bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparativein vitrotranscriptomic analyses of COVID-19 candidate therapy hydroxychloroquine suggest limited immunomodulatory evidence of SARS-CoV-2 host response genes
Authors: Corley Michael J. , Sugai Christopher , Schotsaert Michael , Schwartz Robert E. , Ndhlovu Lishomwa C.
Published: April 2020

Hydroxychloroquine (HCQ) has emerged as a potential and controversial antiviral candidate therapy for COVID-19. While many clinical trials are underway to test the efficacy of HCQ as a treatment for COVID-19, underlying mechanisms of HCQ in the setting of COVID-19 remain unclear. Hence, we examined differential gene expression signatures of HCQ exposure,in vitroSARS-CoV-2 infection, and host signatures of COVID-19 in blood, bronchoalveolar lavage, and postmortem lung to evaluate whether HCQ transcriptome signatures associate with restoration of SARS-CoV-2-related host transcriptional responses. Here, we show that 24 hours ofin vitrotreatment of peripheral blood mononuclear cells(PBMC) with HCQ significantly impacted transcription of 16 genes involved in immune regulation and lipid metabolism. Using transcriptome data fromin vitroSARS-CoV-2 infected NHBE and A549 cells and PBMC derived from confirmed COVID-19 infected patients, we determined that only 0.24% of the COVID-19 PBMC differentially expressed gene set and 0.39% of thein vitroSARS-CoV-2 cells differentially expressed gene set overlapped with HCQ-related differentially expressed genes. Moreover, we observed that HCQ treatment significantly impacted transcription of 159 genes in human primary monocyte-derived macrophages involved in cholesterol biosynthetic process and chemokine activity. Notably, when we compared the macrophage HCQ-related gene lists with genes transcriptionally altered during SARS-CoV-2 infection and in bronchoalveolar lavage of COVID-19+ patients, theCXCL6gene was impacted in all three transcriptional signatures revealing evidence in favor of chemokine modulation. HCQ-related transcriptional changes minimally overlapped with host genes altered in postmortem lung biopsies from COVID-19 participants. These results may provide insight into the immunomodulation mechanisms of HCQ treatment in the setting of COVID-19 and suggest HCQ is not a panacea to SARS-CoV-2 infection.
Small molecule cognitive enhancer reverses age-related memory decline in mice
Authors: Krukowski Karen , Nolan Amber , Frias Elma S. , Boone Morgane , Ureta Gonzalo , Grue Katherine , Paladini Maria-Serena , Elizarraras Edward , Delgado Luz , Bernales Sebastian , Walter Peter , Rosi Susanna
Published: April 2020

With increased life expectancy age-associated cognitive decline becomes a growing concern, even in the absence of recognizable neurodegenerative disease. The integrated stress response (ISR) is activated during aging and contributes to age-related brain phenotypes. We demonstrate that treatment with the drug-like small-molecule ISR inhibitor ISRIB reverses ISR activation in the brain, as indicated by decreased levels of activating transcription factor 4 (ATF4) and phosphorylated eukaryotic translation initiation factor eIF2. Furthermore, ISRIB treatment reverses spatial memory deficits and ameliorates working memory in old mice. At the cellular level in the hippocampus, ISR inhibition i) rescues intrinsic neuronal electrophysiological properties, ii) restores spine density and iii) reduces immune profiles, specifically interferon and T cell-mediated responses. Thus, pharmacological interference with the ISR emerges as a promising intervention strategy for combating age-related cognitive decline in otherwise healthy individuals.

ONE SENTENCE SUMMARY

Inhibition of the integrated stress response restores neuronal and immune dysfunction and alleviates memory deficits in aged mice.
Mapping the genetic and environmental aetiology of autistic traits in Sweden and the United Kingdom
Authors: Reed Zoe E. , Larsson Henrik , Haworth Claire M.A. , Rai Dheeraj , Lundström Sebastian , Ronald Angelica , Reichenberg Abraham , Lichtenstein Paul , Davis Oliver S.P.
Published: April 2020

Background

Autistic traits are influenced by both genetic and environmental factors, and are known to vary geographically in prevalence. But to what extent does their aetiology also vary from place to place?

Methods

We applied a novel spatial approach to data on autistic traits from two large twin studies, the Child and Adolescent Twin Study in Sweden (CATSS; N=16,677, including 8,307 twin pairs) and the Twins Early Development Study in the UK (TEDS; N=11,594, including 5,796 twin pairs), to explore how the influence of nature and nurture on autistic traits varies from place to place.

Results

We present maps of gene- and environment-by geography interactions in Sweden and the United Kingdom (UK), showing geographical variation in both genetic and environmental influences across the two countries. In Sweden genetic influences appear higher in the far south and in a band running across the centre of the country. Environmental influences appear greatest in the south and north, with reduced environmental influence across the central band. In the UK genetic influences appear greater in the south, particularly in more central southern areas and the southeast, the Midlands and the north of England. Environmental influences appear greatest in the south and east of the UK, with less influence in the north and the west.

Conclusions

We hope this systematic approach to identifying aetiological interactions will inspire research to examine a wider range of previously unknown environmental influences on the aetiology of autistic traits. By doing so, we will gain greater understanding of how these environments draw out or mask genetic predisposition and interact with other environmental influences in the development of autistic traits.
Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å
Authors: Flores Jonathan A. , Haddad Bassam G. , Dolan Kimberly A. , Myers Janette B. , Yoshioka Craig C. , Copperman Jeremy , Zuckerman Daniel M. , Reichow Steve L.
Published: April 2020

Gap junctions establish direct pathways for connected cells and tissues to transfer metabolic and electrical messages1. The local lipid environment is known to affect the structure, stability and intercellular channel activity of gap junctions2-5; however, the molecular basis for these effects remains unknown. To gain insight toward how gap junctions interact with their local membrane environment, we used lipid nanodisc technology to incorporate native connexin-46/50 (Cx46/50) intercellular channels into a dual lipid membrane system, closely mimicking a native cell-to-cell junction. Structural characterization of Cx46/50 lipid-embedded channels by single particle CryoEM revealed a lipid-induced stabilization to the channel, resulting in a 3D reconstruction at 1.9 Å resolution. Together with all-atom molecular dynamics (MD) simulations and 3D heterogeneity analysis of the ensemble CryoEM data, it is shown that Cx46/50 in turn imparts long-range stabilization to the dynamic local lipid environment that is specific to the extracellular lipid leaflet of the two opposed membranes. In addition, nearly 400 water molecules are resolved in the CryoEM map, localized throughout the intercellular permeation pathway and contributing to the channel architecture. These results illustrate how the aqueous-lipid environment is integrated with the architectural stability, structure and function of gap junction communication channels, and demonstrates the ability of CryoEM to effectively characterize dynamical protein-lipid interactions.
A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity
Authors: Driscoll Timothy P. , Verhoeve Victoria I. , Gillespie Joseph J. , Johnston J. Spencer , Guillotte Mark L. , Rennoll-Bankert Kristen E. , Rahman M. Sayeedur , Hagen Darren , Elsik Christine G. , Macaluso Kevin R. , Azad Abdu F.
Published: April 2020

Background

Fleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e. the etiological agents of bubonic plague, endemic and murine typhus). The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea,Ctenocephalides felis, an insect with substantial human health and veterinary importance across the globe.

Results

By combining Illumina and PacBio sequencing with Hi-C scaffolding techniques, we generated a chromosome-level genome assembly forC.felis. Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by ∼38% of protein-coding genes with two or more copies and over 4,000 tRNA genes. A broad range of genome size determinations (433-551 Mb) for individual fleas sampled across different populations supports the widespread presence of fluctuating copy number variation (CNV) inC. felis. Similarly broad genome sizes were also calculated for individuals ofXenopsylla cheopis(Oriental rat flea), indicating that this remarkable “genome-in-flux” phenomenon could be a siphonapteran-wide trait. Finally, from theC. felissequence reads we also generated closed genomes for two novel strains ofWolbachia, one parasitic and one symbiotic, found to co-infect individual fleas.

Conclusion

Rampant CNV inC.felishas dire implications for gene-targeting pest control measures and stands to complicate standard normalization procedures utilized in comparative transcriptomics analysis. Coupled with co-infection by novelWolbachiaendosymbionts – potential tools for blocking pathogen transmission – these oddities highlight a unique and underappreciated disease vector.
Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees
Authors: Romiguier Jonathan , Weyna Arthur
Published: April 2020

With one of the highest number of parasite, eusocial and pollinator species among all insect orders, Hymenoptera features a great diversity of specific lifestyles. At the population genetic level, such life-history strategies are expected to decrease effective population size and efficiency of purifying selection. In this study, we tested this hypothesis by estimating the relative rate of non-synonymous substitution in 169 species to investigate the variation in natural selection efficiency throughout the hymenopteran tree of life. We found no effect of parasitism or body size, but show that relaxed selection is associated with eusociality, suggesting that the division of reproductive labour decreases effective population size in ants, bees and wasps. Unexpectedly, the effect of eusociality is marginal compared to a striking and widespread relaxation of selection in both social and non social bees, which indicates that these keystone pollinator species generally feature low effective population sizes. This widespread pattern suggests specific constraints in pollinating bees potentially linked to limited resource and high parental investment. The particularly high load of deleterious mutations we report in the genome of these crucial ecosystem engineer species also raises new concerns about their ongoing population decline.
Microbial interactions in the mosquito gut determineSerratiacolonization and blood feeding propensity
Authors: Kozlova Elena V. , Hegde Shivanand , Roundy Christopher M. , Golovko George , Saldaña Miguel A. , Hart Charles E. , Anderson Enyia R , Hornett Emily A , Khanipov Kamil , Popov Vsevolod L. , Pimenova Maria , Zhou Yiyang , Fovanov Yuriy , Weaver Scott C. , Routh Andrew L. , Heinz Eva , Hughes Grant L.
Published: April 2020

How microbe-microbe interactions dictate microbial complexity in the mosquito gut is unclear. Previously we found thatSerratia, a gut symbiont that alters vector competence and is being considered for vector control, poorly colonizedAedes aegyptiyet was abundant inCulex quinquefasciatusreared under identical conditions. To investigate the incompatibility betweenSerratiaandAe. aegypti, we characterized two distinct strains ofSerratia marcescensfromCx. quinquefasciatusand examined their ability to infectAe. aegypti. BothSerratiastrains poorly infectedAe. aegypti, but when microbiome homeostasis was disrupted, the prevalence and titers ofSerratiawere similar to the infection in its native host. Examination of multiple genetically diverseAe. aegyptilines found microbial interference toS. marcescenswas commonplace, however one line ofAe. aegyptiwas susceptible to infection. Microbiome analysis of resistant and susceptible lines indicated an inverse correlation betweenEnterobacteriaceaebacteria andSerratia, and experimental co-infections in a gnotobiotic system recapitulated the interference phenotype. Furthermore, we observed an effect on host behaviour;Serratiaexposure toAe. aegyptidisrupted their feeding behaviour, and this phenotype was also reliant on interactions with their native microbiota. Our work highlights the complexity of host-microbe interactions and provides evidence that microbial interactions influence mosquito behaviour.
Molecular basis for the recognition of steroidogenic acute regulatory protein by the 14-3-3 protein family
Authors: Tugaeva Kristina V. , Titterington James , Sotnikov Dmitriy V. , Maksimov Eugene G. , Antson Alfred A. , Sluchanko Nikolai N.
Published: April 2020

Steroidogenesis in adrenals and gonads starts from cholesterol transport to mitochondria by the steroidogenic acute regulatory protein STARD1, containing a mitochondrial import sequence followed by a cholesterol-binding START domain. Although mutations in this protein have been linked to lipoid congenital adrenal hyperplasia, the mechanism of steroidogenesis regulation by the STARD1 remains debatable, hypothetically involving a molten-globule structural transition and interaction with 14-3-3 proteins. We show that, while the isolated START domain does not interact with 14-3-3, interaction is enabled by STARD1 phosphorylation at Ser57, close to the mitochondrial peptide cleavage site. Biochemical analysis of the STARD1 affinity towards 14-3-3 and crystal structures of 14-3-3 complexes with Ser57 and Ser195 phosphopeptides, suggest distinct roles of site-specific phosphorylations in recruiting 14-3-3, to modulate STARD1 activity, processing and import to mitochondria. Phosphorylation at Ser195 creates a unique conditional site, that could only bind to 14-3-3 upon partial unfolding of the START domain.
Integrin-linked kinase is a key signal factor involved in Nogo-66-induced inhibition of neurite outgrowth
Authors: Yu Ya-ping , Wang Qiang-ping , Shen Jian-Ying , Xiong Nan-xiang , Yu Hua , Fu Peng , Wang Lei , Yuan Ye , Zhao Hong-yang , Zhang Fang-cheng , Pool Hendrik
Published: April 2020

Nogo-66, the extracellular domain of Nogo-A, has been identified as the most important myelin-associated neuronal growth inhibitor. Evidence suggested that Nogo-66 exert its neurite inhibition effect via a Nogo-66/Protein kinase B (PKB)/Glycogen synthase kinase-3β (GSK-3β)/tau signaling pathway. Integrin-linked kinase (ILK) is a serine/threonine kinase mediating axon upstream growth of PKB and GSK-3β. However, the contribution of ILK to the Nogo-66-induced inhibition of neurite, is not clear. In this study, we set out to reveal the role of ILK on Nogo-66 signalingin vitroandin vivo. To deteremine this directly, Recombinant adenoviruses were constructed to upregulate or downregulate the expresioon of ILK in Neuro 2a (N2a)and analysis the change of downstream molecule and neurite length. The results showed that Nogo-66 inhibited the phosphorylation of ILK, while ILK regulated the phosphorylation of PKB and GSK-3β, and the expression of tau in Nogo-66-treated N2a cells. ILK overexpression through lentivirus vector transfection reduced the inhibitory effect of neurite outgrowth induced by Nogo-66 in cortical neurons. The Tau expression in the complete spinal cord transection rat model was promoted by the overexpression of ILK. Our findings indicated that ILK is a key signal factor involved in Nogo-66-induced inhibition of neurite outgrowth. The mechanism of Nogo-66 signaling pathway was further explained and a proper target for the promotion of neural regeneration was also provided by this study.
Regional transmission and reassortment of 2.3.4.4b highly pathogenic avian influenza (HPAI) viruses in Bulgarian poultry 2017/18
Authors: Venkatesh Divya , Brouwer Adam , Ellis Richard , Goujgoulova Gabriela , Seekings James , Brown Ian H. , Lewis Nicola S.
Published: April 2020

Between 2017 and 2018, several farms across Bulgaria reported outbreaks of H5 HPAI viruses. In this study we use genomic and traditional epidemiological analyses to trace the origin and subsequent spread of these outbreaks within Bulgaria. Both methods indicate two separate incursions, one restricted to the North-Eastern region of Dobrich, and another largely restricted to Central and Eastern Bulgaria including places such as Plovdiv, Sliven and Stara Zagora, as well as one virus from the Western region of Vidin. Both outbreaks likely originate from different European 2.3.4.4b virus ancestors circulating in 2017. The viruses were likely introduced by wild birds or poultry trade links in 2017 and have continued to circulate, but due to lack of contemporaneous sampling and sequences from wild bird viruses in Bulgaria, the precise route and timing of introduction cannot be determined. Analysis of whole genomes indicates complete lack of reassortment in all segments but the MP, which presents as multiple smaller clusters associated with different European 2.3.4.4b viruses. Ancestral reconstruction of host states of the HA gene of viruses involved in the outbreaks suggests that transmission is driven by domestic ducks into galliform poultry. Thus, according to present evidence we suggest that surveillance of domestic ducks as epidemiologically relevant species for subclinical infection. Monitoring spread due to movement between farms within regions and links to poultry production systems in European countries can help to predict and prevent future outbreaks.
Spatiotemporal development of cuticular ridges on leaf surfaces ofHevea brasiliensisalters insect attachment
Authors: Surapaneni Venkata A. , Bold Georg , Speck Thomas , Thielen Marc
Published: April 2020

Cuticular ridges on plant surfaces can control insect adhesion and wetting behaviour and might also offer stability to underlying cells during growth. The growth of the plant cuticle and its underlying cells possibly results in changes in the morphology of cuticular ridges and may also affect their function. We present spatial and temporal patterns in cuticular ridge development on the leaf surfaces of the model plant,Hevea brasiliensis. We have identified, by confocal laser scanning microscopy of polymer leaf replicas, an acropetally directed progression of ridges during the ontogeny ofHevea brasiliensisleaf surfaces. The use of Colorado potato beetles(Leptinotarsa decemlineata)as a model insect species has shown that the changing dimensions of cuticular ridges on plant leaves during ontogeny have a significant impact on insect traction forces and act as an effective indirect defence mechanism. The traction forces of walking insects are significantly lower on mature leaf surfaces compared with young leaf surfaces. The measured walking traction forces exhibit a strong negative correlation with the dimensions of the cuticular ridges.
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology
Authors: Domingo-Fernández Daniel , Baksi Shounak , Schultz Bruce , Gadiya Yojana , Karki Reagon , Raschka Tamara , Ebeling Christian , Hofmann-Apitius Martin , Kodamullil Alpha Tom
Published: April 2020

The past few weeks have witnessed a worldwide mobilization of the research community in response to the novel coronavirus (COVID-19). This global response has led to a burst of publications on the pathophysiology of the virus, yet without coordinated efforts to organize this knowledge, it can remain hidden away from individual research groups. By extracting and formalizing this knowledge in a structured and computable form, as in the form of a knowledge graph, researchers can readily reason and analyze this information on a much larger scale. Here, we present the COVID-19 Knowledge Graph, an expansive cause-and-effect network constructed from scientific literature on the new coronavirus that aims to provide a comprehensive view of its pathophysiology. To make this resource available to the research community and facilitate its exploration and analysis, we also implemented a web application and released the KG in multiple standard formats.

Availability

The COVID-19 Knowledge Graph is publicly available under CC-0 license athttps://github.com/covid19kgandhttps://bikmi.covid19-knowledgespace.de.

Contact

alpha.tom.kodamullil@scai.fraunhofer.de

Supplementary information

Supplementary data are available online.
Mating-type locus rearrangement leads to shift from homothallism to heterothallism inCitrus-associatedPhyllostictaspecies
Authors: Petters-Vandresen Desirrê Alexia Lourenço , Rossi Bruno Janoski , Groenewald Johannes Z. , Crous Pedro W. , Machado Marcos Antonio , Stukenbrock Eva H. , Glienke Chirlei
Published: April 2020

Currently, eightPhyllostictaspecies are known to be associated withCitrushosts, incorporating endophytic and pathogenic lifestyles. As sexual reproduction is a key factor involved in host-interaction, it could be related to the differences in lifestyle. To evaluate this hypothesis, we characterized the mating-type loci of sixCitrus-associatedPhyllostictaspecies from whole genome assemblies. Mating-type genes are highly variable in their sequence content, but the genomic locations and organization of the mating-type loci are conserved.Phyllosticta citriasiana, P. citribraziliensisandP. paracitricarpaare heterothallic, andP. citrichinaensiswas confirmed to be homothallic. In addition, theP. citrichinaensis MAT1-2idiomorph occurs in a separate location from the mating-type locus. Ancestral state reconstruction suggests that homothallism is the ancestral thallism state inPhyllosticta, with a shift to heterothallism inPhyllostictaspecies that are pathogenic toCitrus. Moreover, the homothallic strategies ofP. capitalensisandP. citrichinaensisresult from independent evolutionary events. As the pathogenic speciesP. citriasiana, P. citricarpaandP. paracitricarpaare heterothallic and incapable of selfing, disease management practices focused in preventing the occurrence of sexual reproduction could assist in the control of Citrus Black Spot and Citrus Tan Spot diseases. This study emphasizes the importance of studyingCitrus-Phyllostictainteractions under evolutionary and genomic perspectives, as these approaches can provide valuable information about the association betweenPhyllostictaspecies and their hosts, and also serve as guidance for the improvement of disease management practices.
Apoptotic cells induce CD103 expression and immunoregulatory function in myeloid dendritic cell precursors through integrin αv and TGF-β activation
Authors: Zhang Ailiang , Paidassi Helena , Lacy-Hulbert Adam , Savill John
Published: April 2020

In the mammalian gut CD103+ve myeloid DCs are known to suppress inflammation threatened by luminal bacteria, but stimuli driving DC precursor differentiation towards this beneficial phenotype are incompletely understood. We isolated CD11+ve DCs from mesenteric lymph nodes (MLNs) of healthy mice; CD103+ve DCs were 8-24 folds more likely than CD103-ve DCs to exhibit extensive of prior phagocytosis of apoptotic intestinal epithelial cells. However, CD103+ve and CD103-ve MLN DCs exhibited similar ex vivo capacity to ingest apoptotic cells, indicating that apoptotic cells might drive immature DC differentiation towards the CD103+ve phenotype. When cultured with apoptotic cells, myeloid DC precursors isolated from murine bone marrow and characterised as lineage-ve CD103-ve, displayed enhanced expression of CD103 and β8 integrin and acquired increased capacity to induce Tregs after 7d in vitro. However, DC precursors isolated from α v -tie2 mice lacking α v integrins in the myeloid line exhibited reduced binding of apoptotic cells and complete deficiency in the capacity of apoptotic cells and/or latent TGF-β1 to enhance CD103 expression in culture, whereas active TGF-β1 increased DC precursor CD103 expression irrespective of α v expression. Fluorescence microscopy revealed clustering of α v integrin chains and latent TGF-β1 at points of contact between DC precursors and apoptotic cells. We conclude that myeloid DC precursors can deploy α v integrin to orchestrate binding of apoptotic cells, activation of latent TGF-β1 and acquisition of the immunoregulatory CD103+ve β8+ve DC phenotype. This implies that a hitherto unrecognised consequence of apoptotic cell interaction with myeloid phagocytes is programming that prevents inflammation.
Suitability of resampled multispectral datasets for mapping flowering plants in the Kenyan savannah
Authors: Makori David M. , Abdel-Rahman Elfatih M. , Landmann Tobias , Mutanga Onisimo , Odindi John , Nguku Evelyn , Tonnang Henry E. Z , Raina Suresh
Published: April 2020

Pollination services and honeybee health in general are important in the African savannahs particularly to farmers who often rely on honeybee products as a supplementary source of income. Therefore, it is imperative to understand the floral cycle, abundance and spatial distribution of melliferous plants in the African savannah landscapes. Furthermore, placement of apiaries in the landscapes could benefit from information on spatiotemporal patterns of flowering plants, by optimising honeybees’ foraging behaviours, which could improve apiary productivity. This study sought to assess the suitability of simulated multispectral data for mapping melliferous (flowering) plants in the African savannahs. Bi-temporal AISA Eagle hyperspectral images, resampled to four sensors (i.e. WorldView-2, RapidEye, Spot-6 and Sentinel-2) spatial and spectral resolutions, and a 10-cm ultra-high spatial resolution aerial imagery coinciding with onset and peak flowering periods were used in this study. Ground reference data was collected at the time of imagery capture. The advanced machine learning random forest (RF) classifier was used to map the flowering plants at a landscape scale and a classification accuracy validated using 30% independent test samples. The results showed that 93.33%, 69.43%, 67.52% and 82.18% accuracies could be achieved using WorldView-2, RapidEye, Spot-6 and Sentinel-2 data sets respectively, at the peak flowering period. Our study provides a basis for the development of operational and cost-effective approaches for mapping flowering plants in an African semiarid agroecological landscape. Specifically, such mapping approaches are valuable in providing timely and reliable advisory tools for guiding the implementation of beekeeping systems at a landscape scale.
Ecological and anthropogenic drivers of large carnivore depredation on sheep in Europe
Authors: Gervasi Vincenzo , Linnell John D. C. , Berce Tomaž , Boitani Luigi , Cerne Rok , Cretois Benjamin , Ciucci Paolo , Duchamp Christophe , Gastineau Adrienne , Grente Oksana , Hilfiker Daniela , Huber Djuro , Iliopoulos Yorgos , Karamanlidis Alexandros A. , Marucco Francesca , Mertzanis Yorgos , Männil Peep , Norberg Harri , Pagon Nives , Pedrotti Luca , Quenette Pierre-Yves , Reljic Slaven , Salvatori Valeria , Talvi Tõnu , von Arx Manuela , Gimenez Olivier
Published: April 2020

Sharing space with large carnivores on a human-dominated continent like Europe results in multiple conflictful interactions with human interests, of which depredation on livestock is the most widespread. Wildlife management agencies maintain compensation programs for the damage caused by large carnivores, but the long-term effectiveness of such programs is often contested. Therefore, understanding the mechanisms driving large carnivore impact on human activities is necessary to identify key management actions to reduce it.

We conducted an analysis of the impact by all four European large carnivores on sheep husbandry in 10 European countries, during the period 2010-2015. We ran a hierarchical Simultaneous Autoregressive model, to assess the influence of ecological and anthropogenic factors on the spatial and temporal patterns in the reported depredation levels across the continent.

On average, about 35,000 sheep were compensated in the ten countries as killed by large carnivores annually, representing about 0.5% of the total sheep stock. Of them, 45% were recognized as killed by wolves, 24% by wolverines, 19% by lynx and 12% by bears. At the continental level, we found a positive relationship between wolf distribution and the number of compensated sheep, but not for the other three species. Impact levels were lower in the areas where large carnivore presence has been continuous compared to areas where they disappeared and recently returned. The model explained 62% of the variation in the number of compensated sheep per year in each administrative unit. Only 13% of the variation was related to the ecological components of the process.

Synthesis and Applications:Large carnivore distribution and local abundance alone are poor predictors of large carnivore impact on livestock at the continental level. A few individuals can produce high damage, when the contribution of environmental, social and economic systems predisposes for it, whereas large populations can produce a limited impact when the same components of the system reduce the probability that depredations occur. Time seems to play in favour of a progressive reduction in the costs associated with coexistence, provided that the responsible agencies focus their attention both on compensation and co-adaptation.
Genomics of experimental diversification ofPseudomonas aeruginosain cystic fibrosis lung-like conditions
Authors: Schick Alana , Kassen Rees
Published: April 2020

Pseudomonas aeruginosais among the most problematic opportunistic pathogens for adults with cystic fibrosis (CF), causing repeated and resilient infections in the lung and surrounding airways. Evidence suggests that long-term infections are associated with diversification into specialized types but the underlying cause of that diversification and the effect it has on the persistence of infections remains poorly understood. Here, we use evolve and resequence experiments to investigate the genetic changes accompanying rapid,de novophenotypic diversification in lab environments designed to mimic two aspects of human lung ecology: spatial structure and complex nutritional content. After ∼220 generations of evolution, we find extensive genetic variation present in all environments, including those that most closely resemble the CF lung, attributable to a combination of high mutation supply rates resulting from large population sizes and the complex ecological conditions imposed by resource complexity and spatial structure. We use the abundance and frequency of nonsynonymous and synonymous mutations to estimate the ratio of mutations that are selectively neutral (hitchhikers) to those that are under selection (drivers). A significantly lower proportion of driver mutations in spatially structured populations suggests that reduced dispersal generates subpopulations with reduced effective population size, decreasing the supply of beneficial mutations and causing more divergent evolutionary trajectories. The genes most commonly mutated tend to impact regulatory functions linked to a range of CF-associated phenotypes, including one gene that confers antibiotic resistance despite the absence of antibiotic selection in our experiment, but do not appear to be specific to CF-like conditions arising from antimicrobial treatment, immune system suppression, or competition from other microbial species. Our results are consistent with models of adaptation that see the first mutations fixed during adaptation to a stressful environment being those that are broadly beneficial across a range of environments.
Viscoelasticity in simple indentation-cycle experiments: a computational study
Authors: Efremov Yu.M. , Kotova S.L. , Timashev P.S.
Published: April 2020

Instrumented indentation has become an indispensable tool for quantitative analysis of the mechanical properties of soft polymers and biological samples at different length scales. These types of samples are known for their prominent viscoelastic behavior, and attempts to calculate such properties from the indentation data are constantly made. The simplest indentation experiment presents a cycle of approach (deepening into the sample) and retraction of the indenter, with the output of the force and indentation depth as functions of time and a force versus indentation dependency (force curve). The linear viscoelastic theory based on the elastic-viscoelastic correspondence principle might predict the shape of force curves based on the experimental conditions and underlying relaxation function of the sample. Here, we conducted a computational analysis based on this theory and studied how the force curves were affected by the indenter geometry, type of indentation (triangular or sinusoidal ramp), and the relaxation functions. The relaxation functions of both traditional and fractional viscoelastic models were considered. The curves obtained from the analytical solutions, numerical algorithm and finite element simulations matched each other well. Common trends for the curve-related parameters (apparent Young’s modulus, normalized hysteresis area, and curve exponent) were revealed. Importantly, the apparent Young’s modulus, obtained by fitting the approach curve to the elastic model, demonstrated a direct relation to the relaxation function for all the tested cases. The study will help researchers to verify which model is more appropriate for the sample description without extensive calculations from the basic curve parameters and their dependency on the indentation rate.
Customer incivility and service sabotage in the hotel industry
Authors: Cheng Bao , Guo Gongxing , Tian Jian , Shaalan Ahmed
Published: April 2020

Purpose

Using equity theory, this study aims to examine the role of customer incivility in effecting service sabotage among hotel employees by recognizing the mediating role of revenge motivation and the moderating effect of emotion regulation.

Design/methodology/approach

A multi-wave, multi-source questionnaire survey was conducted with 291 employee–supervisor dyads at chain hotels in Shenzhen, China. Previously developed and validated measures for customer incivility, revenge motivation, emotion regulation and service sabotage were adopted to test the hypotheses.

Findings

Customer incivility increased employees’ revenge motivation and service sabotage. Emotion regulation acted as a boundary condition for customer incivility’s direct effect on revenge motivation and its indirect effect on service sabotage through revenge motivation. Cognitive reappraisal mitigated the detrimental influence of customer incivility, whereas expressive suppression worsened its adverse effects.

Practical implications

Managers should monitor and deter the emergence of uncivil behaviors, provide psychological support for employees experiencing customer incivility and encourage these employees to use cognitive reappraisal rather than expressive suppression as an emotion regulation strategy.

Originality/value

To the authors’ knowledge, no prior research has investigated the customer incivility–service sabotage relationship in the hotel industry. This study sheds light on how customer incivility can motivate service sabotage among hotel employees. Furthermore, the authors used equity theory rather than the commonly adopted resources perspective to offer new insights into the customer incivility–service sabotage relationship.
Micro-crack detection of solar cell based on adaptive deep features and visual saliency
Authors: Qian Xiaoliang , Li Jing , Zhang Jianwei , Zhang Wenhao , Yue Weichao , Wu Qing-E , Zhang Huanlong , Wu Yuanyuan , Wang Wei
Published: April 2020

Purpose

An effective machine vision-based method for micro-crack detection of solar cell can economically improve the qualified rate of solar cells. However, how to extract features which have strong generalization and data representation ability at the same time is still an open problem for machine vision-based methods.

Design/methodology/approach

A micro-crack detection method based on adaptive deep features and visual saliency is proposed in this paper. The proposed method can adaptively extract deep features from the input image without any supervised training. Furthermore, considering the fact that micro-cracks can obviously attract visual attention when people look at the solar cell’s surface, the visual saliency is also introduced for the micro-crack detection.

Findings

Comprehensive evaluations are implemented on two existing data sets, where subjective experimental results show that most of the micro-cracks can be detected, and the objective experimental results show that the method proposed in this study has better performance in detecting precision.

Originality/value

First, an adaptive deep features extraction scheme without any supervised training is proposed for micro-crack detection. Second, the visual saliency is introduced for micro-crack detection.
Compressed sensing grid-based target stepwise location method in underground tunnel
Authors: Tian ZiJian , Gong XiaoWei , He FangYuan , He JiaLuan , Wang XuQi
Published: April 2020

Purpose

To solve the problem that the traditional received signal strength indicator real-time location method does not test the attenuation characteristics of the electromagnetic wave transmission in the location area, which cannot guarantee the accuracy of the location, resulting in a large location error.

Design/methodology/approach

At present, the compressed sensing (CS) reconstruction algorithm can be roughly divided into the following two categories (Zhouzhou and Fubao, 2014; Lagunas et al., 2016): one is the greedy iterative algorithm proposed for combinatorial optimization problems, which includes matching pursuit algorithm (MP), positive cross matching tracking algorithm (OMP), greedy matching tracking algorithm, segmented orthogonal matching tracking algorithm (StOMP) and so on. The second kind is the convex optimization algorithm, which also called the optimization approximation method. The common method is the basic tracking algorithm, which uses the norm instead of the norm to solve the optimization problem. In this paper, based on the piecewise orthogonal MP algorithm, the improved StOMP reconstruction algorithm is obtained.

Findings

In this paper, the MP algorithm (OMP), the StOMP and the improved StOMP algorithm are used as simulation reconstruction algorithms to achieve the comparison of location performance. It can be seen that the estimated position of the target is very close to the original position of the target. It is concluded that the CS grid-based target stepwise location method in underground tunnel can accurately locate the target in such specific region.

Originality/value

In this paper, the offline fingerprint database in offline phase of location method is established and the measurement of the electromagnetic noise distribution in different localization areas is considered. Furthermore, the offline phase shares the work of the location process, which greatly reduces the algorithm complexity of the online phase location process and the power consumption of the reference node, meanwhile is easy to implement under the same conditions, as well as conforms to the location environment.
Botulinum toxin type A in chronic non‐dyshidrotic palmar eczema: A side‐by‐side comparative study
Authors: Ismail Aisha , El‐Kholy Samar , Farid Carmen
Published: April 2020

New indications are being reported for intradermal botulinum toxin type A (BTX‐A) owing to its anti‐inflammatory and antipruritic actions. Its successful use for dyshidrotic hand eczema and lichen simplex has been reported in a few cases, while its utility in dry palmar eczema not associated with hyperhidrosis has not yet been investigated. The aim of this study was the assessment of the additive efficacy and tolerability of BTX‐A in chronic dry palmar eczema. This prospective non‐randomized side‐by‐side comparative study included 30 cases of chronic bilateral dry palmar eczema with no associated hyperhidrosis. Combined emollients and topical mid‐potency steroid on one side were compared with an additive 100 units of intradermal BTX‐A on the other side for efficacy and tolerability using both patient‐ and physician‐oriented scores over a period of 6 months. Timing and extent of improvement and relapse were recorded on both sides, together with the frequency of development of side‐effects. Both lines were effective and well tolerated, with significantly greater reduction of symptom and sign scores and higher overall patient satisfaction on the side receiving BTX‐A, an effect which lasted for a significantly longer duration on this side (4 months) as compared with the other side (1 month). In conclusion, intradermal BTX‐A at a dose of 100 units/palm is beneficial and well tolerated in chronic dry palmar eczema. Compared with topical steroid and emollients alone, its addition yielded superior efficacy that was longer lasting and more satisfactory to the patients, while exerting a steroid‐sparing effect.
Spillover of an alien parasite reduces expression of costly behaviour in native host species
Authors: Santicchia Francesca , Wauters Lucas A. , Piscitelli Anna Pia , Van Dongen Stefan , Martinoli Adriano , Preatoni Damiano , Romeo Claudia , Ferrari Nicola
Published: April 2020

Understanding the effects of invasive alien species (IAS) on native host–parasite relationships is of importance for enhancing ecological theory and IAS management. When IAS and their parasite(s) invade a guild, the effects of interspecific resource competition and/or parasite‐mediated competition can alter existing native host–parasite relationships and the dependent biological traits such as native species' behaviour.

We used a natural experiment of populations of native red squirrelsSciurus vulgaristhat were colonized by the alien grey squirrelSciurus carolinensis, comparing repeated measurements of red squirrel parasite infection and personality with those taken in sites where only the native species occurred.

We explored two alternative hypotheses: (a) individual differences in personality traits (activity and/or sociability) of native red squirrel positively affect the probability of macroparasite spillover and thus the likelihood to acquire the alien's parasitic helminthStrongyloides robustus; (b) the combined effects of grey squirrel presence and parasite infection result in a reduction of costly personality traits (activity and/or exploration).

Using data from 323 arena tests across three experimental (native species and IAS) and three control sites (only native species), we found negative correlations between native species' activity and infection withS. robustusin the sites invaded by the alien species. Activity was also negatively correlated with infection by its native helminthTrypanoxyuris sciuribut only when grey squirrels were present, while in the red‐only sites there was no relationship ofT. sciuriinfection with any of the personality traits. Moreover, individuals that acquiredS. robustusduring the study reduced their activity after infection, while this was not the case for animals that remained uninfected.

Our results show that parasite‐mediated competition is costly, reducing activity in individuals of the native species, and altering the native host–native parasite relationships.
Mutational landscape and characteristics of ERBB2 in non‐small cell lung cancer
Authors: Wei Xue‐Wu , Gao Xin , Zhang Xu‐Chao , Yang Jin‐Ji , Chen Zhi‐Hong , Wu Yi‐Long , Zhou Qing
Published: April 2020

Background

Tyrosine kinase domain (TKD) mutation and particularly exon 20 insertion mutations of ERBB2 have been extensively reported in non‐small cell lung cancer (NSCLC). Due to the increased accessibility of next‐generation sequencing, more ERBB2 mutations within the non‐TKD can be detected in clinical practice. Nevertheless, the clinical significance of non‐TKD mutations remains unknown. Hence, this study was designed to comprehensively outline the landscape and characteristics of ERBB2 mutations in NSCLC.

Methods

A total of 1934 patients with NSCLC from cBioPortal were included in the study. An ERBB2 mutation cohort was identified, while subsequent analyses revealed clinical and genomic characteristics.

Results

The frequency of ERBB2 mutation was 4.5%, and it was determined to be more likely to occur in never‐smokers. ERBB2 mutations occurring in the non‐TKD accounted for 57.5% of ERBB2 mutations. In the non‐TKD, missense mutation was the most recurrent mutation type, and S310F was the most recurrent mutation variant. ERBB2 mutations within non‐TKD also had a strong oncogenic ability where up to 37.5% of ERBB2 oncogenic mutations were within non‐TKD. The co‐mutation of EGFR or KRAS was higher in the non‐TKD mutation compared to the TKD mutation. Shorter overall survival was observed in ERBB2‐mutant patients compared with ERBB2 wild‐type patients. There was no significant difference in overall survival between patients with non‐TKD mutations and TKD mutations.

Conclusions

The present study showed that a considerable portion of non‐TKD mutations were oncogenic. ERBB2 mutation was a poor prognostic factor. The non‐TKD mutation might also be used as a therapeutic target in ERBB2‐directed target therapy.

Key points

• Significant findings of the study

ERBB2 mutations were more abundant within a nontyrosine domain than those within the tyrosine domain. Up to 37.5% of ERBB2 oncogenic mutations were within the nontyrosine domain. ERBB2 mutation was a poor prognostic factor.

• What this study adds

The frequency of EGFR or KRAS co‐mutations were significantly higher in ERBB2 mutations within the nontyrosine kinase domain compared to ERBB2 mutations within the tyrosine kinase domain. Nontyrosine domain mutations confer equal overall survival to tyrosine domain mutations.