bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding Preservation of Primary Signatures in Apatite by Comparing Matrix and Zircon‐Hosted Crystals From the Eoarchean Acasta Gneiss Complex (Canada)
Authors: Antoine C. , Bruand E. , Guitreau M. , Devidal J.‐L. 
Published: May 2020

AbstractA novel way to investigate the petrogenesis of ancient polymetamorphosed terranes is to study zircon‐hosted mineral inclusions, which are sensitive to melt evolution such as apatite. Recent contributions on such inclusions in unmetamorphosed granitoids can provide valuable petrogenetic information and, in turn, represent a way to circumvent effects of metamorphism. Yet the impact of metamorphism on apatite inclusion has never been studied in detail. To address the issue of chemical and isotopic preservation of primary signals in apatite crystals both in the matrix and armored within zircons, we have studied apatite crystals from four 3.6–4.0 Ga TTG granitoids from the Acasta Gneiss Complex (Canada). Our results demonstrate that U‐Th‐Pb isotope systematics in matrix apatite crystals were reset at 1.8–1.7 Ga (Wopmay orogen) whereas primary REE signatures were preserved in many crystals. In contrast, zircon‐hosted apatite inclusions all preserved primary REE signatures despite variable ages between 1.7 and 4.0 Ga. We interpret reset ages to be a consequence of metamorphism that managed to affect U‐Th‐Pb systematics because of advanced radiation damage accumulation in host‐zircon lattices. Only the most pristine zircon crystal has an apatite inclusion with a concordant age consistent with the magmatic age of the zircon (4.0 Ga). In addition, our results show that apatite crystals from TTG have distinct REE composition from post‐Archean granitoids apatites, that is preserved even in some apatites with reset ages. This capacity to retain primary information and discriminate granitoid types makes apatite a very valuable tool for reconstructing the nature and evolution of ancient crustal rocks through the use of detrital minerals.
Hydrological Model Calibration for Dammed Basins Using Satellite Altimetry Information
Authors: Zhong Ruida , Zhao Tongtiegang , Chen Xiaohong 
Published: May 2020

AbstractDownstream stakeholders are often hindered when performing water management decision making based on effective hydrological modeling and streamflow anticipation, due to alterations of river flow caused by upstream damming. Meanwhile, spaceborne altimeters and imagers can provide valuable data for the upper data‐limited reservoirs by monitoring their operations. This study proposes a novel modeling approach that incorporates reservoir levels from satellite altimetry into hydrological model calibration. Doing so enables model parameter determination and retrieval of upper reservoir inflow for dammed basins, when only the altered downstream flow observations are available. Case studies are performed for two large reservoirs in the Dongjiang basin, a typical dam‐affected area in South China. Two settings for determining the stage‐volume (S‐V) curve are tested: (1) The curves are prefitted by satellite information and (2) the curves are optimized by calibration in conjunction with the model parameters. Results show that the proposed approach is effective in identifying the hydrological model parameters and retrieving the upper reservoir inflow of data‐limited dammed basins. Our analyses also show that the error in satellite altimetry has significant influences and can impede reasonable determination of the model parameters, and the fitted S‐V curves perform more reasonably and robustly than calibrated S‐V curves with respect to retrieving reservoir inflow, and thus, the fitted S‐V curve is more highly recommended. Overall, our approach provides an effective solution for aiding downstream stakeholders and researchers in understanding the upper reservoir operation and analyzing the hydrology of dammed basins, when knowledge about the upstream area is limited.
Isatuximab plus pomalidomide and dexamethasone in relapsed/refractory multiple myeloma patients with renal impairment: ICARIA-MM subgroup analysis
Authors: Dimopoulos Meletios A. , Leleu Xavier , Moreau Philippe , Richardson Paul G. , Liberati Anna Marina , Harrison Simon J. , Miles Prince H. , Ocio Enrique M. , Assadourian Sylvie , Campana Frank , Malinge Laure , Sémiond Dorothée , van de Velde Helgi , Yong Kwee 
Published: May 2020

AbstractThe randomized, phase 3 ICARIA-MM study investigated isatuximab (Isa) with pomalidomide and dexamethasone (Pd) versus Pd in patients with relapsed/refractory multiple myeloma and ≥2 prior lines. This prespecified subgroup analysis examined efficacy in patients with renal impairment (RI; estimated glomerular filtration rate <60 mL/min/1.73 m²). Isa 10 mg/kg was given intravenously once weekly in cycle 1, and every 2 weeks in subsequent 28-day cycles. Patients received standard doses of Pd. Median progression-free survival (PFS) for patients with RI was 9.5 months with Isa-Pd (n = 55) and 3.7 months with Pd (n = 49; hazard ratio [HR] 0.50; 95% confidence interval [CI], 0.30–0.85). Without RI, median PFS was 12.7 months with Isa-Pd (n = 87) and 7.9 months with Pd (n = 96; HR 0.58; 95% CI, 0.38–0.88). The overall response rate (ORR) with and without RI was higher with Isa-Pd (56 and 68%) than Pd (25 and 43%). Complete renal response rates were 71.9% (23/32) with Isa-Pd and 38.1% (8/21) with Pd; these lasted ≥60 days in 31.3% (10/32) and 19.0% (4/21) of patients, respectively. Isa pharmacokinetics were comparable between the subgroups, suggesting no need for dose adjustment in patients with RI. In summary, the addition of Isa to Pd improved PFS, ORR and renal response rates.
Diverse coral reef invertebrates exhibit patterns of phylosymbiosis
Authors: O’Brien Paul A , Tan Shangjin , Yang Chentao , Frade Pedro R , Andreakis Nikos , Smith Hillary A , Miller David J , Webster Nicole S , Zhang Guojie , Bourne David G 
Published: May 2020

Abstract
Microbiome assemblages of plants and animals often show a degree of correlation with host phylogeny; an eco-evolutionary pattern known as phylosymbiosis. Using 16S rRNA gene sequencing to profile the microbiome, paired with COI, 18S rRNA and ITS1 host phylogenies, phylosymbiosis was investigated in four groups of coral reef invertebrates (scleractinian corals, octocorals, sponges and ascidians). We tested three commonly used metrics to evaluate the extent of phylosymbiosis: (a) intraspecific versus interspecific microbiome variation, (b) topological comparisons between host phylogeny and hierarchical clustering (dendrogram) of host-associated microbial communities, and (c) correlation of host phylogenetic distance with microbial community dissimilarity. In all instances, intraspecific variation in microbiome composition was significantly lower than interspecific variation. Similarly, topological congruency between host phylogeny and the associated microbial dendrogram was more significant than would be expected by chance across all groups, except when using unweighted UniFrac distance (compared with weighted UniFrac and Bray–Curtis dissimilarity). Interestingly, all but the ascidians showed a significant positive correlation between host phylogenetic distance and associated microbial dissimilarity. Our findings provide new perspectives on the diverse nature of marine phylosymbioses and the complex roles of the microbiome in the evolution of marine invertebrates.
Drought and plant litter chemistry alter microbial gene expression and metabolite production
Authors: Malik Ashish A , Swenson Tami , Weihe Claudia , Morrison Eric W , Martiny Jennifer B H , Brodie Eoin L , Northen Trent R , Allison Steven D 
Published: May 2020

Abstract
Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic and metabolomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems. We hypothesised that drought causes greater microbial allocation to stress tolerance relative to growth pathways. In grass litter, communities from the decade-long ambient and reduced precipitation treatments had distinct taxonomic and functional profiles. The most discernable physiological signatures of drought were production or uptake of compatible solutes to maintain cellular osmotic balance, and synthesis of capsular and extracellular polymeric substances as a mechanism to retain water. The results show a clear functional response to drought in grass litter communities with greater allocation to survival relative to growth that could affect decomposition under drought. In contrast, communities on chemically more diverse and complex shrub litter had smaller physiological differences in response to long-term drought but higher investment in resource acquisition traits across precipitation treatments, suggesting that the functional response to drought is constrained by substrate quality. Our findings suggest, for the first time in a field setting, a trade off between microbial drought stress tolerance, resource acquisition and growth traits in plant litter microbial communities.
Combining gene expression profiling and machine learning to diagnose B-cell non-Hodgkin lymphoma
Authors: Bobée Victor , Drieux Fanny , Marchand Vinciane , Sater Vincent , Veresezan Liana , Picquenot Jean-Michel , Viailly Pierre-Julien , Lanic Marie-Delphine , Viennot Mathieu , Bohers Elodie , Oberic Lucie , Copie-Bergman Christiane , Molina Thierry Jo , Gaulard Philippe , Haioun Corinne , Salles Gilles , Tilly Hervé , Jardin Fabrice , Ruminy Philippe 
Published: May 2020

AbstractNon-Hodgkin B-cell lymphomas (B-NHLs) are a highly heterogeneous group of mature B-cell malignancies. Their classification thus requires skillful evaluation by expert hematopathologists, but the risk of error remains higher in these tumors than in many other areas of pathology. To facilitate diagnosis, we have thus developed a gene expression assay able to discriminate the seven most frequent B-cell NHL categories. This assay relies on the combination of ligation-dependent RT-PCR and next-generation sequencing, and addresses the expression of more than 130 genetic markers. It was designed to retrieve the main gene expression signatures of B-NHL cells and their microenvironment. The classification is handled by a random forest algorithm which we trained and validated on a large cohort of more than 400 annotated cases of different histology. Its clinical relevance was verified through its capacity to prevent important misclassification in low grade lymphomas and to retrieve clinically important characteristics in high grade lymphomas including the cell-of-origin signatures and the MYC and BCL2 expression levels. This accurate pan-B-NHL predictor, which allows a systematic evaluation of numerous diagnostic and prognostic markers, could thus be proposed as a complement to conventional histology to guide the management of patients and facilitate their stratification into clinical trials.
Osteogenesis imperfecta mutations in plastin 3 lead to impaired calcium regulation of actin bundling
Authors: Schwebach Christopher L. , Kudryashova Elena , Zheng Weili , Orchard Matthew , Smith Harper , Runyan Lucas A. , Egelman Edward H. , Kudryashov Dmitri S. 
Published: May 2020

AbstractMutations in actin-bundling protein plastin 3 (PLS3) emerged as a cause of congenital osteoporosis, but neither the role of PLS3 in bone development nor the mechanisms underlying PLS3-dependent osteoporosis are understood. Of the over 20 identified osteoporosis-linked PLS3 mutations, we investigated all five that are expected to produce full-length protein. One of the mutations distorted an actin-binding loop in the second actin-binding domain of PLS3 and abolished F-actin bundling as revealed by cryo-EM reconstruction and protein interaction assays. Surprisingly, the remaining four mutants fully retained F-actin bundling ability. However, they displayed defects in Ca2+ sensitivity: two of the mutants lost the ability to be inhibited by Ca2+, while the other two became hypersensitive to Ca2+. Each group of the mutants with similar biochemical properties showed highly characteristic cellular behavior. Wild-type PLS3 was distributed between lamellipodia and focal adhesions. In striking contrast, the Ca2+-hyposensitive mutants were not found at the leading edge but localized exclusively at focal adhesions/stress fibers, which displayed reinforced morphology. Consistently, the Ca2+-hypersensitive PLS3 mutants were restricted to lamellipodia, while chelation of Ca2+ caused their redistribution to focal adhesions. Finally, the bundling-deficient mutant failed to co-localize with any F-actin structures in cells despite a preserved F-actin binding through a non-mutation-bearing actin-binding domain. Our findings revealed that severe osteoporosis can be caused by a mutational disruption of the Ca2+-controlled PLS3’s cycling between adhesion complexes and the leading edge. Integration of the structural, biochemical, and cell biology insights enabled us to propose a molecular mechanism of plastin activity regulation by Ca2+.
Loss of Spry1 reduces growth of BRAFV600-mutant cutaneous melanoma and improves response to targeted therapy
Authors: Montico Barbara , Colizzi Francesca , Giurato Giorgio , Rizzo Aurora , Salvati Annamaria , Baboci Lorena , Benedetti Dania , Pivetta Eliana , Covre Alessia , Bo Michele Dal , Weisz Alessandro , Steffan Agostino , Maio Michele , Sigalotti Luca , Fratta Elisabetta 
Published: May 2020

AbstractMitogen-activated protein kinase (MAPK) pathway activation is a central step in BRAFV600-mutant cutaneous melanoma (CM) pathogenesis. In the last years, Spry1 has been frequently described as an upstream regulator of MAPK signaling pathway. However, its specific role in BRAFV600-mutant CM is still poorly defined. Here, we report that Spry1 knockdown (Spry1KO) in three BRAFV600-mutant CM cell lines markedly induced cell cycle arrest and apoptosis, repressed cell proliferation in vitro, and impaired tumor growth in vivo. Furthermore, our findings indicated that Spry1KOreduced the expression of several markers of epithelial–mesenchymal transition, such as MMP-2 both in vitro and in vivo. These effects were associated with a sustained and deleterious phosphorylation of ERK1/2. In addition, p38 activation along with an increase in basal ROS levels were found in Spry1KOclones compared to parental CM cell lines, suggesting that BRAFV600-mutant CM may restrain the activity of Spry1 to avoid oncogenic stress and to enable tumor growth. Consistent with this hypothesis, treatment with the BRAF inhibitor (BRAFi) vemurafenib down-regulated Spry1 levels in parental CM cell lines, indicating that Spry1 expression is sustained by the MAPK/ERK signaling pathway in a positive feedback loop that safeguards cells from the potentially toxic effects of ERK1/2 hyperactivation. Disruption of this feedback loop rendered Spry1KOcells more susceptible to apoptosis and markedly improved response to BRAFi both in vitro and in vivo, as a consequence of the detrimental effect of ERK1/2 hyperactivation observed upon Spry1 abrogation. Therefore, targeting Spry1 might offer a treatment strategy for BRAFV600-mutant CM by inducing the toxic effects of ERK-mediated signaling.
BBMRI-ERIC’s contributions to research and knowledge exchange on COVID-19
Authors:   on behalf of the BBMRI-ERIC community, Holub Petr , Kozera Lukasz , Florindi Francesco , van Enckevort Esther , Swertz Morris , Reihs Robert , Wutte Andrea , Valík Dalibor , Mayrhofer Michaela Th. 
Published: May 2020

AbstractDuring the COVID-19 pandemic, the European biobanking infrastructure is in a unique position to preserve valuable biological material complemented with detailed data for future research purposes. Biobanks can be either integrated into healthcare, where preservation of the biological material is a fork in clinical routine diagnostics and medical treatment processes or they can also host prospective cohorts or material related to clinical trials. The paper discussed objectives of BBMRI-ERIC, the European research infrastructure established to facilitate access to quality-defined biological materials and data for research purposes, with respect to the COVID-19 crisis: (a) to collect information on available European as well as non-European COVID-19-relevant biobanking resources in BBMRI-ERIC Directory and to facilitate access to these via BBMRI-ERIC Negotiator platform; (b) to help harmonizing guidelines on how data and biological material is to be collected to maximize utility for future research, including large-scale data processing in artificial intelligence, by participating in activities such as COVID-19 Host Genetics Initiative; (c) to minimize risks for all involved parties dealing with (potentially) infectious material by developing recommendations and guidelines; (d) to provide a European-wide platform of exchange in relation to ethical, legal, and societal issues (ELSI) specific to the collection of biological material and data during the COVID-19 pandemic.
A mechanistic explanation of the transition to simple multicellularity in fungi
Authors: Heaton Luke L. M. , Jones Nick S. , Fricker Mark D. 
Published: May 2020

AbstractDevelopment of multicellularity was one of the major transitions in evolution and occurred independently multiple times in algae, plants, animals, and fungi. However recent comparative genome analyses suggest that fungi followed a different route to other eukaryotic lineages. To understand the driving forces behind the transition from unicellular fungi to hyphal forms of growth, we develop a comparative model of osmotrophic resource acquisition. This predicts that whenever the local resource is immobile, hard-to-digest, and nutrient poor, hyphal osmotrophs outcompete motile or autolytic unicellular osmotrophs. This hyphal advantage arises because transporting nutrients via a contiguous cytoplasm enables continued exploitation of remaining resources after local depletion of essential nutrients, and more efficient use of costly exoenzymes. The model provides a mechanistic explanation for the origins of multicellular hyphal organisms, and explains why fungi, rather than unicellular bacteria, evolved to dominate decay of recalcitrant, nutrient poor substrates such as leaf litter or wood.
Using publicly available satellite imagery and deep learning to understand economic well-being in Africa
Authors: Yeh Christopher , Perez Anthony , Driscoll Anne , Azzari George , Tang Zhongyi , Lobell David , Ermon Stefano , Burke Marshall 
Published: May 2020

AbstractAccurate and comprehensive measurements of economic well-being are fundamental inputs into both research and policy, but such measures are unavailable at a local level in many parts of the world. Here we train deep learning models to predict survey-based estimates of asset wealth across ~ 20,000 African villages from publicly-available multispectral satellite imagery. Models can explain 70% of the variation in ground-measured village wealth in countries where the model was not trained, outperforming previous benchmarks from high-resolution imagery, and comparison with independent wealth measurements from censuses suggests that errors in satellite estimates are comparable to errors in existing ground data. Satellite-based estimates can also explain up to 50% of the variation in district-aggregated changes in wealth over time, with daytime imagery particularly useful in this task. We demonstrate the utility of satellite-based estimates for research and policy, and demonstrate their scalability by creating a wealth map for Africa’s most populous country.
Colossal flexoresistance in dielectrics
Authors: Park Sung Min , Wang Bo , Paudel Tula , Park Se Young , Das Saikat , Kim Jeong Rae , Ko Eun Kyo , Lee Han Gyeol , Park Nahee , Tao Lingling , Suh Dongseok , Tsymbal Evgeny Y. , Chen Long-Qing , Noh Tae Won , Lee Daesu 
Published: May 2020

AbstractDielectrics have long been considered as unsuitable for pure electrical switches; under weak electric fields, they show extremely low conductivity, whereas under strong fields, they suffer from irreversible damage. Here, we show that flexoelectricity enables damage-free exposure of dielectrics to strong electric fields, leading to reversible switching between electrical states—insulating and conducting. Applying strain gradients with an atomic force microscope tip polarizes an ultrathin film of an archetypal dielectric SrTiO3 via flexoelectricity, which in turn generates non-destructive, strong electrostatic fields. When the applied strain gradient exceeds a certain value, SrTiO3 suddenly becomes highly conductive, yielding at least around a 108-fold decrease in room-temperature resistivity. We explain this phenomenon, which we call the colossal flexoresistance, based on the abrupt increase in the tunneling conductance of ultrathin SrTiO3 under strain gradients. Our work extends the scope of electrical control in solids, and inspires further exploration of dielectric responses to strong electromechanical fields.
Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion
Authors: Ke Wenfan , Saba James A. , Yao Cong-Hui , Hilzendeger Michael A. , Drangowska-Way Anna , Joshi Chintan , Mony Vinod K. , Benjamin Shawna B. , Zhang Sisi , Locasale Jason , Patti Gary J. , Lewis Nathan , O’Rourke Eyleen J. 
Published: May 2020

AbstractThe gut microbiota metabolizes drugs and alters their efficacy and toxicity. Diet alters drugs, the metabolism of the microbiota, and the host. However, whether diet-triggered metabolic changes in the microbiota can alter drug responses in the host has been largely unexplored. Here we show that dietary thymidine and serine enhance 5-fluoro 2′deoxyuridine (FUdR) toxicity in C. elegans through different microbial mechanisms. Thymidine promotes microbial conversion of the prodrug FUdR into toxic 5-fluorouridine-5′-monophosphate (FUMP), leading to enhanced host death associated with mitochondrial RNA and DNA depletion, and lethal activation of autophagy. By contrast, serine does not alter FUdR metabolism. Instead, serine alters E. coli’s 1C-metabolism, reduces the provision of nucleotides to the host, and exacerbates DNA toxicity and host death without mitochondrial RNA or DNA depletion; moreover, autophagy promotes survival in this condition. This work implies that diet-microbe interactions can alter the host response to drugs without altering the drug or the host.