bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marine reserve benefits and recreational fishing yields: the winners and the losers
Authors: Kayal Mohsen , Cigala Marine , Cambra Eléonore , Soulat Nelly , Mercader Manon , Lebras Audrey , Ivanoff Pauline , Sébési Léa , Lassus-Debat Aurélie , Hartmann Virginie , Bradtke Mélissa , Lenfant Philippe , Jabouin Coraline , Dubreuil Julien , Pelletier Dominique , Joguet Manon , Le Mellionnec Solène , Brichet Marion , Binche Jean-Louis , Payrot Jérôme , Saragoni Gilles , Crec’hriou Romain , Verdoit-Jarraya Marion 
Published: August 2020

AbstractMarine reserves constitute effective tools for preserving fish stocks and associated human benefits. However, not all reserves perform equally, and predicting the response of marine communities to management actions in the long run is challenging. Our decadal-scale survey of recreational fishing yields at France’s 45-year old Cerbère-Banyuls marine reserve indicated significant protection benefits, with 40-50% higher fishing yields per unit effort in the partial-protection zone of the reserve (where fishing is permitted but at a lower level) than in surrounding non-reserve areas. Over the period 2005-2014, catch per unit effort (CPUE) showed a similar pattern of decline inside and outside the reserve while weight per unit effort (WPUE) increased by 131% inside and decreased by 60% outside. Different CPUE and WPUE trajectories among fish families indicated changing catch assemblages, with yields increasing for the family most valued by fisheries, Sparidae (the ecological winners). However, reserve benefits were restricted to off-shore fishermen (the social winners), as on-shore yields were ∼4 times lower and declining, even inside the reserve. Our study illustrates how surveys of recreational fishing yields can help evaluate the effectiveness of marine protected areas for key social and ecological protagonists. We show that, more than four decades after its establishment, fishing efficiencies at the historical Cerbère-Banyuls marine reserve are still changing, but benefits in terms of catch abundance, weight, and composition remain predominantly restricted to off-shore fishermen. Further regulations appear necessary to guarantee that conservation strategies equitably benefit societal groups.
Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic
Authors: Klimczak Leszek J. , Randall Thomas A. , Saini Natalie , Li Jian-Liang , Gordenin Dmitry A. 
Published: August 2020

AbstractGenomes of tens of thousands of SARS-CoV2 isolates have been sequenced across the world and the total number of changes (predominantly single base substitutions) in these isolates exceeds ten thousand. We compared the mutational spectrum in the new SARS-CoV-2 mutation dataset with the previously published mutation spectrum in hypermutated genomes of rubella - another positive single stranded (ss) RNA virus. Each of the rubella isolates arose by accumulation of hundreds of mutations during propagation in a single subject, while SARS-CoV-2 mutation spectrum represents a collection events in multiple virus isolates from individuals across the world. We found a clear similarity between the spectra of single base substitutions in rubella and in SARS-CoV-2, with C to U as well as A to G and U to C being the most prominent in plus strand genomic RNA of each virus. Of those, U to C changes universally showed preference for loops versus stems in predicted RNA secondary structure. Similarly, to what was previously reported for rubella, C to U changes showed enrichment in the uCn motif, which suggested a subclass of APOBEC cytidine deaminase being a source of these substitutions. We also found enrichment of several other trinucleotide-centered mutation motifs only in SARS-CoV-2 - likely indicative of a mutation process characteristic to this virus. Altogether, the results of this analysis suggest that the mutation mechanisms that lead to hypermutation of the rubella vaccine virus in a rare pathological condition may also operate in the background of the SARS-CoV-2 viruses currently propagating in the human population.
CRISPR interference as low burden logic inverters in synthetic circuits: characterization and tuning
Authors: Bellato Massimo , Chiacchiera Angelica Frusteri , Salibi Elia , Casanova Michela , De Marchi Davide , De Angelis Maria Gabriella Cusella , Pasotti Lorenzo , Magni Paolo 
Published: August 2020

AbstractThe rational design of complex biological systems through the interconnection of single functional building blocks is hampered by many unpredictability sources; this is mainly due to the tangled context-dependency behavior of those parts once placed into an intrinsically complex living system. Among others, the finite amount of translational resources in prokaryotic cells leads to load effects in heterologous protein expression. As a result, hidden interactions among protein synthesis rates arise, leading to unexpected and counterintuitive behaviors. To face this issue in rational design of synthetic circuits in bacterial cells, CRISPR interference is here evaluated as genetic logic inverters with low translational resource usage, compared with traditional transcriptional regulators. This system has been studied and characterized in several circuit configurations. Each module composing the circuit architecture has been optimized in order to meet the desired specifications, and its reduced metabolic load has been eventually demonstrated via in-vivo assays.
Modular low-cost homemade radiation shields for forest ecology field experiments
Authors: Morales N.S. 
Published: August 2020

SummaryAbiotic variables are important in understanding several forest ecosystems processes. Hence, temporal, accurate, and precise measurements are vital to any experiment including abiotic variables as part of its objectives.In general, field experiments require several types of sensors to represent intra-site variability. For temperature and humidity measurements in particular, accessories to decrease biases such as radiation shields are indispensable. However, this kind of experimental setup can make project costs escalate quickly.Low-cost alternatives to commercially available radiation shields have proven to be adequate in their ability to decrease measurement bias. Despite this advantage (low cost), the materials used in some of these cannot last long under field conditions (e.g. cardboard, aluminium foil).A custom-made low-cost solution was designed to withstand rugged conditions to perform temporal measurements using sensors. The radiation shields proved to meet the technical and budgetary needs of the project while lasting the entire duration of the project (approx. 3 years). At the end of the project they were still in good enough condition to use in future studies, and they were donated to the School of Environmental Sciences (University of Auckland).
Separating noise and function in systems of animal communication: a comparative study of aggressive signaling in crayfish
Authors: Graham Zackary A. , Angilletta Michael J. 
Published: August 2020

ABSTRACTA primary issue in the study of dishonest signaling is the researcher’s ability to detect and describe a signal as being dishonest. However, by understanding the relative honesty of a signal as a statistical property of an individual or population, researchers have recently quantitively describe dishonest communication. Thus, dishonesty signals can be understood as when there is a breakdown in the correlation between a signal and its underlying meaning; creating variation within a signaling system. However, such variation in signaling systems may not be attributed to dishonesty, because of inherent noise within biological systems driven by evolutionary or physiological noise. Here, we try to separate out functional variation within honest or dishonesty signaling systems from inherent biological noise by leveraging homologous structures that have evolved for separate functions – the enlarged claws of freshwater crayfish. Because burrowing species of freshwater crayfish claws have not evolved as signals, the variability in the size and strength of their claws should be minimal when compared to claws of non-burrowing species that evolved as signals during aggression. We found that despite the claws of burrowing and nonburrowing crayfish claws having evolved to serve difference functions, the claws of all species in our study were inherently noisy. Furthermore, although claws that unreliably correlate to the strengthen the wielder may function as dishonest signals in other crustaceans, we did not find support for this hypothesis; because crayfish escalated aggression based on relative body size.
Central and peripheral GLP-1 systems independently and additively suppress eating
Authors: Brierley Daniel I. , Holt Marie K. , Singh Arashdeep , de Araujo Alan , Vergara Macarena , Afaghani Majd H. , Lee Shin Jae , Scott Karen , Langhans Wolfgang , Krause Eric , de Kloet Annette , Gribble Fiona M. , Reimann Frank , Rinaman Linda , de Lartigue Guillaume , Trapp Stefan 
Published: August 2020

AbstractThe anorexigenic peptide glucagon-like peptide-1 (GLP-1) is secreted from gut enteroendocrine cells and brain preproglucagon (PPG) neurons, which respectively define the peripheral and central GLP-1 systems. As peripheral satiation signals are integrated in the nucleus tractus solitarius (NTS), PPGNTSneurons are assumed to link the peripheral and central GLP-1 systems, forming a unified GLP-1 gut-brain satiation circuit. This hypothesis, however, remains unsubstantiated. We report that PPGNTSneurons encode satiation in mice, consistent with vagal gastrointestinal distension signalling. However, PPGNTSneurons predominantly receive vagal input from oxytocin receptor-expressing vagal neurons, rather than those expressing GLP-1 receptors. Furthermore, PPGNTSneurons are not necessary for eating suppression induced by the GLP-1 receptor agonists liraglutide or semaglutide, and semaglutide and PPGNTSneuron activation additively suppress eating. Central and peripheral GLP-1 systems thus suppress eating via independent gut-brain circuits, hence PPGNTSneurons represent a rational pharmacological target for anti-obesity combination therapy with GLP-1 receptor agonists.Abstract FigureGraphical Abstract:
Pairwise Linkage Disequilibrium Estimation for Polyploids
Authors: Gerard David 
Published: August 2020

AbstractMany tasks in statistical genetics involve pairwise estimation of linkage disequilibrium (LD). The study of LD in diploids is mature. However, in polyploids, the field lacks a comprehensive characterization of LD. Polyploids also exhibit greater levels of genotype uncertainty than diploids, and yet no methods currently exist to estimate LD in polyploids in the presence of such genotype uncertainty. Furthermore, most LD estimation methods do not quantify the level of uncertainty in their LD estimates. Our paper contains three major contributions. (i) We characterize haplotypic and composite measures of LD in polyploids. These composite measures of LD turn out to be functions of common statistical measures of association. (ii) We derive procedures to estimate haplotypic and composite LD in polyploids in the presence of genotype uncertainty. We do this by estimating LD directly from genotype likelihoods, which may be obtained from many genotyping platforms. (iii) We derive standard errors of all LD estimators that we discuss. We validate our methods on both real and simulated data. Our methods are implemented in the R package ldsep, available on the Comprehensive R Archive Networkhttps://cran.r-project.org/package=ldsep.
How do zebrafish respond to MK-801 and amphetamine? Relevance for assessing schizophrenia-relevant endophenotypes in alternative model organisms
Authors: Benvenutti Radharani , Gallas-Lopes Matheus , Sachett Adrieli , Marcon Matheus , Strogulski Nathan Ryzewski , Rosa Reis Carlos Guilherme , Chitolina Rafael , Piato Angelo , Herrmann Ana Paula 
Published: August 2020

ABSTRACTBackground and PurposeSchizophrenia pathophysiology has been associated with dopaminergic hyperactivity, loss of parvalbumin-positive GABAergic interneurons, NMDA receptor hypofunction, and redox dysregulation. Most behavioral assays and animal models to study this condition were developed in rodents, leaving room for species-specific biases that could be avoided by cross-species approaches. As MK-801 and amphetamine are largely used in mice and rats to mimic schizophrenia features, this study aimed to investigate the effects of these drugs in zebrafish.Experimental ApproachAdult zebrafish were exposed to MK-801 (1, 5, and 10 μM) or amphetamine (0.625, 2.5, and 10 mg·L-1) and observed in paradigms of locomotor activity and social behavior. Oxidative parameters relevant to schizophrenia were quantified in brain tissue.Key ResultsMK-801 disrupted social interaction, an effect that resembles the negative symptoms of schizophrenia. It also altered locomotion in a context-dependent manner, with hyperactivity when fish were tested in the presence of social cues and hypoactivity when tested alone. On the other hand, exposure to amphetamine was devoid of effects on locomotion and social behavior, while increased lipid peroxidation in the brain.Conclusion and ImplicationsKey outcomes induced by MK-801 in rodents were replicated in zebrafish, which suggests this species is suitable as an alternative model animal to study psychotic disorders. More studies are necessary to further develop preclinical paradigms with this species and ultimately optimize the screening of potential novel treatments.
Human vulnerability to cancer malignancy is enhanced by evolution of higher mesenchymal CD44 expression compared to other mammals
Authors: Ma Xinghong , Dighe Anasuya , Maziarz Jamie , Neumann Edwin , Erkenbrack Eric , Hei Yuan-Yuan , Liu Yansheng , Suhail Yasir , Kshitiz  , Pak Irene , Levchenko Andre , Wagner Günter P. 
Published: August 2020

AbstractCD44 is a membrane-bound extracellular matrix (ECM) receptor interacting, among others, with hyaluronic acid (HA) and osteopontin (OPN). Cancer progression and metastasis are greatly influenced by the cancer micro-environment, consisting of ECM, immune cells and cancer-associated fibroblasts (CAF). Recruitment of fibroblasts (FB) into the role as CAFs is caused by paracrine signals from the tumor, including TGFb1, PDGF and OPN. The effect of OPN on the transformation of FB into CAF is mediated by CD44. CD44 expression in human skin and endometrial stromal fibroblasts (SF and ESF, respectively) also enhances invasibility of stroma by trophoblast as well as cancer cells. Here we study the evolution ofCD44expression in therian mammals in both SF as well as ESF and demonstrate that the human lineage has experienced a concerted evolutionary enhancement of CD44 expression in SF and ESF, correlating with an increase in human vulnerability to cancer malignancy. In both human and cattle (Bos taurus), the dominant isoforms are CD44s and CD44v10 with 9 and 10 exons, respectively. CD44s is an isoform strongly associated with malignancy. In humans, an additional isoform is expressed: HsaCD44-205 with 8 exons not found in cattle. We show that the concerted increase ofCD44expression in SF and ESF is largely due to cis-regulatory effects in the proximal promoter ofCD44. We identify a primate specific acquisition of CEBPB binding sites in the CD44 promoter. Recruitment of CEBPB into CD44 regulation explains almost 50% of the lineage-specific increasedCD44expression in primate skin fibroblasts but is not necessary for high CD44 expression in ESF. All these results suggest that selective modulation ofCD44expression in skin fibroblasts could attenuate the cancer-promoting effect of CAF recruitment in the skin with minimal side effects on other cell types. Additional experimental data is needed to explore this possibility.
In vitromodeling of tumor spheroid interactions to perfused blood vessels
Authors: Kwak Tae Joon , Lee Esak 
Published: August 2020

AbstractTumor angiogenesis, the formation of new blood vessels from existing blood vessels in and around the tumor stroma, is orchestrated by multiple biological factors in the tumor microenvironment, including tumor stromal cells, extracellular matrices, and secreted growth factors. Here, we present the processes to define and optimize the biological conditions for robust interactions between tumor spheroids and engineered blood vessels in a microfluidic organ-on-a-chip devicein vitro. Within the device, vascular lumen formation and vessel sprouting in human umbilical vein endothelial cell based engineered blood vessels are observed in a variety of extracellular matrices (collagen, Matrigel, and fibrin), containing metastatic breast tumor cells (MDA-MB-231), and tumor stromal cells (mesenchymal stem cells, and human lung fibroblasts) to show the crosstalk between the tumor spheroids and the perfused blood vasculaturesin vitro.
Centrosomal P4.1-associated protein (CPAP) positively regulates endocytic vesicular transport and lysosome targeting of EGFR
Authors: Gudi Radhika , Palanisamy Viswanathan , Vasu Chenthamarakshan 
Published: August 2020

AbstractCentrosomal P4.1-associated protein (CPAP) plays a critical role in restricting the centriole length in human cells. Here, we report a novel, positive regulatory role for CPAP in endocytic vesicular transport (EVT) and lysosome targeting of internalized-cell surface receptor EGFR. We observed that higher CPAP levels cause an increase in the abundance of multi-vesicular body (MVB) and EGFR is detectable in CPAP-overexpression induced puncta. While the surface levels, and total and phosphorylated cellular levels of EGFR are higher under CPAP deficiency, ligandengagement induced internalization of this receptor is not impacted by CPAP levels. Furthermore, routing of EGFR into early endosomes is not influenced by CPAP. However, most importantly, we found that CPAP is required for targeting ligand-activated, internalized EGFR to lysosome. Transport of ligand-bound EGFR from early endosome to late endosome/MVB and lysosome is severely diminished in CPAP-depleted cells. Moreover, CPAP depleted cells showed diminished ability to form MVB structures upon EGFR activation. These observations show a positive regulatory role for CPAP in early endosome to late endosome transport and lysosome targeting of ligand-bound EGFR-like cell surface receptors. Overall, identification of this regulatory role for CPAP in endocytic trafficking of EGFR provides new insights in understanding the cellular functions of CPAP.
Structure of SARS-CoV-2 2′-O-methyltransferase heterodimer with RNA Cap analog and sulfates bound reveals new strategies for structure-based inhibitor design
Authors: Rosas-Lemus Monica , Minasov George , Shuvalova Ludmilla , Inniss Nicole , Kiryukhina Olga , Brunzelle Joseph , Satchell Karla J. F. 
Published: August 2020

AbstractThere are currently no antiviral therapies specific against SARS-CoV-2, the virus responsible for the global pandemic disease COVID-19. To facilitate structure-based drug design, we conducted an X-ray crystallographic study of the nsp16/nsp10 2′-O-methyltransferase complex that methylates Cap-0 viral mRNAs to improve viral protein translation and to avoid host immune detection. Heterodimer structures are determined with the methyl donorS-adenosylmethionine (SAM), the reaction productS-adenosylhomocysteine (SAH) or the SAH analog sinefungin (SFG). Furthermore, structures of nsp16/nsp10 with the methylated Cap-0 analog (m7GpppA) and SAM or SAH bound were obtained. Comparative analysis revealed flexible loops in open and closed conformations at the m7GpppA binding pocket. Bound sulfates in several structures suggested the location of the phosphates in the ribonucleotide binding groove. Additional nucleotide binding sites were found on the face of the protein opposite the active site. These various sites and the conserved dimer interface could be exploited for development of antiviral inhibitors.
A dynamical system model for predicting gene expression from the epigenome
Authors: Brunner James D. , Kim Jacob , Downing Timothy , Mjolsness Eric , Kober Kord M. 
Published: August 2020

AbstractGene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigentic processes (e.g., DNA methylation). Understanding the role of epigenetic changes in gene expression is a fundamental question of molecular biology. Predictions of gene expression values from epigenetic data have tremendous research and clinical potential. Despite active research, studies to date have focused on using statistical models to predict gene expression from methylation data. In contrast, dynamical systems can be used to generate a model to predict gene expression using epigenetic data and a gene regulatory network (GRN) which can also serve as a mechanistic hypothesis. Here we present a novel stochastic dynamical systems model that predicts gene expression levels from methylation data of genes in a given GRN. Software for dataset preparation, model parameter fitting and prediction generation, and reporting are available athttps://github.com/kordk/stoch_epi_lib.
Dimension reduction and denoising of single-cell RNA sequencing data in the presence of observed confounding variables
Authors: Huang Mo , Zhang Zhaojun , Zhang Nancy R. 
Published: August 2020

AbstractConfounding variation, such as batch effects, are a pervasive issue in single-cell RNA sequencing experiments. While methods exist for aligning cells across batches, it is yet unclear how to correct for other types of confounding variation which may be observed at the subject level, such as age and sex, and at the cell level, such as library size and other measures of cell quality. On the specific problem of batch alignment, many questions still persist despite recent advances: Existing methods can effectively align batches in low-dimensional representations of cells, yet their effectiveness in aligning the original gene expression matrices is unclear. Nor is it clear how batch correction can be performed alongside data denoising, the former treating technical biases due to experimental stratification while the latter treating technical variation due inherently to the random sampling that occurs during library construction and sequencing. Here, we propose SAVERCAT, a method for dimension reduction and denoising of single-cell gene expression data that can flexibly adjust for arbitrary observed covariates. We benchmark SAVERCAT against existing single-cell batch correction methods and show that while it matches the best of the field in low-dimensional cell alignment, it significantly improves upon existing methods on the task of batch correction in the high-dimensional expression matrix. We also demonstrate the ability of SAVERCAT to effectively integrate batch correction and denoising through a data down-sampling experiment. Finally, we apply SAVERCAT to a single cell study of Alzheimer’s disease where batch is confounded with the contrast of interest, and demonstrate how adjusting for covariates other than batch allows for more interpretable analysis.