• Building a consistent parton shower

      Forshaw, Jeffrey R.; Holguin, Jack; orcid: 0000-0001-5183-2673; email: jack.holguin@manchester.ac.uk; Plätzer, Simon (Springer Berlin Heidelberg, 2020-09-01)
      Abstract: Modern parton showers are built using one of two models: dipole showers or angular ordered showers. Both have distinct strengths and weaknesses. Dipole showers correctly account for wide-angle, soft gluon emissions and track the leading flows in QCD colour charge but they are known to mishandle partonic recoil. Angular ordered showers keep better track of partonic recoil and correctly include large amounts of wide-angle, soft physics but azimuthal averaging means they are known to mishandle some correlations. In this paper, we derive both approaches from the same starting point; linking our under- standing of the two showers. This insight allows us to construct a new dipole shower that has all the strengths of a standard dipole shower together with the collinear evolution of an angular-ordered shower. We show that this new approach corrects the next-to-leading- log errors previously observed in parton showers and improves their sub-leading-colour accuracy.
    • Cell-specific conditional deletion of interleukin-1 (IL-1) ligands and its receptors: a new toolbox to study the role of IL-1 in health and disease

      Pinteaux, Emmanuel; orcid: 0000-0002-9986-4401; email: emmanuel.pinteaux@manchester.ac.uk; Abdulaal, Wesam H; Mufazalov, Ilgiz A; Humphreys, Neil E; Simonsen-Jackson, Maj; Francis, Sheila; Müller, Werner; Waisman, Ari (Springer Berlin Heidelberg, 2020-05-29)
      Abstract: The pro-inflammatory cytokine interleukin-1 (IL-1) plays a key role in many physiological processes and during the inflammatory and immune response to most common diseases. IL-1 exists as two agonists, IL-1α and IL-1β that bind to the only signaling IL-1 type 1 receptor (IL-1R1), while a second decoy IL-1 type 2 receptor (IL-1R2) binds both forms of IL-1 without inducing cell signaling. The field of immunology and inflammation research has, over the past 35 years, unraveled many mechanisms of IL-1 actions, through in vitro manipulation of the IL-1 system or by using genetically engineered mouse models that lack either member of the IL-1 family in ubiquitous constitutive manner. However, the limitation of global mouse knockout technology has significantly hampered our understanding of the precise mechanisms of IL-1 actions in animal models of disease. Here we report and review the recent generation of new conditional mouse mutants in which exons of Il1a, Il1b, Il1r1, and Il1r2 genes flanked by loxP sites (fl/fl) can be deleted in cell-/tissue-specific constitutive or inducible manner by Cre recombinase expression. Hence, IL-1αfl/fl, IL-1βfl/fl, IL-1R1fl/fl, and IL-1R2fl/fl mice constitute a new toolbox that will provide a step change in our understanding of the cell-specific role of IL-1 and its receptor in health and disease and the potential development of targeted IL-1 therapies.
    • Direct comparison of sterile neutrino constraints from cosmological data, ν e disappearance data and ν μ → ν e appearance data in a 3 + 1 model

      Adams, Matthew; Bezrukov, Fedor; Elvin-Poole, Jack; Evans, Justin J.; orcid: 0000-0003-4697-3337; email: justin.evans@manchester.ac.uk; Guzowski, Pawel; Fearraigh, Brían Ó; Söldner-Rembold, Stefan (Springer Berlin Heidelberg, 2020-08-19)
      Abstract: We present a quantitative, direct comparison of constraints on sterile neutrinos derived from neutrino oscillation experiments and from Planck data, interpreted assuming standard cosmological evolution. We extend a 1+1 model, which is used to compare exclusion contours at the 95% Cl derived from Planck data to those from νe-disappearance measurements, to a 3+1 model. This allows us to compare the Planck constraints with those obtained through νμ→νe appearance searches, which are sensitive to more than one active-sterile mixing angle. We find that the cosmological data fully exclude the allowed regions published by the LSND, MiniBooNE and Neutrino-4 collaborations, and those from the gallium and rector anomalies, at the 95% Cl. Compared to the exclusion region from the Daya Bay νe-disappearance search, the Planck data are more strongly excluding above |Δm412|≈0.1eV2 and meffsterile≈0.2eV, with the Daya Bay exclusion being stronger below these values. Compared to the combined Daya Bay/Bugey/MINOS exclusion region on νμ→νe appearance, the Planck data is more strongly excluding above Δm412≈5×10-2eV2, with the exclusion strengths of the Planck data and the Daya Bay/Bugey/MINOS combination becoming comparable below this value.
    • Discrete beliefs space and equilibrium: a cautionary note

      Berardi, Michele; orcid: 0000-0001-8145-5207; email: michele.berardi@manchester.ac.uk (Springer Berlin Heidelberg, 2020-06-29)
      Abstract: Bounded rationality requires assumptions about ways in which rationality is constrained and agents form their expectations. Evolutionary schemes have been used to model beliefs dynamics, with agents choosing endogenously among a limited number of beliefs heuristics according to their relative performance. This work shows that arbitrarily constraining the beliefs space to a finite (small) set of possibilities can generate artificial equilibria that can be stable under evolutionary dynamics. Only when “enough” heuristics are available are beliefs in equilibrium not artificially constrained. I discuss these findings in light of an alternative approach to modelling beliefs dynamics, namely, adaptive learning.
    • Discrete beliefs space and equilibrium: a cautionary note

      Berardi, Michele; orcid: 0000-0001-8145-5207; email: michele.berardi@manchester.ac.uk (Springer Berlin Heidelberg, 2020-06-29)
      Abstract: Bounded rationality requires assumptions about ways in which rationality is constrained and agents form their expectations. Evolutionary schemes have been used to model beliefs dynamics, with agents choosing endogenously among a limited number of beliefs heuristics according to their relative performance. This work shows that arbitrarily constraining the beliefs space to a finite (small) set of possibilities can generate artificial equilibria that can be stable under evolutionary dynamics. Only when “enough” heuristics are available are beliefs in equilibrium not artificially constrained. I discuss these findings in light of an alternative approach to modelling beliefs dynamics, namely, adaptive learning.
    • Does posture explain the kinematic differences in a grounded running gait between male and female Svalbard rock ptarmigan ( Lagopus muta hyperborea ) moving on snow?

      Marmol-Guijarro, Andres; orcid: 0000-0001-9316-540X; Nudds, Robert; orcid: 0000-0002-7627-6324; Folkow, Lars; orcid: 0000-0002-6580-9156; Lees, John; orcid: 0000-0002-9627-1790; Codd, Jonathan; orcid: 0000-0003-0211-1786; email: jonathan.codd@manchester.ac.uk (Springer Berlin Heidelberg, 2021-05-05)
      Abstract: The majority of locomotor research is conducted on treadmills and few studies attempt to understand the differences between this and animals moving in the wild. For example, animals may adjust their gait kinematics or limb posture, to a more compliant limb, to increase stability of locomotion to prevent limb failure or falling on different substrates. Here, using video recordings, we compared locomotor parameters (speed range, stride length, stride frequency, stance duration, swing duration and duty factor) of female Svalbard rock ptarmigan (Lagopus muta hyperborea) moving in the wild over snow to previous treadmill-based research. We also compared the absolute and body size (body mass and limb length)-corrected values of kinematic parameters to published data from males to look for any sex differences across walking and grounded running gaits. Our findings indicate that the kinematics of locomotion are largely conserved between the field and laboratory in that none of the female gaits were drastically affected by moving over snow, except for a prolonged swing phase at very slow walking speeds, likely due to toe dragging. Comparisons between the sexes indicate that the differences observed during a walking gait are likely due to body size. However, sexual dimorphism in body size could not explain the disparate grounded running kinematics of the female and male ptarmigan, which might be linked to a more crouched posture in females. Our findings provide insight into how males and females moving in situ may use different strategies to alleviate the effects of a variable substrate.
    • EFT for soft drop double differential cross section

      Pathak, Aditya; orcid: 0000-0001-8149-2817; email: aditya.pathak@manchester.ac.uk; Stewart, Iain W.; Vaidya, Varun; Zoppi, Lorenzo; orcid: 0000-0002-9157-6907 (Springer Berlin Heidelberg, 2021-04-06)
      Abstract: We develop a factorization framework to compute the double differential cross section in soft drop groomed jet mass and groomed jet radius. We describe the effective theories in the large, intermediate, and small groomed jet radius regions defined by the interplay of the jet mass and the groomed jet radius measurement. As an application we present the NLL′ results for the perturbative moments that are related to the coefficients C1 and C2 that specify the leading hadronization corrections up to three universal parameters. We compare our results with Monte Carlo simulations and a calculation using the coherent branching method.
    • Frame covariant formalism for fermionic theories

      Finn, Kieran; orcid: 0000-0002-9840-2264; email: kieran.finn@manchester.ac.uk; Karamitsos, Sotirios; Pilaftsis, Apostolos (Springer Berlin Heidelberg, 2021-07-02)
      Abstract: We present a frame- and reparametrisation-invariant formalism for quantum field theories that include fermionic degrees of freedom. We achieve this using methods of field-space covariance and the Vilkovisky–DeWitt (VDW) effective action. We explicitly construct a field-space supermanifold on which the quantum fields act as coordinates. We show how to define field-space tensors on this supermanifold from the classical action that are covariant under field reparametrisations. We then employ these tensors to equip the field-space supermanifold with a metric, thus solving a long-standing problem concerning the proper definition of a metric for fermionic theories. With the metric thus defined, we use well-established field-space techniques to extend the VDW effective action and express any fermionic theory in a frame- and field-reparametrisation-invariant manner.
    • From parametric trace slicing to rule systems

      Reger, Giles; email: giles.reger@manchester.ac.uk; Rydeheard, David (Springer Berlin Heidelberg, 2021-02-27)
      Abstract: Parametric runtime verification is the process of verifying properties of execution traces of (data carrying) events produced by a running system. This paper continues our work exploring the relationship between specification techniques for parametric runtime verification. Here we consider the correspondence between trace-slicing automata-based approaches and rule systems. The main contribution is a translation from quantified automata to rule systems, which has been implemented in Scala. This then allows us to highlight the key differences in how the two formalisms handle data, an important step in our wider effort to understand the correspondence between different specification languages for parametric runtime verification. This paper extends a previous conference version of this paper with further examples, a proof of correctness, and an optimisation based on a notion of redundancy observed during the development of the translation.
    • Herwig 7.2 release note

      Bellm, Johannes; Bewick, Gavin; Ferrario Ravasio, Silvia; Gieseke, Stefan; Grellscheid, David; Kirchgaeßer, Patrick; Loshaj, Frashër; Masouminia, Mohammad R.; Nail, Graeme; Papaefstathiou, Andreas; et al. (Springer Berlin Heidelberg, 2020-05-20)
      Abstract: A new release of the Monte Carlo event generator Herwig (version 7.2) is now available. This version introduces a number of improvements over the major version 7.0, notably: multi-jet merging with the dipole shower at LO and NLO QCD; spin correlations in both the dipole and angular-ordered parton showers; an improved choice of evolution variable in the angular-ordered parton shower; improvements to mass effects and top decays in the dipole shower, improvements to the simulation of multiple-parton interactions, including diffractive processes; a new model for baryonic colour reconnection; improvements to strangeness production; as well as a new tune of the hadronisation parameters and support for generic Lorentz structures in BSM models. This article illustrates new features of versions 7.1 and 7.2.
    • Improvements on dipole shower colour

      Holguin, Jack; orcid: 0000-0001-5183-2673; email: jack.holguin@manchester.ac.uk; Forshaw, Jeffrey R.; Plätzer, Simom (Springer Berlin Heidelberg, 2021-04-27)
      Abstract: The dipole formalism provides a powerful framework from which parton showers can be constructed. In a recent paper (Forshaw et al. 2020), we proposed a dipole shower with improved colour accuracy and in this paper we show how it can be further improved. After an explicit check at O(αs2) we confirm that our original shower performs as it was designed to, i.e. inheriting its handling of angular-ordered radiation from a coherent branching algorithm. We also show how other dipole shower algorithms fail to achieve this. Nevertheless, there is an O(αs2) topology where it differs at sub-leading Nc from a coherent branching algorithm. This erroneous topology can contribute a leading logarithm to some observables and corresponds to emissions that are ordered in kt but not angle. We propose a simple, computationally efficient way to correct this and assign colour factors in accordance with the coherence properties of QCD to all orders in αs.
    • Investigating the importance of B cells and antibodies during Trichuris muris infection using the IgMi mouse

      Sahputra, Rinal; orcid: 0000-0001-6612-0417; email: rinal.sahputra@manchester.ac.uk; Murphy, Emma A; Forman, Ruth; Mair, Iris; Fadlullah, Muhammad Z. H.; Waisman, Ari; Muller, Werner; Else, Kathryn J.; email: kathryn.j.else@manchester.ac.uk (Springer Berlin Heidelberg, 2020-08-10)
      Abstract: The IgMi mouse has normal B cell development; its B cells express an IgM B cell receptor but cannot class switch or secrete antibody. Thus, the IgMi mouse offers a model system by which to dissect out antibody-dependent and antibody-independent B cell function. Here, we provide the first detailed characterisation of the IgMi mouse post-Trichuris muris (T. muris) infection, describing expulsion phenotype, cytokine production, gut pathology and changes in T regulatory cells, T follicular helper cells and germinal centre B cells, in addition to RNA sequencing (RNA seq) analyses of wild-type littermates (WT) and mutant B cells prior to and post infection. IgMi mice were susceptible to a high-dose infection, with reduced Th2 cytokines and elevated B cell-derived IL-10 in mesenteric lymph nodes (MLN) compared to controls. A low-dose infection regime revealed IgMi mice to have significantly more apoptotic cells in the gut compared to WT mice, but no change in intestinal inflammation. IL-10 levels were again elevated. Collectively, this study showcases the potential of the IgMi mouse as a tool for understanding B cell biology and suggests that the B cell plays both antibody-dependent and antibody-independent roles post high- and low-dose T. muris infection. Key messages: During a high-dose T. muris infection, B cells are important in maintaining the Th1/Th2 balance in the MLN through an antibody-independent mechanism. High levels of IL-10 in the MLN early post-infection, and the presence of IL-10-producing B cells, correlates with susceptibility to T. muris infection. B cells maintain gut homeostasis during chronic T. muris infection via an antibody-dependent mechanism.
    • Physiological and anthropometric determinants of critical power, W ′ and the reconstitution of W ′ in trained and untrained male cyclists

      Chorley, Alan; orcid: 0000-0003-0000-3394; email: a.chorley@chester.ac.uk; Bott, Richard P.; orcid: 0000-0002-7842-2436; Marwood, Simon; orcid: 0000-0003-4668-1131; Lamb, Kevin L.; orcid: 0000-0003-4481-4711 (Springer Berlin Heidelberg, 2020-08-09)
      Abstract: Purpose: This study examined the relationship of physiological and anthropometric characteristics with parameters of the critical power (CP) model, and in particular the reconstitution of W′ following successive bouts of maximal exercise, amongst trained and untrained cyclists. Methods: Twenty male adults (trained nine; untrained 11; age 39 ± 15 year; mass 74.7 ± 8.7 kg; V̇O2max 58.0 ± 8.7 mL kg−1 min−1) completed three incremental ramps (20 W min−1) to exhaustion interspersed with 2-min recoveries. Pearson’s correlation coefficients were used to assess relationships for W′ reconstitution after the first recovery (W′rec1), the delta in W′ reconstituted between recoveries (∆W′rec), CP and W′. Results: CP was strongly related to V̇O2max for both trained (r = 0.82) and untrained participants (r = 0.71), whereas W′ was related to V̇O2max when both groups were considered together (r = 0.54). W′rec1 was strongly related to V̇O2max for the trained (r = 0.81) but not untrained (r = 0.18); similarly, ∆W′rec was strongly related to V̇O2max (r = − 0.85) and CP (r = − 0.71) in the trained group only. Conclusions: Notable physiological relationships between parameters of aerobic fitness and the measurements of W′ reconstitution were observed, which differed among groups. The amount of W′ reconstitution and the maintenance of W′ reconstitution that occurred with repeated bouts of maximal exercise were found to be related to key measures of aerobic fitness such as CP and V̇O2max. This data demonstrates that trained cyclists wishing to improve their rate of W′ reconstitution following repeated efforts should focus training on improving key aspects of aerobic fitness such as V̇O2max and CP.
    • Practical Demonstration of a Hybrid Model for Optimising the Reliability, Risk, and Maintenance of Rolling Stock Subsystem

      Appoh, Frederick; orcid: 0000-0003-4228-5799; email: frederick.appoh@manchester.ac.uk; Yunusa-Kaltungo, Akilu; orcid: 0000-0001-5138-3783; Sinha, Jyoti Kumar; orcid: 0000-0001-9202-1789; Kidd, Moray; orcid: 0000-0003-4185-5788 (Springer Berlin Heidelberg, 2021-05-11)
      Abstract: Railway transport system (RTS) failures exert enormous strain on end-users and operators owing to in-service reliability failure. Despite the extensive research on improving the reliability of RTS, such as signalling, tracks, and infrastructure, few attempts have been made to develop an effective optimisation model for improving the reliability, and maintenance of rolling stock subsystems. In this paper, a new hybrid model that integrates reliability, risk, and maintenance techniques is proposed to facilitate engineering failure and asset management decision analysis. The upstream segment of the model consists of risk and reliability techniques for bottom-up and top-down failure analysis using failure mode effects and criticality analysis and fault tree analysis, respectively. The downstream segment consists of a (1) decision-making grid (DMG) for the appropriate allocation of maintenance strategies using a decision map and (2) group decision-making analysis for selecting appropriate improvement options for subsystems allocated to the worst region of the DMG map using the multi-criteria pairwise comparison features of the analytical hierarchy process. The hybrid model was illustrated through a case study for replacing an unreliable pneumatic brake unit (PBU) using operational data from a UK-based train operator where the frequency of failures and delay minutes exceeded the operator’s original target by 300% and 900%, respectively. The results indicate that the novel hybrid model can effectively analyse and identify a new PBU subsystem that meets the operator’s reliability, risk, and maintenance requirements.
    • Predictive approaches to guide the expression of recombinant vaccine targets in Escherichia coli: a case study presentation utilising Absynth Biologics Ltd. proprietary Clostridium difficile vaccine antigens

      Hussain, Hirra; McKenzie, Edward A; Robinson, Andrew M; Gingles, Neill A; Marston, Fiona; Warwicker, Jim; Dickson, Alan J; orcid: 0000-0001-9490-645X; email: alan.dickson@manchester.ac.uk (Springer Berlin Heidelberg, 2021-06-28)
      Abstract: Bacterial expression systems remain a widely used host for recombinant protein production. However, overexpression of recombinant target proteins in bacterial systems such as Escherichia coli can result in poor solubility and the formation of insoluble aggregates. As a consequence, numerous strategies or alternative engineering approaches have been employed to increase recombinant protein production. In this case study, we present the strategies used to increase the recombinant production and solubility of ‘difficult-to-express’ bacterial antigens, termed Ant2 and Ant3, from Absynth Biologics Ltd.’s Clostridium difficile vaccine programme. Single recombinant antigens (Ant2 and Ant3) and fusion proteins (Ant2-3 and Ant3-2) formed insoluble aggregates (inclusion bodies) when overexpressed in bacterial cells. Further, proteolytic cleavage of Ant2-3 was observed. Optimisation of culture conditions and changes to the construct design to include N-terminal solubility tags did not improve antigen solubility. However, screening of different buffer/additives showed that the addition of 1–15 mM dithiothreitol alone decreased the formation of insoluble aggregates and improved the stability of both Ant2 and Ant3. Structural models were generated for Ant2 and Ant3, and solubility-based prediction tools were employed to determine the role of hydrophobicity and charge on protein production. The results showed that a large non-polar region (containing hydrophobic amino acids) was detected on the surface of Ant2 structures, whereas positively charged regions (containing lysine and arginine amino acids) were observed for Ant3, both of which were associated with poor protein solubility. We present a guide of strategies and predictive approaches that aim to guide the construct design, prior to expression studies, to define and engineer sequences/structures that could lead to increased expression and stability of single and potentially multi-domain (or fusion) antigens in bacterial expression systems.
    • Primary glomus tumour of the pituitary gland: diagnostic challenges of a rare and potentially aggressive neoplasm

      Quah, Boon Leong; orcid: 0000-0001-9094-5857; Donofrio, Carmine Antonio; orcid: 0000-0002-9123-8158; La Rosa, Stefano; orcid: 0000-0003-1941-2403; Brouland, Jean-Philippe; orcid: 0000-0003-3475-0101; Cossu, Giulia; orcid: 0000-0003-0913-8965; Djoukhadar, Ibrahim; Mayers, Helen; Shenjere, Patrick; orcid: 0000-0001-9627-6914; Pereira, Marta; Pathmanaban, Omar N.; et al. (Springer Berlin Heidelberg, 2020-09-12)
      Abstract: Primary non-neuroendocrine tumours of the pituitary gland and sella are rare lesions often challenging to diagnose. We describe two cases of clinically aggressive primary glomus tumour of the pituitary gland. The lesions occurred in a 63-year-old male and a 30-year-old female who presented with headache, blurred vision and hypopituitarism. Neuroimaging demonstrated large sellar and suprasellar tumours invading the surrounding structures. Histologically, the lesions were characterised by angiocentric sheets and nests of atypical cells that expressed vimentin, smooth muscle actin and CD34. Perivascular deposition of collagen IV was also a feature. Case 2 expressed synaptophysin. INI-1 (SMARCB1) expression was preserved. Both lesions were mitotically active and demonstrated a Ki-67 labelling index of 30%. Next-generation sequencing performed in case 1 showed no mutations in the reading frame of 37 commonly mutated oncogenes, including BRAF and KRAS. Four pituitary glomus tumours have previously been reported, none of which showed features of malignant glomus tumour. Similar to our two patients, three previous examples displayed aggressive behaviour.
    • Probing the ∆ U = 0 rule in three body charm decays

      Dery, Avital; Grossman, Yuval; Schacht, Stefan; email: stefan.schacht@manchester.ac.uk; Soffer, Abner (Springer Berlin Heidelberg, 2021-05-20)
      Abstract: CP violation in charm decay was observed in the decays D0→ P±P∓ of a D0 meson to two pseudoscalars. When interpreted within the SM, the results imply that the ratio of the relevant rescattering amplitudes has a magnitude and phase that are both of O(1). We discuss ways to probe similar ratios in D0→ V±P∓ decays, where V is a vector that decays to two pseudoscalars, from the Dalitz-plot analysis of time-integrated three-body decays. Compared to two-body decays, three-body decays have the advantage that the complete system can be solved without the need for time-dependent CP violation measurements or use of correlated D0−D¯0 production. We discuss the decays D0→ π+π−π0 and D0→ K+K−π0 as examples by considering a toy model of only two overlapping charged resonances, treating the underlying pseudo two-body decays in full generality.
    • Probing the ∆ U = 0 rule in three body charm decays

      Dery, Avital; Grossman, Yuval; Schacht, Stefan; email: stefan.schacht@manchester.ac.uk; Soffer, Abner (Springer Berlin Heidelberg, 2021-05-20)
      Abstract: CP violation in charm decay was observed in the decays D0→ P±P∓ of a D0 meson to two pseudoscalars. When interpreted within the SM, the results imply that the ratio of the relevant rescattering amplitudes has a magnitude and phase that are both of O(1). We discuss ways to probe similar ratios in D0→ V±P∓ decays, where V is a vector that decays to two pseudoscalars, from the Dalitz-plot analysis of time-integrated three-body decays. Compared to two-body decays, three-body decays have the advantage that the complete system can be solved without the need for time-dependent CP violation measurements or use of correlated D0−D¯0 production. We discuss the decays D0→ π+π−π0 and D0→ K+K−π0 as examples by considering a toy model of only two overlapping charged resonances, treating the underlying pseudo two-body decays in full generality.
    • Redistribution, power sharing and inequality concern

      Debowicz, Dario; orcid: 0000-0003-0944-3097; Saporiti, Alejandro; orcid: 0000-0002-9156-464X; email: alejandro.saporiti@manchester.ac.uk; Wang, Yizhi; orcid: 0000-0002-5723-2609 (Springer Berlin Heidelberg, 2021-03-10)
      Abstract: We analyze a political competition model of redistributive policies. We provide an equilibrium existence result and a full characterization of the net transfers to the different income groups. We also derive several testable predictions about the way in which the net group transfers and the after-tax Gini coefficient vary with the main parameters of the model. In accordance with the theory, the empirical evidence from a sample of developed and developing democracies supports a highly statistically significant association between: (i) the net group transfer and the gap between the population and the group mean initial income, and (ii) the net group transfer (and resp., the Gini coefficient) and power sharing disproportionality. In addition, the data also provide some empirical evidence confirming a significant relationship between the net transfers to the poor (and resp., the Gini) and the concern of the political parties with income inequality.
    • Reliability and prognostic value of radiomic features are highly dependent on choice of feature extraction platform

      Fornacon-Wood, Isabella; orcid: 0000-0002-3736-2967; email: Isabella.fornacon-wood@postgrad.manchester.ac.uk; Mistry, Hitesh; Ackermann, Christoph J.; Blackhall, Fiona; McPartlin, Andrew; Faivre-Finn, Corinne; Price, Gareth J.; O’Connor, James P. B. (Springer Berlin Heidelberg, 2020-06-01)
      Abstract: Objective: To investigate the effects of Image Biomarker Standardisation Initiative (IBSI) compliance, harmonisation of calculation settings and platform version on the statistical reliability of radiomic features and their corresponding ability to predict clinical outcome. Methods: The statistical reliability of radiomic features was assessed retrospectively in three clinical datasets (patient numbers: 108 head and neck cancer, 37 small-cell lung cancer, 47 non-small-cell lung cancer). Features were calculated using four platforms (PyRadiomics, LIFEx, CERR and IBEX). PyRadiomics, LIFEx and CERR are IBSI-compliant, whereas IBEX is not. The effects of IBSI compliance, user-defined calculation settings and platform version were assessed by calculating intraclass correlation coefficients and confidence intervals. The influence of platform choice on the relationship between radiomic biomarkers and survival was evaluated using univariable cox regression in the largest dataset. Results: The reliability of radiomic features calculated by the different software platforms was only excellent (ICC > 0.9) for 4/17 radiomic features when comparing all four platforms. Reliability improved to ICC > 0.9 for 15/17 radiomic features when analysis was restricted to the three IBSI-compliant platforms. Failure to harmonise calculation settings resulted in poor reliability, even across the IBSI-compliant platforms. Software platform version also had a marked effect on feature reliability in CERR and LIFEx. Features identified as having significant relationship to survival varied between platforms, as did the direction of hazard ratios. Conclusion: IBSI compliance, user-defined calculation settings and choice of platform version all influence the statistical reliability and corresponding performance of prognostic models in radiomics. Key Points: • Reliability of radiomic features varies between feature calculation platforms and with choice of software version. • Image Biomarker Standardisation Initiative (IBSI) compliance improves reliability of radiomic features across platforms, but only when calculation settings are harmonised. • IBSI compliance, user-defined calculation settings and choice of platform version collectively affect the prognostic value of features.