bluuebunny/crossref_metadata_2025 huggingface dataset:
Facial expressions of emotional stress in horses
Authors: Lundblad Johan , Rashid Maheen , Rhodin Marie , Andersen Pia Haubro
Published: October 2020

Horses have the ability to generate a remarkable repertoire of facial expressions, some which have been linked to certain emotional states, for example pain. Studies suggest that facial expressions may be a more ‘honest’ expression of emotional state in horses than behavioral or physiological parameters. This study sought to describe the facial expressions during stress of healthy horses free of pain, using a standardized method of recording facial expressions in video. Stress was induced in 28 horses by subjecting them to road transport and 10 of these horses were also subjected to social isolation. The horses served as their own control. A body-mounted, remote controlled heart rate monitor provided continuous heart rate measurements during the interventions. The horses’ facial expressions were video-recorded during the interventions. Frequency and duration of each facial expression were then determined, according to the Equine Facial Action Coding System. Heart rate increased during the stressful interventions (p=0.01), confirming that the interventions were stressful. Using both the human investigation- and the co-occurrence methods, the following facial traits could be observed during stress:eye white increase(p<0.001),nostril dilator(p<0.001),upper eyelid raiser(p<0.001),inner brow raiser(p=0.042),tongue show(p<0.001) along with an increase in ‘ear flicker’ (p<0.001) and blink frequency (p<0.001). The facial actions were successfully used to train a machine-learning classifier to discriminate between stressed and calm horses, with an accuracy of 74.2 %. Most of the facial features identified correspond well with previous research on the subject, for example flared nostrils, repetitive mouth behaviors, increased eye white, tongue show and ear movements. Some features selected as indicative of emotional pain-free stress are used in face-based pain assessment tools, such as dilated nostrils, eye white increase or inner brow raiser. The relation between facial expressions of stress and pain should therefore further be studied.
Information Confusion Reveals an Innate Limit of the Information Processing by Neurons
Authors: Tian Yang , Gardner Justin L. , Li Guoqi , Sun Pei
Published: October 2020

Information experiences complex transformation processes in the brain, involving various errors. A daunting and critical challenge in neuroscience is to understand the origin of these errors and their effects on neural information processing. While previous efforts have made substantial progresses in studying the information errors in bounded, unreliable and noisy transformation cases, it still remains elusive whether the neural system is inherently error-free under an ideal and noise-free condition. This work brings the controversy to an end with a negative answer. We propose a novel neural information confusion theory, indicating the widespread presence of information confusion phenomenon after the end of transmission process, which originates from innate neuron characteristics rather than external noises. Then, we reformulate the definition of zero-error capacity under the context of neuroscience, presenting an optimal upper bound of the zero-error transformation rates determined by the tuning properties of neurons. By applying this theory to neural coding analysis, we unveil the multi-dimensional impacts of information confusion on neural coding. Although it reduces the variability of neural responses and limits mutual information, it controls the stimulus-irrelevant neural activities and improves the interpretability of neural responses based on stimuli. Together, the present study discovers an inherent and ubiquitous precision limitation of neural information transformation, which shapes the coding process by neural ensembles. These discoveries reveal that the neural system is intrinsically error-prone in information processing even in the most ideal cases.

Author summary

One of the most central challenges in neuroscience is to understand the information processing capacity of the neural system. Decades of efforts have identified various errors in nonideal neural information processing cases, indicating that the neural system is not optimal in information processing because of the widespread presences of external noises and limitations. These incredible progresses, however, can not address the problem about whether the neural system is essentially error-free and optimal under ideal information processing conditions, leading to extensive controversies in neuroscience. Our work brings this well-known controversy to an end with a negative answer. We demonstrate that the neural system is intrinsically error-prone in information processing even in the most ideal cases, challenging the conventional ideas about the superior neural information processing capacity. We further indicate that the neural coding process is shaped by this innate limit, revealing how the characteristics of neural information functions and further cognitive functions are determined by the inherent limitation of the neural system.
Evaluation of CRISPR gene-editing tools in zebrafish
Authors: Uribe-Salazar José M. , Kaya Gulhan , Sekar Aadithya , Weyenberg KaeChandra , Ingamells Cole , Dennis Megan Y.
Published: October 2020

Background

Zebrafish have practical features that make them a useful model for higher-throughput tests of gene function using CRISPR/Cas9 editing to create ‘knockout’ models. In particular, the use of G0mosaic mutants has potential to increase throughput of functional studies significantly but may suffer from transient effects of introducing Cas9 via microinjection. Further, a large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods leaving uncertainty in choosing an optimal approach for zebrafish studies.

Methods

To systematically assess accuracy of tool predictions of on- and off-target gene editing, we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs (gRNAs) targeting 14 genes. We also investigate potential confounders of G0-based CRISPR screens by screening control embryos for spurious mutations and altered gene expression.

Results

We compared our experimentalin vivoediting efficiencies in mosaic G0embryos with those predicted by eight commonly used gRNA design tools and found large discrepancies between methods. Assessing off-target mutations (predictedin silicoandin vitro) found that the majority of tested loci had lowin vivofrequencies (<1%). To characterize if commonly used ‘mock’ CRISPR controls (larvae injected with Cas9 enzyme or mRNA with no gRNA) exhibited spurious molecular features that might exacerbate studies of G0mosaic CRISPR knockout fish, we generated an RNA-seq dataset of various control larvae at 5 days post fertilization. While we found no evidence of spontaneous somatic mutations of injected larvae, we did identify several hundred differentially-expressed genes with high variability between injection types. Network analyses of shared differentially-expressed genes in the ‘mock’ injected larvae implicated a number of key regulators of common metabolic pathways, and gene-ontology analysis revealed connections with response to wounding and cytoskeleton organization, highlighting a potentially lasting effect from the microinjection process that requires further investigation.

Conclusion

Overall, our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.
Internalization of the host alkaline pH signal in a fungal pathogen
Authors: Brown Hannah E. , Pianalto Kaila M. , Fernandes Caroline M. , Mueller Katherine D. , Del Poeta Maurizio , Alspaugh J. Andrew
Published: October 2020

The ability for cells to internalize extracellular cues allows them to adapt to novel and stressful environments. This adaptability is especially important for microbial pathogens that must sense and respond to drastic changes when encountering the human host.Cryptococcus neoformansis an environmental fungus and opportunistic pathogen that naturally lives in slightly acidic reservoirs, but must adapt to the relative increase in alkalinity in the human host in order to effectively cause disease. The fungal-specific Rim alkaline response signaling pathway effectively converts this extracellular signal into an adaptive cellular response allowing the pathogen to survive in its new environment. The newly identified Rra1 protein, the most upstream component of theC. neoformansRim pathway, is an essential component of this alkaline response. Previous work connected Rra1-mediated signaling to the dynamics of the plasma membrane. Here we identify the specific mechanisms of Rim pathway signaling through detailed studies of the activation of the Rra1 protein. Specifically, we observe that the Rra1 protein is internalized and recycled in a pH-dependent manner, and that this dynamic pattern of localization further depends on specific residues in its C-terminal tail, clathrin-mediated endocytosis, and the integrity of the plasma membrane. The data presented here continue to unravel the complex and intricate processes of pH-sensing in a relevant human fungal pathogen. These studies will further elucidate general mechanisms by which cells respond to and internalize extracellular stress signals.

Author Summary

The work described here explores the genetics and mechanics of a cellular signaling pathway in a relevant human fungal pathogen,Cryptococcus neoformans. The findings presented in this manuscript untangle the complex interactions involved in the activation of a fungal-specific alkaline response pathway, the Rim pathway. Specifically, we find thatC. neoformansis able to sense an increase in pH within the human host, internalize a membrane-bound pH-sensor, and activate a downstream signaling pathway enabling this pathogen to adapt to a novel host environment and effectively cause disease. Revealing the mechanisms of Rim pathway activation within the larger context of the fungal cell allows us to understand how and when this microorganism interprets relevant host signals. Furthermore, understanding how this pathogenic organism converts extracellular stress signals into an adaptive cellular response will elucidate more general mechanisms of microbial environmental sensing and stress response.
Rethinking Pleijel’s (1995) characters under a hierarchical point of view
Authors: Faure-Brac Mathieu G. , Rineau Valentin , Bagils René Zaragüeta
Published: October 2020

In 1995, Pleijel raised an issue on the coding of complex (multistate) characters: to find a unique coding approach satisfying both informational and semantical criteria. Following Pleijel’s work, this study aims to propose a new answer to this problematic. We proposed here to use hierarchical characters instead of classical partitional ones as hierarchy allows to deal effectively with the different uncertainties met by phylogeneticists since the beginning of phylogenetic data matrices: missing data, inapplicable data and polymorphism. We translated all previous proposed approaches into hierarchical ones and add three new approaches, only coded using hierarchy. Using phylogenetic and show with different metric how one of these new approaches displaces the other ones. The results from this study then supports the idea than phylogenetic characters should be coded using only hierarchies, as they offer a better management of uncertainties and propose new approaches more informative.
Consensus clustering applied to multi-omic disease subtyping
Authors: Brière Galadriel , Darbo Élodie , Thébault Patricia , Uricaru Raluca
Published: October 2020

Background

Facing the diversity of omic data and the difficulty of selecting one result over all those produced by several methods, consensus strategies have the potential to reconcile multiple inputs and to produce robust results.

Results

Here, we introduce ClustOmics, a generic consensus clustering tool that we use in the context of cancer subtyping. ClustOmics relies on a non-relational graph database, which allows for the simultaneous integration of both multiple omic data and results from various clustering methods. This new tool conciliates input clusterings, regardless of their origin, their number, their size or their shape. ClustOmics implements an intuitive and flexible strategy, based upon the idea ofevidence accumulation clustering. It computes co-occurrences of pairs of samples in input clusters and uses this score as a similarity measure to reorganise data into consensus clusters.

Conclusion

We applied ClustOmics to multi-omic disease subtyping on real TCGA cancer data from ten different cancer types. We showed that ClustOmics is robust to heterogeneous qualities of input partitions, smoothing and reconciling preliminary predictions into high quality consensus clusters, both from a computational and a biological point of view. The comparison to a state-of-the-art consensus based integration tool, COCA, further corroborated this statement. However, the main interest of ClustOmics is not to compete with other tools, but rather to make profit from their various predictions when no gold-standard metric is available to assess their significance.

Availability

ClustOmics’ source code, released under MIT licence, as well as the results obtained on TCGA cancer data are available on Github:https://github.com/galadrielbriere/ClustOmics.
Juvenile corals inherit mutations acquired during the parent’s lifespan
Authors: Kuntz Kate L. Vasquez , Kitchen Sheila A. , Conn Trinity L. , Vohsen Samuel A. , Chan Andrea N. , Vermeij Mark J. A. , Page Christopher , Marhaver Kristen L. , Baums Iliana B.
Published: October 2020

128 years ago, August Weismann proposed that the only source of inherited genetic variation in animals is the germline1. Julian Huxley reasoned that if this were true, it would falsify Jean-Baptiste Lamarck’s theory that acquired characteristics are heritable2. Since then, scientists have discovered that not all animals segregate germline cells from somatic cells permanently and early in development3. In fact, throughout their lives, Cnidaria4–6and Porifera7maintain primordial stem cells that continuously give rise to both germline and somatic cells. The fate of mutations generated in this primordial stem cell line during adulthood remains an open question. It was unknown whether post-embryonic mutations could be heritable in animals8–10—until now. Here we use two independent genetic marker analyses to show that post-embryonic mutations are inherited in the coralAcropora palmata(Cnidaria, Anthozoa). This discovery upends the long-held supposition that post-embryonic genetic mutations acquired over an animal’s lifetime in non-germline tissues are not heritable2. Over the centuries-long lifespan of a coral, the inheritance of post-embryonic mutations may not only change allele frequencies in the local larval pool but may also spread novel alleles across great distances via larval dispersal. Thus, corals may have the potential to adapt to changing environments via heritable somatic mutations10. This mechanism challenges our understanding of animal adaptation and prompts a deeper examination of both the process of germline determination in Cnidaria and the role of post-embryonic genetic mutations in adaptation and epigenetics of modular animals. Understanding the role of post-embryonic mutations in animal adaptation will be crucial as ecological change accelerates in the Anthropocene.
Lentiviral vectors transduce lung stem cells without disrupting plasticity
Authors: Cooney Ashley L. , Thurman Andrew L. , McCray Paul B. , Pezzulo Alejandro A. , Sinn Patrick L.
Published: October 2020

Life-long expression of a gene therapy agent likely requires targeting stem cells. Here we ask the question: does viral vector transduction or ectopic expression of a therapeutic transgene preclude airway stem cell function? We used a lentiviral vector containing a GFP or cystic fibrosis transmembrane conductance regulator (CFTR) transgene to transduce primary airway basal cells from human cystic fibrosis (CF) or non-CF lung donors and monitored expression and function after differentiation. Ussing chamber measurements confirmed CFTR-dependent chloride channel activity in CF donor cells. Immunostaining, quantitative real-time PCR, and single-cell sequencing analysis of cell-type markers indicated that vector transduction or CFTR expression does not alter the formation of pseudostratified, fully-differentiated epithelial cell cultures or cell type distribution. These results have important implications for use of gene addition or gene editing strategies as life-long curative approaches for lung genetic diseases.
Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases
Authors: Hoque M. Nazmul , Rahman M. Shaminur , Ahmed Rasel , Hossain Md. Sabbir , Islam Md. Shahidul , Crandall Keith A , Islam Md Tofazzal , Hossain M. Anwar , Siddiki AMAM Zonaed
Published: October 2020

The novel coronavirus disease 2019 (COVID-19) is a rapidly emerging and highly transmissible disease caused by the Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2). Understanding the microbiomes associated with the upper respiratory tract infection (URTI), chronic obstructive pulmonary disease (COPD) and COVID-19 diseases has clinical interest. We hypothesized that the diversity of microbiome compositions and their genomic features are associated with different pathological conditions of these human respiratory tract diseases (COVID-19 and non-COVID; URTI and COPD). To test this hypothesis, we analyzed 21 whole metagenome sequences (WMS) including eleven COVID-19 (BD = 6 and China = 5), six COPD (UK = 6) and four URTI (USA = 4) samples to unravel the diversity of microbiomes, their genomic features and relevant metabolic functions. The WMS data mapped to 534 bacterial, 60 archaeal and 61 viral genomes with distinct variation in the microbiome composition across the samples (COVID-19>COPD>URTI). Notably, 94.57%, 80.0% and 24.59% bacterial, archaeal and viral genera shared between the COVID-19 and non-COVID samples, respectively, however, the COVID-19 related samples had sole association with 16 viral genera other than SARS-CoV-2. Strain-level virome profiling revealed 660 and 729 strains in COVID-19 and non-COVID sequence data, respectively and of them 34.50% strains shared between the conditions. Functional annotation of metagenomics sequences of thevCOVID-19 and non-COVID groups identified the association of several biochemical pathways related to basic metabolism (amino acid and energy), ABC transporters, membrane transport, replication and repair, clustering-based subsystems, virulence, disease and defense, adhesion, regulation of virulence, programmed cell death, and primary immunodeficiency. We also detected 30 functional gene groups/classes associated with resistance to antibiotics and toxic compounds (RATC) in both COVID-19 and non-COVID microbiomes. Furthermore, a predominant higher abundance of cobalt-zinc-cadmium resistance (CZCR) and multidrug resistance to efflux pumps (MREP) genes were detected in COVID-19 metagenome. The profiles of microbiome diversity and associated microbial genomic features found in both COVID-19 and non-COVID (COPD and URTI) samples might be helpful for developing the microbiome-based diagnostics and therapeutics for COVID-19 and non-COVID respiratory diseases. However, future studies might be carried out to explore the microbiome dynamics and the cross-talk between host and microbiomes employing larger volume of samples from different ethnic groups and geoclimatic conditions.
Stem bending generates electrical response in poplar
Authors: Tinturier Erwan , Badel Éric , Leblanc-Fournier Nathalie , Julien Jean-Louis
Published: October 2020

Under natural conditions, plants experience external mechanical stresses such as wind and touch that impact their growth. A remarkable feature of this mechanically induced growth response is that it may occur at distance from the stimulation site, suggesting the existence of a signal propagating through the plant. In this study, we investigated the electrical response of poplar trees to a transient controlled bending stimulation of the stem that mimics the mechanical effect of wind. Stem bending was found to cause an electrical response that we called ‘gradual’ potential, similar in shape to an action potential. However, this signal distinguished from the well-known plant action potential by its propagation up to 20 cm along the stem and its strong dumping in velocity and amplitude. Two hypotheses regarding the mode of propagation of the ‘gradual’ potential are discussed.

One sentence summary

Poplar stem bending induces an electrical response with high speed and strong decrement.
APOE4 Lowers Energy Expenditure and Impairs Glucose Oxidation by Increasing Flux through Aerobic Glycolysis
Authors: Farmer Brandon C. , Williams Holden C. , Devanney Nicholas , Piron Margaret A. , Nation Grant K. , Carter David J. , Walsh Adeline E. , Khanal Rebika , Young Lyndsay E. A. , Kluemper Jude C. , Hernandez Gabriela , Allenger Elizabeth J. , Mooney Rachel , Brandon J. Anthony , Gupta Vedant A. , Kern Philip A. , Gentry Matthew S. , Morganti Josh M. , Sun Ramon C. , Johnson Lance A.
Published: October 2020

Cerebral glucose hypometabolism is consistently observed in individuals with Alzheimer’s disease (AD), as well as in young cognitively normal carriers of the E4 allele of Apolipoprotein E (APOE), the strongest genetic predictor of late-onset AD. While this clinical feature has been described for over two decades, the mechanism underlying these changes in cerebral glucose metabolism remains a critical knowledge gap in the field. Here, we undertook a multi-omic approach by combining single-cell RNA sequencing (scRNAseq) and stable isotope resolved metabolomics (SIRM) to define a metabolic rewiring across astrocytes, brain tissue, mice, and human subjects expressing APOE4. Single-cell analysis of brain tissue from mice expressing human APOE revealed E4-associated decreases in genes related to oxidative phosphorylation, particularly in astrocytes. This shift was confirmed on a metabolic level with isotopic tracing of13C-glucose in E4 mice and astrocytes, which showed decreased pyruvate entry into the TCA cycle and increases in lactate synthesis. Metabolic phenotyping of E4 astrocytes showed elevated glycolytic activity, decreased oxygen consumption, blunted oxidative flexibility, and a lower rate of glucose oxidation in the presence of lactate. Together, these cellular findings suggested an E4 associated increase in aerobic glycolysis (i.e. the Warburg effect). To test whether this phenomenon translated to APOE4 humans, we analyzed the plasma metabolome of young and middle-aged human participants with and without the E4 allele, and used indirect calorimetry to measure whole body oxygen consumption and energy expenditure. In line with data from E4-expressing mice, young female E4 carriers showed a striking decrease in energy expenditure compared to non-carriers. This decrease in energy expenditure was primarily driven by a lower rate of oxygen consumption, and was exaggerated following a dietary glucose challenge. Further, the stunted oxygen consumption was accompanied by markedly increased lactate in the plasma of E4 carriers, and a pathway analysis of the plasma metabolome suggested an increase in aerobic glycolysis. Together, these results suggest astrocyte, brain and system-level metabolic reprogramming in the presence of APOE4, a ‘Warburg like’ endophenotype that is observable in young humans decades prior to clinically manifest AD.
Investigation of biochemical changes in barley inoculated withTrichoderma harzianumT-22 under salt stress
Authors: Gupta Sneha , Smith Penelope M. C. , Boughton Berin A. , Rupasinghe Thusitha W. T. , Natera Siria H.A. , Roessner Ute
Published: October 2020

Increases in soil salinity impacts growth and yield of agricultural plants by inhibiting plant functions. Soil salinization is increasing because of the pressure of a growing population on food supply. Genetically modified crops and plant breeding techniques are being used to produce plants tolerant to salt stress. However, interactions of fungal endophytes with crop plants can also improve tolerance and is a less expensive approach. Here, the role ofTrichoderma harzianumT-22 in alleviating NaCl-induced stress in two barley genotypes (cv. Vlamingh and cv. Gairdner) has been investigated. Metabolomics using GC-MS for polar metabolites and LC-MS for lipids was employed to provide insights into the biochemical changes in barley roots inoculated with fungus during the early stages of interaction.T. harzianumincreased the root length of both genotypes under controlled and saline conditions. The fungus reduced the relative concentration of sugars in both genotypes and caused no change in organic acids under saline conditions. Amino acids decreased only in cv. Gairdner in fungus-inoculated roots under saline conditions. Lipid analyses suggest that salt stress causes large changes in the lipid profile of roots but that inoculation with fungus greatly reduces the extent of these changes. By studying a tolerant and a sensitive genotype and their responses to salt and inoculation we have been able to develop hypotheses about what lipid species and metabolites may be involved in the tolerant genotype for its tolerance to salt and how fungal inoculation changes the response of the sensitive genotype to improve its tolerance.
Enrichment of genomic variation in pathways linked to autism
Authors: Esteban Francisco J. , Tonellato Peter J. , Wall Dennis P.
Published: October 2020

The genetic heterogeneity of autism has stymied the search for causes and cures. Even whole-genomic studies on large numbers of families have yielded results of relatively little impact. In the present work, we analyze two genomic databases using a novel strategy that takes prior knowledge of genetic relationships into account and that was designed to boost signal important to our understanding of the molecular basis of autism. Our strategy was designed to identify significant genomic variation withina prioridefined biological concepts and improves signal detection while lessening the severity of multiple test correction seen in standard analysis of genome-wide association data. Upon application of our approach using 3,244 biological concepts, we detected genomic variation in 68 biological concepts with significant association to autism in comparison to family-based controls. These concepts clustered naturally into a total of 19 classes, principally including cell adhesion, cancer, and immune response. The top-ranking concepts contained high percentages of genes already suspected to play roles in autism or in a related neurological disorder. In addition, many of the sets associated with autism at the DNA level also proved to be predictive of changes in gene expression within a separate population of autistic cases, suggesting that the signature of genomic variation may also be detectable in blood-based transcriptional profiles. This robust cross-validation with gene expression data from individuals with autism coupled with the enrichment within autism-related neurological disorders supported the possibility that the mutations play important roles in the onset of autism and should be given priority for further study. In sum, our work provides new leads into the genetic underpinnings of autism and highlights the importance of reanalysis of genomic studies of complex disease using prior knowledge of genetic organization.

Author Summary

The genetic heterogeneity of autism has stymied the search for causes and cures. Even whole-genomic studies on large numbers of families have yielded results of relatively little impact. In the present work, we reanalyze two of the most influential whole-genomic studies using a novel strategy that takes prior knowledge of genetic relationships into account in an effort to boost signal important to our understanding of the molecular structure of autism. Our approach demonstrates that these genome wide association studies contain more information relevant to autism than previously realized. We detected 68 highly significant collections of mutations that map to genes with measurable and significant changes in gene expression in autistic individuals, and that have been implicated in other neurological disorders believed to be closely related, and genetically linked, to autism. Our work provides leads into the genetic underpinnings of autism and highlights the importance of reanalysis of genomic studies of disease using prior knowledge of genetic organization.
Cohesin components Stag1 and Stag2 differentially influence haematopoietic mesoderm development in zebrafish embryos
Authors: Ketharnathan Sarada , Labudina Anastasia , Horsfield Julia A.
Published: October 2020

Cohesin is a multiprotein complex made up of core subunits Smc1, Smc3 and Rad21, and either Stag1 or Stag2. Normal haematopoietic development relies on crucial functions of cohesin in cell division and regulation of gene expression via three-dimensional chromatin organisation. Cohesin subunit STAG2 is frequently mutated in myeloid malignancies, but the individual contributions of Stag variants to haematopoiesis or malignancy are not fully understood. Zebrafish have four Stag paralogues (Stag1a, Stag1b, Stag2a and Stag2b), allowing detailed genetic dissection of the contribution of Stag1-cohesin and Stag2-cohesin to development. Here we characterize for the first time the expression patterns and functions of zebrafishstaggenes during embryogenesis. Using loss-of-function CRISPR-Cas9 zebrafish mutants, we show thatstag1aandstag2bcontribute to primitive embryonic haematopoiesis. Bothstag1aandstag2bmutants present with erythropenia by 24 hours post-fertilisation. Homozygous loss of either paralog alters the number of haematopoietic/vascular progenitors in the lateral plate mesoderm. The lateral plate mesoderm zone ofscl-positive cells is expanded instag1amutants with concomitant loss of kidney progenitors, and the number ofspi1-positive cells are increased, consistent with skewing toward primitive myelopoiesis. In contrast,stag2bmutants have reduced haematopoietic/vascular mesoderm and downregulation of primitive erythropoiesis. Our results suggest that Stag1 and Stag2 proteins cooperate to balance the production of primitive haematopoietic/vascular progenitors from mesoderm.
Phospholipid flippases and Sfk1 are essential for the retention of ergosterol in the plasma membrane
Authors: Kishimoto Takuma , Mioka Tetsuo , Itoh Eriko , Williams David E. , Andersen Raymond J. , Tanaka Kazuma
Published: October 2020

Sterols are important lipid components of the plasma membrane (PM) in eukaryotic cells, but it is unknown how the PM retains sterols at a high concentration. Phospholipids are asymmetrically distributed in the PM, and phospholipid flippases play an important role in generating this phospholipid asymmetry. Here, we provide evidence that phospholipid flippases are essential for retaining ergosterol in the PM of yeast. A mutant in three flippases, Dnf1-Lem3, Dnf2-Lem3, and Dnf3-Crf1, and a membrane protein, Sfk1, showed a severe growth defect. We recently identified Sfk1 as a PM protein involved in phospholipid asymmetry. The PM of this mutant showed high permeability and low density, and many nutrient transporters failed to localize to the PM. Staining with the sterol probe filipin and the expression of a sterol biosensor revealed that ergosterol was not retained in the PM. Instead, ergosterol accumulated in an esterified form in lipid droplets. We propose that ergosterol is retained in the PM by the asymmetrical distribution of phospholipids and the action of Sfk1. Once phospholipid asymmetry is severely disrupted, sterols might be exposed on the cytoplasmic leaflet of the PM and actively transported to the endoplasmic reticulum by sterol transfer proteins.
Large, stable spikes exhibit differential broadening in excitatory and inhibitory neocortical boutons
Authors: Ritzau-Jost Andreas , Tsintsadze Timur , Krueger Martin , Ader Jonas , Bechmann Ingo , Eilers Jens , Barbour Boris , Smith Stephen M. , Hallermann Stefan
Published: October 2020

Presynaptic action potential spikes control neurotransmitter release and thus interneuronal communication. However, the properties and the dynamics of presynaptic spikes in the neocortex remain enigmatic because boutons in the neocortex are small and direct patch-clamp recordings have not been performed. Here we report direct recordings from boutons of neocortical pyramidal neurons and interneurons. Our data reveal rapid and large presynaptic action potentials in layer 5 neurons and fast-spiking interneurons reliably propagating into axon collaterals. For in-depth analyses we validate boutons of mature cultured neurons as models for excitatory neocortical boutons, demonstrating that the presynaptic spike amplitude was unaffected by potassium channels, homeostatic long-term plasticity, and high-frequency firing. In contrast to the stable amplitude, presynaptic spikes profoundly broadened for example during high-frequency firing in layer 5 pyramidal neurons but not in fast-spiking interneurons. Thus, our data demonstrate large presynaptic spikes and fundamental differences between excitatory and inhibitory boutons in the neocortex.
Dendritic spines are lost in clusters in Alzheimer’s disease
Authors: Mijalkov Mite , Volpe Giovanni , Fernaud-Espinosa Isabel , DeFelipe Javier , Pereira Joana B. , Merino-Serrais Paula
Published: October 2020

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by a deterioration of neuronal connectivity. The pathological accumulation of tau in neurons is one of the hallmarks of AD and has been connected to the loss of dendritic spines of pyramidal cells, which are the major targets of cortical excitatory synapses and key elements in memory storage. However, the detailed mechanisms underlying the loss of dendritic spines in individuals with AD are still unclear. Here, we used graph-theory approaches to compare the distribution of dendritic spines from neurons with and without tau pathology of AD individuals. We found that the presence of tau pathology determines the loss of dendritic spines in clusters, ruling out alternative models where spine loss occurs at random locations. Since memory storage has been associated with synaptic clusters, the present results provide a new insight into the mechanisms by which tau drives synaptic damage in AD, paving the way to memory deficits through alterations of spine organization.
eEF1A2 controls local translation and actin dynamics in structural synaptic plasticity
Authors: Mendoza Mònica B. , Gutierrez Sara , Ortiz Raúl , Moreno David F. , Dermit Maria , Dodel Martin , Rebollo Elena , Bosch Miquel , Mardakheh Faraz K. , Gallego Carme
Published: October 2020

Synaptic plasticity involves structural modifications in dendritic spines. Increasing evidence suggests that structural plasticity is modulated by local protein synthesis and actin remodeling in a synapsis-specific manner. However, the precise molecular mechanisms connecting synaptic stimulation to these processes in dendritic spines are still unclear. In the present study, we demonstrate that the configuration of phosphorylation sites in eEF1A2, an essential translation elongation factor in neurons, is a key modulator of structural plasticity in dendritic spines. A mutant that cannot be phosphorylated stimulates translation but reduces actin dynamics and spine density. By contrast, the phosphomimetic variant loosens its association with F-actin and becomes inactive as a translation elongation factor. Metabotropic glutamate receptor signaling triggers a transient dissociation of eEF1A2 from its GEF protein in dendritic spines, in a phospho-dependent manner. We propose that eEF1A2 establishes a crosstalk mechanism that coordinates local translation and actin dynamics during spine remodeling.
Focusing a round coherent beam by spatial filtering the horizontal source
Authors: Dufresne Eric M. , Narayanan Suresh , Reininger Ruben , Sandy Alec R. , Lurio Larry
Published: October 2020

This paper illustrates the use of spatial filtering with a horizontal slit near the source to enlarge the horizontal coherence in an experimental station and produce a diffraction-limited round focus at an insertion device beamline for X-ray photon correlation spectroscopy experiments. Simple expressions are provided to guide the optical layout, and wave propagation simulations confirm their applicability. The two-dimensional focusing performance of Be compound refractive lenses to produce a round diffraction-limited focus at 11 keV capable of generating a high-contrast speckle pattern of an aerogel sample is demonstrated. The coherent scattering patterns have comparable speckle sizes in both horizontal and vertical directions. The focal spot sizes are consistent with hybrid ray-tracing calculations. Producing a two-dimensional focus on the sample can be helpful to resolve speckle patterns with modern pixel array detectors with high visibility. This scheme has now been in use since 2019 for the 8-ID beamline at the Advanced Photon Source, sharing the undulator beam with two separate beamlines, 8-ID-E and 8-ID-I at 7.35 keV, with increased partially coherent flux, reduced horizontal spot sizes on samples, and good speckle contrast.
Self-regulation failure as a moderator of the pops–work outcomes relationships
Authors: Palmer Joshua C. , Hochwarter Wayne A. , Ma Shuang (Sara) , Ferris Gerald R. , Kiewitz Christian
Published: October 2020

Purpose

Drawing upon cognitive control theory, we examine the effects of self-regulation failure (SRF) on the relationships between perceptions of organizational politics (POPs) and tension, exhaustion, satisfaction, work effort, perceived resource availability and performance/contribution.

Design/methodology/approach

We test hypotheses across three unique studies (Study 1: 310 employees from various occupations; Study 2: 124 administrative/support employees; Study 3: 271 Chinese hotel managers) using hierarchical moderated regression analyses.

Findings

Across studies, results suggest that POPs had a minimal impact on work attitudes, behaviors and health-related outcomes when SRF was low. However, employees experiencing high SRF reported adverse consequences in high POPS settings.

Research limitations/implications

These studies relied on self-report data. However, we implemented design features to mitigate potential concerns and analytic techniques to determine method effects. This paper contributed to the POPs literature by explaining how SRF and POPs interact to impact meaningful work outcomes.

Practical implications

Leaders should receive training to help them identify and address indicators of SRF. Leaders can also implement intervention programs to help calm employees who experience SRF.

Social implications

Leaders should receive training to help them identify and address indicators of SRF. Leaders can also implement programs to help assist employees who demonstrate adverse effects from SRF.

Originality/value

This paper integrates the research on SRF and politics to examine the collective impact these variables have on workers. Our three-study package also addresses the call for more studies to examine how politics operate across cultures.
An experimental study on characterizing damage and fracture of a rock-like material based on three-dimensional magnetic field imaging
Authors: Yue Wenping , Yang Mingyang
Published: October 2020

Purpose

The results showed that the use of a magnetic marker could relatively accurately reflect the fracture pattern inside the rock-like material (RLM).

Design/methodology/approach

This study investigated the internal structure and fracture pattern of a fractured RLM. Magnetized iron oxide powder, which was used as a magnetic marker, was mixed with water and glue to form a magnetic slurry, which was subsequently injected into a fractured RLM. After the magnetic slurry completely filled the cracks inside the RLM and became cemented, the distribution and magnitude of the magnetic field inside the RLM were determined using a three-dimensional (3D) magnetic field imaging system.

Findings

A model for determining the magnetic field strength was developed using MATLAB.

Originality/value

This model of 3D magnetic will further be used as a finite element tool to simulate and image cracks inside the rock.
Forecasting cocoa production of six major producers through ARIMA and grey models
Authors: Quartey-Papafio Tawiah Kwatekwei , Javed Saad Ahmed , Liu Sifeng
Published: October 2020

Purpose

In the current study, two grey prediction models, Even GM (1, 1) and Non-homogeneous discrete grey model (NDGM), and ARIMA models are deployed to forecast cocoa bean production of the six major cocoa-producing countries. Furthermore, relying on Relative Growth Rate (RGR) and Doubling Time (Dt), production growth is analyzed.

Design/methodology/approach

The secondary data were extracted from the United Nations Food and Agricultural Organization (FAO) database. Grey forecasting models are applied using the data covering 2008 to 2017 as their performance on the small sample size is well-recognized. The models' performance was estimated through MAPE, MAE and RMSE.

Findings

Results show the two grey models fell below 10% of MAPE confirming their high accuracy and forecasting performance against that of the ARIMA. Therefore, the suitability of grey models for the cocoa production forecast is established. Findings also revealed that cocoa production in Côte d'Ivoire, Cameroon, Ghana and Brazil is likely to experience a rise with a growth rate of 2.52, 2.49, 2.45 and 2.72% by 2030, respectively. However, Nigeria and Indonesia are likely to experience a decrease with a growth rate of 2.25 and 2.21%, respectively.

Practical implications

For a sustainable cocoa industry, stakeholders should investigate the decline in production despite the implementation of advanced agricultural mechanization in cocoa farming, which goes further to put food security at risk.

Originality/value

The study presents a pioneering attempt of using grey forecasting models to predict cocoa production.
Sustainable utilization of recycled aggregates: robust construction and demolition waste reduction strategies
Authors: De Luca Angelo , Chen Linda , Gharehbaghi Koorosh
Published: October 2020

Purpose

Due to the high demand of concrete, significant volume of natural resources is required, including virgin aggregates. Many studies have shown that the production of concrete has one of the highest CO2 levels. Although efforts are in place to recycle, enormous effects on landfill and the wider environment remain. Research has suggested the importance of reusing construction and demolition waste such as aggregate for use in recycled concrete. However, robust construction and demolition waste reduction strategies are required. There have been numerous researches on the use of recycled concrete and its management in the construction industry. This paper further consolidates this position.

Design/methodology/approach

This paper exhibits the barriers and benefits of using recycled aggregates for construction industry. This is achieved via reviewing the current construction and demolition waste reduction strategies used mainly in three countries: the UK, Australia and Japan. These countries were selected since they seemingly have similar construction industry and environment. Subsequently, evolving barriers and benefits of using recycled aggregates for construction industry are also reviewed and discussed. And to support such focus, robust construction and demolition waste reduction strategies will be advocated.

Findings

The findings are summarized as follows. The recycling construction and demolition waste could have a positive net benefit compared to the procurement and production of virgin aggregate materials with the same properties. This is not only financially beneficial but also environmentally viable, as fewer resources would be required to produce the same aggregate material. There are effective ways to achieve a high recycle rate target, as demonstrated by Japan. The implementation of a similar recycling process could be implemented globally to achieve a more effective recycle rate through the help of governments at all levels. By creating awareness about the financial and environmental benefits of using recycled aggregate products, large recycling companies can be also enticed to follow suit.

Practical implications

The findings from this paper can ultimately support the construction industry to further consolidate and advocate the use of recycled aggregates.

Originality/value

To achieve the research aim, this paper reviews some of the main sustainability factors of recycled aggregates (including coarse and fine aggregates) and provides comparison to virgin aggregates.
Links between well-being and communication with friends and family in one’s country of origin amongst migrants in Australia
Authors: du Plooy Daniel Rupert , Lyons Anthony , Kashima Emiko S.
Published: October 2020

Purpose

This paper aims to examine the relationship between migrants’ psychological well-being and the extent to which they keep in touch with people in their country of origin.

Design/methodology/approach

An online survey completed by 1,328 Australian migrants from 4 cultural groups (Anglo, Southern Asian, Confucian Asian and other European) assessed 2 facets of well-being, namely, flourishing and psychological distress and the use of 3 modes of online communication, namely, social media, messaging services and phone/video services.

Findings

Overall, keeping in touch with family and friends in their country of origin was associated with more flourishing and less distress amongst migrants. Nonetheless, the preferred modes of communication and how those usages relate with well-being varied considerably across cultural groups. In the Anglo group, communicating through messaging and phone/video services was associated with lower distress and communicating in all modes was associated with higher flourishing. Furthermore, the latter link was accounted for by having a meaningful conversation.

Originality/value

These findings suggest that the psychological well-being of migrant populations may be supported by an understanding of the distinct roles played by specific communication modes that are used to stay in touch with family and friends back home.
Pandemic and teacher retention: empirical evidence from expat teachers in Southeast Asia during COVID-19
Authors: Hoang Anh-Duc
Published: October 2020

Purpose

This research aims to explore the influence of expat teachers' attitude about local policies, and their subjective norms of social engagement during COVID-19 over their intention to leave the current country, due to COVID-19.

Design/methodology/approach

This study uses analysis of variance (ANOVA) and structural equation model (SEM) to examine the perception of crisis and the intention to leave among 307 expat teachers in Southeast Asia during COVID-19 and highlights the importance of policy responses and social engagement toward the minimum teacher turnover rate.

Findings

The study reveals that, the higher perceived policy responses and community engagement the teachers acknowledge, the lower chance they will move to another country. Also, this paper presents the differences in expat teachers' perceptions and intentions among demographic factors such as teaching qualification, their current country of teaching, experience at the current country, income before, during and expected income after COVID-19.

Originality/value

The paper justifies a conceptual framework which provides a hypothetical explanation about the influence of perceived policy responses and community engagement over expat teachers' intention to leave.