 School of Mathematics and Statistics  Research Publications
School of Mathematics and Statistics  Research Publications
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ItemMetaGenePipe: An Automated, Portable Pipeline for Contigbased Functional and Taxonomic AnalysisShaban, B ; Quiroga, M ; Turnbull, R ; Tescari, E ; Lê Cao, KA ; Verbruggen, H (The Open Journal, 2023)MetaGenePipe (MGP) is an efficient, flexible, portable, and scalable metagenomics pipeline that uses performant bioinformatics software suites and genomic databases to create an accurate taxonomic and functional characterization of the prokaryotic fraction of sequenced microbiomes. Written in the Workflow Definition Language (WDL), MGP produces output that can be explored and interpreted directly, or can be used for downstream analysis. MGP is a pipelinedevelopment best practice tool that uses Singularity for containerization and includes a setup script that downloads the necessary databases for setup. The source code for MGP is freely available and distributed under the Apache 2.0 license.

ItemSharp phase transition for Cox percolationHirsch, C ; Jahnel, B ; Muirhead, S (Institute of Mathematical Statistics, 20220101)We prove the sharpness of the percolation phase transition for a class of Cox percolation models, i.e., models of continuum percolation in a random environment. The key requirements are that the environment has a finite range of dependence, satisfies a local boundedness condition and can be constructed from a discrete iid random field, however the FKG inequality need not hold. The proof combines the OSSS inequality with a coarsegraining construction that allows us to compare different notions of influence.

ItemUpper bounds on the onearm exponent for dependent percolation modelsDewan, V ; Muirhead, S (Springer Science and Business Media LLC, 20230201)We prove upper bounds on the onearm exponent η1 for a class of dependent percolation models which generalise Bernoulli percolation; while our main interest is level set percolation of Gaussian fields, the arguments apply to other models in the Bernoulli percolation universality class, including Poisson–Voronoi and Poisson–Boolean percolation. More precisely, in dimension d= 2 we prove that η1≤ 1 / 3 for continuous Gaussian fields with rapid correlation decay (e.g. the Bargmann–Fock field), and in d≥ 3 we prove η1≤ d/ 3 for finiterange fields, both discrete and continuous, and η1≤ d 2 for fields with rapid correlation decay. Although these results are classical for Bernoulli percolation (indeed they are bestknown in general), existing proofs do not extend to dependent percolation models, and we develop a new approach based on exploration and relative entropy arguments. The proof also makes use of a new Russotype inequality for Gaussian fields, which we apply to prove the sharpness of the phase transition and the meanfield bound for finiterange fields.

ItemPregnant women maintain body temperatures within safe limits during moderateintensity aquaaerobic classes conducted in pools heated up to 33 degrees Celsius: an observational studyBrearley, AL ; Sherburn, M ; Galea, MP ; Clarke, SJ (AUSTRALIAN PHYSIOTHERAPY ASSOC, 20151001)QUESTION: What is the body temperature response of healthy pregnant women exercising at moderate intensity in an aquaaerobics class where the water temperature is in the range of 28 to 33 degrees Celsius, as typically found in community swimming pools? DESIGN: An observational study. PARTICIPANTS: One hundred and nine women in the second and third trimester of pregnancy who were enrolled in a standardised aquaaerobics class. OUTCOME MEASURES: Tympanic temperature was measured at rest preimmersion (T1), after 35minutes of moderateintensity aquaaerobic exercise (T2), after a further 10minutes of light exercise while still in the water (T3) and finally on departure from the facility (T4). The range of water temperatures in seven indoor community pools was 28.8 to 33.4 degrees Celsius. RESULTS: Body temperature increased by a mean of 0.16 degrees Celsius (SD 0.35, p<0.001) at T2, was maintained at this level at T3 and had returned to preimmersion resting values at T4. Regression analysis demonstrated that the temperature response was not related to the water temperature (T2 r = 0.01, p = 0.9; T3 r = 0.02, p=0.9; T4 r=0.03, p=0.8). Analysis of variance demonstrated no difference in body temperature response between participants when grouped in the cooler, medium and warmer water temperatures (T2 F=0.94, p=0.40; T3 F=0.93, p=0.40; T4 F=0.70, p=0.50). CONCLUSIONS: Healthy pregnant women maintain body temperatures within safe limits during moderateintensity aquaaerobic exercise conducted in pools heated up to 33 degrees Celsius. The study provides evidence to inform guidelines for safe water temperatures for aquaaerobic exercise during pregnancy.

ItemA statistical approach to knot confinement via persistent homologyCeloria, D ; Mahler, BI (ROYAL SOC, 20220525)In this paper, we study how randomly generated knots occupy a volume of space using topological methods. To this end, we consider the evolution of the first homology of an immersed metric neighbourhood of a knot's embedding for growing radii. Specifically, we extract features from the persistent homology (PH) of the VietorisRips complexes built from point clouds associated with knots. Statistical analysis of our data shows the existence of increasing correlations between geometric quantities associated with the embedding and PHbased features, as a function of the knots' lengths. We further study the variation of these correlations for different knot types. Finally, this framework also allows us to define a simple notion of deviation from ideal configurations of knots.

ItemModel Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility.Karr, J ; MalikSheriff, RS ; Osborne, J ; GonzalezParra, G ; Forgoston, E ; Bowness, R ; Liu, Y ; Thompson, R ; Garira, W ; Barhak, J ; Rice, J ; Torres, M ; Dobrovolny, HM ; Tang, T ; Waites, W ; Glazier, JA ; Faeder, JR ; Kulesza, A (Frontiers Media SA, 2022)During the COVID19 pandemic, mathematical modeling of disease transmission has become a cornerstone of key state decisions. To advance the stateoftheart host viral modeling to handle future pandemics, many scientists working on related issues assembled to discuss the topics. These discussions exposed the reproducibility crisis that leads to inability to reuse and integrate models. This document summarizes these discussions, presents difficulties, and mentions existing efforts towards future solutions that will allow future model utility and integration. We argue that without addressing these challenges, scientists will have diminished ability to build, disseminate, and implement highimpact multiscale modeling that is needed to understand the health crises we face.

ItemClassical Length5 PatternAvoiding PermutationsClisby, N ; Conway, AR ; Guttmann, AJ ; Inoue, Y (The Electronic Journal of Combinatorics, 20220101)We have made a systematic numerical study of the 16 Wilf classes of length5 classical patternavoiding permutations from their generating function coefficients. We have extended the number of known coefficients in fourteen of the sixteen classes. Careful analysis, including sequence extension, has allowed us to estimate the growth constant of all classes, and in some cases to estimate the subdominant powerlaw term associated with the exponential growth. In six of the sixteen classes we find the familiar powerlaw behaviour, so that the coefficients behave like $s_n \sim C \cdot \mu^n \cdot n^g,$ while in the remaining ten cases we find a stretched exponential as the most likely subdominant term, so that the coefficients behave like $s_n \sim C \cdot \mu^n \cdot \mu_1^{n^\sigma} \cdot n^g,$ where $0 < \sigma < 1.$ We have also classified the 120 possible permutations into the 16 distinct classes. We give compelling numerical evidence, and in one case a proof, that all 16 Wilfclass generating function coefficients can be represented as moments of a nonnegative measure on $[0,\infty)$. Such sequences are known as Stieltjes moment sequences. They have a number of nice properties, such as logconvexity, which can be used to provide quite strong rigorous lower bounds. Stronger bounds still can be established under plausible monotonicity assumptions about the terms in the continuedfraction expansion of the generating functions implied by the Stieltjes property. In this way we provide strong (nonrigorous) lower bounds to the growth constants, which are sometimes within a few percent of the exact value.

ItemPredicting Safe Regions Within Lava Flows Over TopographySaville, JM ; Hinton, EM ; Huppert, HE (AMER GEOPHYSICAL UNION, 20220901)

ItemA representation learning framework for detection and characterization of dead versus strain localization zones from preto postfailureTordesillas, A ; Zhou, S ; Bailey, J ; Bondell, H (SPRINGER, 20220801)Abstract Experiments have long shown that zones of near vanishing deformation, socalled “dead zones”, emerge and coexist with strain localization zones inside deforming granular media. To date, a method that can disentangle these dynamically coupled structures from each other, from pre to post failure, is lacking. Here we develop a framework that learns a new representation of the kinematic data, based on the complexity of a grain’s neighborhood structure in the kinematicstatespace, as measured by a recently introduced metric called sLID. Dead zones (DZ) are first distinguished from strain localization zones (SZ) throughout loading history. Next the coupled dynamics of DZ and SZ are characterized using a range of discriminative features representing: local nonaffine deformation, contact topology and force transmission properties. Data came from discrete element simulations of biaxial compression tests. The deformation is found to be essentially dual in nature. DZ and SZ exhibit distinct yet coupled dynamics, with the separation in dynamics increasing in the lead up to failure. Force congestion and plastic deformation mainly concentrate in SZ. Although the 3core of the contact network is highly prone to damage in SZ, it is robust to prefailure microbands but is decimated in the shearband, leaving a fragmented 3core in DZ at failure. We also show how loading condition and rolling resistance influence SZ and DZ differently, thus casting new light on controls on plasticity from the perspective of emergent deformation structures. Graphic abstract

ItemEstimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.Cao, S ; Wang, JR ; Ji, S ; Yang, P ; Dai, Y ; Guo, S ; Montierth, MD ; Shen, JP ; Zhao, X ; Chen, J ; Lee, JJ ; Guerrero, PA ; Spetsieris, N ; Engedal, N ; Taavitsainen, S ; Yu, K ; Livingstone, J ; Bhandari, V ; Hubert, SM ; Daw, NC ; Futreal, PA ; Efstathiou, E ; Lim, B ; Viale, A ; Zhang, J ; Nykter, M ; Czerniak, BA ; Brown, PH ; Swanton, C ; Msaouel, P ; Maitra, A ; Kopetz, S ; Campbell, P ; Speed, TP ; Boutros, PC ; Zhu, H ; Urbanucci, A ; Demeulemeester, J ; Van Loo, P ; Wang, W (Springer Science and Business Media LLC, 202211)Singlecell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded atscale pancancer examination of total mRNA content. Here we present a method to quantify tumorspecific total mRNA expression (TmS) from bulk sequencing data, taking into account tumor transcript proportion, purity and ploidy, which are estimated through transcriptomic/genomic deconvolution. We estimate and validate TmS in 6,590 patient tumors across 15 cancer types, identifying significant intertumor variability. Across cancers, high TmS is associated with increased risk of disease progression and death. TmS is influenced by cancerspecific patterns of gene alteration and intratumor genetic heterogeneity as well as by pancancer trends in metabolic dysregulation. Taken together, our results indicate that measuring celltypespecific total mRNA expression in tumor cells predicts tumor phenotypes and clinical outcomes.