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  • Characterization of microwave and terahertz dielectric properties of single crystal La2Ti2O7 along one single direction

    Zhang, Man; orcid: 0000-0002-1094-7279; Tang, Zhiyong; orcid: 0000-0002-1921-6034; Zhang, Hangfeng; Smith, Graham; orcid: 0000-0003-3273-7085; Jiang, Qinghui; Saunders, Theo; orcid: 0000-0003-4250-3071; Yang, Bin; Yan, Haixue; orcid: 0000-0002-4563-1100
    New generation wireless communication systems require characterisations of dielectric permittivity and loss tangent at microwave and terahertz bands. La2Ti2O7 is a candidate material for microwave application. However, all the reported microwave dielectric data are average value from different directions of a single crystal, which could not reflect its anisotropic nature due to the layered crystal structure. Its dielectric properties at the microwave and terahertz bands in a single crystallographic direction have rarely been reported. In this work, a single crystal ferroelectric La2Ti2O7 was prepared by floating zone method and its dielectric properties were characterized from 1 kHz to 1 THz along one single direction. The decrease in dielectric permittivity with increasing frequency is related to dielectric relaxation from radio frequency to microwave then to terahertz band. The capability of characterizing anisotropic dielectric properties of a single crystal in this work opens the feasibility for its microwave and terahertz applications.
  • Flow Control Techniques for Enhancing the Bio-Recognition Performance of Microfluidic-Integrated Biosensors

    Shahbazi, Fatemeh; orcid: 0000-0001-9326-1741; email: fatemeh.shahbazi@manchester.ac.uk; Souri, Mohammad; orcid: 0000-0003-0225-6328; email: msouri@seas.harvard.edu; Jabbari, Masoud; email: m.jabbari@manchester.ac.uk; Keshmiri, Amir; email: a.keshmiri@manchester.ac.uk (MDPI, 2021-08-03)
    Biosensors are favored devices for the fast and cost-effective detection of biological species without the need for laboratories. Microfluidic integration with biosensors has advanced their capabilities in selectivity, sensitivity, controllability, and conducting multiple binding assays simultaneously. Despite all the improvements, their design and fabrication are still challenging and time-consuming. The current study aims to enhance microfluidic-integrated biosensors’ performance. Three different functional designs are presented with both active (with the help of electroosmotic flow) and passive (geometry optimization) methods. For validation and further studies, these solutions are applied to an experimental setup for DNA hybridization. The numerical results for the original case have been validated with the experimental data from previous literature. Convection, diffusion, migration, and hybridization of DNA strands during the hybridization process have been simulated with finite element method (FEM) in 3D. Based on the results, increasing the velocity on top of the functionalized surface, by reducing the thickness of the microchamber in that area, would increase the speed of surface coverage by up to 62%. An active flow control with the help of electric field would increase this speed by 32%. In addition, other essential parameters in the fabrication of the microchamber, such as changes in pressure and bulk concentration, have been studied. The suggested designs are simple, applicable and cost-effective, and would not add extra challenges to the fabrication process. Overall, the effect of the geometry of the microchamber on the time and effectiveness of biosensors is inevitable. More studies on the geometry optimization of the microchamber and position of the electrodes using machine learning methods would be beneficial in future works.
  • Editorial for the Special Issue on “Emerging Trends in Phononic Crystals”

    Nouh, Mostafa; orcid: 0000-0002-2135-5391; email: mnouh@buffalo.edu; Parnell, William J.; email: william.parnell@manchester.ac.uk; Hussein, Mahmoud I.; email: mih@colorado.edu (MDPI, 2021-08-03)
    Over the past three decades, the study of phononic crystals (PCs) has rapidly evolved into a prominent research field offering a versatile platform for the creation of structured materials with salient properties [...]
  • Utilising Patient and Public Involvement in Stated Preference Research in Health: Learning from the Existing Literature and a Case Study

    Shields, Gemma E.; orcid: 0000-0003-4869-7524; email: gemma.shields@manchester.ac.uk; Brown, Lindsey; Wells, Adrian; orcid: 0000-0001-7713-1592; Capobianco, Lora; orcid: 0000-0001-6877-8650; Vass, Caroline; orcid: 0000-0002-6385-2812 (Springer International Publishing, 2020-08-04)
    Abstract: Publications reporting discrete choice experiments of healthcare interventions rarely discuss whether patient and public involvement (PPI) activities have been conducted. This paper presents examples from the existing literature and a detailed case study from the National Institute for Health Research-funded PATHWAY programme that comprehensively included PPI activities at multiple stages of preference research. Reflecting on these examples, as well as the wider PPI literature, we describe the different stages at which it is possible to effectively incorporate PPI across preference research, including the design, recruitment and dissemination of projects. Benefits of PPI activities include gaining practical insights from a wider perspective, which can positively impact experiment design as well as survey materials. Further benefits included advice around recruitment and reaching a greater audience with dissemination activities, amongst others. There are challenges associated with PPI activities; examples include time, cost and outlining expectations. Overall, although we acknowledge practical difficulties associated with PPI, this work highlights that it is possible for preference researchers to implement PPI across preference research. Further research systematically comparing methods related to PPI in preference research and their associated impact on the methods and results of studies would strengthen the literature.
  • Functional diversity and identity of plant genotypes regulate rhizodeposition and soil microbial activity

    Semchenko, Marina; orcid: 0000-0001-6196-3562; email: marina.semchenko@manchester.ac.uk; Xue, Piao; Leigh, Tomas; orcid: 0000-0003-4103-8649 (2021-08-04)
    Summary: Our understanding of the linkages between plant diversity and soil carbon and nutrient cycling is primarily derived from studies at the species level, while the importance and mechanisms of diversity effects at the genotype level are poorly understood. Here we examine how genotypic diversity and identity, and associated variation in functional traits, within a common grass species, Anthoxanthum odoratum, modified rhizodeposition, soil microbial activity and litter decomposition. Root litter quality was not significantly affected by plant genotypic diversity, but decomposition was enhanced in soils with the legacy of higher genotypic diversity. Plant genotypic diversity and identity modified rhizodeposition and associated microbial activity via two independent pathways. Plant genotypic diversity enhanced soil functioning via positive effects on variation in specific leaf area and total rhizodeposition. Genotype identity affected both rhizodeposit quantity and quality, and these effects were mediated by differences in mean specific leaf area, shoot mass and plant height. Rhizodeposition was more strongly predicted by aboveground than belowground traits, suggesting strong linkages between photosynthesis and root exudation. Our study demonstrates that functional diversity and identity of plant genotypes modulates belowground carbon supply and quality, representing an important but overlooked pathway by which biodiversity affects ecosystem functioning.
  • Transactions between Big‐5 personality traits and job characteristics across 20 years

    Holman, David J.; email: david.holman@manchester.ac.uk; Hughes, David J. (2021-02-04)
    Although understanding the relationship between the individual and work environment is a core concern of organizational research, few studies have examined longitudinal transactions between Big‐5 personality traits and job characteristics. Building on research in personality and job design we develop hypotheses detailing transactions between Big‐5 personality traits (i.e., openness, conscientiousness, extraversion, agreeableness, neuroticism) and two key job characteristics (i.e., job discretion and workload). Specifically, we hypothesize and test transactions with regard to the effects of job characteristics on personality, the effects of personality on job characteristics, and the reciprocal effects between these constructs. Our findings, based on a latent change score analysis of data collected over three waves across 20 years, show strongest support for the effects of job characteristics on personality, particularly the effects of workload on personality change in openness, extraversion, and agreeableness. We found no effects of job discretion on personality, limited support for the effects of personality on job characteristics (except a positive effect of neuroticism on job discretion), and no evidence of reciprocal effects. Practitioner points: Job demands can alter employee personality. Employees who consistently experienced high workloads over a 20‐year period incurred developmental increases in three personality traits – extraversion, openness, and agreeableness – such that they became more outgoing and assertive, more curious, and broadminded, as well as more helpful and sympathetic. Employees who experienced high job discretion did not incur similar development changes in personality.
  • A diagnostic evaluation of single screen testing for malaria in the returning traveler: A large retrospective cohort study

    editor: Runyon, Michael S.; Reynard, Charles; orcid: 0000-0002-7534-2668; email: Charles.reynard@postgrad.manchester.ac.uk; Geary, Katie; Chiodini, Peter; Brereton, Michelle; Burthem, John; McDermott, John; van den Berg, Patricia; Body, Richard (2021-02-27)
    Abstract: Background: Screening for malaria in the returning traveler has often required repeat testing; however, audit data suggest that patients have not been reattending. We sought to ascertain if this was safe by examining the diagnostic efficacy of a single screen consisting of a rapid diagnostic test (RDT) and a thin film. Methods: We conducted a retrospective cohort study of patients with suspected malaria who attended in the past 5 years from two large teaching hospitals. We assessed the diagnostic accuracy of a single screen, reporting measures of sensitivity and specificity. To establish a reference standard, we cross‐linked data with the national malaria registry held at Public Health England and regional centers. Results: The cohort consisted of 1365 patients, of whom 33 opted out of the research and one did not have a complete initial screen. Of those 1331 screens there were 74 cases of Plasmodium falciparum (prevalence of 5.6%) and 104 of any malaria species (prevalence of 7.8%). Sensitivity for the detection of P. falciparum was 100.00% (95% confidence interval [CI] = 95.1 to 100), with a specificity of 99.4% (95% CI = 98.9 to 99.8). For the detection of any species of malaria the sensitivity was slightly lower due to the presence of one false negative; sensitivity was 99.0% (95% CI = 94.8 to 100) and specificity was 99.5% (95% CI = 98.9 to 99.8). Conclusions: A single thin film and RDT is likely to be sufficient as a first screen for falciparum malaria in the returning traveler with important caveats. For those sent home from emergency departments, appropriate safety netting must be provided. Further prospective study is required to investigate this approach.
  • The plasma membrane calcium ATPase 4 does not influence parasite levels but partially promotes experimental cerebral malaria during murine blood stage malaria.

    Villegas-Mendez, Ana; Stafford, Nicholas; Haley, Michael J; Pravitasari, Normalita Eka; Baudoin, Florence; Ali, Adnan; Asih, Puji Budi Setia; Siregar, Josephine E; Baena, Esther; Syafruddin, Din; et al. (2021-07-02)
    <h4>Background</h4>Recent genome wide analysis studies have identified a strong association between single nucleotide variations within the human ATP2B4 gene and susceptibility to severe malaria. The ATP2B4 gene encodes the plasma membrane calcium ATPase 4 (PMCA4), which is responsible for controlling the physiological level of intracellular calcium in many cell types, including red blood cells (RBCs). It is, therefore, postulated that genetic differences in the activity or expression level of PMCA4 alters intracellular Ca<sup>2+</sup> levels and affects RBC hydration, modulating the invasion and growth of the Plasmodium parasite within its target host cell.<h4>Methods</h4>In this study the course of three different Plasmodium spp. infections were examined in mice with systemic knockout of Pmca4 expression.<h4>Results</h4>Ablation of PMCA4 reduced the size of RBCs and their haemoglobin content but did not affect RBC maturation and reticulocyte count. Surprisingly, knockout of PMCA4 did not significantly alter peripheral parasite burdens or the dynamics of blood stage Plasmodium chabaudi infection or reticulocyte-restricted Plasmodium yoelii infection. Interestingly, although ablation of PMCA4 did not affect peripheral parasite levels during Plasmodium berghei infection, it did promote slight protection against experimental cerebral malaria, associated with a minor reduction in antigen-experienced T cell accumulation in the brain.<h4>Conclusions</h4>The finding suggests that PMCA4 may play a minor role in the development of severe malarial complications, but that this appears independent of direct effects on parasite invasion, growth or survival within RBCs.
  • The T cell receptor repertoire of tumor infiltrating T cells is predictive and prognostic for cancer survival.

    Valpione, Sara; Mundra, Piyushkumar A; Galvani, Elena; Campana, Luca G; orcid: 0000-0002-8466-8459; Lorigan, Paul; orcid: 0000-0002-8875-2164; De Rosa, Francesco; orcid: 0000-0003-0511-1298; Gupta, Avinash; Weightman, John; Mills, Sarah; Dhomen, Nathalie; et al. (2021-07-02)
    Tumor infiltration by T cells is paramount for effective anti-cancer immune responses. We hypothesized that the T cell receptor (TCR) repertoire of tumor infiltrating T lymphocytes could therefore be indicative of the functional state of these cells and determine disease course at different stages in cancer progression. Here we show that the diversity of the TCR of tumor infiltrating T cell at baseline is prognostic in various cancers, whereas the TCR clonality of T cell infiltrating metastatic melanoma pre-treatment is predictive for activity and efficacy of PD1 blockade immunotherapy.
  • Testing the Efficacy of the Synthesis of Iron Antimony Sulfide Powders from Single Source Precursors

    Makin, Fadiyah; email: fadiyah.makin@postgrad.manchester.ac.uk; Alzahrani, Dalal; email: dalal.alzahrani@postgrad.manchester.ac.uk; Alam, Firoz; orcid: 0000-0002-5070-5899; email: firoz.alam@manchester.ac.uk; Tuna, Floriana; email: Floriana.Tuna@manchester.ac.uk; Lewis, David J.; orcid: 0000-0001-5950-1350; email: david.lewis-4@manchester.ac.uk (MDPI, 2021-08-02)
    The antimony-iron sulfide system in general does not produce alloys below 540 °C from traditional solid-state methods. However, single source precursors have been known to produce unexpected products that arise from kinetically trapped polymorphs. In this paper, we test the efficacy of this approach toward the Fe-Sb-S system. Antimony and iron diethyldithiocarbamate complexes of the form Sb[S2CN(Et2)]3 (1) and Fe[S2CN(Et2)]3 (2) were synthesised, characterised, and used as single-source precursors for the preparation of Sb2S3, FexSy, and mixed iron antimony sulfide Sb2(1−x)Fe2xS3 (0 ≥ x ≥ 1) powders using the solvent-less thermolysis method at different temperatures ranging from 300 to 475 °C. The effect of different mole fractions of the iron precursor was evaluated on morphology, shape, and optical and magnetic properties of Sb2(1−x)Fe2xS3 (0 ≥ x ≥ 1). The obtained powders were characterized by X-ray diffraction (XRD), Raman spectroscopy scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, magnetometer measurement, and UV/vis/NIR spectroscopy. The results demonstrated that the crystalline structure, morphology, and elemental composition of the samples changed with the mole fraction of the precursor. There was significant phase separation between Sb and Fe sulfides noted from EDX spectroscopic mapping, yet an optoelectronic study monitoring the direct band gap energy of antimony sulfide shows that the band gap energy increases as a function of Fe content, which suggests limited alloying is possible from the single source route.
  • Re-purposing evaluation to learn about social justice: Reconfiguring epistemological politics through the regulative ideal of ‘participatory parity’

    Silver, Daniel; orcid: 0000-0001-7316-5146; email: daniel.silver@manchester.ac.uk (SAGE Publications, 2020-12-24)
    The article aims to re-purpose evaluation to learn about social justice by anchoring evaluation in normative dimensions. This article demonstrates the ways in which evaluation with an establishment orientation can limit the scope for dialogue and neglect narratives that contest the status quo. It explains how a more participatory approach that engages with the standpoints of marginalised participants can enhance the potential to learn about social justice. An ethical commitment to social justice does not mean a rejection of rigour in evidence-based evaluation. Relating Fraser’s critical theory of participatory parity to the regulative ideal of evaluation creates a foundation to systematically foreground explanations about how an intervention has delivered social justice.
  • Detection of early changes in the post-radiosurgery vestibular schwannoma microenvironment using multinuclear MRI

    Lewis, Daniel; email: daniel.lewis-3@postgrad.manchester.ac.uk; McHugh, Damien J.; Li, Ka-loh; Zhu, Xiaoping; Mcbain, Catherine; Lloyd, Simon K.; Jackson, Alan; Pathmanaban, Omar N.; King, Andrew T.; Coope, David J. (Nature Publishing Group UK, 2021-08-03)
    Abstract: Stereotactic radiosurgery (SRS) is an established, effective therapy against vestibular schwannoma (VS). The mechanisms of tumour response are, however, unknown and in this study we sought to evaluate changes in the irradiated VS tumour microenvironment through a multinuclear MRI approach. Five patients with growing sporadic VS underwent a multi-timepoint comprehensive MRI protocol, which included diffusion tensor imaging (DTI), dynamic contrast-enhanced (DCE) MRI and a spiral 23Na-MRI acquisition for total sodium concentration (TSC) quantification. Post-treatment voxelwise changes in TSC, DTI metrics and DCE-MRI derived microvascular biomarkers (Ktrans, ve and vp) were evaluated and compared against pre-treatment values. Changes in tumour TSC and microvascular parameters were observable as early as 2 weeks post-treatment, preceding changes in structural imaging. At 6 months post-treatment there were significant voxelwise increases in tumour TSC (p < 0.001) and mean diffusivity (p < 0.001, repeated-measures ANOVA) with marked decreases in tumour microvascular parameters (p < 0.001, repeated-measures ANOVA). This study presents the first in vivo evaluation of alterations in the VS tumour microenvironment following SRS, demonstrating that changes in tumour sodium homeostasis and microvascular parameters can be imaged as early as 2 weeks following treatment. Future studies should seek to investigate these clinically relevant MRI metrics as early biomarkers of SRS response.
  • A consideration of publication-derived immune-related associations in Coronavirus and related lung damaging diseases

    Geifman, Nophar; orcid: 0000-0003-2956-6676; email: nophar.geifman@manchester.ac.uk; Whetton, Anthony D. (BioMed Central, 2020-08-03)
    Abstract: Background: The severe acute respiratory syndrome virus SARS-CoV-2, a close relative of the SARS-CoV virus, is the cause of the recent COVID-19 pandemic affecting, to date, over 14 million individuals across the globe and demonstrating relatively high rates of infection and mortality. A third virus, the H5N1, responsible for avian influenza, has caused infection with some clinical similarities to those in COVID-19 infections. Cytokines, small proteins that modulate immune responses, have been directly implicated in some of the severe responses seen in COVID-19 patients, e.g. cytokine storms. Understanding the immune processes related to COVID-19, and other similar infections, could help identify diagnostic markers and therapeutic targets. Methods: Here we examine data of cytokine, immune cell types, and disease associations captured from biomedical literature associated with COVID-19, Coronavirus in general, SARS, and H5N1 influenza, with the objective of identifying potentially useful relationships and areas for future research. Results: Cytokine and cell-type associations captured from Medical Subject Heading (MeSH) terms linked to thousands of PubMed records, has identified differing patterns of associations between the four corpuses of publications (COVID-19, Coronavirus, SARS, or H5N1 influenza). Clustering of cytokine-disease co-occurrences in the context of Coronavirus has identified compelling clusters of co-morbidities and symptoms, some of which already known to be linked to COVID-19. Finally, network analysis identified sub-networks of cytokines and immune cell types associated with different manifestations, co-morbidities and symptoms of Coronavirus, SARS, and H5N1. Conclusion: Systematic review of research in medicine is essential to facilitate evidence-based choices about health interventions. In a fast moving pandemic the approach taken here will identify trends and enable rapid comparison to the literature of related diseases.
  • Studying Effects of Calcium Oxide Nanoparticles on Dentinogenesis in Male Wistar Rats

    Academic Editor: Mallineni, Sreekanth Kumar; Al-Maula, Bushra Habeeb; orcid: 0000-0002-2293-4897; email: bushraalmaula@gmail.com; Wally, Zena Jehad; orcid: 0000-0002-0885-0179; email: zinah.alnuaimi@uokufa.edu.iq; Al-Magsoosi, Mohanad Jameel Najm; orcid: 0000-0002-9007-2870; email: muhanned72@yahoo.com; Dosh, Rasha Hatem; orcid: 0000-0002-2318-6608; email: rasha.dosh@uokufa.edu.iq; Mustafa, Ruba M.; orcid: 0000-0002-3425-459X; email: rmmustafa@just.edu.jo; Al-Nasrawi, Suhad Jabbar Hamed; orcid: 0000-0003-3045-7389; email: suhad.alnasrawi@uokufa.edu.iq; Alfutimie, Abdullatif; orcid: 0000-0002-2531-3762; email: abdullatif.alfutimie@manchester.ac.uk; Haider, Julfikar; orcid: 0000-0001-7010-8285; email: j.haider@mmu.ac.uk (Hindawi, 2021-07-26)
    This study aimed to evaluate potential impacts of calcium oxide nanoparticles (CaO-NPs) at different dosages on predentin thickness, number of blood vessels, periodontal ligament thickness, and blood glucose level of Wistar rats. Twelve rats were randomly gathered into four groups, untreated (control) and CaO-NP-treated groups at three concentrations (25, 50, and 100 mg/kg of the body weight) over a period of 60 days. Histological investigation was performed on twenty-four lower incisor teeth extracted from all the tested groups under a light microscope, and an automatic Fujifilm was used to measure the blood glucose level. The results showed that regular nanoparticle treatment significantly increased predentin and periodontal ligament thicknesses, a gradual decrease in vascularization in the pulp tissue, and an increase in the blood glucose level as the dosages of nanoparticles administered to the rats increased. Administration of the CaO-NPs at low dosage (25 mg/kg) could be beneficial for the growth and integrity of teeth and dentinal tissues in rats.
  • An alternative pathway for membrane protein biogenesis at the endoplasmic reticulum.

    O'Keefe, Sarah; orcid: 0000-0002-1744-0198; email: sarah.okeefe@manchester.ac.uk; Zong, Guanghui; orcid: 0000-0002-7335-039X; Duah, Kwabena B; Andrews, Lauren E; Shi, Wei Q; orcid: 0000-0001-5453-1753; High, Stephen; orcid: 0000-0002-4532-8152; email: stephen.high@manchester.ac.uk (2021-07-01)
    The heterotrimeric Sec61 complex is a major site for the biogenesis of transmembrane proteins (TMPs), accepting nascent TMP precursors that are targeted to the endoplasmic reticulum (ER) by the signal recognition particle (SRP). Unlike most single-spanning membrane proteins, the integration of type III TMPs is completely resistant to small molecule inhibitors of the Sec61 translocon. Using siRNA-mediated depletion of specific ER components, in combination with the potent Sec61 inhibitor ipomoeassin F (Ipom-F), we show that type III TMPs utilise a distinct pathway for membrane integration at the ER. Hence, following SRP-mediated delivery to the ER, type III TMPs can uniquely access the membrane insertase activity of the ER membrane complex (EMC) via a mechanism that is facilitated by the Sec61 translocon. This alternative EMC-mediated insertion pathway allows type III TMPs to bypass the Ipom-F-mediated blockade of membrane integration that is seen with obligate Sec61 clients.
  • Insulin protects acinar cells during pancreatitis by preserving glycolytic ATP supply to calcium pumps.

    Bruce, Jason I E; orcid: 0000-0002-4503-1981; email: jason.bruce@manchester.ac.uk; Sánchez-Alvarez, Rosa; Sans, Maria Dolors; orcid: 0000-0002-9271-2106; Sugden, Sarah A; Qi, Nathan; James, Andrew D; orcid: 0000-0002-2432-5948; Williams, John A (2021-07-19)
    Acute pancreatitis (AP) is serious inflammatory disease of the pancreas. Accumulating evidence links diabetes with severity of AP, suggesting that endogenous insulin may be protective. We investigated this putative protective effect of insulin during cellular and in vivo models of AP in diabetic mice (Ins2 ) and Pancreatic Acinar cell-specific Conditional Insulin Receptor Knock Out mice (PACIRKO). Caerulein and palmitoleic acid (POA)/ethanol-induced pancreatitis was more severe in both Ins2 and PACIRKO vs control mice, suggesting that endogenous insulin directly protects acinar cells in vivo. In isolated pancreatic acinar cells, insulin induced Akt-mediated phosphorylation of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (PFKFB2) which upregulated glycolysis thereby preventing POA-induced ATP depletion, inhibition of the ATP-dependent plasma membrane Ca ATPase (PMCA) and cytotoxic Ca overload. These data provide the first mechanistic link between diabetes and severity of AP and suggest that phosphorylation of PFKFB2 may represent a potential therapeutic strategy for treatment of AP. [Abstract copyright: © 2021. The Author(s).]
  • Technical Note: Four‐dimensional deformable digital phantom for MRI sequence development

    Hanson, Hanna M.; email: hanna.hanson@postgrad.manchester.ac.uk; Eiben, Björn; McClelland, Jamie R.; van Herk, Marcel; Rowland, Benjamin C. (2021-08-02)
    Abstract: Purpose: MR‐guided radiotherapy has different requirements for the images than diagnostic radiology, thus requiring development of novel imaging sequences. MRI simulation is an excellent tool for optimizing these new sequences; however, currently available software does not provide all the necessary features. In this paper, we present a digital framework for testing MRI sequences that incorporates anatomical structure, respiratory motion, and realistic presentation of MR physics. Methods: The extended Cardiac‐Torso (XCAT) software was used to create T1, T2, and proton density maps that formed the anatomical structure of the phantom. Respiratory motion model was based on the XCAT deformation vector fields, modified to create a motion model driven by a respiration signal. MRI simulation was carried out with JEMRIS, an open source Bloch simulator. We developed an extension for JEMRIS, which calculates the motion of each spin independently, allowing for deformable motion. Results: The performance of the framework was demonstrated through simulating the acquisition of a two‐dimensional (2D) cine and demonstrating expected motion ghosts from T2 weighted spin echo acquisitions with different respiratory patterns. All simulations were consistent with behavior previously described in literature. Simulations with deformable motion were not more time consuming than with rigid motion. Conclusions: We present a deformable four‐dimensional (4D) digital phantom framework for MR sequence development. The framework incorporates anatomical structure, realistic breathing patterns, deformable motion, and Bloch simulation to achieve accurate simulation of MRI. This method is particularly relevant for testing novel imaging sequences for the purpose of MR‐guided radiotherapy in lungs and abdomen.
  • The unequal-time matter power spectrum: impact on weak lensing observables

    de la Bella, Lucia F.; email: lucia.fonsecadelabella@manchester.ac.uk; Tessore, Nicolas; email: n.tessore@ucl.ac.uk; Bridle, Sarah; email: sarah.bridle@manchester.ac.uk (IOP Publishing, 2021-08-02)
    Abstract: We investigate the impact of a common approximation of weak lensing power spectra: the use of single-epoch matter power spectra in integrals over redshift. We disentangle this from the closely connected Limber's approximation. We derive the unequal-time matter power spectrum at one-loop in standard perturbation theory and effective field theory to deal with non-linear physics. We compare these formalisms and conclude that the unequal-time power spectrum using effective field theory breaks for larger scales. As an alternative we introduce the midpoint approximation. We also provide, for the first time, a fitting function for the time evolution of the effective field theory counterterms based on the Quijote simulations. Then we compute the angular power spectrum using a range of approaches: the Limber approximation, and the geometric and midpoint approximations. We compare our results with the exact calculation at all angular scales using the unequal-time power spectrum. We use DES Y1 and LSST-like redshift distributions for our analysis. We find that the use of the Limber's approximation in weak lensing diverges from the exact calculation of the angular power spectrum on large-angle separations, ℓ < 10. Even though this deviation is of order 2% maximum for cosmic lensing, we find the biggest effect for galaxy clustering and galaxy-galaxy lensing. We show that not only is this true for upcoming galaxy surveys, but also for current data such as DES Y1. Finally, we make our pipeline and analysis publicly available as a Python package called unequalpy.
  • The unequal-time matter power spectrum: impact on weak lensing observables

    de la Bella, Lucia F.; email: lucia.fonsecadelabella@manchester.ac.uk; Tessore, Nicolas; email: n.tessore@ucl.ac.uk; Bridle, Sarah; email: sarah.bridle@manchester.ac.uk (IOP Publishing, 2021-08-02)
    Abstract: We investigate the impact of a common approximation of weak lensing power spectra: the use of single-epoch matter power spectra in integrals over redshift. We disentangle this from the closely connected Limber's approximation. We derive the unequal-time matter power spectrum at one-loop in standard perturbation theory and effective field theory to deal with non-linear physics. We compare these formalisms and conclude that the unequal-time power spectrum using effective field theory breaks for larger scales. As an alternative we introduce the midpoint approximation. We also provide, for the first time, a fitting function for the time evolution of the effective field theory counterterms based on the Quijote simulations. Then we compute the angular power spectrum using a range of approaches: the Limber approximation, and the geometric and midpoint approximations. We compare our results with the exact calculation at all angular scales using the unequal-time power spectrum. We use DES Y1 and LSST-like redshift distributions for our analysis. We find that the use of the Limber's approximation in weak lensing diverges from the exact calculation of the angular power spectrum on large-angle separations, ℓ < 10. Even though this deviation is of order 2% maximum for cosmic lensing, we find the biggest effect for galaxy clustering and galaxy-galaxy lensing. We show that not only is this true for upcoming galaxy surveys, but also for current data such as DES Y1. Finally, we make our pipeline and analysis publicly available as a Python package called unequalpy.
  • The new cold war and the rise of the 21st‐century infrastructure state

    Schindler, Seth; orcid: 0000-0003-2233-0628; email: seth.schindler@manchester.ac.uk; DiCarlo, Jessica; orcid: 0000-0003-1178-5053; Paudel, Dinesh; orcid: 0000-0001-9100-4012 (2021-08-02)
    Abstract: The unipolar international order led by the USA has given way to a multipolar order with the emergence of China as a great power competitor. According to many commentators, the deterioration of Sino–US relations in recent years heralds a “new Cold War.” The new Cold War differs from its namesake in many respects, and in this paper we focus on its novel territorial logic. Containing the USSR was the overriding objective of American foreign policy for nearly four decades, but in contrast, the USA and China are engaged in geopolitical‐economic competition to integrate territory into value chains anchored by their domestic lead firms through the financing and construction of transnational infrastructure (e.g., transportation networks and regional energy grids). We show this competition poses risks as well as opportunities for small states to articulate and realise spatial objectives. We present cases from Nepal and Laos that demonstrate that by hedging between China and the USA and its partners, their governments are able to pursue spatial objectives. In order to achieve them, however, they must implement significant reforms or state restructuring. The result is the emergence of what we term the 21st‐century infrastructure state, which seeks to mobilise foreign capital for infrastructure projects designed to enhance transnational connectivity.

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