A Wireless Gamma-Ray Monitoring System for Cemented Radwaste Drums

In the framework of the PREDIS EU project, a wireless battery-operated gamma-ray detection system was developed in order to provide a medium-to-long-term monitoring system for radioactive waste drums. It was initially proposed to monitor the gamma radioactivity outcoming from steel drums containing cemented radwaste, even though it could be usefully employed in a wider range of applications. Gamma rays are penetrating and convey information from the drum's internal structure, as the count rate measured on the surface depends on the thickness and density of the crossed materials. A number of sensors arranged around a drum, typically four units, provide indications of the emission anisotropy, and any sensitive change in the measured count rate would hint at some anomaly, thus triggering a suitable inspection by operators.

Three-dimensional Element-by-element Surface Topography Reconstruction of Compound Samples Using Multisegment Silicon Drift Detectors

Elemental surface topography information in microscopic material characterization contributes to a better understanding of surfaces, interfaces, substrates, and their applications. Here, a general approach based on microbeam proton-induced X-ray emission (micro-PIXE) to reconstruct the three-dimensional (3D) elemental surface topography using the annular multisegment silicon drift detector has been demonstrated. The proposed method includes four main steps: acquiring four two-dimensional elemental concentration maps using the multichannel spectrometer, reconstructing the local inclination angle from the atomic model of ion-matter interaction, calculating the two independent topography gradient components, and numerical surface topography integration. In this study, the general algorithm to obtain the gradient components has been successfully tested on a four-segment configuration to reconstruct the 3D surface topography of compound alloys with different microstructure scales. In synchrotron and accelerator facilities dealing with elemental X-ray mapping where the development of customized multisegment detectors is needed, the introduced method is applicable to elemental surface/interface roughness reconstruction in microscale for cultural heritage samples, fusion plasma-facing materials, and microelectronic devices.

Experimental results on nonlinear distortion compensation using photonic reservoir computing with a single set of weights for different wavelengths

Photonics-based computing approaches in combination with wavelength division multiplexing offer a potential solution to modern data and bandwidth needs. This paper experimentally takes an important step towards wavelength division multiplexing in an integrated waveguide-based photonic reservoir computing platform by using a single set of readout weights for up to at least 3 ITU-T channels to efficiently scale the data bandwidth when processing a nonlinear signal equalization task on a 28 Gbps modulated on-off keying signal. Using multiple-wavelength training, we obtain bit error rates well below that of the [Formula: see text] forward error correction limit at high fiber input powers of 18 dBm, which result in high nonlinear distortion. The results of the reservoir chip are compared to a tapped delay line filter and clearly show that the system performs nonlinear equalization. This was achieved using only limited post processing which in future work can be implemented in optical hardware as well.

Chitosan from Marine Amphipods Inhibits the Wilt Banana Pathogen Fusarium oxysporum f. sp. Cubense Tropical Race 4

In this work, we extracted chitosan from marine amphipods associated with aquaculture facilities and tested its use in crop protection. The obtained chitosan was 2.5 ± 0.3% of initial ground amphipod dry weight. The chemical nature of chitosan from amphipod extracts was confirmed via Raman scattering spectroscopy and Fourier transform infrared spectroscopy (FTIR). This chitosan showed an 85.7-84.3% deacetylation degree. Chitosan from biofouling amphipods at 1 mg·mL-1 virtually arrested conidia germination (ca. sixfold reduction from controls) of the banana wilt pathogenic fungus Fusarium oxysporum f. sp cubense Tropical Race 4 (FocTR4). This concentration reduced (ca. twofold) the conidia germination of the biocontrol fungus Pochonia chlamydosporia (Pc123). Chitosan from amphipods at low concentrations (0.01 mg·mL-1) still reduced FocTR4 germination but did not affect Pc123. This is the first time that chitosan is obtained from biofouling amphipods. This new chitosan valorizes aquaculture residues and has potential for biomanaging the diseases of food security crops such as bananas.

The structure of global cultural networks: Evidence from the diffusion of music videos

We apply the independent cascade network inference model to a large database of music videos to infer the structure of the global network of music diffusion. The derived network reveals an intricate topology-fully interconnected, exhibiting a modular structure, and characterized by asymmetric links. We explore the relationship between the identified bilateral cultural diffusion pathways and the geographical and cultural distances among countries, and key socioeconomic interactions such as international trade and migration. Additionally, we use a gravity model to ascertain the factors contributing to both the formation and the intensity of the estimated diffusion channels between countries. Our findings reveal that cultural, geographical, and historical factors serve as primary drivers of musical diffusion, downplaying the importance of economic factors. This study posits that these elements exert considerable force in shaping musical preferences across nations, making the emergence of a homogeneous global musical culture improbable. This exploration adds valuable insights to the discourse on the globalization of music and its potential cultural implications.

Event-driven adaptive optical neural network

We present an adaptive optical neural network based on a large-scale event-driven architecture. In addition to changing the synaptic weights (synaptic plasticity), the optical neural network's structure can also be reconfigured enabling various functionalities (structural plasticity). Key building blocks are wavelength-addressable artificial neurons with embedded phase-change materials that implement nonlinear activation functions and nonvolatile memory. Using multimode focusing, the activation function features both excitatory and inhibitory responses and shows a reversible switching contrast of 3.2 decibels. We train the neural network to distinguish between English and German text samples via an evolutionary algorithm. We investigate both the synaptic and structural plasticity during the training process. On the basis of this concept, we realize a large-scale network consisting of 736 subnetworks with 16 phase-change material neurons each. Overall, 8398 neurons are functional, highlighting the scalability of the photonic architecture.

Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of morbidity and mortality. Colonization by MRSA increases the risk of infection and transmission, underscoring the importance of decolonization efforts. However, success of these decolonization protocols varies, raising the possibility that some MRSA strains may be more persistent than others. Here, we studied how the persistence of MRSA colonization correlates with genomic presence of antibiotic resistance genes. Our analysis using a Bayesian mixed effects survival model found that genetic determinants of high-level resistance to mupirocin was strongly associated with failure of the decolonization protocol. However, we did not see a similar effect with genetic resistance to chlorhexidine or other antibiotics. Including strain-specific random effects improved the predictive performance, indicating that some strain characteristics other than resistance also contributed to persistence. Study subject-specific random effects did not improve the model. Our results highlight the need to consider the properties of the colonizing MRSA strain when deciding which treatments to include in the decolonization protocol.

Dragon's Blood Sap Microencapsulation within Whey Protein Concentrate and Zein Using Electrospraying Assisted by Pressurized Gas Technology

Dragon's blood sap (DBS) obtained from the bark of Croton lechleri (Müll, Arg.) is a complex herbal remedy of pharmacological interest due to its high content in polyphenols, specifically proanthocyanidins. In this paper, electrospraying assisted by pressurized gas (EAPG) was first compared with freeze-drying to dry natural DBS. Secondly, EAPG was used for the first time to entrap natural DBS at room temperature into two different encapsulation matrices, i.e., whey protein concentrate (WPC) and zein (ZN), using different ratios of encapsulant material: bioactive compound, for instance 2:1 w/w and 1:1 w/w. The obtained particles were characterized in terms of morphology, total soluble polyphenolic content (TSP), antioxidant activity, and photo-oxidation stability during the 40 days of the experiment. Regarding the drying process, EAPG produced spherical particles with sizes of 11.38 ± 4.34 µm, whereas freeze-drying produced irregular particles with a broad particle size distribution. However, no significant differences were detected between DBS dried by EAPG or freeze-drying in TSP, antioxidant activity, and photo-oxidation stability, confirming that EAPG is a mild drying process suitable to dry sensitive bioactive compounds. Regarding the encapsulation process, the DBS encapsulated within the WPC produced smooth spherical microparticles, with average sizes of 11.28 ± 4.28 µm and 12.77 ± 4.54 µm for ratios 1:1 w/w and 2:1 w/w, respectively. The DBS was also encapsulated into ZN producing rough spherical microparticles, with average sizes of 6.37 ± 1.67 µm and 7.58 ± 2.54 µm for ratios 1:1 w/w and 2:1 w/w, respectively. The TSP was not affected during the encapsulation process. However, a slight reduction in antioxidant activity measured by DPPH was observed during encapsulation. An accelerated photo-oxidation test under ultraviolet light confirmed that the encapsulated DBS showed an increased oxidative stability in comparison with the non-encapsulated DBS, with the stability being enhanced for the ratio of 2:1 w/w. Among the encapsulating materials and according to the ATR-FTIR results, ZN showed increased protection against UV light. The obtained results demonstrate the potential of EAPG technology in the drying or encapsulation of sensitive natural bioactive compounds in a continuous process available at an industrial scale, which could be an alternative to freeze-drying.

Hyperosmolar environment and salivary gland epithelial cells increase extra-cellular matrix remodeling and lymphocytic infiltration in Sjögren's syndrome

Salivary gland epithelial cells (SGECs) play an active role in primary Sjogren's syndrome (pSS) pathogenesis. Quantitative and qualitative abnormalities of saliva might expose SGECs to chronic hyperosmolarity. We aimed to decipher the links between hyperosmolar stimulation of SGECs and lymphocytic infiltration of the salivary glands (SG) observed in pSS. RNAseq was performed on NS-SV-AC cells stimulated with hyperosmolar media containing NaCl (100 mM) or sucrose (200 mM), or with iso-osmolar (Iso) medium. RNAseq was performed on primary cultured SGECs from pSS and controls, in the presence or not of B cells. Hyperosmolar stimulation of NS-SV-AC-cells identified an upregulation of interferon-induced (MX1, IFIT2) and MMPs genes. Enrichment analysis revealed an over-representation of fibrosis pathway. In parallel, RNAseq of SGECs comparing pSS to controls identified an over-representation of a pathway involving MMPs. Given the unexpected upregulation of collagen (COL3A1, COL1A2) and ADAMTS genes in pSS SGECs, we hypothesized that SGECs might undergo epithelial-mesenchymal transition. ZEB2 was upregulated and SLUG was down regulated in SGECs from pSS versus controls. MMP24 and ZEB2 were higher in SGECs from pSS with a focus score ≥1 versus <1. Lastly, SGECs cocultured with B cells expressed higher levels of COL1A2. These results suggest the existence of a vicious circle. Alteration of SGECs in pSS participates in the establishment of a hyperosmolar microenvironment, which in turn promotes SGECs transcriptomic modifications. These modifications include extracellular matrix remodeling and promote SG lymphocytic infiltration.

Estimation of recurrent atherosclerotic cardiovascular event risk in patients with established cardiovascular disease: the updated SMART2 algorithm

AIMS

The 10-year risk of recurrent atherosclerotic cardiovascular disease (ASCVD) events in patients with established ASCVD can be estimated with the Secondary Manifestations of ARTerial disease (SMART) risk score, and may help refine clinical management. To broaden generalizability across regions, we updated the existing tool (SMART2 risk score) and recalibrated it with regional incidence rates and assessed its performance in external populations.

METHODS AND RESULTS

Individuals with coronary artery disease, cerebrovascular disease, peripheral artery disease, or abdominal aortic aneurysms were included from the Utrecht Cardiovascular Cohort-SMART cohort [n = 8355; 1706 ASCVD events during a median follow-up of 8.2 years (interquartile range 4.2-12.5)] to derive a 10-year risk prediction model for recurrent ASCVD events (non-fatal myocardial infarction, non-fatal stroke, or cardiovascular mortality) using a Fine and Gray competing risk-adjusted model. The model was recalibrated to four regions across Europe, and to Asia (excluding Japan), Japan, Australia, North America, and Latin America using contemporary cohort data from each target region. External validation used data from seven cohorts [Clinical Practice Research Datalink, SWEDEHEART, the international REduction of Atherothrombosis for Continued Health (REACH) Registry, Estonian Biobank, Spanish Biomarkers in Acute Coronary Syndrome and Biomarkers in Acute Myocardial Infarction (BACS/BAMI), the Norwegian COgnitive Impairment After STroke, and Bialystok PLUS/Polaspire] and included 369 044 individuals with established ASCVD of whom 62 807 experienced an ASCVD event. C-statistics ranged from 0.605 [95% confidence interval (CI) 0.547-0.664] in BACS/BAMI to 0.772 (95% CI 0.659-0.886) in REACH Europe high-risk region. The clinical utility of the model was demonstrated across a range of clinically relevant treatment thresholds for intensified treatment options.

CONCLUSION

The SMART2 risk score provides an updated, validated tool for the prediction of recurrent ASCVD events in patients with established ASCVD across European and non-European populations. The use of this tool could allow for a more personalized approach to secondary prevention based upon quantitative rather than qualitative estimates of residual risk.

PYL1- and PYL8-like ABA Receptors of Nicotiana benthamiana Play a Key Role in ABA Response in Seed and Vegetative Tissue

To face the challenges of climate change and sustainable food production, it is essential to develop crop genome editing techniques to pinpoint key genes involved in abiotic stress signaling. The identification of those prevailing abscisic acid (ABA) receptors that mediate plant-environment interactions is quite challenging in polyploid plants because of the high number of genes in the PYR/PYL/RCAR ABA receptor family. Nicotiana benthamiana is a biotechnological crop amenable to genome editing, and given the importance of ABA signaling in coping with drought stress, we initiated the analysis of its 23-member family of ABA receptors through multiplex CRISPR/Cas9-mediated editing. We generated several high-order mutants impaired in NbPYL1-like and NbPYL8-like receptors, which showed certain insensitivity to ABA for inhibition of seedling establishment, growth, and development of shoot and lateral roots as well as reduced sensitivity to the PYL1-agonist cyanabactin (CB). However, in these high-order mutants, regulation of transpiration was not affected and was responsive to ABA treatment. This reveals a robust and redundant control of transpiration in this allotetraploid plant that probably reflects its origin from the extreme habitat of central Australia.

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas.

Genome-wide analysis of 944 133 individuals provides insights into the etiology of haemorrhoidal disease

OBJECTIVE

Haemorrhoidal disease (HEM) affects a large and silently suffering fraction of the population but its aetiology, including suspected genetic predisposition, is poorly understood. We report the first genome-wide association study (GWAS) meta-analysis to identify genetic risk factors for HEM to date.

DESIGN

We conducted a GWAS meta-analysis of 218 920 patients with HEM and 725 213 controls of European ancestry. Using GWAS summary statistics, we performed multiple genetic correlation analyses between HEM and other traits as well as calculated HEM polygenic risk scores (PRS) and evaluated their translational potential in independent datasets. Using functional annotation of GWAS results, we identified HEM candidate genes, which differential expression and coexpression in HEM tissues were evaluated employing RNA-seq analyses. The localisation of expressed proteins at selected loci was investigated by immunohistochemistry.

RESULTS

We demonstrate modest heritability and genetic correlation of HEM with several other diseases from the GI, neuroaffective and cardiovascular domains. HEM PRS validated in 180 435 individuals from independent datasets allowed the identification of those at risk and correlated with younger age of onset and recurrent surgery. We identified 102 independent HEM risk loci harbouring genes whose expression is enriched in blood vessels and GI tissues, and in pathways associated with smooth muscles, epithelial and endothelial development and morphogenesis. Network transcriptomic analyses highlighted HEM gene coexpression modules that are relevant to the development and integrity of the musculoskeletal and epidermal systems, and the organisation of the extracellular matrix.

CONCLUSION

HEM has a genetic component that predisposes to smooth muscle, epithelial and connective tissue dysfunction.

Long-term evolution of the epithelial cell secretome in preclinical 3D models of the human bronchial epithelium

The human bronchial epithelium is the first line of defense against atmospheric particles, pollutants, and respiratory pathogens such as the novel SARS-CoV-2. The epithelial cells form a tight barrier and secrete proteins that are major components of the mucosal immune response. Functional in vitro models of the human lung are essential for screening the epithelial response and assessing the toxicity and barrier crossing of drugs, inhaled particles, and pollutants. However, there is a lack of models to investigate the effect of chronic exposure without resorting to animal testing. Here, we developed a 3D model of the human bronchial epithelium using Calu-3 cell line and demonstrated its viability and functionality for 21 days without subculturing. We investigated the effect of reduced Fetal Bovine Serum supplementation in the basal medium and defined the minimal supplementation needed to maintain a functional epithelium, so that the amount of exogenous serum proteins could be reduced during drug testing. The long-term evolution of the epithelial cell secretome was fully characterized by quantitative mass spectrometry in two preclinical models using Calu-3 or primary NHBE cells. 408 common secreted proteins were identified while significant differences in protein abundance were observed with time, suggesting that 7-10 days are necessary to establish a mature secretome in the Calu-3 model. The associated Reactome pathways highlight the role of the secreted proteins in the immune response of the bronchial epithelium. We suggest this preclinical 3D model can be used to evaluate the long-term toxicity of drugs or particles on the human bronchial epithelium, and subsequently to investigate their effect on the epithelial cell secretions.

Human-Robot Perception in Industrial Environments: A Survey

Perception capability assumes significant importance for human-robot interaction. The forthcoming industrial environments will require a high level of automation to be flexible and adaptive enough to comply with the increasingly faster and low-cost market demands. Autonomous and collaborative robots able to adapt to varying and dynamic conditions of the environment, including the presence of human beings, will have an ever-greater role in this context. However, if the robot is not aware of the human position and intention, a shared workspace between robots and humans may decrease productivity and lead to human safety issues. This paper presents a survey on sensory equipment useful for human detection and action recognition in industrial environments. An overview of different sensors and perception techniques is presented. Various types of robotic systems commonly used in industry, such as fixed-base manipulators, collaborative robots, mobile robots and mobile manipulators, are considered, analyzing the most useful sensors and methods to perceive and react to the presence of human operators in industrial cooperative and collaborative applications. The paper also introduces two proofs of concept, developed by the authors for future collaborative robotic applications that benefit from enhanced capabilities of human perception and interaction. The first one concerns fixed-base collaborative robots, and proposes a solution for human safety in tasks requiring human collision avoidance or moving obstacles detection. The second one proposes a collaborative behavior implementable upon autonomous mobile robots, pursuing assigned tasks within an industrial space shared with human operators.

Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability

Differences between sexes contribute to variation in the levels of fasting glucose and insulin. Epidemiological studies established a higher prevalence of impaired fasting glucose in men and impaired glucose tolerance in women, however, the genetic component underlying this phenomenon is not established. We assess sex-dimorphic (73,089/50,404 women and 67,506/47,806 men) and sex-combined (151,188/105,056 individuals) fasting glucose/fasting insulin genetic effects via genome-wide association study meta-analyses in individuals of European descent without diabetes. Here we report sex dimorphism in allelic effects on fasting insulin at IRS1 and ZNF12 loci, the latter showing higher RNA expression in whole blood in women compared to men. We also observe sex-homogeneous effects on fasting glucose at seven novel loci. Fasting insulin in women shows stronger genetic correlations than in men with waist-to-hip ratio and anorexia nervosa. Furthermore, waist-to-hip ratio is causally related to insulin resistance in women, but not in men. These results position dissection of metabolic and glycemic health sex dimorphism as a steppingstone for understanding differences in genetic effects between women and men in related phenotypes.

'Not only faces': specialized visual representation of human hands revealed by adaptation

Classical neurophysiological studies demonstrated that the monkey brain is equipped with neurons selectively representing the visual shape of the primate hand. Neuroimaging in humans provided data suggesting that a similar representation can be found in humans. Here, we investigated the selectivity of hand representation in humans by means of the visual adaptation technique. Results showed that participants' judgement of human-likeness of a visual probe representing a human hand was specifically reduced by a visual adaptation procedure when using a human hand adaptor but not when using an anthropoid robotic hand or a non-primate animal paw adaptor. Instead, human-likeness of the anthropoid robotic hand was affected by both human and robotic adaptors. No effect was found when using a non-primate animal paw as adaptor or probe. These results support the existence of specific neural mechanisms encoding human hand in the human's visual system.

Development of Active Barrier Multilayer Films Based on Electrospun Antimicrobial Hot-Tack Food Waste Derived Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) and Cellulose Nanocrystal Interlayers

Active multilayer films based on polyhydroxyalkanoates (PHAs) with and without high barrier coatings of cellulose nanocrystals (CNCs) were herein successfully developed. To this end, an electrospun antimicrobial hot-tack layer made of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) derived from cheese whey, a by-product from the dairy industry, was deposited on a previously manufactured blown film of commercial food contact PHA-based resin. A hybrid combination of oregano essential oil (OEO) and zinc oxide nanoparticles (ZnONPs) were incorporated during the electrospinning process into the PHBV nanofibers at 2.5 and 2.25 wt%, respectively, in order to provide antimicrobial properties. A barrier CNC coating was also applied by casting from an aqueous solution of nanocellulose at 2 wt% using a rod at 1m/min. The whole multilayer structure was thereafter assembled in a pilot roll-to-roll laminating system, where the blown PHA-based film was located as the outer layers while the electrospun antimicrobial hot-tack PHBV layer and the barrier CNC coating were placed as interlayers. The resultant multilayer films, having a final thickness in the 130-150 µm range, were characterized to ascertain their potential in biodegradable food packaging. The multilayers showed contact transparency, interlayer adhesion, improved barrier to water and limonene vapors, and intermediate mechanical performance. Moreover, the films presented high antimicrobial and antioxidant activities in both open and closed systems for up to 15 days. Finally, the food safety of the multilayers was assessed by migration and cytotoxicity tests, demonstrating that the films are safe to use in both alcoholic and acid food simulants and they are also not cytotoxic for Caco-2 cells.

Facile fabrication of Mn2+-doped ZnO photocatalysts by electrospinning

In this study, a high-efficiency photocatalyst was synthesized by Mn2+-doped ZnO nanofibres (NFs) fabricated by facile electrospinning and a following annealing process, in which Mn2+ successes incorporate to ZnO NFs lattice without changing any morphology and crystalline structure of ZnO. The photodegradation properties of ZnO loading with different concentrations of Mn2+ (5, 10, 15 and 50 at%) were investigated. The 50% MnO-ZnO composite owns excellent active photocatalytic performance (quantum efficiency up to 7.57%) compared to pure ZnO (0.16%) under visible light and can be considered as an efficient visible light photocatalyst material. We systematically analysed its catalytic mechanism and found that the enhancement belongs to the Mn doping effect and the phase junction between MnO and ZnO. The dominant mechanism of Mn doping leads to the presence of impurity levels in the band gap of ZnO, narrowing the optical band gap of ZnO. In addition, doped Mn2+ ions can be used as electron traps that inhibit the recombination process and promote electron-hole pair separation. In summary, this paper provides a convenient method for fabricating highly efficient visible light photocatalysts using controlled annealing.

Dynamic characterization of a periodic microstructured flexural system with rotational inertia

We consider the propagation of waves in a flexural medium composed of massless beams joining a periodic array of elements, elastically supported and possessing mass and rotational inertia. The dispersion properties of the system are determined and the influence and interplay between the dynamic parameters on the structure of the pass and stop bands are analysed in detail. We highlight the existence of three special dynamic regimes corresponding to a low stiffness in the supports and/or low rotational inertia of the masses; to a high stiffness and/or high rotational inertia regime; and to a transition one where dispersion degeneracies are encountered. In the low-frequency regime, a rigorous asymptotic analysis shows that the structure approximates a continuous Rayleigh beam on an elastic foundation. This article is part of the theme issue 'Modelling of dynamic phenomena and localization in structured media (part 1)'.

Flexural vibration systems with gyroscopic spinners

In this paper, we study the spectral properties of a finite system of flexural elements connected by gyroscopic spinners. We determine how the eigenfrequencies and eigenmodes of the system depend on the gyricity of the spinners. In addition, we present a transient numerical simulation that shows how a gyroscopic spinner attached to the end of a hinged beam can be used as a 'stabilizer', reducing the displacements of the beam. We also discuss the dispersive properties of an infinite periodic system of beams with gyroscopic spinners at the junctions. In particular, we investigate how the band-gaps of the structure can be tuned by varying the gyricity of the spinners. This article is part of the theme issue 'Modelling of dynamic phenomena and localization in structured media (part 1)'.

Big data: the end of the scientific method?

For it is not the abundance of knowledge, but the interior feeling and taste of things, which is accustomed to satisfy the desire of the soul. (Saint Ignatius of Loyola). We argue that the boldest claims of big data (BD) are in need of revision and toning-down, in view of a few basic lessons learned from the science of complex systems. We point out that, once the most extravagant claims of BD are properly discarded, a synergistic merging of BD with big theory offers considerable potential to spawn a new scientific paradigm capable of overcoming some of the major barriers confronted by the modern scientific method originating with Galileo. These obstacles are due to the presence of nonlinearity, non-locality and hyperdimensions which one encounters frequently in multi-scale modelling of complex systems. This article is part of the theme issue 'Multiscale modelling, simulation and computing: from the desktop to the exascale'.

ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS-STING

A coding variant of the inflammatory bowel disease (IBD) risk gene ATG16L1 has been associated with defective autophagy and deregulation of endoplasmic reticulum (ER) function. IL-22 is a barrier protective cytokine by inducing regeneration and antimicrobial responses in the intestinal mucosa. We show that ATG16L1 critically orchestrates IL-22 signaling in the intestinal epithelium. IL-22 stimulation physiologically leads to transient ER stress and subsequent activation of STING-dependent type I interferon (IFN-I) signaling, which is augmented in Atg16l1 ΔIEC intestinal organoids. IFN-I signals amplify epithelial TNF production downstream of IL-22 and contribute to necroptotic cell death. In vivo, IL-22 treatment in Atg16l1 ΔIEC and Atg16l1 ΔIEC/Xbp1 ΔIEC mice potentiates endogenous ileal inflammation and causes widespread necroptotic epithelial cell death. Therapeutic blockade of IFN-I signaling ameliorates IL-22-induced ileal inflammation in Atg16l1 ΔIEC mice. Our data demonstrate an unexpected role of ATG16L1 in coordinating the outcome of IL-22 signaling in the intestinal epithelium.

Temporal walk based centrality metric for graph streams

A plethora of centrality measures or rankings have been proposed to account for the importance of the nodes of a network. In the seminal study of Boldi and Vigna (2014), the comparative evaluation of centrality measures was termed a difficult, arduous task. In networks with fast dynamics, such as the Twitter mention or retweet graphs, predicting emerging centrality is even more challenging. Our main result is a new, temporal walk based dynamic centrality measure that models temporal information propagation by considering the order of edge creation. Dynamic centrality measures have already started to emerge in publications; however, their empirical evaluation is limited. One of our main contributions is creating a quantitative experiment to assess temporal centrality metrics. In this experiment, our new measure outperforms graph snapshot based static and other recently proposed dynamic centrality measures in assigning the highest time-aware centrality to the actually relevant nodes of the network. Additional experiments over different data sets show that our method perform well for detecting concept drift in the process that generates the graphs.

The Global Phylogeography of Lyssaviruses - Challenging the 'Out of Africa' Hypothesis

Rabies virus kills tens of thousands of people globally each year, especially in resource-limited countries. Yet, there are genetically- and antigenically-related lyssaviruses, all capable of causing the disease rabies, circulating globally among bats without causing conspicuous disease outbreaks. The species richness and greater genetic diversity of African lyssaviruses, along with the lack of antibody cross-reactivity among them, has led to the hypothesis that Africa is the origin of lyssaviruses. This hypothesis was tested using a probabilistic phylogeographical approach. The nucleoprotein gene sequences from 153 representatives of 16 lyssavirus species, collected between 1956 and 2015, were used to develop a phylogenetic tree which incorporated relevant geographic and temporal data relating to the viruses. In addition, complete genome sequences from all 16 (putative) species were analysed. The most probable ancestral distribution for the internal nodes was inferred using three different approaches and was confirmed by analysis of complete genomes. These results support a Palearctic origin for lyssaviruses (posterior probability = 0.85), challenging the ‘out of Africa’ hypothesis, and suggest three independent transmission events to the Afrotropical region, representing the three phylogroups that form the three major lyssavirus clades.

Rabies virus kills tens of thousands of people globally each year and causes indescribable misery and family disturbance, especially in developing countries. Yet in much of the world there are related viruses, called lyssaviruses, which circulate among bats without causing conspicuous outbreaks. The greater diversity of African lyssaviruses has led to the hypothesis that Africa is the origin of these viruses. To test this hypothesis, the genetic data from 153 representative viruses from 16 available lyssavirus species from across the world dated between 1956 and 2015 were analysed. Statistical models were used to reconstruct the historical processes that lead to the contemporary distribution of these viruses. Our results support a Palearctic origin for lyssaviruses, not Afrotropic, and suggest three independent transmission events to Africa from the Palearctic region.

A metadata schema for data objects in clinical research

BACKGROUND

A large number of stakeholders have accepted the need for greater transparency in clinical research and, in the context of various initiatives and systems, have developed a diverse and expanding number of repositories for storing the data and documents created by clinical studies (collectively known as data objects). To make the best use of such resources, we assert that it is also necessary for stakeholders to agree and deploy a simple, consistent metadata scheme.

METHODS

The relevant data objects and their likely storage are described, and the requirements for metadata to support data sharing in clinical research are identified. Issues concerning persistent identifiers, for both studies and data objects, are explored.

RESULTS

A scheme is proposed that is based on the DataCite standard, with extensions to cover the needs of clinical researchers, specifically to provide (a) study identification data, including links to clinical trial registries; (b) data object characteristics and identifiers; and (c) data covering location, ownership and access to the data object. The components of the metadata scheme are described.

CONCLUSIONS

The metadata schema is proposed as a natural extension of a widely agreed standard to fill a gap not tackled by other standards related to clinical research (e.g., Clinical Data Interchange Standards Consortium, Biomedical Research Integrated Domain Group). The proposal could be integrated with, but is not dependent on, other moves to better structure data in clinical research.