bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of claw colouration in fiddler crabs’ mate choice: Private communication channel or handicap?
Authors: Silva Diogo Jackson Aquino , Erickson Marilia Fernandes , Guidi Raiane dos Santos , Pessoa Daniel Marques Almeida 
Published: February 2021

AbstractColour cues play an important role in sexual selection and conspecific recognition. Literature shows that conspecifics might enjoy their everyday chat, without ever worrying about occasional eavesdroppers (e.g., predators), when information interchange evolves into a private communication channel. Yet, when signalling is converted into foraging cues by predators, their prey must pay the due cost for sustaining conversation. For that matter, fiddler crabs draw attention for having flashy enlarged claws that could potentially attract the attention of many predators. Surprisingly, the costs associated with claw colouration in fiddler crabs are still poorly understood and have never been studied in American species. Here, we initially examine whether hypertrophied claws of American thin-fingered fiddler crabs (Leptuca leptodactyla) reflect UV-light and how conspecific females react to these cues. Then we test two alternative hypotheses concerning the role of claw colouration in fiddler crabs’ mate choice: a) that claw colouration evolved into a private communication channel, which could have significantly lowered signalling costs for males; b) that claw colouration is conspicuous to potential reproductive partners, as well as to predators, making colour signalling by males very costly (i.e., a handicap). Thereafter, we measured the reflectance spectra from several enlarged claws and modelled their chromatic contrast against the background spectrum, considering the visual systems of conspecific fiddler crabs and two kinds of predators (terns and plovers). We also tested female conspecifics’ preference towards enlarged claws that reflected UV-light or other colour cues, by artificially altering claw colouration. Our results show a clear female preference for UV reflecting males. We also found that natural enlarged claws should be highly detectable by avian predators, refuting the private communication channel hypothesis. Furthermore, since female fiddler crabs select the most flamboyant claws from the sandy background, claw colouration in fiddler crabs can be understood as an honest signal.HIGHLIGHTSThe hypertrophied claws of maleLeptuca leptodactylareflect UV light.Female fiddler crabs display a natural preference for UV light cues.Conspicuous claws function as handicaps and may honestly signal individual quality.Male enlarged claws are more conspicuous to birds than to crabs.Our data refute the presence of a private communication channel inL. leptodactyla.
Pre-pandemic cognitive function and COVID-19 mortality: prospective cohort study
Authors: Batty G. David , Deary Ian J. , Gale Catharine R. 
Published: February 2021

AbstractBackgroundPoorer performance on standard tests of cognitive function is related to an elevated risk of death from lower respiratory tract infections. Whether pre-pandemic measures of cognition are related to COVID-19 mortality is untested.MethodsUK Biobank, a prospective cohort study, comprises around half a million people who were aged 40 to 69 years at study induction between 2006 and 2010 when a reaction time test was administered to the full sample, and verbal-numeric reasoning assessed in a subgroup. Death from COVID-19 was ascertained from participant linkage to a UK-wide national registry.ResultsBetween April 1st and September 23rd 2020, there were 388 deaths (138 women) ascribed to COVID-19 in the 494,932 individuals (269,602 women) with a reaction time test result, and 125 such deaths (38 women) in the 180,198 (97,794 women) for whom there were data on verbal-numeric reasoning. In analyses adjusted for age, sex, and ethnicity, a one standard deviation (118.2 msec) slower reaction time was related to a higher rate of death from COVID-19 (hazard ratio; 95% confidence interval: 1.18; 1.09, 1.28). A one standard deviation disadvantage (2.16 point) on the verbal-numeric reasoning test was also associated with an elevated risk of death (1.32; 1.09, 1.59). Attenuation after adjustment for additional covariates followed a similar pattern for both measures of cognition. For verbal-numeric reasoning, for instance, the hazard ratios were 1.22 (0.98, 1.51) after control for socioeconomic status, 1.16 (0.96, 1.41) after lifestyle factors, 1.25 (1.04, 1.52) after co-morbidity, and 1.29 (1.01, 1.64) after physiological indices.ConclusionsIn the present study, poorer performance on two pre-pandemic indicators of cognitive function, including reaction time, a knowledge-reduced measure, was related to death ascribed to COVID-19.
Dynamic Gene-Based Ecophysiological Models to Predict Phenotype from Genotype and Environment Data
Authors: Vallejos C. Eduardo , Jones James W. , Bhakta Mehul S. , Gezan Salvador A. , Correll Melanie J. 
Published: February 2021

ABSTRACTPredicting the phenotype from the genotype is one of the major contemporary challenges in biology. This challenge is greater in plants because their development occurs mostly post-embryonically under diurnal and seasonal environmental fluctuations. Current phenotype prediction models do not adequately capture all of these fluctuations or effectively use genotype information. Instead, we have developed a dynamic modular approach that captures the genotype, environment, and Genotype-by-Environment effects to express the time-to-flowering phenotype in real time inPhaseolus vulgaris. The module we describe can be applied to different plant processes and can gradually replace processes in existing crop models. Our model can enable accelerated progress in diverse breeding programs, particularly with the prospects of climate change. Finally, a gene-based simulation model can assist policy decision makers in matters pertaining to prediction of food supplies.
Long non-coding RNAs bind to proteins relevant to the ethanol tolerance in yeast: a systems biology view
Authors: Marques Lucas Farinazzo , Wolf Ivan Rodrigo , Lazari Lucas Cardoso , de Almeida Lauana Fogaça , Schnepper Amanda Piveta , Cardoso Luiz Henrique , de Moraes Leonardo Nazário , Grotto Rejane Maria Tommasini , Simões Rafael Plana , Ramos Érica , Valente Guilherme Targino 
Published: February 2021

AbstractThe ethanol disturbs the cell cycle, transcription, translation, protein folding, cell wall, membranes, and manySaccharomyces cerevisiaemetabolic processes. Long non-coding RNAs (lncRNAs) are regulatory molecules binding onto the genome or proteins. The number of lncRNAs described for yeast is still scarce, and little is known concerning their roles in the system. There is a lack of knowledge concerning how lncRNAs are responsive to the ethanol tolerance in yeast and whether they act in this tolerance. Hence, by using RNA-Seq data fromS. cerevisiaestrains with different ethanol tolerance phenotypes, we found the severe ethanol responsive lncRNAs. We modeled how they participate in the ethanol tolerance by analyzing lncRNA-protein interactions. The results showed that the EtOH tolerance responsive lncRNAs, in both higher tolerant and lower tolerant phenotypes, work on different pathways: cell wall, cell cycle, growth, longevity, cell surveillance, ribosome biogenesis, intracellular transport, trehalose metabolism, transcription, and nutrient shifts. In summary, lncRNAs seems to interconnect essential systems’ modules to overcome the ethanol stress. Finally, here we also found the most extensive catalog of lncRNAs in yeast.
Investigation of layer specific BOLD in the human visual cortex during visual attention
Authors: van Mourik Tim , Koopmans Peter J. , Bains Lauren J. , Norris David G. , Jehee Janneke F.M. 
Published: February 2021

AbstractDirecting spatial attention towards a particular stimulus location enhances cortical responses at corresponding regions in cortex. How attention modulates the laminar response profile within the attended region, however, remains unclear. In this paper, we use high field (7T) fMRI to investigate the effects of attention on laminar activity profiles in areas V1-V3; both when a stimulus was presented to the observer, and in the absence of visual stimulation. Replicating previous findings, we find robust increases in the overall BOLD response for attended regions in cortex, both with and without visual stimulation. When analyzing the BOLD response across the individual layers in visual cortex, we observed no evidence for laminar-specific differentiation with attention. We offer several potential explanations for these results, including theoretical, methodological and technical reasons. Additionally, we provide all data and pipelines openly, in order to promote analytic consistency across layer-specific studies, improve reproducibility, and decrease the false positive rate as a result of analytical flexibility.
Validation of biosignatures confirms the informative nature of fossil organic Raman spectra
Authors: Wiemann Jasmina , Briggs Derek E. G. 
Published: February 2021

AbstractRaman spectroscopy has facilitated rapid progress in the understanding of patterns and processes associated with biomolecule fossilization and revealed the preservation of biological and geological signatures in fossil organic matter. Nonetheless six large-scale statistical studies of Raman spectra of carbonaceous fossils, selected from a number of independent assessments producing similar trends, have been disputed. Alleon et al. (21) applied a wavelet transform analysis in an unconventional way to identify frequency components contributing to two baselined spectra selected from these studies and claimed similarities with a downloaded edge filter transmission spectrum. On the basis of indirect comparisons and qualitative observations they argued that all spectral features detected, including significant mineral peaks, can be equated to edge filter ripples and are therefore artefactual. Alleon et al. (21) extrapolated this conclusion to dispute not only the validity of n>200 spectra in the studies in question, but also the utility of Raman spectroscopy, a well established method, for analysing organic materials in general. Here we test the claims by Alleon et al. (21) using direct spectral comparisons and statistical analyses. We present multiple independent lines of evidence that demonstrate the original, biologically and geologically informative nature of the Raman spectra in question. We demonstrate that the methodological approach introduced by Alleon et al. (21) is unsuitable for assessing the quality of spectra and identifying noise within them. Statistical analyses of large Raman spectral data sets provide a powerful tool in the search for compositional patterns in biomaterials and yield invaluable insights into the history of life.
Kaposi’s sarcoma-associated herpesvirus (KSHV) utilizes the NDP52/CALCOCO2 selective autophagy receptor to disassemble processing bodies
Authors: Robinson Carolyn-Ann , Singh Gillian K. , Kleer Mariel , Castle Elizabeth L. , Boudreau Bre Q. , Corcoran Jennifer A. 
Published: February 2021

AbstractKaposi’s sarcoma-associated herpesvirus (KSHV) causes the inflammatory and angiogenic endothelial cell neoplasm, Kaposi’s sarcoma (KS). We previously demonstrated that expression of the KSHV protein, Kaposin B (KapB), promoted inflammation via the disassembly of cytoplasmic ribonucleoprotein granules called processing bodies (PBs). Processing bodies (PBs) modify gene expression by silencing or degrading labile messenger RNAs (mRNAs) including many transcripts that encode inflammatory or angiogenic proteins that are associated with KS disease. Although our work implicated PB disassembly as one of the causes of inflammation during KSHV infection, the precise mechanism used by KapB to elicit PB disassembly was unclear. Here we reveal a new connection between the degradative process of autophagy and PB disassembly. We show that both latent KSHV infection and KapB expression enhanced autophagic flux via the phosphorylation of the autophagy regulatory protein, Beclin 1. KapB was necessary for this effect, as infection with a recombinant virus that does not express the KapB protein did not induce Beclin 1 phosphorylation or autophagic flux. Moreover, we reveal that PB disassembly mediated by KSHV or KapB depended on canonical autophagy genes and the selective autophagy receptorNDP52/CALCOCO2and that the PB scaffolding protein, Pat1b, co-immunoprecipitated with NDP52. These studies reveal a new role for autophagy and the selective autophagy receptor NDP52 in promoting PB turnover and the concomitant synthesis of inflammatory molecules during KSHV infection.Author SummaryKaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of the inflammatory, endothelial cell cancer, Kaposi’s Sarcoma (KS). KSHV induces a pro-tumourigenic inflammatory environment which aids in the establishment and maintenance of the KS lesion. Processing bodies (PBs) are cellular structures that dampen inflammatory gene expression by suppression or decay of their cognate RNA molecules. We previously showed that the viral protein KapB caused PB disappearance during KSHV infection, identifying a new pathway used by KSHV to elicit inflammation. Now, we show that KSHV and KapB hijack the cellular degradative process of autophagy to promote PB disassembly and increase inflammatory gene expression. This places autophagy as central to the regulation of inflammation by KSHV and illustrates another remarkable strategy used by these viruses to create a tumourigenic microenvironment.
Autism-associated protein POGZ maintains embryonic stem cells by association with esBAF and HP1γ
Authors: Sun Xiaoyun , Cheng Linxi , Sun Yuhua 
Published: February 2021

AbstractPOGZ, which encodes a multi-domain transcription factor, has been found frequently mutated in neurodevelopmental disorders, particularly autism spectrum disorder (ASD) and intellectual disability (ID). However, little is known about its functions in embryonic stem cells (ESCs) and in transcriptional regulation. Here, we show that POGZ plays key roles in the maintenance of ESCs by association with the SWI-SNF (BAF) chromatin remodeler complex and heterochromatin protein 1 (HP1) proteins. Loss of POGZ induces differentiation of ESCs, likely by up-regulation of primitive endoderm and mesoderm lineage genes and by down-regulation of pluripotency-related and cell cycle genes. Genome-wide binding analysis shows that POGZ is primarily localized to gene promoter and enhancer regions where POGZ is required to maintain an open chromatin. Regulation of chromatin under control of POGZ depends on esBAF complex. Furthermore, there is an extensive overlap of POGZ and OCT4 peaks genome-wide, and both factors interact with each other. We propose that POGZ is an important pluripotency-associated factor, and its absence causes failure to maintain a proper ESC-specific chromatin state and transcriptional circuitry, which eventually leads to loss of ESC phenotype. Our work provides important insights into the roles of POGZ in the maintenance of ESC identity as well as regulation of transcription, which will be useful for understanding the etiology of neurodevelopmental disorders byPOGZmutation.
Global impact and cost-effectiveness of one-dose versus two-dose human papillomavirus vaccination schedules: a comparative modelling analysis
Authors: Prem Kiesha , Choi Yoon Hong , Bénard Élodie , Burger Emily A , Hadley Liza , Laprise Jean-François , Regan Mary Caroline , Drolet Mélanie , Sy Stephen , Abbas Kaja , Portnoy Allison , Kim Jane J , Brisson Marc , Jit Mark 
Published: February 2021

AbstractBackgroundTo eliminate cervical cancer as a public health problem, the World Health Organization currently recommends routine vaccination of adolescent girls with two doses of the human papillomavirus (HPV) vaccine before sexual initiation. However, many countries have yet to implement HPV vaccination because of financial or logistical barriers to delivering two doses outside the infant immunisation programme.MethodsUsing three independent HPV transmission models, we estimated the long-term health benefits and cost-effectiveness of one-dose versus two-dose HPV vaccination, in 188 countries, assuming that one dose of the vaccine gives either a shorter duration of full protection (20 or 30 years) or lifelong protection but lower vaccine efficacy (e.g., 80%) compared to two doses. We simulated routine vaccination with the 9-valent HPV vaccine in 10-year-old girls at 80% coverage for the years 2021–2120, with a one-year catch-up campaign of 11–14-year-old girls at 80% coverage in the first year of the programme.ResultsOver the years 2021–2120, one-dose vaccination at 80% coverage was projected to avert 112.9 million (range of medians: 75.8–176.2) and 148.0 million (111.6–187.6) cervical cancer cases assuming one dose of the vaccine confers 20 and 30 years of protection, respectively. Should one dose of the vaccine provide lifelong protection at 80% vaccine efficacy, 155.2 million (143.7–170.3) cervical cancer cases could be prevented. Around 65 to 889 additional girls would need to be vaccinated with the second dose to prevent one cervical cancer case, depending on the epidemiological profiles of the country. Across all income groups, the threshold cost for the second dose was low: from 0.85 (0.07–3.82) USD in low-income countries to 18.08 (−3.62–85.64) USD in high-income countries, assuming one-dose confers 30-year protection.ConclusionsResults were consistent across the three independent models and suggest that one-dose vaccination has similar health benefits to a two-dose programme while simplifying vaccine delivery, reducing costs, and alleviating vaccine supply constraints. The second dose may be cost-effective if there is a shorter duration of protection from one dose, cheaper vaccine and vaccination delivery strategies, and high burden of cervical cancer.
Nucleosomal Asymmetry Shapes Histone Mark Binding and Promotes Poising at Bivalent Domains
Authors: Bryan Elana , Warburton Marie , Webb Kimberly M. , McLaughlin Katy A. , Spanos Christos , Ambrosi Christina , Major Viktoria , Baubec Tuncay , Rappsilber Juri , Voigt Philipp 
Published: February 2021

SummaryPromoters of developmental genes in embryonic stem cells (ESCs) are marked by histone H3 lysine 4 trimethylation (H3K4me3) and H3K27me3 in an asymmetric nucleosomal conformation, with each sister histone H3 carrying only one mark. These bivalent domains are thought to poise genes for timely activation upon differentiation. Here we show that asymmetric bivalent nucleosomes recruit repressive H3K27me3 binders but fail to enrich activating H3K4me3 binders, despite presence of H3K4me3, thereby promoting a poised state. Strikingly, the bivalent mark combination further attracts chromatin proteins that are not recruited by each mark individually, including the histone acetyltransferase complex KAT6B (MORF). Knockout of KAT6B blocks neuronal differentiation, demonstrating that bivalency-specific readers are critical for proper ESC differentiation. These findings reveal how histone mark bivalency directly promotes establishment of a poised state at developmental genes, while highlighting how nucleosomal asymmetry is critical for histone mark readout and function.
A systematic approach for finding herbicide synergies
Authors: Sukhoverkov Kirill V. , Mylne Joshua S. 
Published: February 2021

ABSTRACTCombining herbicides into a double dose is a common approach to overcome the potential for herbicide resistance by weeds. Many herbicide mixtures can be antagonistic and they are rarely synergistic. Here, 24 commercial herbicides, each representing a mode of action were used to create a matrix of all 276 unique combinations to search for new synergies in agar withArabidopsis thaliana. Herbicides were used at an appropriate sub-lethal dose such that any synergies gave visible growth inhibition. We found five synergies including three new ones, namely mesotrione-norflurazon, mesotrione-clethodim and paraquat-clomazone. All three new synergies were reproducible in soil-grown conditions. Interestingly, all three new combinations included a bleaching herbicide, suggesting synergy might be a class specific phenomenon. We also found that mesotrione-norflurazon and mesotrione-clethodim combinations remained synergistic against lettuce(Lactuca sativa), but not tef(Eragrostis tef). Our study shows that screening herbicide mixtures againstA. thalianais an efficient approach for finding rare herbicide synergies.
Bidirectional neuronal migration coordinates retinal morphogenesis by preventing spatial competition
Authors: Rocha-Martins Mauricio , Kretzschmar Jenny , Nerli Elisa , Weigert Martin , Icha Jaroslav , Myers Eugene W. , Norden Caren 
Published: February 2021

AbstractWhile the design of industrial products is often optimized for the sequential assembly of single components, organismal development is hallmarked by the concomitant occurrence of tissue growth and organization. Often this means that proliferating and differentiating cells occur at the same time in a shared tissue environment that continuously changes. How cells adapt to architectural changes in order to prevent spatial interference remains unclear. To understand how cell movements important for growth and organization are orchestrated, we here study the emergence of photoreceptor neurons that occur during the peak of retinal growth using zebrafish, human tissue and human organoids. Quantitative imaging reveals that successful retinal morphogenesis depends on active bidirectional photoreceptor translocation. This leads to a transient transfer of the entire cell population away from the apical proliferative zone. This migration pattern is driven by distinct cytoskeletal machineries, depending on direction: microtubules are required for basal translocation, while actomyosin drives apical movement. Blocking photoreceptor translocation leads to apical overcrowding that hampers progenitor movements. Thus, photoreceptor migration is crucial to prevent competition for space and thereby allows concurrent tissue growth and lamination. This shows that neuronal migration, in addition to its canonical role in cell positioning, is involved in coordinating morphogenesis.
Productivity estimation of cutter suction dredger operation through data mining and learning from real-time big data
Authors: Fu Jiake , Tian Huijing , Song Lingguang , Li Mingchao , Bai Shuo , Ren Qiubing 
Published: February 2021

PurposeThis paper presents a new approach of productivity estimation of cutter suction dredger operation through data mining and learning from real-time big data.Design/methodology/approachThe paper used big data, data mining and machine learning techniques to extract features of cutter suction dredgers (CSD) for predicting its productivity. ElasticNet-SVR (Elastic Net-Support Vector Machine) method is used to filter the original monitoring data. Along with the actual working conditions of CSD, 15 features were selected. Then, a box plot was used to clean the corresponding data by filtering out outliers. Finally, four algorithms, namely SVR (Support Vector Regression), XGBoost (Extreme Gradient Boosting), LSTM (Long-Short Term Memory Network) and BP (Back Propagation) Neural Network, were used for modeling and testing.FindingsThe paper provided a comprehensive forecasting framework for productivity estimation including feature selection, data processing and model evaluation. The optimal coefficient of determination (R2) of four algorithms were all above 80.0%, indicating that the features selected were representative. Finally, the BP neural network model coupled with the SVR model was selected as the final model.Originality/valueMachine-learning algorithm incorporating domain expert judgments was used to select predictive features. The final optimal coefficient of determination (R2) of the coupled model of BP neural network and SVR is 87.6%, indicating that the method proposed in this paper is effective for CSD productivity estimation.