bluuebunny/crossref_metadata_2025 huggingface dataset:
Environmental heterogeneity ruling the action of ecological processes over the bacterial metacommunity assembly
Authors: Huber Paula , Metz Sebastian , Unrein Fernando , Mayora Gisela , Sarmento Hugo , Devercelli Melina
Published: January 2020

Determining which processes take place in the spatial distribution of bacterioplankton metacommunities has been a central goal of microbial ecology. In freshwater ecosystems, selection has been spotted as the main driver shaping bacterial community. However, its relative importance compared with others processes (dispersal, drift, diversification) may depend on spatial heterogeneity and dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating the bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of Paraná River. The bacterioplankton metacommunity was studied by a step-forward analysis combining different statistical inferences based on the phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the complexity and randomness of bacterial networks. The heterogeneous selection promoted greater network complexity increasing the β-diversity, and bacterial associations were more random with the increasing influence of stochasticity. Finally, the spatiotemporal heterogeneity was an important factor determining the number and identity of keystone taxa in the system. Integrating all these empirical evidences we propose a new conceptual model that elucidates how the environmental heterogeneity guides the action of ecological processes shaping the bacterial metacommunity.
Automated Workflow For Peptide-level Quantitation From DIA/ SWATH-MS Data
Authors: Gupta Shubham , Röst Hannes
Published: January 2020

Data Independent Acquisition (DIA) is a powerful method to acquire spectra from all ionized precursors of a sample. Considering the complexity of the highly multiplexed spectral data, sophisticated workflows have been developed to obtain peptides quantification. Here we describe an open-source and easy-to-use workflow to obtain a quantitative matrix from multiple DIA runs. This workflow requires as prior information an “assay library”, which contains the MS coordinates of peptides. It consists of OpenSWATH, pyProphet and DIAlignR software. For the ease of installation and to isolate operating system related dependency, docker-based containerization is utilized in this workflow.
Genome-wide scale analyses identify novel BMI genotype-environment interactions using a conditional false discovery rate
Authors: Moore R. , Georgatou-Politou L. , Liley J. , Stegle O. , Barroso I.
Published: January 2020

Genotype-environment interaction (G×E) studies typically focus on variants with previously known marginal associations. While such two-step filtering greatly reduces the multiple testing burden, it can miss loci with pronounced G×E effects, which tend to have weaker marginal associations. To test for G×E effects on a genome-wide scale whilst leveraging information from marginal associations in a flexible manner, we combine the conditional false discovery rate with interaction test results obtained from StructLMM. After validating our approach, we applied this strategy to UK Biobank (UKBB) data to probe for G×E effects on BMI. Using 126,077 UKBB individuals for discovery, we identified known (FTO, MC4R, SEC16B) and novel G×E signals, many of which replicated (FAM150B/ALKAL2,TMEM18, EFR3B, ZNF596-FAM87A, LIN7C-BDNF, FAIM2, UNC79, LAT)in an independent subset of UKBB (n=126,076). Finally, when analysing the full UKBB cohort, we identified 140 candidate loci with G×E effects, highlighting the advantages of our approach.
Fluorescence Labeling of Circulating Tumor Cells with Folate Receptor Targeted Molecular Probes for DiffuseIn VivoFlow Cytometry
Authors: Patil Roshani , Srinivasarao Madduri , Amiji Mansoor , Low Philip S. , Niedre Mark
Published: January 2020

Purpose

We recently developed a new instrument called ‘diffusein vivoflow cytometry’ (DiFC) for enumeration of rare fluorescently-labeled circulating tumor cells (CTCs) in small animals without drawing blood samples. Until now, we have used cell lines that express fluorescent proteins, or were pre-labeled with a fluorescent dyeex-vivo. In this work, we investigated the use of two folate receptor (FR)-targeted fluorescence molecular probes forin vivolabeling of FR+ CTCs for DiFC.

Methods

We used EC-17 and Cy5-PEG-FR fluorescent probes. We studied the affinity of these probes for L1210A and KB cancer cells, both of which over-express FR. We tested the labeling specificity in cells in culturein vitro, in whole blood, and in micein vivo. We also studied detectability of labeled cells with DiFC.

Results

Both EC-17 and Cy5-PEG-FR probes had high affinity for FR+ CTCs in cell culturein vitro. However, only EC-17 had sufficient specificity for CTCs in whole blood. EC-17 labeled CTCs were also readily detectable in circulation in mice with DiFC.

Conclusions

This work demonstrates the feasibility of labeling CTCs for DiFC with a cell surface receptor targeted probe, greatly expanding the utility of the method for pre-clinical animal models. Because DiFC uses diffuse light, this method could be also used to enumerate CTCs in larger animal models and potentially even in humans.
Automatic Three-Dimensional Reconstruction of Fascicles in Peripheral Nerves from Histological Images
Authors: Tovbis Daniel , Agur Anne , Mogk Jeremy P.M. , Zariffa José
Published: January 2020

Computational studies can be used to support the development of peripheral nerve interfaces, but currently use simplified models of nerve anatomy, which may impact the applicability of simulation results. To better quantify and model neural anatomy across the population, we have developed an algorithm to automatically reconstruct accurate peripheral nerve models from histological cross-sections. We acquired serial median nerve cross-sections from human cadaveric samples, staining one set with hematoxylin and eosin (H&E) and the other using immunohistochemistry (IHC) with anti-neurofilament antibody. We developed a four-step processing pipeline involving registration, fascicle detection, segmentation, and reconstruction. We compared the output of each step to manual ground truths, and additionally compared the final models to commonly used extrusions, via intersection-over-union (IOU). Fascicle detection and segmentation required the use of a neural network and active contours in H&E-stained images, but only simple image processing methods for IHC-stained images. Reconstruction achieved an IOU of 0.42±0.07 for H&E and 0.37±0.16 for IHC images, with errors partially attributable to global misalignment at the registration step, rather than poor reconstruction. This work provides a quantitative baseline for fully automatic construction of peripheral nerve models. Our models provided fascicular shape and branching information that would be lost via extrusion.
Lineage reversion drives WNT independence in intestinal cancer
Authors: Han Teng , Goswami Sukanya , Hu Yang , Tang Fanying , Zafra Maria Paz , Murphy Charles , Cao Zhen , Poirier John T , Khurana Ekta , Elemento Olivier , Hechtman Jaclyn F. , Yaeger Rona , Dow Lukas E.
Published: January 2020

The WNT pathway is a fundamental regulator of intestinal homeostasis and hyperactivation of WNT signaling is the major oncogenic driver in colorectal cancer (CRC). To date, there are no described mechanisms that bypass WNT dependence in intestinal tumors. Here, we show that while WNT suppression blocks tumor growth in most organoid and in vivo CRC models, the accumulation of CRC-associated genetic alterations enables drug resistance and WNT-independent growth. In intestinal epithelial cells harboring mutations in KRAS or BRAF, together with disruption of p53 and SMAD4, transient TGFβ exposure drives YAP/ TAZ-dependent transcriptional reprogramming and lineage reversion. Acquisition of embryonic intestinal identity is accompanied by a permanent loss of adult intestinal lineages, and long-term WNT-independent growth. This work delineates genetic and microenvironmental factors that drive WNT inhibitor resistance, identifies a new mechanism for WNT-independent CRC growth and reveals how integration of associated genetic alterations and extracellular signals can overcome lineage-dependent oncogenic programs.
Cerebellar and Prefrontal-Cortical Engagement During Higher-Order Rule Learning in Older Adulthood
Authors: Jackson T. Bryan , Maldonado Ted , Eakin Sydney M. , Orr Joseph M. , Bernard Jessica A.
Published: January 2020

To date most aging research has focused on cortical systems and networks, ignoring the cerebellum which has been implicated in both cognitive and motor function. Critically, older adults (OA) show marked differences in cerebellar volume and functional networks, suggesting it may play a key role in the behavioral differences observed in advanced age. OA may be less able to recruit cerebellar resources due to network and structural differences. Here, 26 young adults (YA) and 25 OA performed a second-order learning task, known to activate the cerebellum in the fMRI environment. Behavioral results indicated that YA performed significantly better and learned more quickly compared to OA. Functional imaging detailed robust parietal and cerebellar activity during learning (compared to control) blocks within each group. OA showed increased activity (relative to YA) in the left inferior parietal lobe in response to instruction cues during learning (compared to control); whereas, YA showed increased activity (relative to OA) in the left anterior cingulate to feedback cues during learning, potentially explaining age-related performance differences. Visual interpretation of effect size maps showed more bilateral posterior cerebellar activation in OA compared to YA during learning blocks, but early learning showed widespread cerebellar activation in YA compared to OA. There were qualitatively large age-related differences in cerebellar recruitment in terms of effect sizes, yet no statistical difference. These findings serve to further elucidate age-related differences and similarities in cerebellar and cortical brain function and implicate the cerebellum and its networks as regions of interest in aging research.
Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin
Authors: Zhou Peng , Yang Xing-Lou , Wang Xian-Guang , Hu Ben , Zhang Lei , Zhang Wei , Si Hao-Rui , Zhu Yan , Li Bei , Huang Chao-Lin , Chen Hui-Dong , Chen Jing , Luo Yun , Guo Hua , Jiang Ren-Di , Liu Mei-Qin , Chen Ying , Shen Xu-Rui , Wang Xi , Zheng Xiao-Shuang , Zhao Kai , Chen Quan-Jiao , Deng Fei , Liu Lin-Lin , Yan Bing , Zhan Fa-Xian , Wang Yan-Yi , Xiao Gengfu , Shi Zheng-Li
Published: January 2020

Since the SARS outbreak 18 years ago, a large number of severe acute respiratory syndrome related coronaviruses (SARSr-CoV) have been discovered in their natural reservoir host, bats. Previous studies indicated that some of those bat SARSr-CoVs have the potential to infect humans. Here we report the identification and characterization of a novel coronavirus (nCoV-2019) which caused an epidemic of acute respiratory syndrome in humans, in Wuhan, China. The epidemic, started from December 12th, 2019, has caused 198 laboratory confirmed infections with three fatal cases by January 20th, 2020. Full-length genome sequences were obtained from five patients at the early stage of the outbreak. They are almost identical to each other and share 79.5% sequence identify to SARS-CoV. Furthermore, it was found that nCoV-2019 is 96% identical at the whole genome level to a bat coronavirus. The pairwise protein sequence analysis of seven conserved non-structural proteins show that this virus belongs to the species of SARSr-CoV. The nCoV-2019 virus was then isolated from the bronchoalveolar lavage fluid of a critically ill patient, which can be neutralized by sera from several patients. Importantly, we have confirmed that this novel CoV uses the same cell entry receptor, ACE2, as SARS-CoV.
Breastmilk-promoted bifidobacteria produce aromatic amino acids in the infant gut
Authors: Laursen Martin F. , Sakanaka Mikiyasu , von Burg Nicole , Mörbe Urs , Andersen Daniel , Moll Janne Marie , Pekmez Ceyda T. , Rivollier Aymeric , Michaelsen Kim F. , Mølgaard Christian , Lind Mads Vendelbo , Dragsted Lars O. , Katayama Takane , Frandsen Henrik L. , Vinggaard Anne Marie , Bahl Martin I. , Brix Susanne , Agace William , Licht Tine R. , Roager Henrik M.
Published: January 2020

Breastfeeding profoundly shapes the infant gut microbiota, which is critical for early life immune development. However, few breastmilk-dependent microbial metabolites mediating host-microbiota interactions are currently known. We here demonstrate that breastmilk-promotedBifidobacteriumspecies convert aromatic amino acids (tryptophan, phenylalanine and tyrosine) into their respective aromatic lactic acids (indolelactate, phenyllactate and 4-hydroxyphenyllactate) via a previously unrecognised aromatic lactate dehydrogenase. By longitudinal profiling of the gut microbiota composition and metabolome of stool samples of infants obtained from birth until 6 months of age, we show that stool concentrations of aromatic lactic acids are determined by the abundance of human milk oligosaccharide degradingBifidobacteriumspecies containing the aromatic lactate dehydrogenase. We demonstrate that stool concentrations ofBifidobacterium-derived indolelactate, the most abundant aromatic lactic acidin vivo, are associated with the capacity of infant stool samples to activate the aryl hydrocarbon receptor (AhR), a receptor important for controlling intestinal homeostasis and immune responses. Finally, we show that indolelactate modulatesex vivoimmune responses of human CD4+ T-cells and monocytes in a dose-dependent manner by acting as an agonist of both, the AhR and hydroxycarboxylic acid receptor 3 (HCAR3). Our findings reveal that breastmilk-promotedBifidobacteriumproduce aromatic lactic acids in the gut of infants and suggest that these microbial metabolites may impact immune function in early life.
Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples
Authors: Carøe Christian , Bohmann Kristine
Published: January 2020

Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called ‘tag-jumps’ can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5’ nucleotide-tagged amplicons have been suggested to cause tag-jumps; i) T4 DNA polymerase blunt-ending in the end-repair step and ii) post-ligation PCR amplification of amplicon libraries. The discovery of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag-jumps cannot result in false assignments of sequences to samples. As this increases both cost and workload, a metabarcoding library preparation protocol which circumvents the two steps that causes tag-jumps is needed. Here, we demonstrate Tagsteady, a metabarcoding Illumina library preparation protocol for pools of nucleotide-tagged amplicons that enables efficient and cost-effective generation of metabarcoding data with virtually no tag-jumps. We use pools of twin-tagged amplicons to investigate the effect of T4 DNA polymerase blunt-ending and post-ligation PCR on the occurrence of tag-jumps. We demonstrate that both blunt-ending and post-ligation PCR, alone or together, can result in detrimental amounts of tag-jumps (here, up to ca. 49% of total sequences), while leaving both steps out (the Tagsteady protocol) results in amounts of sequences carrying new combinations of used tags (tag-jumps) comparable to background contamination.
Linguistic input drives brain network configuration during language comprehension
Authors: Quiñones Ileana , Molinaro Nicola , Caballero-Gaudes César , Mancini Simona , Hernández-Cabrera Juan Andrés , Barber Horacio , Carreiras Manuel
Published: January 2020

Assessing the synchrony and interplay between distributed neural regions is critical to understanding how language is processed. Here, we investigated possible neuro-functional links between form and meaning during sentence comprehension combining a classical whole-brain approach, which characterizes patterns of brain activation resulting from our experimental manipulation, and a novel multivariate network-based approach, which uses graph-theory measures to unravel the architectural configuration of the language system. Capitalizing on the Spanish gender agreement system, we experimentally manipulated formal and conceptual factors: whether the noun-adjective grammatical gender relationship was congruent or not and whether the noun gender type was semantically informative or strictly formal. Left inferior and middle frontal gyri, as well as left MTG/STG emerged as critical areas for the computation of grammatical relations. We demonstrate how the interface between formal and conceptual features depends on the synergic articulation of brain areas divided in three subnetworks that extend beyond the classical left-lateralized perisylvian language circuit. Critically, we isolated a subregion of the left angular gyrus showing a significant interaction between gender congruency and gender type. The functional interplay between the angular gyrus and left perisylvian language-specific circuit proves crucial for constructing coherent and meaningful messages. Importantly, using graph theory we show that this complex system is functionally malleable: the role each node plays within the network changes depending on the available linguistic cues.

Significance Statement

Neural networks can be described as graphs comprising distributed and interconnected nodes. These nodes share functional properties but also differ in terms of functional specialization and the number of interconnections mediating the efficient transfer of information. Previous work has shown functional connectivity differences based on graph-theory properties between typical and atypical samples. However, here we have used concepts from graph theory to characterize connectivity during language processing using task-related fMRI. This approach allowed us to demonstrate how linguistic input drives brain network configuration during language comprehension. This is the first evidence of functional flexibility in language networks: the communicative capacity of each hub changes depending on whether the linguistic input grants access to meaning or is purely formal.
Not only compulsivity: The SAPAP3-KO mouse reconsidered as a comorbid model expressing a spectrum of pathological repetitive behaviors
Authors: Lamothe H , Schreiweis C , Lavielle O , Mallet L , Burguière E
Published: January 2020

Symptom comorbidity is present amongst neuropsychiatric disorders with repetitive behaviours, complicating clinical diagnosis and impeding appropriate treatments. This is of particular importance for obsessive-compulsive disorder (OCD) and Tourette syndrome. Here, we meticulously analysed the behaviour of Sapap3 knockout mice, the recent rodent model predominantly used to study compulsive-like behaviours, and found that its behaviour is more complex than originally and persistently described. Indeed, we detected previously unreported elements of distinct pathologically repetitive behaviours, which do not form part of rodent syntactic cephalo-caudal self-grooming. These repetitive behaviours include sudden, rapid body and head twitches, resembling tic-like movements. We also observed that another type of repetitive behaviours, aberrant hindpaw scratching, is responsible for the flagship-like skin lesions of this mouse model, rather than originally suspected self-grooming. In order to characterize the symptomatological nature of observed repetitive behaviours, we pharmacologically challenged these phenotypes by systemic aripiprazole administration, a first-line treatment for tic-like symptoms in Tourette Syndrome and trichotillomania. A single treatment of aripiprazole significantly reduced the number of tic-like movements but not syntactic grooming events. These observations are in line with the high comorbidity of tic- and compulsive-like symptoms in Tourette, OCD and trichotillomania patients as well as with the hypothesis of shared neurobiological mechanisms.
Structured clustering of the glycosphingolipid GM1 is required for membrane curvature induced by cholera toxin
Authors: Kabbani Abir Maarouf , Raghunathan Krishnan , Lencer Wayne I. , Kenworthy Anne K. , Kelly Christopher V.
Published: January 2020

AB5bacterial toxins and polyomaviruses induce membrane curvature as a mechanism to facilitate their entry into host cells. How membrane bending is accomplished is not yet fully understood but has been linked to the simultaneous binding of the pentameric B-subunit to multiple copies of their glycosphingolipid receptors. Here, we probe the toxin membrane binding and internalization mechanisms by using a combination of super-resolution and polarized localization microscopy. We show that cholera toxin subunit B (CTxB) can induce membrane curvature only when bound to multiple copies of its glycosphingolipid receptor, GM1, and the ceramide structure of GM1 is likely not a determinant of this activity as assessed in model membranes. A mutant CTxB capable of binding only a single GM1 fails to generate curvature either in model membranes or in cells and clustering the mutant CTxB-single-GM1 complexes by antibody cross-linking does not rescue the membrane curvature phenotype. We conclude that both the multiplicity and specific geometry of GM1 binding sites are necessary for the induction of membrane curvature. We expect this to be a general rule of membrane behavior for all AB5toxins and polyomaviruses that bind glycosphingolipids to invade host cells.

SIGNIFICANCE STATEMENT

Membrane binding toxins demonstrate both a public health challenge and a bioengineering opportunity due to their efficient internalization into cells. These toxins multivalently bind to naturally occurring lipid receptors at the plasma membrane and initiate endocytosis. This manuscript reports the importance of structured lipid-receptor clustering for the induction of membrane bending. We also observed that the magnitude of membrane curvature was correlated to the stoichiometry of toxin-bound receptors. By identifying how these bacterial proteins initiate membrane curvature, these findings provide mechanistic insights into the early steps of pathogenic endocytosis.
Anillin propels myosin-independent constriction of actin rings
Authors: Kučera Ondřej , Janda Daniel , Siahaan Valerie , Dijkstra Sietske H. , Pilátová Eliška , Zatecka Eva , Diez Stefan , Braun Marcus , Lansky Zdenek
Published: January 2020

Constriction of the actin cytokinetic ring is an essential step of cell division. In a generally accepted view, the constriction is driven by relative sliding of actin filaments propelled by myosin motors. However, in multiple organisms, the ring constriction is myosin independent. How actin rings constrict in the absence of motor activity remains unclear. Here, we demonstrate that actin contractility can be propelled by anillin, a diffusible non-motor actin crosslinker, localising to the cytokinetic ring. We in vitro observed the formation and constriction of rings comprising multiple actin filaments bundled by anillin. Rings constricted due to anillin-generated forces maximising the overlap lengths between the filaments. Actin disassembly promoted constriction. We propose that actin crosslinkers, generating forces complementary to molecular motors, contribute to the contractility of diverse actin structures, including the cytokinetic ring.
Using visual encounter data to improve capture-recapture abundance estimates
Authors: Joseph Maxwell B. , Knapp Roland A.
Published: January 2020

Capture-recapture studies are widely used in ecology to estimate population sizes and demographic rates. In some capture-recapture studies, individuals may be visually encountered but not identified. For example, if individual identification is only possible upon capture and individuals escape capture, visual encounters can result in failed captures where individual identities are unknown. In such cases, the data consist of capture histories with known individual identities, and counts of failed captures for individuals with unknown identities. These failed captures are ignored in traditional capture-recapture analyses that require known individual identities. Here we show that if animals can be encountered at most once per sampling occasion, failed captures provide lower bounds on population size that can increase the precision of abundance estimates. Analytical results and simulations indicate that visual encounter data improve abundance estimates when capture probabilities are low, and when there are few repeat surveys. We present a hierarchical Bayesian approach for integrating failed captures and auxiliary encounter data in statistical capture-recapture models. This approach can be integrated with existing capture-recapture models, and may prove particularly useful for hard to capture species in data-limited settings.
Behavioural traits and feeding ecology of Mediterranean lionfish and native species naiveté to lionfish predation
Authors: D’Agostino Daniele , Jimenez Carlos , Reader Tom , Hadjioannou Louis , Heyworth Stephanie , Aplikioti Marilena , Argyrou Marina , Feary David A.
Published: January 2020

The detrimental effects of invasion by Indo-Pacific lionfish (Pterois volitans/miles) on western Atlantic fishes have spurred concerns for Mediterranean fish biodiversity, where a Lessepsian invasion of lionfish has recently begun. In order to assess the potential impact on biodiversity, we examine key behavioural and ecological traits of lionfish, and the resident fish community in the Mediterranean, that may contribute to lionfish invasion success. We focus on Cyprus, where lionfish populations were first sighted in 2012 and have now established abundant and stable populations. Using field observations, we examine lionfish predatory behaviour and feeding ecology, and resident fish species naiveté to hunting lionfish. Our findings suggest that lionfish in the Mediterranean are crepuscular generalist predators, with prey targeted dominated by small-bodied benthic or bentho-pelagic associated species. Such prey are more likely to be native than introduced (Lessepsian) fishes, with native prey fishes showing greater naiveté towards lionfish than Lessepsian prey species. Notably, one of the Mediterranean’s key ecological fish species (the native damselfishChromis chromis), showed the highest level of naiveté and was the most heavily targeted prey. Overall, lionfish in the Mediterranean show similar predatory behaviour and ecology to their western Atlantic counterparts. Although the Mediterranean invasion is still relatively recent, it may result in a similar disruption to reef fish biomass to that recorded in the Atlantic, with impact to the structure and biodiversity of reef fish communities and the services they provide.
The effect of genetic architecture and selfing on the capacity of a population to expand its range
Authors: Eriksson Martin , Rafajlović Marina
Published: January 2020

Previous theoretical work on range expansions over heterogeneous environments showed that there is a critical environmental gradient where range expansion stops. For populations with freely recombining loci underlying the trait under selection (hereafteradaptive loci), the critical gradient in one-dimensional habitats depends on the fitness cost of dispersal, and the strength of selection relative to genetic drift. Here, we extend the previous work in two directions and ask: What is the role of the genetic architecture of adaptive loci during range expansions? And what effect does the ability of selfing have on range expansions? To answer these questions, we use computer simulations. We demonstrate that, while reduced recombination rates between adaptive loci slow down range expansions due to poor purging of locally deleterious alleles at the expansion front, they may also allow a species to occupy a greater range. In fact, for some parameter values, we find that a population with freely recombining adaptive loci experiences global extinction, whereas reduced recombination rates allow for a successful expansion over a wide geographic range. In addition, we find that allowance of selfing may improve the ability of populations to expand their ranges. We discuss the mechanisms underlying these results.
Functional assessment of cell entry and receptor usage for lineage B β-coronaviruses, including 2019-nCoV
Authors: Letko Michael , Munster Vincent
Published: January 2020

Over the past 20 years, several coronaviruses have crossed the species barrier into humans, causing outbreaks of severe, and often fatal, respiratory illness. Since SARS- CoV was first identified in animal markets, global viromics projects have discovered thousands of coronavirus sequences in diverse animals and geographic regions. Unfortunately, there are few tools available to functionally test these novel viruses for their ability to infect humans, which has severely hampered efforts to predict the next zoonotic viral outbreak. Here we developed an approach to rapidly screen lineage B betacoronaviruses, such as SARS-CoV and the recent 2019-nCoV, for receptor usage and their ability to infect cell types from different species. We show that host protease processing during viral entry is a significant barrier for several lineage B viruses and that bypassing this barrier allows several lineage B viruses to enter human cells through an unknown receptor. We also demonstrate how different lineage B viruses can recombine to gain entry into human cells and confirm that human ACE2 is the receptor for the recently emerging 2019-nCoV.
Stator–rotor interaction in the tip leakage flow of an inlet vaned low-speed axial fan
Authors: Vazquez Gonzalez Adrián , Meana-Fernández Andrés , Fernández Jesús Manuel
Published: January 2020

Purpose

The purpose of the paper is to quantify the impact of the non-uniform flow generated by the upstream stator on the generation and convection of the tip leakage flow (TLF) structures in the passages of the rotor blades in a low-speed axial fan.

Design/methodology/approach

A full three dimensional (3D)-viscous unsteady Reynolds-averaged Navier-stokes (RANS) (URANS) simulation of the flow within a periodic domain of the axial stage has been performed at three different flow rate coefficients (φ = 0.38, 0.32, 0.27) using ReNormalization Group k-ε turbulence modelling. A typical tip clearance of 2.3 per cent of the blade span has been modelled on a reduced domain comprising a three-vaned stator and a two-bladed rotor with circumferential periodicity. A non-conformal grid with hybrid meshing, locally refined O-meshes on both blades and vanes walls with (100 × 25 × 80) elements, a 15-node meshed tip gap and circumferential interfaces for sliding mesh computations were also implemented. The unsteady motion of the rotor has been covered with 60 time steps per blade event. The simulations were validated with experimental measurements of the static pressure in the shroud of the blade tip region.

Findings

It has been observed that both TLF and intensities of the tip leakage vortex (TLV) are significantly influenced by upstream stator wakes, especially at nominal and partial load conditions. In particular, the leakage flow, which represents 12.4 per cent and 11.3 per cent of the working flow rate, respectively, has shown a clear periodic fluctuation clocked with the vane passing period in the relative domain. The periodic fluctuation of the TLF is in the range of 2.8-3.4 per cent of the mean value. In addition, the trajectory of the tip vortex is also notably perturbed, with root-mean squared fluctuations reaching up to 18 per cent and 6 per cent in the regions of maximum interaction at 50 per cent and 25 per cent of the blade chord for nominal and partial load conditions, respectively. On the contrary, the massive flow separation observed in the tip region of the blades for near-stall conditions prevents the formation of TLV structures and neglects any further interaction with the upstream vanes.

Research limitations/implications

Despite the increasing use of large eddy simulation modelling in turbomachinery environments, which requires extremely high computational costs, URANS modelling is still revealed as a useful technique to describe highly complex viscous mechanisms in 3D swirl flows, such as unsteady tip flow structures, with reasonable accuracy.

Originality/value

The paper presents a validated numerical model that simulates the unsteady response of the TLF to upstream perturbations in an axial fan stage. It also provides levels of instabilities in the TLV derived from the deterministic non-uniformities associated to the vane wakes.
Second law analysis on Hall effect of natural convection flow through vertical channel in the presence of uniform heat source/sink
Authors: Roja A. , Gireesha B.J.
Published: January 2020

Purpose

Microfluidics is one of the extensive elaborated technologies in thermal and engineering fields due to its wide range of applications, such as micro heat exchangers, micro mixture and microchannel heat sinks, which is used to develop a large number of microscopic devices and systems. Enhancement of thermal energy using verity of nanoliquids is one of the challenges in these applications of microfluidics. Therefore, using single wall carbon nanotubes for enhancement of thermal energy in microchannel is the main purpose of this study. Hall effect of natural convection flow in a vertical channel with slip and temperature jump condition is considered. The impacts of radiative heat flux, uniform heat source/sink, viscous dissipation and joule heating are also taken into account.

Design/methodology/approach

Suitable non-dimension variables are applied to the governing equations to reduce the system into ordinary differential equations. The reduced nonlinear system is then solved numerically using Runge–Kutta–Fehlberg fourth–fifth-order method along with shooting technique. The impact of different pertinent parameters on numerical solutions of primary velocity, secondary velocity, temperature, entropy generation and Bejan number is comprehensively discussed in detail. Also, the obtained numerical results are compared with existing one which perfectly found to be in good agreement.

Findings

It is established that, with the aspects of Joule heating, viscous dissipation, radiative heat flux and uniform heat source/sink, the production in the entropy can be improved. Further, it is found that the increasing ratio of wall ambient temperature difference and nanoparticle volume fraction leads to enhance the entropy generation. The same effect reverses with increasing values of fluid wall interaction parameter (FWIP) and rare faction. The irreversibility ratio enhances with larger values of nanoparticle volume fraction and decelerates with increment values of FWIP.

Originality/value

The impact of single wall carbon nanoliquid in a vertical channel flow by using radiative heat flux, heat source/sink, joule heating and viscous dissipation is first time investigated. Further, the influence of Hall current is explored in detail.
The hunt for computerized support in information security policy management
Authors: Rostami Elham , Karlsson Fredrik , Kolkowska Ella
Published: January 2020

Purpose

The purpose of this paper is to survey existing information security policy (ISP) management research to scrutinise the extent to which manual and computerised support has been suggested, and the way in which the suggested support has been brought about.

Design/methodology/approach

The results are based on a literature review of ISP management research published between 1990 and 2017.

Findings

Existing research has focused mostly on manual support for managing ISPs. Very few papers have considered computerised support. The entire complexity of the ISP management process has received little attention. Existing research has not focused much on the interaction between the different ISP management phases. Few research methods have been used extensively and intervention-oriented research is rare.

Research limitations/implications

Future research should to a larger extent address the interaction between the ISP management phases, apply more intervention research to develop computerised support for ISP management, investigate to what extent computerised support can enhance integration of ISP management phases and reduce the complexity of such a management process.

Practical implications

The limited focus on computerised support for ISP management affects the kind of advice and artefacts the research community can offer to practitioners.

Originality/value

Today, there are no literature reviews on to what extent computerised support the ISP management process. Findings on how the complexity of ISP management has been addressed and the research methods used extend beyond the existing knowledge base, allowing for a critical discussion of existing research and future research needs.
Evaluating graphical user interfaces for buildings
Authors: Halmetoja Esa , Forns-Samso Francisco
Published: January 2020

Purpose

The purpose of this paper is to evaluate six different graphical user interfaces (GUIs) for facilities operations using human–machine interaction (HMI) theories.

Design/methodology/approach

The authors used a combined multi-functional method that includes a review of the theories behind HMI for GUIs as its first approach. Consequently, heuristic evaluations were conducted to identify usability problems in a professional context. Ultimately, thematic interviews were conducted with property managers and service staff to determine special needs for the interaction of humans and the built environment.

Findings

The heuristic evaluation revealed that not all the studied applications were complete when the study was done. The significant non-motivational factor was slowness, and a lighter application means the GUI is more comfortable and faster to use. The evaluators recommended not using actions that deviate from regular practice. Proper implementation of the GUI would make it easier and quicker to work on property maintenance and management. The thematic interviews concluded that the GUIs form an excellent solution that enables communication between the occupant, owner and service provider. Indoor conditions monitoring was seen as the most compelling use case for GUIs. Two-dimensional (2D) layouts are more demonstrative and faster than three-dimensional (3D) layouts for monitoring purposes.

Practical implications

The study provides an objective view of the strengths and weaknesses of specific types of GUI. So, it can help to select a suitable GUI for a particular environment. The 3D view is not seen as necessary for monitoring indoor conditions room by room or sending a service request. Many occupants’ services can be implemented without any particular layout. On the other hand, some advanced services were desired for the occupants, such as monitoring occupancy, making space reservations and people tracking. These aspects require a 2D layout at least. The building information model is seen as useful, especially when monitoring complex technical systems.

Originality/value

Earlier investigations have primarily concentrated on investigating human–computer interaction. The authors’ studied human–building interaction instead. The notable difference to previous efforts is that the authors considered the GUI as a medium with which to communicate with the built environment, and looked at its benefits for top-level processes, not for the user interface itself.
Bond–slip constitutive relation of mortar anchor under different loading rates
Authors: Wang Haitao , Guo Tao , Sun Haoyu
Published: January 2020

Purpose

This paper aims to focus on establishing the bond-slip constitutive relation of mortar anchor under high loading rates by the dynamic pull-out test.

Design/methodology/approach

Self-made specimens were made for the dynamic pull-out test to explore the bond performance of mortar anchor, and the bond-slip constitutive relation of mortar anchor under high loading rates was established according to the analysis of test data.

Findings

During the loading process, the position of the peak bond stress was observed to translate to the free end. The bearing capacity of the mortar anchor was enhanced to some extent due to the increase of the loading rate.

Originality/value

The bond-slip constitutive relation of mortar anchor under high loading rates was established with the introduction of the position function and dynamic-load expanded coefficient.
Reduced biodiversity in modernized villages: A conflict between sustainable development goals
Authors: Rosin Zuzanna M. , Hiron Matthew , Żmihorski Michał , Szymański Paweł , Tobolka Marcin , Pärt Tomas
Published: January 2020

Despite large conservation efforts to halt the loss of farmland biodiversity in Europe, negative population trends are still observed, especially for common species. Old villages and human settlements are biodiversity hotspots and important breeding habitats for farmland birds, but recent requirements for energy saving measures and improved living comfort have changed their architecture and habitats. Consequently, modernization of villages may negatively affect bird diversity due to the loss of nesting and foraging sites.

We investigated how the abundance and diversity of birds breeding in 104 Polish villages varied in relation to the degree of modernization as estimated by the proportion of new and renovated homesteads.

Abundance of building‐nesting species, but not tree‐nesting species, declined by 50% across a gradient of old to highly modernized villages. The contribution of new versus renovated houses to the observed decline was similar.

Synthesis and applications. Rural modernization may have a dramatic effect on abundance of birds nesting on buildings, thus may be an important and overlooked contributor to farmland bird population declines in Europe. Villages and rural properties fall outside of current conservation policy as they are neither protected areas nor agricultural lands (where agri‐environmental schemes can be applied). The observed conflict between sustainability goals such as increased building energy efficiency and biodiversity conservation suggests that sustainable rural development should better link modernization with conservation measures, for example, by constructing nesting sites when renovating and building new houses. The challenge is to design modern buildings that are both energy‐efficient and biodiversity‐friendly to generally improve quality of life for rural communities and to halt or reduce farmland bird declines in rural landscapes. Designers and architects can find inspiration from traditional architecture and add a variety of nest‐box types.
Measures of care fragmentation: Mathematical insights from population genetics
Authors: Rosenberg Noah A. , Zulman Donna M.
Published: January 2020

Objective

To identify novel properties of health care fragmentation measures, drawing on insights from mathematically equivalent measures of genetic diversity.

Study Design

We describe mathematical relationships between two measures: (a) Breslau's Usual Provider of Care (UPC), the proportion of care with the most frequently visited provider, analogous to the “frequency of the most frequent allele” at a genetic locus; and (b) Bice‐Boxerman's Continuity of Care Index (COCI), a measure of care dispersion across multiple providers, analogous to “Nei's estimator of homozygosity” in genetics.

Principal Findings

Just as the frequency of the most frequent allele places a tight constraint on homozygosity, the proportion of care with the most frequently visited provider (UPC) places lower and upper bounds on dispersion of care (COCI), and vice versa. This property presents the possibility of a normalized COCI given UPC (NCGU) measure, which reflects a bounded range of care dispersion dependent on the number of visits with the most frequently visited provider. Mathematical aspects of UPC and COCI also suggest thresholds for the minimal number of patient visits to use when studying fragmentation.

Conclusions

Applying knowledge from population genetics elucidated relationships between care fragmentation measures and produced novel insights for care fragmentation studies.
A Behavioral Perspective on Saving Decisions. Empirical Evidence for Policymakers in the European Union
Authors: Clifton Judith , Díaz‐Fuentes Daniel , Llamosas García Gonzalo
Published: January 2020

Evidence is mounting that individuals do not always behave as strictly ‘rational’ customers of the banking sector as neoclassical models of economics would assume. Instead, scholars and policymakers are increasingly arguing that behavioral economics offers a more useful and realistic means of understanding customer behavior in the real economy. Drawing on data from the first European Central Bank harmonized household survey at the European level and Eurostat, this paper develops a multi‐level model to investigate how individuals actually save. We find evidence that loss aversion bias exists in saving behavior as regards an individual's current level of income, and that evidence of this effect is also supported at the country level. We also find strong evidence that socio‐demographic factors and cross‐country differences influence individuals' saving behavior. We argue that behavioral approaches can – and should – be used to understand saving behavior of individuals, and that this insight should be used towards the ongoing quest to improve future banking practice and financial reform, particularly in the aftermath of the 2008 financial crisis.
The mechanism of propofol in cancer development: An updated review
Authors: Gao Xingchun , Mi Yajing , Guo Na , Luan Jing , Xu Hao , Hu Zhifang , Wang Ning , Zhang Dian , Gou Xingchun , Xu Lixian
Published: January 2020

Cancer is a key cause of death worldwide. Despite the development of radiotherapy, chemotherapy and even immunotherapy, surgery remains the standard treatment for cancer patients. Recently, many studies have shown that propofol, a commonly used anesthetic drug, can affect the prognosis of cancer. In this review, we provide an overview of the molecular mechanisms of propofol in the development of cancer. Propofol not only affects epigenetic pathways, such as those involving miRNA, lncRNA and histone acetylation, but also modulates genetic signaling pathways, including the hypoxia, NF‐κB, MAPK, SLUG and Nrf2 pathways. In addition, propofol influences the immune function of patients and impacts the degree of immunosuppression. Furthermore, we briefly summarize the clinical trials on the effect of propofol in cancer development. Ultimately, further studies distinguishing the types of tumors in clinical trials are needed to clarify the correlation between propofol and cancer.