Pseudofinite proofs of the stable graph regularity lemma

This expository article is based on two lectures given by the first author at the Fields Institute in the Fall 2021 Thematic Program on Trends in Pure and Applied Model Theory. We give a detailed proof of a qualitative version of the Mallaris-Shelah regularity lemma for stable graphs using only basic local stability theory and an ultraproduct construction. This proof strategy was first established by Malliaris and Pillay, and later simplified by Pillay. We provide some further simplifications, and also explain how the pseudofinite approach can be used to obtain a qualitative strengthening (compared to previous proofs) in terms of "functional error". To illustrate the extra leverage obtained by functional error, we give an elementary argument for extracting equipartitions from arbitrary partitions.Comment: 15 pages, submitted as a chapter in a forthcoming title of the Fields Institute Monographs book serie

Nonrandom Survival of Gene Conversions among Yeast Ribosomal Proteins Duplicated through Genome Doubling

By comparing the patterns of evolution in the coding and upstream noncoding regions of yeast ribosomal protein (RP) genes duplicated in a genome duplication, we find that although nonsynonymous sites in the coding sequences show strong evidence for the fixation of recent gene conversion events, similar patterns are less evident among the synonymous positions and noncoding regulatory elements. This result suggests a potential explanation for the somewhat puzzling fact that duplicated RP genes are not functionally redundant despite their very high protein sequence identity. An analysis of the patterns of regulatory network evolution after genome duplication also indicates that the duplicated proteins have diverged considerably in expression despite their similar protein sequences

Symbols in Wittgenstein's Tractatus

This paper is concerned with the status of a symbol in Wittgenstein’s Tractatus. It is claimed in the first section that a Tractarian symbol, whilst essentially a syntactic entity to be distinguished from the mark or sound that is its sign, bears its semantic significance only inessentially. In the second and third sections I pursue this point of exegesis through the Tractarian discussions of nonsense and the context principle respectively. The final section of the paper places the forgoing work in a secondary context, addressing in particular a debate regarding the realism of the Tractatus

Intratumoral T-cell receptor repertoire composition predicts overall survival in patients with pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy that is refractory to immune checkpoint inhibitor therapy. However, intratumoral T-cell infiltration correlates with improved overall survival (OS). Herein, we characterized the diversity and antigen specificity of the PDAC T-cell receptor (TCR) repertoire to identify novel immune-relevant biomarkers. Demographic, clinical, and TCR-beta sequencing data were collated from 353 patients across three cohorts that underwent surgical resection for PDAC. TCR diversity was calculated using Shannon Wiener index, Inverse Simpson index, and True entropy. Patients were clustered by shared repertoire specificity. TCRs predictive of OS were identified and their associated transcriptional states were characterized by single-cell RNAseq. In multivariate Cox regression models controlling for relevant covariates, high intratumoral TCR diversity predicted OS across multiple cohorts. Conversely, in peripheral blood, high abundance of T-cells, but not high diversity, predicted OS. Clustering patients based on TCR specificity revealed a subset of TCRs that predicts OS. Interestingly, these TCR sequences were more likely to encode CD

Aerosol–cloud drop concentration closure in warm cumulus

Our understanding of the activation of aerosol particles into cloud drops during the formation of warm cumulus clouds presently has a limited observational foundation. Detailed observations of aerosol size and composition, cloud microphysics and dynamics, and atmospheric thermodynamic state were collected in a systematic study of 21 cumulus clouds by the Center for Interdisciplinary Remotely-Piloted Aircraft Studies (CIRPAS) Twin Otter aircraft during NASA's Cirrus Regional Study of Tropical Anvils and Cirrus Layers–Florida Area Cirrus Experiment (CRYSTAL-FACE). An “aerosol-cloud” closure study was carried out in which a detailed cloud activation parcel model, which predicts cloud drop concentration using observed aerosol concentration, size distribution, cloud updraft velocity, and thermodynamic state, is evaluated against observations. On average, measured droplet concentration in adiabatic cloud regions is within 15% of the predictions. This agreement is corroborated by independent measurements of aerosol activation carried out by two cloud condensation nucleus (CCN) counters on the aircraft. Variations in aerosol concentration, which ranged from 300 to 3300 cm^(−3), drives large microphysical differences (250–2300 cm^(−3)) observed among continental and maritime clouds in the South Florida region. This is the first known study in which a cloud parcel model is evaluated in a closure study using a constraining set of data collected from a single platform. Likewise, this is the first known study in which relationships among aerosol size distribution, CCN spectrum, and cloud droplet concentration are all found to be consistent with theory within experimental uncertainties much less than 50%. Vertical profiles of cloud microphysical properties (effective radius, droplet concentration, dispersion) clearly demonstrate the boundary layer aerosol's effect on cloud microphysics throughout the lowest 1 km of cloud depth. Onboard measurements of aerosol hygroscopic growth and the organic to sulfate mass ratio are related to CCN properties. These chemical data are used to quantify the range of uncertainty associated with the simplified treatment of aerosol composition assumed in the closure study

'Sexercise': Working out heterosexuality in Jane Fonda’s fitness books

This is an Author's Accepted Manuscript of an article published in Leisure Studies, 30(2), 237 - 255, 2011, copyright Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/02614367.2010.523837.This paper explores the connection between the promotion of heterosexual norms in women’s fitness books written by or in the name of Jane Fonda during the 1980s and the commodification of women’s fitness space in both the public and private spheres. The paper is set in the absence of overt discussions of normative heterosexuality in leisure studies and draws on critical heterosexual scholarship as well as the growing body of work theorising geographies of corporeality and heterosexuality. Using the principles of media discourse analysis, the paper identifies three overlapping characteristics of heterosexuality represented in Jane Fonda’s fitness books, and embodied through the exercise regimes: respectable heterosexual desire, monogamous procreation and domesticity. The paper concludes that the promotion and prescription of exercise for women in the Jane Fonda workout books centred on the reproduction and embodiment of heterosexual corporeality. Set within an emerging commercial landscape of women’s fitness in the 1980s, such exercise practices were significant in the legitimation and institutionalisation of heteronormativity

LPMLE3 : a novel 1-D approach to study water flow in streambeds using heat as a tracer

We introduce LPMLE3, a new 1-D approach to quantify vertical water flow components at streambeds using temperature data collected in different depths. LPMLE3 solves the partial differential equation for coupled water flow and heat transport in the frequency domain. Unlike other 1-D approaches it does not assume a semi-infinite halfspace with the location of the lower boundary condition approaching infinity. Instead, it uses local upper and lower boundary conditions. As such, the streambed can be divided into finite subdomains bound at the top and bottom by a temperature-time series. Information from a third temperature sensor within each subdomain is then used for parameter estimation. LPMLE3 applies a low order local polynomial to separate periodic and transient parts (including the noise contributions) of a temperature-time series and calculates the frequency response of each subdomain to a known temperature input at the streambed top. A maximum-likelihood estimator is used to estimate the vertical component of water flow, thermal diffusivity, and their uncertainties for each streambed subdomain and provides information regarding model quality. We tested the method on synthetic temperature data generated with the numerical model STRIVE and demonstrate how the vertical flow component can be quantified for field data collected in a Belgian stream. We show that by using the results in additional analyses, nonvertical flow components could be identified and by making certain assumptions they could be quantified for each subdomain. LPMLE3 performed well on both simulated and field data and can be considered a valuable addition to the existing 1-D methods

High Energy Physics Opportunities Using Reactor Antineutrinos

Nuclear reactors are uniquely powerful, abundant, and flavor-pure sources ofantineutrinos that continue to play a vital role in the US neutrino physicsprogram. The US reactor antineutrino physics community is a diverse interestgroup encompassing many detection technologies and many particle physicstopics, including Standard Model and short-baseline oscillations, BSM physicssearches, and reactor flux and spectrum modeling. The community's aims offerstrong complimentary with numerous aspects of the wider US neutrino program andhave direct relevance to most of the topical sub-groups composing the Snowmass2021 Neutrino Frontier. Reactor neutrino experiments also have a directsocietal impact and have become a strong workforce and technology developmentpipeline for DOE National Laboratories and universities. This white paper,prepared as a submission to the Snowmass 2021 community organizing exercise,will survey the state of the reactor antineutrino physics field and summarizethe ways in which current and future reactor antineutrino experiments can playa critical role in advancing the field of particle physics in the next decade.<br

Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

Markov models of codon substitution are powerful inferential tools for studying biological processes such as natural selection and preferences in amino acid substitution. The equilibrium character distributions of these models are almost always estimated using nucleotide frequencies observed in a sequence alignment, primarily as a matter of historical convention. In this note, we demonstrate that a popular class of such estimators are biased, and that this bias has an adverse effect on goodness of fit and estimates of substitution rates. We propose a “corrected” empirical estimator that begins with observed nucleotide counts, but accounts for the nucleotide composition of stop codons. We show via simulation that the corrected estimates outperform the de facto standard estimates not just by providing better estimates of the frequencies themselves, but also by leading to improved estimation of other parameters in the evolutionary models. On a curated collection of sequence alignments, our estimators show a significant improvement in goodness of fit compared to the approach. Maximum likelihood estimation of the frequency parameters appears to be warranted in many cases, albeit at a greater computational cost. Our results demonstrate that there is little justification, either statistical or computational, for continued use of the -style estimators