Theory and Simulation of the diffusion of kinks on dislocations in bcc metals

Isolated kinks on thermally fluctuating (1/2) screw, edge and (1/2) edge dislocations in bcc iron are simulated under zero stress conditions using molecular dynamics (MD). Kinks are seen to perform stochastic motion in a potential landscape that depends on the dislocation character and geometry, and their motion provides fresh insight into the coupling of dislocations to a heat bath. The kink formation energy, migration barrier and friction parameter are deduced from the simulations. A discrete Frenkel-Kontorova-Langevin (FKL) model is able to reproduce the coarse grained data from MD at a fraction of the computational cost, without assuming an a priori temperature dependence beyond the fluctuation-dissipation theorem. Analytic results reveal that discreteness effects play an essential r\^ole in thermally activated dislocation glide, revealing the existence of a crucial intermediate length scale between molecular and dislocation dynamics. The model is used to investigate dislocation motion under the vanishingly small stress levels found in the evolution of dislocation microstructures in irradiated materials

Imperfect identity

Questions of identity over time are often hard to answer. A long tradition has it that such questions are somehow soft: they have no unique, determinate answer, and disagreements about them are merely verbal. I argue that this claim is not the truism it is taken to be. Depending on how it is understood, it turns out either to be false or to presuppose a highly contentious metaphysical claim

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes

The quantification of cell shape, cell migration, and cell rearrangements is important for addressing classical questions in developmental biology such as patterning and tissue morphogenesis. Time-lapse microscopic imaging of transgenic embryos expressing fluorescent reporters is the method of choice for tracking morphogenetic changes and establishing cell lineages and fate maps in vivo. However, the manual steps involved in curating thousands of putative cell segmentations have been a major bottleneck in the application of these technologies especially for cell membranes. Segmentation of cell membranes while more difficult than nuclear segmentation is necessary for quantifying the relations between changes in cell morphology and morphogenesis. We present a novel and fully automated method to first reconstruct membrane signals and then segment out cells from 3D membrane images even in dense tissues. The approach has three stages: 1) detection of local membrane planes, 2) voting to fill structural gaps, and 3) region segmentation. We demonstrate the superior performance of the algorithms quantitatively on time-lapse confocal and two-photon images of zebrafish neuroectoderm and paraxial mesoderm by comparing its results with those derived from human inspection. We also compared with synthetic microscopic images generated by simulating the process of imaging with fluorescent reporters under varying conditions of noise. Both the over-segmentation and under-segmentation percentages of our method are around 5%. The volume overlap of individual cells, compared to expert manual segmentation, is consistently over 84%. By using our software (ACME) to study somite formation, we were able to segment touching cells with high accuracy and reliably quantify changes in morphogenetic parameters such as cell shape and size, and the arrangement of epithelial and mesenchymal cells. Our software has been developed and tested on Windows, Mac, and Linux platforms and is available publicly under an open source BSD license (https://github.com/krm15/ACME)

The Platform Carbonates of Monte Jouf, Maniago, and the Cretaceous Stratigraphy of the Italian Carnian Prealps

The Late Cretaceous strata of Monte Jouf are reasonably pure, white limestones, and are part of the stratigraphic unit known as Calcari del Monte Cavallo. M. Jouf is the original locality of two genera of rudists Joufia and Colveraia, which are used as biostratigraphic markers for shallow water carbonate facies in central-western Tethys. The limestone sequence has been subdivided into 4 units on the basis of facies and these have been dated using Sr-isotope chronology. This technique gives an independent age for the units and of the fossils as they occur on M. Jouf, and thus provides an accurate and precise timescale to present the evolution of the palaeoenvironment in this part of the Adriatic Carbonate Platform. Unit 1 is Late Cenomanian, as dated by the caprinid rudist Caprinula boissyi. Unit 2 ranges from the earliest to middle/late of the Campanian according to the Sr-isotope results. Unit 3 is Late Campanian to Campanian/Maastrichtian boundary, as dated by Sr-isotopes. Unit 4 is of earliest Maastrichtian age (placing the Campanian/Maastrichtian boundary at the extinction of the planktonic foraminifer Globotruncana calcarata). Two main epochs of broad, shallow carbonate platforms, covered by a diverse rudist fauna with large individuals, including recumbent forms are noted. The first of these was in the Late Cenomanian and the second in the latest Campanian. The Late Cenomanian event was ended by downfaulting of the platform margin, possibly preceded by a regression. Sediment wedges then began to build out again over the Late Cenomanian deposits, though in the interval Turonian-Santonian sediment by-passed the M. Jouf area. In the latest Campanian platform carbonate deposition was ended by a regression and by subsequent downfaulting in the Maastrichtian and Palaeocene

New remarks on the Cosmological Argument

We present a formal analysis of the Cosmological Argument in its two main forms: that due to Aquinas, and the revised version of the Kalam Cosmological Argument more recently advocated by William Lane Craig. We formulate these two arguments in such a way that each conclusion follows in first-order logic from the corresponding assumptions. Our analysis shows that the conclusion which follows for Aquinas is considerably weaker than what his aims demand. With formalizations that are logically valid in hand, we reinterpret the natural language versions of the premises and conclusions in terms of concepts of causality consistent with (and used in) recent work in cosmology done by physicists. In brief: the Kalam argument commits the fallacy of equivocation in a way that seems beyond repair; two of the premises adopted by Aquinas seem dubious when the terms `cause' and `causality' are interpreted in the context of contemporary empirical science. Thus, while there are no problems with whether the conclusions follow logically from their assumptions, the Kalam argument is not viable, and the Aquinas argument does not imply a caused origination of the universe. The assumptions of the latter are at best less than obvious relative to recent work in the sciences. We conclude with mention of a new argument that makes some positive modifications to an alternative variation on Aquinas by Le Poidevin, which nonetheless seems rather weak.Comment: 12 pages, accepted for publication in International Journal for Philosophy of Religio

Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells

BACKGROUND: Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination. Accumulation of RNA polymerase II at particular locations across genes can be indicative of sites of regulation. RNA polymerase II is thought to accumulate at the promoter and at sites of co-transcriptional alternative splicing where the rate of RNA synthesis slows. RESULTS: To further understand transcriptional regulation at a global level, we determined the distribution of RNA polymerase II within regions of the human genome designated by the ENCODE project. Hypophosphorylated RNA polymerase II localizes almost exclusively to 5' ends of genes. On the other hand, localization of total RNA polymerase II reveals a variety of distinct landscapes across many genes with 74% of the observed enriched locations at exons. RNA polymerase II accumulates at many annotated constitutively spliced exons, but is biased for alternatively spliced exons. Finally, RNA polymerase II is also observed at locations not in gene regions. CONCLUSION: Localizing RNA polymerase II across many millions of base pairs in the human genome identifies novel sites of transcription and provides insights into the regulation of transcription elongation. These data indicate that RNA polymerase II accumulates most often at exons during transcription. Thus, a major factor of transcription elongation control in mammalian cells is the coordination of transcription and pre-mRNA processing to define exons

Evaluating associations between fitspiration and thinspiration content on Instagram and disordered-eating behaviors using ecological momentary assessment: A registered report

This is the peer reviewed version of the following article: Christensen, KA, Forbush, KT, Cushing, CC, Lejuez, CW, Fleming, KK, Swinburne Romine, RE. Evaluating associations between fitspiration and thinspiration content on Instagram and disordered-eating behaviors using ecological momentary assessment: A registered report. Int J Eat Disord. 2021; 54: 1307– 1315. https://doi.org/10.1002/eat.23518, which has been published in final form at https://doi.org/10.1002/eat.23518. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.Introduction Greater use of appearance-focused social media, such as Instagram, is associated with increased body dissatisfaction and eating disorder (ED) symptoms; however, questions remain about the mechanism connecting social media use to disordered-eating behaviors (DEBs). The proposed study evaluates how and for whom exposure to fitspiration or thinspiration on Instagram is associated with DEBs. Methods We will evaluate a hypothesized pathway from Instagram use to disordered-eating mediated by negative affect. We will test how individual differences in internalized weight stigma, trait self-esteem, and trait self-comparison moderate the pathway from social media use to negative affect. We will recruit 175 undergraduate women who report engaging in DEBs on average at least once per week over the past 3 months. Participants will complete a 7-day ecological momentary assessment protocol, during which they will report their Instagram use, affect, and engagement in DEBs. Results Multi-level modeling will be used to assess moderated mediation. Results from this study will provide increased specificity about how Instagram usage is linked to eating pathology and who may be most vulnerable to experiencing distress. Discussion Information about negative affect from Instagram and engagement in DEBs could contribute to the development of Just-In-Time Interventions for problematic social media use

Lanthanide speciation in potential SANEX and GANEX actinide/ 2 lanthanide separations using Tetra-N-Donor extractants

Lanthanide(III) complexes with N-donor ex-tractants, which exhibit the potential for the separation of minor actinides from lanthanides in the management of spent nuclear fuel, have been directly synthesized and characterized in both solution and solid states. Crystal structures of the Pr3+, Eu3+, Tb3+, and Yb3+ complexes of 6,6′-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzotriazin3-yl)-1,10-phenanthroline(CyMe4-BTPhen) and the Pr3+, Eu3+, and Tb3+ complexes of 2,9-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzotria-zin-3-yl)-2,2′-bypyridine (CyMe4-BTBP) were obtained. The majority of these structures displayed coordination of two ofthe tetra-N-donor ligands to each Ln3+ ion, even when in some cases the complexations were performed with equimolar amounts of lanthanide and N-donor ligand. The structures showed that generally the lighter lanthanides had their coordination spheres completed by a bidentate nitrate ion, giving a 2+ charged complex cation, whereas the structures of the heavier lanthanides displayed tricationic complex species with a single water molecule completing their coordination environments. Electronic absorption spectroscopic titrations showed formation of the 1:2 Ln3+/LN4‑donor species (Ln = Pr3+, Eu3+, Tb3+) in methanol when the N-donor ligand was in excess. When the Ln3+ ion was in excess, evidence for formation of a 1:1 Ln3+/LN4‑donor complex species was observed. Luminescent lifetime studies of mixtures of Eu3+ with excess CyMe4-BTBP and CyMe4-BTPhen in methanol indicated that the nitrate-coordinated species is dominant in solution. X-ray absorption spectra of Eu3+ and Tb3+ species, formed by extraction from an acidic aqueous phase into an organic solution consisting of excess N-donor extractant in pure cyclohexanone or 30% tri-n-butyl phosphate (TBP) in cyclohexanone, were obtained. The presence of TBP in the organic phase did not alter lanthanide speciation. Extended X-ray absorption fine structure data from these spectra were fitted using chemical models established by crystallography and solution spectroscopy and showed the dominant lanthanide species in the bulk organic phase was a 1:2 Ln3+/LN‑donor species

The Ontology of Intentional Agency in Light of Neurobiological Determinism: Philosophy Meets Folk Psychology

The moot point of the Western philosophical rhetoric about free will consists in examining whether the claim of authorship to intentional, deliberative actions fits into or is undermined by a one-way causal framework of determinism. Philosophers who think that reconciliation between the two is possible are known as metaphysical compatibilists. However, there are philosophers populating the other end of the spectrum, known as the metaphysical libertarians, who maintain that claim to intentional agency cannot be sustained unless it is assumed that indeterministic causal processes pervade the action-implementation apparatus employed by the agent. The metaphysical libertarians differ among themselves on the question of whether the indeterministic causal relation exists between the series of intentional states and processes, both conscious and unconscious, and the action, making claim for what has come to be known as the event-causal view, or between the agent and the action, arguing that a sort of agent causation is at work. In this paper, I have tried to propose that certain features of both event-causal and agent-causal libertarian views need to be combined in order to provide a more defendable compatibilist account accommodating deliberative actions with deterministic causation. The ‘‘agent-executed-eventcausal libertarianism’’, the account of agency I have tried to develop here, integrates certain plausible features of the two competing accounts of libertarianism turning them into a consistent whole. I hope to show in the process that the integration of these two variants of libertarianism does not challenge what some accounts of metaphysical compatibilism propose—that there exists a broader deterministic relation between the web of mental and extra-mental components constituting the agent’s dispositional system—the agent’s beliefs, desires, short-term and long-term goals based on them, the acquired social, cultural and religious beliefs, the general and immediate and situational environment in which the agent is placed, etc. on the one hand and the decisions she makes over her lifetime on the basis of these factors. While in the ‘‘Introduction’’ the philosophically assumed anomaly between deterministic causation and the intentional act of deciding has been briefly surveyed, the second section is devoted to the task of bridging the gap between compatibilism and libertarianism. The next section of the paper turns to an analysis of folk-psychological concepts and intuitions about the effects of neurochemical processes and prior mental events on the freedom of making choices. How philosophical insights can be beneficially informed by taking into consideration folk-psychological intuitions has also been discussed, thus setting up the background for such analysis. It has been suggested in the end that support for the proposed theory of intentional agency can be found in the folk-psychological intuitions, when they are taken in the right perspective