bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transition path properties for one-dimensional non-Markovian models
Authors: Li Hua , Xu Yong , Metzler Ralf , Shen Jianwei 
Published: August 2024

Abstract
Transitions between long-lived states are rare but important. The statistic of successful transitions is considered in transition path theory. We here consider the transition path properties of a generalized Langevin equation with built-in memory. The general form of the approximate theoretical solutions to the transition path time distribution, mean transition path time, and coefficient of variation are obtained from the generalized Smoluchowski equation. Then, the accuracy of our theoretical results is verified by the Forward Fluxing Sampling scheme. Finally, two examples are worked out in detail. We quantify how the potential function and the memory parameters affect the transition path properties. The short time limit of transition path time distribution always has an exponential decay. For the parabolic potential case, the memory strongly affects the long-time behavior of the transition path time distribution. Our results show that the behavior of the mean transition path time is dominated by the smaller of the two memory times when both memory times exceed the intrinsic diffusion time. Interestingly, the results also show that the memory can effect a coefficient of variation of transition path times exceeding unity, in contrast to Markovian case.
Estimating Bethe roots with VQE
Authors: Raveh David , Nepomechie Rafael I 
Published: August 2024

AbstractBethe equations, whose solutions determine exact eigenvalues and eigenstates of corresponding integrable Hamiltonians, are generally hard to solve. We implement a Variational Quantum Eigensolver approach to estimating Bethe roots of the spin-1/2 XXZ quantum spin chain, by using Bethe states as trial states, and treating Bethe roots as variational parameters. In numerical simulations of systems of size up to 6, we obtain estimates for Bethe roots corresponding to both ground states and excited states with up to 5 down-spins, for both the closed and open XXZ chains. This approach is not limited to real Bethe roots.
Bessel–Bessel–Gaussian vortex laser beams
Authors: Kotlyar Victor V , Abramochkin Eugeny G , Kovalev Alexey A 
Published: August 2024

Abstract
We obtain and investigate Bessel–Bessel–Gaussian vortex beams (BBG beams) with the complex amplitude being equal to a product of the Gaussian function with two Bessel functions, whose arguments are expressed as complicated radicals including the cylindrical coordinates and a free parameter that defines the shape of the intensity distribution. If this parameter is small, the intensity has the shape of an inhomogeneous ring. For larger values of this parameter, the intensity has the shape of two arcs or ‘crescents’, oriented by their concave sides to each other. The complex amplitude of such beams is derived in explicit form for an arbitrary distance from the waist. We demonstrate that the BBG beams rotate upon propagation anomalously fast: at a distance much shorter than the Rayleigh length, the intensity distribution is already rotated by almost 45°, whereas typically, the rotation angle of vortex Gaussian beams is equal to the Gouy phase. It is also shown that the parameter of the BBG beam allows controlling its topological charge (TC): when the parameter value is positive and increases, the beam TC also increases stepwise by an even number. Besides, we study two other similar vortex BBG beams: either with four local intensity maxima, lying on the Cartesian coordinates axes, or with one intensity maximum with a crescent shape, whose center is on the horizontal axis. The derived three new families of asymmetric vortex laser beams, whose complex amplitude is described by explicit analytical expressions at an arbitrary distance from the waist, extend the variety of laser beams that can be used for manipulating and rotating microparticles, free space data transmission, and in quantum informatics.
A practical guide to digital micro-mirror devices (DMDs) for wavefront shaping
Authors: Popoff Sébastien M , Gutiérrez-Cuevas Rodrigo , Bromberg Yaron , Matthés Maxime W 
Published: August 2024

Abstract
Digital micromirror devices have gained popularity in wavefront shaping, offering a high frame rate alternative to liquid crystal spatial light modulators. They are relatively inexpensive, offer high resolution, are easy to operate, and a single device can be used in a broad optical bandwidth. However, some technical drawbacks must be considered to achieve optimal performance. These issues, often undocumented by manufacturers, mostly stem from the device’s original design for video projection applications. Herein, we present a guide to characterize and mitigate these effects. Our focus is on providing simple and practical solutions that can be easily incorporated into a typical wavefront shaping setup.
A research agenda for economic resilience in fossil fuel–dependent communities
Authors: Clarke Leon , Curtis Mark , Eisenberg Ann , Grubert Emily , Haggerty Julia Hobson , James Alexander , Jensen Nathan , Kaufman Noah , Krause Eleanor , Raimi Daniel , Tingley Dustin , Weber Jeremy 
Published: August 2024

Abstract
World leaders have committed to a transition away from fossil fuels in the energy system. Yet&#xD;local communities across the United States depend on fossil fuel industries for high-paying&#xD;jobs and essential public services. Building economic resilience in these communities will&#xD;increase the likelihood of a successful response to climate threats and help ensure that the&#xD;benefits and burdens of an energy transition are broadly shared.&#xD;&#xD;Policy support for fossil fuel–dependent local economies in the United States is growing&#xD;but remains limited. Only a scant body of rigorous evidence exists on how to effectively and&#xD;equitably increase economic resilience in these communities. This article describes the&#xD;critical need for additional scholarship to help policymakers design, implement, and evaluate&#xD;strategies for supporting the economies of fossil fuel–dependent regions. It also highlights key&#xD;research questions that can inform decisionmakers in the years ahead.
Continuity and Discontinuity between the Tractatus Theologico-Politicus and the Ethics
Authors: Totaro Pina 
Published: August 2024

Abstract
This chapter aims to analyze the relationship between the Tractatus theologico-politicus and the Ethics. On the proposed reading, Spinoza carries out his biblical exegesis in the TTP according to the “ex sola Scriptura” principle (adherence to the “letter”) in order to show that even though the biblical texts are interpreted differently, their moral meaning, i.e. the “spirit,” remains unchanged. It is argued that the same spirit that Spinoza finds in his secularized reading of Scripture can also be found in the Ethics, where Spinoza develops a philosophical reflection on the good and on justice, according to principles of love and knowledge, as well as a political reflection on common human salvation and bliss. Spinoza’s insistence on a literal reading of the Bible also offers a model that seeks to avoid the “lucubrations of theologians” and the attribution of mysterious and mystifying meanings to the text. This model of reading will have a profound impact on later literature.
‘Divine Law’ in Spinoza’s Tractatus Theologico-Politicus
Authors: Verbeek Theo 
Published: August 2024

Abstract
Starting from an analysis of chapter 4 of Spinoza’s Tractatus theologico-politicus the relation between ‘Divine Law’ and Spinoza’s claim that God cannot be a lawgiver is further examined. It is shown that Spinoza’s reinterpretation of the notion of ‘Divine Law’ as the rule of life leading to human perfection, that is, the intellectual knowledge and love of God is not consistent with some of the central tenets of the Ethics; that, as opposed to what is claimed by Spinoza himself, it is irrelevant to political philosophy; and that it mainly serves as a smoke screen for the denial of God’s legislative will, which in the seventeenth century was associated with atheism.
Is Wonder a Remedy against the Passions?
Authors: Sangiacomo Andrea 
Published: August 2024

Abstract
This chapter reconstructs Spinoza’s ambivalent treatment of wonder across his works. I argue that in the TTP, Spinoza took into serious consideration Descartes’s own account and his suggestion that wonder can play the role of a remedy against other, more dangerous passions. Nonetheless, I also maintain that this solution is dismissed in the Ethics. Here, affects are more or less useful or dangerous depending on whether and how they foster agreement in nature among individuals. Spinoza’s account of agreement in nature builds on the bodily aptitude to be affected in a great many ways at the same time by external causes. Since wonder results from affections produced by isolated and exceptional objects, it tends to produce fixation and hinders the bodily ability to be affected in a great many ways. Spinoza considers the fixation as a threat to the bodily capacity to foster the body’s agreement with external causes.
Finalism, Religion, and Miracles
Authors: Scribano Emanuela 
Published: August 2024

Abstract
In the TTP, Spinoza attributes the origin of belief in miracles to the ancient Jews as part of the belief that God arranged natural events to benefit the chosen people. Anthropocentric finalism would, therefore, be a belief originating within a particular group of people. In Ethics, however, the human people are considered inclined to believe in anthropocentric finalism of nature. Furthermore, in Ethics, Spinoza argues that finalism is by its nature anthropocentric. Finalism is judged responsible not only for prejudices concerning metaphysics and theology but also for those concerning the investigation of nature. Therefore, the entire natural philosophy of Aristotle is involved in the criticism of finalism conducted by Spinoza in Ethics.
Spinoza’s Views on Prophecy and the Prophets Revisited
Authors: Renz Ursula , Waldner Philip 
Published: August 2024

Abstract
Elaborating on Spinoza’s definitions established in the first two chapters in the TTP and discussing them in light of the analysis of the process of the imagination as developed in the Ethics, this chapter argues that Spinoza’s attitude toward the phenomenon of prophecy and the prophets is far less critical than often assumed. In particular, Spinoza’s naturalism with respect to causation of prophecy does not undermine the notion that he takes prophets to play an important role in society. Concretely, it is argued that following Spinoza’s views, prophets may serve as leaders in situations where people lack firm knowledge. The chapter concludes by pointing out that the very problem to which the idea of prophets responds is a problem sub specie durationis. The need for prophets—or leaders—typically arises where knowledge is not available.
Reason and Scripture in the Ethics and Tractatus Theologico-Politicus
Authors: Leo Russ 
Published: August 2024

Abstract
Baruch Spinoza’s friend Jarig Jelles delivers an account of the philosopher’s thought in the Preface to the posthumous Dutch edition of Spinoza’s writings. Spinoza’s philosophy, Jelles argues, neither contradicts nor challenges the basic principles of Christianity. To make this point, Jelles describes how everything that is required for salvation is evident in nature and may be understood by the light of reason alone. In other words, Jelles insists that Spinoza, Christ, and the Apostles all share an ethics that Jesus summarized when he asserted that “God must be loved above all, and our neighbors as ourselves.” In the Preface, however, Jelles derives these principles solely from the Ethics; by reading the Ethics and the Tractatus theologico-politicus together, in turn, Jelles directs scrupulous readers to distinguish between these crucial minimal principles in Scripture and its many other aspects. Jelles’s Preface affords us insight into how contemporary readers understood Spinoza’s thought not as distinct from Christianity but as a summary account of its basic principles.
Will, Sovereignty, and the Self in the Ethics and the Tractatus Theologico-Politicus
Authors: Rosenthal Michael A 
Published: August 2024

Abstract
In chapter IV of the Tractatus theologico-politicus (TTP), Spinoza distinguishes between two kinds of law, one that “depends … on a necessity of nature,” the other “on a human decision.” This chapter considers the relation of these two kinds of law to each other and to the ground of sovereign authority. Although Spinoza attacks the idea of a free will, he insists that we treat the second kind of law as if it resulted from a free decision of the human sovereign. His view that it is a practical necessity to hold the second view—a quasi-free-will—has consequences for his later work, particularly the structure of the Ethics. Achieving the highest good is no longer simply a matter of using reason to correct the mistaken notion of the free will. Instead, we must recognize that the quasi-free will is itself part of the process of ethical self-improvement. Spinoza uses a concept that is explicit in his early works—a “being of reason”—to make sense of the human will, the sovereign will, and the product of those acts.
Where Is the Collective Morality in Spinoza’s Ethics?
Authors: Israel Jonathan 
Published: August 2024

Abstract
This essay examines several of Spinoza’s key political ideas with a special focus on how these ideas are presented respectively in the TTP and the Ethics in an attempt to coax out what is argued to be the essential coherence of Spinoza’s political thought and its centrality to his philosophy as a whole. The main concepts discussed are Spinoza’s notion of ‘positive liberty’, ‘forced to be free’, ‘common good,’ ‘general will’, and the common mass of humanity or the ‘vulgus.’ Offering several contrasts in Spinoza’s use of key political concepts with Hobbes and Rousseau, the essay ends with a discussion of where Spinoza’s thought fits into the Dutch tradition of political thought in the late seventeenth century and the commencement of the ‘radical Enlightenment.’
Thinking with Concepts
Authors: Shea Nicholas 
Published: August 2024

Abstract
This chapter introduces the topic of conceptual thinking. Conceptual thinking involves conscious, deliberate thought processes that rely on working memory and are subject to cognitive load. Concepts are mental representations that serve as freely-recombinable components of thoughts. When combined in working memory, concepts provide access to a variety of information stored in other systems, allowing the construction of rich, cross-domain models of situations. Inference includes both step-by-step reasoning and non-local processes that draw conclusions from larger models or representations as a whole. Concepts act as an interface between general-purpose, broadly-logical reasoning and special-purpose informational models that represent domains like space and social relations. Thinking brings these elements together in an integrated ‘cognitive playground’. Metacognition monitors and controls conceptual thinking by assessing confidence in the concepts, information, and inferences involved. The book develops these ideas into a novel, empirically-grounded account that explains central features of human cognition and inference.
Representational Structure
Authors: Shea Nicholas 
Published: August 2024

Abstract
This chapter examines semantically-significant representational structure and distinguishes two broad kinds: structural representation and general-purpose compositional structure. Structural representations rely on a structural correspondence between representation and world, like maps. General-purpose compositional structure is exemplified by natural language sentences and conscious deliberate thoughts composed out of concepts. This allows any concept to be combined with any other concept(s) of the right type, unlike structural representations where the relations that define structure have specific representational contents. After defining representational structure, the chapter surveys different varieties found in mental representations. It then characterizes structural representation, distinguishing this from mere representational organization. Next it focuses on the general-purpose compositionality of language and thought, arguing that this is not a form of structural representation, or if it is, then only of a very abstract kind. The chapter clarifies terminology and draws connections between representational structure, computational processes, and informational models.
Computational Processes
Authors: Shea Nicholas 
Published: August 2024

Abstract
This chapter draws a distinction between two types of computational process that mental representations can enter into. Content-specific transitions are transitions between representations that are faithful to representational content due to the specific non-logical concepts involved. Content-general transitions, e.g. deductive inferences, depend only on broadly-logical concepts in order to be faithful to content. Structural representations, which rely on special-purpose compositional principles, tend to enter into content-specific computations rather than broadly-logical inferences. Conceptual representations, relying as they do on general-purpose compositionality, are well suited for content-general computations. However, concepts can also participate in content-specific transitions. The chapter argues that content-specific and content-general computational processes need to be integrated in order to explain concept-driven thinking. The former capture transitions based on pattern recognition and statistical structure, while the latter underpin logical inferences. An account of thinking needs to incorporate both special-purpose and general-purpose inferences involving concepts.
Drawing on Meaning
Authors: Shea Nicholas 
Published: August 2024

Abstract
This chapter examines the phenomenon of drawing on meaning: transitions between mental representations seem to depend on or draw on the semantic content of those representations. It argues that there are two distinct ways this occurs. First, some transitions rely only on the logical form of representations and the content of logical concepts (content-general transitions). Second, content-specific transitions rely on the specific, non-logical concepts involved, demonstrating an understanding or grasp of their meaning. For example, inferring that a dog barks by a direct-CS inference relies on drawing on the meaning of the concepts of dog and of barking. The chapter defends and elaborates this distinction and its implications. Representing information explicitly can enable content-general transitions that rely less directly on drawing on content.
Epigenome-wide differential methylation and differential variability as predictors of high-grade cervical intraepithelial neoplasia (CIN2+)
Authors: Bukowski Alexandra , Hoyo Cathrine , Graff Misa , Vielot Nadja A , Kosorok Michael R , Brewster Wendy R , Maguire Rachel L , Murphy Susan K , Nedjai Belinda , Ladoukakis Efthymios , North Kari E , Smith Jennifer S 
Published: August 2024

Abstract
CpG site methylation patterns have potential to improve differentiation of high-grade screening-detected cervical abnormalities. We assessed CpG differential methylation (DM) and differential variability (DV) in high-grade (CIN2+) vs low-grade (≤ CIN1) lesions. In ≤ CIN1 (n = 117) and CIN2+ (n = 31) samples, cervical sample DNA underwent testing with Illumina HumanMethylation arrays. We assessed DM and DV of CpG methylation M-values among 9 cervical cancer–associated genes. We fit CpG-specific linear models and estimated empirical Bayes standard errors and false discovery rates (FDRs). An exploratory epigenome-wide association study (EWAS) aimed to detect novel DM and DV CpGs (FDR &lt; 0.05) and Gene Ontology (GO) term enrichment. Compared to ≤ CIN1, CIN2+ exhibited greater methylation at CCNA1 cluster 1 (M-value difference 0.24; 95% CI, 0.04-0.43) and RARB cluster 2 (0.16; 95% CI, 0.05-0.28), and lower methylation at CDH1 cluster 1 (–0.15; 95% CI, –0.26 to –0.04). CIN2+ exhibited lower variability at CDH1 cluster 2 (variation difference –0.24; 95% CI, –0.41 to –0.05) and FHIT cluster 1 (–0.30; 95% CI, –0.50 to –0.09). EWAS detected 3534 DM and 270 DV CpGs. Forty-four GO terms were enriched with DM CpGs related to transcriptional, structural, developmental, and neuronal processes. Methylation patterns may help triage screening-detected cervical abnormalities and inform US screening algorithms.
This article is part of a Special Collection on Gynecological Cancer.
The Camp fire and perinatal health: an example of the generalized synthetic control method to identify susceptible windows of exposure
Authors: Goin Dana E , Benmarhnia Tarik , Huang ShihMing , Lurmann Fred , Mukherjee Anondo , Morello-Frosch Rachel , Padula Amy M 
Published: August 2024

Abstract
The November 2018 Camp fire was the most destructive wildfire in California history, but its effects on reproductive health are not known. We linked California birth records from 2017-2019 to daily smoke levels using US EPA Air Quality System (AQS) PM2.5 data and NOAA Hazard Mapping System smoke plume polygons during the Camp fire. In the main analysis, pregnancies were considered exposed if they had median AQS PM2.5 levels above 50 μg/m3 for at least 7 days during November 8-22, 2018. We calculated rates of preterm birth and the infant sex ratio based on week of conception and used the generalized synthetic control method to estimate the average treatment effect on the treated and to propose a novel approach to identify potential critical weeks of exposure during pregnancy. We found associations between Camp fire-related smoke exposure and rates of preterm birth, with a risk difference (RD) of 0.005 and a 95% confidence interval (CI) of 0.001-0.010. Exposure during week 10 of pregnancy was consistently associated with increased preterm birth (RD, 0.030; 95% CI, 0.004-0.056). We did not observe differences in the infant sex ratio. Camp fire smoke exposure was associated with increased rates of preterm birth, with sensitive windows in the first trimester.
This article is part of a Special Collection on Environmental Epidemiology.
The mediating role of SARS-CoV-2 variants between income and hospitalization due to COVID-19: a period-based mediation analysis
Authors: Harrigan Sean P , Fibke Chad D , Velásquez García Héctor A , Mak Sunny , Wilton James , Prystajecky Natalie , Tyson John , Wang Linwei , Sander Beate , Baral Stefan , Mishra Sharmistha , Janjua Naveed Z , Sbihi Hind 
Published: August 2024

Abstract
The mechanisms facilitating the relationship between low income and COVID-19 severity have not been partitioned in the presence of SARS-CoV-2 variants of concern (VOCs). To address this, we used causal mediation analysis to quantify the possible mediating role infection with VOC has on the relationship between neighborhood income (exposure) and hospitalization due to COVID-19 among cases (outcome). A population-based cohort of 65 629 individuals residing in British Columbia, Canada, was divided into 3 periods of VOC co-circulation in the 2021 calendar year, whereby each period included co-circulation of an emerging and an established VOC. Each cohort was subjected to g-formula mediation techniques to decompose the relationship between exposure and outcome into total, direct, and indirect effects. In the mediation analysis, the total effects indicated that low income was associated with increased odds of hospitalization across all periods. Further decomposition of the effects revealed that income is directly and indirectly associated with hospitalization. The resulting indirect effect through VOC accounted for approximately between 6% and 13% of the total effect of income on hospitalization. This study underscores, conditional on the analysis, the importance of addressing underlying inequities to mitigate the disproportionate impact on historically marginalized communities by adopting an equity lens as central to pandemic preparedness and response from the onset.