Miracle-dz/UniFAR-FTUs huggingface dataset:
Is More Different? Emergent Properties in Physics

This thesis gives a philosophical assessment of a contemporary movement, influential amongst physicists, about the status of microscopic and macroscopic properties. The fountainhead for the movement was a short 1972 paper `More is Different', written by the condensed-matter physicist, Philip Anderson. Each of the chapters is concerned with themes mentioned in that paper, or subsequently expounded by Anderson and his followers. In Chapter 1, I aim to locate Anderson's existence claims for `emergent properties' within the metaphysical, epistemological and methodological doctrines that identify themselves as `emergentist'. I argue, against the commentators' consensus, that the New Emergentists make claims about the metaphysical status of physical properties, and should not be read as concerned only with matters of research methodology for physics. In Chapter 2, I look at the physical examples that the New Emergentists appeal to, and propose a way of formulating their main claims within modern analytic metaphysics. I argue that it is possible to view their thesis as an updated version of `British Emergentism' a movement popular in the early years of the twentieth century. I support this contention by comparing examples of emergent properties put forward by the British and the New Emergentists. Chapter 3 is a discussion of the significance of renormalisation techniques. I attack a set of claims by Robert Batterman, who presents renormalisation as an explanatory strategy unrecognised by the philosophy of science. I separate several different methods of renormalisation analysis, and argue that he has conflated them. In Chapter 4, I discuss the theoretical representation of phase transitions in condensed matter physics; in particular, their appeal to the limit of an infinite system. I examine and refute various claims to the effect that the ineliminability of this limit in modelling phase transitions is of great metaphysical significance. I suggest a definition of phase transitions for finite systems that dissolves this illusion, and gives us reason to trust the results of the theories that only apply in the infinite limit. %I then comment on the significance of these results for a suggestion of Laura Ruetsche, that quantum statistical mechanics should be used as a guide to the interpretation of quantum field theory. Chapter 5 revisits the doctrines of the New Emergentists in order to place their views within some wider philosophical debates. I look at how their doctrines bear on issues in the interpretation of quantum mechanics, in the philosophy of mind and the philosophy of science. I close by returning to the context within physics, in which the New Emergentists originally made their presence felt: the controversy over whether elementary particle physics should enjoy greater status than other areas.
Automatic mechanistic inference from large families of Boolean models generated by Monte Carlo tree search

Motivation Many important processes in biology, such as signaling and gene regulation, can be described using logic models. These logic models are typically built to behaviorally emulate experimentally observed phenotypes, which are assumed to be steady states of a biological system. Most models are built by hand and therefore researchers are only able to consider one or perhaps a few potential mechanisms. We present a method to automatically synthesize Boolean logic models with a specified set of steady states. Our method, called MC-Boomer, is based on Monte Carlo Tree Search (MCTS), an efficient, parallel search method using reinforcement learning. Our approach enables users to constrain the model search space using prior knowledge or biochemical interaction databases, thus leading to generation of biologically plausible mechanistic hypotheses. Our approach can generate very large numbers of data-consistent models. To help develop mechanistic insight from these models, we developed analytical tools for multi-model inference and model selection. These tools reveal the key sets of interactions that govern the behavior of the models. Results We demonstrate that MC-Boomer works well at reconstructing randomly generated models. Then, using single time point measurements and reasonable biological constraints, our method generates hundreds of thousands of candidate models that match experimentally validated in-vivo behaviors of the Drosophila segment polarity network. Finally we outline how our multimodel analysis procedures elucidate potentially novel biological mechanisms and provide opportunities for model-driven experimental validation. Availability Code is available at: www.github. com/bglazer/mcboomer
Testing the Triggering Hypothesis: Effect of Cognate Status on Code-Switching and Disfluencies

“Triggered switching” is the theory that code-switching happens more often with words connected to both languages, such as cognates. Corpus analyses have supported this theory; however, they do not allow testing for directional causality. Here, we test the triggering hypothesis through a picture-naming task, and examine whether cognates trigger code-switches, as well as more subtle interference effects resulting in disfluencies. Forty English-Spanish bilinguals completed a picture-cued sentence production task in three conditions: English-only, Spanish-only, and mixed. Half of the pictures represented Spanish-English cognates. Unsurprisingly, participants were more likely to code-switch when asked to use both their languages compared to only their dominant or non-dominant language. However, participants were not more likely to switch languages for cognate than for non-cognate trials. Participants tended to be more fluent on cognate trials in the dominant and the non-dominant condition, and on non-cognate trials in the mixed-language condition, although these effects were not significant. These findings suggest that both language context and cognate status are important to consider when testing both overt switches and disfluencies in bilingual speech production.
Visualizing the Obvious: A Concreteness-based Ensemble Model for Noun Property Prediction

Neural language models encode rich knowledge about entities and their relationships which can be extracted from their representations using probing. Common properties of nouns (e.g., red strawberries, small ant) are, however, more challenging to extract compared to other types of knowledge because they are rarely explicitly stated in texts. We hypothesize this to mainly be the case for perceptual properties which are obvious to the participants in the communication. We propose to extract these properties from images and use them in an ensemble model, in order to complement the information that is extracted from language models. We consider perceptual properties to be more concrete than abstract properties (e.g., interesting, flawless). We propose to use the adjectives' concreteness score as a lever to calibrate the contribution of each source (text vs. images). We evaluate our ensemble model in a ranking task where the actual properties of a noun need to be ranked higher than other non-relevant properties. Our results show that the proposed combination of text and images greatly improves noun property prediction compared to powerful text-based language models.
Strong-field cyclotron scattering. I - Scattering amplitudes and natural line width. [in spectra of accretion-powered X-ray pulsars

The introduction of resonance line width into the QED cyclotron scattering amplitudes is considered. It is shown that the width arises from loop corrections to the electron propagator, which also bring about shifts in the Landau energy levels. A formalism is developed that allows the dressed electron propagator to be derived. It is shown that the states of Herold, Ruder, & Wunner, and of Sokolov & Ternov, which diagonalize the component of the magnetic moment operator parallel to the external magnetic field, are appropriate for calculation of the scattering amplitudes, whereas the states of Johnson & Lippmann are not
Running title: ANTILIPEMIC EFFECT OF HEDERAGENIN in vivo AND in vitro Academy Section: BIOMEDICAL SCIENCES

Hederagenin, a natural compound distributed in many medicinal plants, has a variety of pharmacological properties including anti-bacteria, anti-infl ammation, antioxidation, and antiapoptosis. The aim of this study was to evaluate the effects of hederagenin on decreasing blood lipid and anti-oxidative stress in oleic acid-induced HepG2 cells and hyperlipidemic rats, and explore underlying mechanisms. In vitro, TG was used as the index to verify the lipid-lowering effect of hederagenin in oleic acid-induced HepG2 cells. In vivo, TC, TG, LDL-C, and HDL-C were used as direct indicators to study the antilipemic effect of hederagenin in hyperlipidemic rats. MDA, SOD, and GSH-PX were measured to analyze the anti-oxidative effect of hederagenin. The signaling pathways of anti-oxidation were evaluated using Western blot. Our results showed that hederagenin (250μmol/L) increased signifi cantly TG clearance rate. In addition, treatment with hederagenin, XZK and simvastatin reduced effectively TC, TG, LDL-C and MDA content, and increased HDL-C, SOD and GSH-PX in HFD rats. Moreover, the phosphorylation level of p38 MAPK was inhibited after administration of hederagenin, XZK and simvastatin. Our results revealed that hederagenin possessed benefi cial potentials for hypolipidemic effects, especially in TG clearance. The mechanism might be associated with inhibition of lipid absorption, reduction of lipid oxidation, and down-regulation of p38MAPK
Running Ontogenic changes in soybean radiation-use efficiency Leaf nitrogen does not explain changes in soybean radiation-use efficiency in 3 vegetative and early reproductive stages

33 Ontogenic changes in soybean radiation-use efficiency (RUE) have been attributed to variation 34 in specific leaf nitrogen (SLN) based only on data collected during seed filling. We evaluated 35 this hypothesis using data on leaf area, absorbed photosynthetically active radiation (APAR), 36 aboveground dry matter (ADM), and plant nitrogen (N) concentration collected during the entire 37 crop season from seven field experiments conducted in a stress-free environment. Each 38 experiment included a full N treatment that received ample N fertilizer and a zero N treatment 39 that relied on N fixation and soil N mineralization. We estimated RUE based on changes in 40 ADM between sampling times and associated APAR, accounting for changes in biomass 41 composition. The SLN and RUE exhibited different seasonal patterns: a bell-shaped pattern with 42 a peak around the beginning of seed filling, and a convex pattern followed by an abrupt decline 43 during late seed filling, respectively. The level of N supply influenced SLN more than RUE via 44 changes in leaf N concentration, with small changes in specific leaf weight. Changes in SLN 45 explained the decline in RUE during seed filling but failed to predict changes in RUE in earlier 46 stages. A simple approach based on phenological stages may give more realistic estimates of 47 RUE before seed filling, improving crop growth and yield prediction via crop models and remote 48 sensing. 49
BIOLOGICAL RELEVANCE OF INTESTINAL GASES IN HEALTY HUMANS

Intestinal gases are usually discarded as physiologically inert, useless sub-products of colonic fermentation that must be expelled to prevent discomfort and meteorism. Starting from the observation that many living beings use exogenous and/or endogenous gases to attain evolutionary benefits, we question whether intestinal gases in healthy humans could have underestimated physiological effects, either intestinal or extra-intestinal. We examine gaseous volume, composition, source and local distribution in proximal as well as distal gut, providing extensive data that may serve as reference for future studies. We analyze each one of the most abundant intestinal gases and describe their diffusive patterns, active trans-barrier transport dynamics, chemical properties, intra-/extra-intestinal metabolic effects mediated by intracellular, extracellular, paracrine and distant actions. Discussing the physical properties of the whole intestinal gaseous mixture, we illustrate how changes in volume/pressure can be generated by two different mechanisms, namely, physical muscular gut contraction and biological colonic fermentation, with quite different metabolic outcomes. The experimental gas laws suggest that the gaseous exchanges between lumen and bloodstream are impaired by muscular contraction and improved by muscular relaxation. In turn, the surface-area-to-volume ratio suggests that the gaseous exchanges are impaired by microorganismal overproduction and improved by microorganismal reduction. Further, theoretical stochastic approaches from probability theory indicate that the non-turbulent, random paths of gas molecules inside colonic haustra do not homogenously spread over the whole mucosal surface. This means that the intestinal area available for lumen/blood metabolic exchanges is much less than expected not just in disease states, but also in healthy individuals.
Comprehensive Analysis of the Oncogenic Role of Targeting Protein for Xklp2 (TPX2) in Human Malignancies

Mitosis and spindle assembly require the microtubule-associated protein Xenopus kinesin-like protein 2 (TPX2). Although TPX2 is highly expressed in several malignant tumor forms, little is known about its role in cancer. In this study, we performed the gene set enrichment analysis of TPX2 in 33 types of cancers and an extensive pan-cancer bioinformatic analysis using prognosis, tumor mutational burdens, microsatellite instability, tumor microenvironment, and immune cell infiltration data. According to the differential expression study, TPX2 was found to be overexpressed across all studied cancer types. Based on the survival analysis, increased TPX2 expression was associated with a poor prognosis for most cancers. The TPX2 expression level was confirmed to correlate with the clinical stage, microsatellite instability, and tumor mutational burden across all cancer types. Furthermore, TPX2 expression has been linked to tumor microenvironments and immune cell infiltration, particularly in bladder urothelial carcinoma, liver hepatocellular carcinoma, lung adenocarcinoma, stomach adenocarcinoma, and uterine corpus endometrial carcinoma. Finally, the gene set enrichment analysis implicated TPX2 in the regulation of aminoacyl tRNA biosynthesis, which is the most important tumor cell cycle signaling pathway. This comprehensive pan-cancer analysis shows that TPX2 is a prognostic molecular biomarker for most cancers and suggests its potential as an effective therapeutic target for the treatment of these diseases.
FedLN: Federated Learning with Label Noise

Federated Learning (FL) is a distributed machine learning paradigm that enables 1 learning models from decentralized private datasets, where the labeling effort is 2 entrusted to the clients. While most existing FL approaches assume high-quality 3 labels are readily available on users’ devices; in reality, label noise can naturally 4 occur in FL and follows a non-i.i. d. distribution among clients. Due to the “ non-iid-5 ness ” challenges, existing state-of-the-art centralized approaches exhibit unsatis-6 factory performance, while previous FL studies rely on data exchange or repeated 7 server-side aid to improve model’s performance. Here, we propose FedLN , a frame-8 work to deal with label noise across different FL training stages; namely, FL 9 initialization, and server-side model aggregation. Extensive experiments on various 10 publicly available vision and audio datasets demonstrate an improvement of 24 % 11 on average compared to state-of-the-art methods for a label noise level of 70 %. 12
DISTFOLD: Distance-guided Protein Folding DISTFOLD: Distance-guided Protein Folding

Background: Protein structure prediction and its associated key sub-problems such as distance map prediction are of signiﬁcant importance in biology and bioinformatics. The inter-residue distance prediction problem, or distance prediction in short, is to predict the physical distance between amino acids in a three-dimensional (3D) space, given a protein’s one-dimensional sequence information. While there exist many methods to predict distance maps, there are currently no methods that can take those predicted distance maps and build 3D models from them in an ab initio way, i.e., without using any other information. This works aims to ﬁll this gap by: a) developing a method that accepts predicted distance maps (2D information) as input and builds 3D models, and, b) investigating the prospect and limitations of distance-guided 3D modeling (reconstruction). Methods: DISTFOLD is a Perl based script that wraps around a well-established 3D modeling tool known as CNS-Suite. To test our DISTFOLD implementation, we ﬁrst benchmarked it on a small subset of the SCOPe dataset representative of the entire protein data bank. In addition to developing DISTFOLD, we also investigated (a) how various distance thresholds for selecting distance restraints impact the reconstruction accuracy, (b) how secondary structure information in-ﬂuences the reconstruction accuracy, (c) how the reconstruction accuracy changes when predicted distances are used instead of true, (d) how accuracy changes with a distance based method as we increase the number of models generated, and (e) how long the process took using elapsed time as a criterion. Results: Using two representative sets consisting of 1583 proteins and 259 proteins, we show that our method, DISTFOLD, is capable of building accurate models in an array of settings. Our results also show that the value of threshold chosen to ﬁlter-out/keep distances can drastically aﬀect reconstruction accuracy. We also show that including secondary structures, when available, can beneﬁt
EVOLUTION OF THE CRAB NEBULA IN A LOW ENERGY SUPERNOVA

The nature of the supernova leading to the Crab Nebula has long been controversial because of the low energy that is present in the observed nebula. One possibility is that there is significant energy in extended fast material around the Crab but searches for such material have not led to detections. An electron capture supernova model can plausibly account for the low energy and the observed abundances in the Crab. Here, we examine the evolution of the Crab pulsar wind nebula inside a freely expanding supernova and find that the observed properties are most consistent with a low energy event. Both the velocity and radius of the shell material, and the amount of gas swept up by the pulsar wind point to a low explosion energy (∼1050 erg). We do not favor a model in which circumstellar interaction powers the supernova luminosity near maximum light because the required mass would limit the freely expanding ejecta.
Transfer of Self-Fruitfulness to Cultivated Almond from Peach and Wild Almond

The almond [Prunus dulcis (Mill.) D.A. Webb] is normally self-sterile, requiring orchard placement of pollinizer cultivars and insect pollinators. Honeybees are the primary insect pollinators utilized, but climate change and the higher frequency of extreme weather events have reduced their availability to levels insufficient to meet the demands of current and anticipated almond acreage. The incorporation of self-fruitfulness may eliminate the need for both pollinizers and pollinators and allow the planting of single cultivar orchards that facilitate orchard management and reduce agrochemical inputs. Self-fruitfulness requires self-compatibility of self-pollen tube growth to fertilization, as well as a high level of consistent self-pollination or autogamy over the range of anticipated bloom environments. The Italian cultivar Tuono has been the sole source of self-compatibility for breeding programs world-wide, leading to high levels of inbreeding in current almond improvement programs. Both self-compatibility and autogamy have been successfully transferred to commercial almonds from cultivated peaches (Prunus persica L.), as well as wild peach and almond species. Self-compatibility was inherited as a novel major gene, but was also influenced by modifiers. Molecular markers developed for one species source often failed to function for other species’ sources. Autogamy was inherited as a quantitative trait. Breeding barriers were more severe in the early stages of trait introgression, but rapidly diminished by the second to third backcross. Increasing kernel size, which was similarly inherited as a quantitative trait, was a major regulator of the introgression rate. Self-fruitfulness, along with good commercial performance of tree and nut traits, was recovered from different species sources, including Prunus mira, Prunus webbii, P. persica, and the P. webbii-derived Italian cultivar Tuono. Differences in expression of self-fruitfulness were observed, particularly during field selection at the early growth stages. Introgression of self-fruitfulness from these diverse sources also enriched overall breeding germplasm, allowing the introduction of useful traits that are not accessible within traditional germplasm.
Open Research Online Using Theory-Based Approaches to Embed Evaluation within a Small Specialist Performing Arts Institution

Using Theory-Based Approaches to Embed Evaluation within a Small Specialist Performing Arts Institution Book Section How to cite: Rainford, Jon and Baptista, Vanessa (2022). Using Theory-Based Approaches to Embed Evaluation within a Small Specialist Performing Arts Institution. In: Dent, Samuel; Mountford-Zimdars, Anna and Burke, Ciaran eds. Theory of Change (Great Debates in Higher Education). Bingley: Emerald Publishing Limited, pp. 81–99.
A Whole Genome Sequencing-Based Approach to Track down Genomic Variants in Itraconazole-Resistant Species of Aspergillus from Iran

The antifungal resistance in non-fumigatus Aspergillus spp. , as well as Aspergillus fumigatus, poses a major therapeutic challenge which affects the entire healthcare community. Mutation occurrence of cyp51 gene paralogs is the major cause of azole resistance in Aspergillus spp. To obtain a full map of genomic changes, an accurate scan of the entire length of the Aspergillus genome is necessary. In this study, using whole genome sequencing (WGS) technique, we evaluated the mutation in cyp51A, cyp51B, Cdr1B, AtrR, Hmg1, HapE and FfmA genes in different clinical isolates of Aspergillus fumigatus, Aspergillus niger, Aspergillus tubingensis, Aspergillus welwitschiae and Aspergillus terreus which responded to minimum inhibitory concentrations of itraconazole above 16 µg mL−1. We found different nonsynonymous mutations in the cyp51A, cyp51B, Cdr1B, AtrR, Hmg1, HapE and FfmA gene loci. According to our findings, Aspergillus species isolated from different parts of the world may represent different pattern of resistance mechanisms which may be revealed by WGS.