , Turkheimer Federico , Cash Diana 
Published: April 2021

AbstractMRI data can be used as input to machine learning models to accurately predict brain age in healthy human subjects. A large difference between predicted and chronological brain age (the so-called BrainAGE score) has been associated with disease and neurodegeneration, indicating the potential utility of neuroimaging-based ageing biomarkers. So far, most brain age prediction studies have been carried out on humans. However, it is important for such a biomarker to be validated on laboratory animals too, in order to better account for specific environmental or genetic factors within a more controlled laboratory framework.In this work, we developed a new algorithm for rat brain age prediction based on the combination of Gaussian process regression and a logistic regression classifier. The algorithm was trained on a cohort of 31 normal rats. High prediction accuracy was achieved using leave-one-out cross-validation (mean absolute error = 4.87 weeks, correlation between predicted and chronological ager= 0.92), supporting the validity and potential of the method.Furthermore, the trained model was tested on two independent groups of 24 rats each: a new normal control group and a “healthy lifestyle” group that underwent long-term environmental enrichment and dietary restriction (EEDR) between 3 and 17 months of age. After fitting a linear mixed-effects model, the BrainAGE values were found to increase more slowly with chronological age in the EEDR group than in the controls (slope = 0.52 vs. 0.61;p= 0.015 for the interaction term). When survival analysis was performed with a Cox regression model, the BrainAGE score at 5 months of age had a significant prediction power (p= 0.03).Our results demonstrate that BrainAGE, as computed by the proposed approach, is significantly modulated by EEDR intervention, hence it is a sensitive marker of biological ageing. These findings also support the potential of lifestyle-related prevention approaches to slow down the brain ageing process. Moreover, the results of the survival analysis further demonstrate that BrainAGE is indeed a predictor of ageing outcome.