Miracle-dz/UniFAR-FTUs huggingface dataset:
Calculation of the energies of the multideterminant states of the nitrogen vacancy center in diamond with quantum Monte Carlo

Certain point defects in solids can efficiently be used as qubits for applications in quantum technology. They have spin states that are initializable, readable, robust, and can be manipulated optically. New theoretical methods are needed to find the best host materials and defect configurations. Most methods proposed so far rely either on cluster models or restrict the many-body treatment of the defects to a subspace of single-particle orbitals. We explore best practices and theory for the use of quantum Monte Carlo to predict the excitation spectra for spin defects, by using the negatively charged nitrogen vacancy (NV$^-$) center in diamond as a test system. Quantum Monte Carlo can be used to explicitly simulate electronic correlations with larger systems and sets of orbitals than previous methods due to favourable scaling with respect to system size and computing power. We consider different trial wave functions for variational and diffusion Monte Carlo methods, explore the nodal surface errors of the ground and excited state wave functions and study whether the variational principle holds for the excited states. We compute the vertical excitation energies in different simulation cell sizes and extrapolate to infinite system size, and include backflow corrections to the extrapolated energies. The final results for vertical excitation energies are found to overestimate the experimental estimates, but the triplet-to-triplet and singlet-to-singlet transitions are accurate against experiment. Finally, we list further developments for QMC needed to address the problem of accurately predicting structural and spin properties of the solid-state defects.
Wages and Utilities in a Closed Economy

The broad objective of this paper is to propose a mathematical model for the study of causes of wage inequality and relate it to choices of consumption, the technologies of production, and the composition of labor in an economy. The paper constructs a Simple Closed Model, or an SCM, for short, for closed economies, in which the consumption and the production parts are clearly separated and yet coupled. The model is established as a specialization of the Arrow-Debreu model and its equilibria correspond directly with those of the general Arrow-Debreu model. The formulation allows us to identify the combinatorial data which link parameters of the economic system with its equilibria, in particular, the impact of consumer preferences on wages. The SCM model also allows the formulation and explicit construction of the consumer choice game, where expressed utilities of various labor classes serve as strategies with total or relative wages as the pay-offs. We illustrate, through examples, the mathematical details of the consumer choice game. We show that consumer preferences, expressed through modified utility functions, do indeed percolate through the economy, and influence not only prices but also production and wages. Thus, consumer choice may serve as an effective tool for wage redistribution.
Detection of early proteomic alterations in 5xFAD Alzheimer's disease neonatal mouse model via MALDI‐MSI

Alzheimer's disease (AD) is a debilitating neurodegenerative disorder, characterized by memory deficit and dementia. AD is considered a multifactorial disorder where multiple processes like amyloid‐beta and tau accumulation, axonal degeneration, synaptic plasticity, and autophagic processes plays an important role. In this study, the spatial proteomic differences in the neonatal 5xFAD brain tissue were investigated using MALDI‐MSI coupled to LC‐MS/MS, and the statistically significantly altered proteins were associated with AD. Thirty‐five differentially expressed proteins (DEPs) between the brain tissues of neonatal 5xFAD and their littermate mice were detected via MALDI‐MSI technique. Among the 35 proteins identified, 26 of them were directly associated with AD. Our results indicated a remarkable resemblance in the protein expression profiles of neonatal 5xFAD brain when compared to AD patient specimens or AD mouse models. These findings showed that the molecular alterations in the AD brain existed even at birth and that some proteins are neurodegenerative presages in neonatal AD brain.
Tonic immobility (freezing) during sexual and physical assaults produces stronger memory effects than other characteristics of the assaults

ABSTRACT Tonic immobility (TI) is a phylogenetically conserved, passive, obligatory defense mechanism commonly engaged during sexual and physical assaults. During TI, people become immobile while remaining conscious and later reexperience intrusive memories of both their assault and of its accompanying immobility. Here we show that this well-studied biological process has powerful effects on memory and other processes. Participants had experienced either a serious sexual (n = 234) or physical (n = 137) assault. For both the assault and its accompanying immobility, the standard measure of the peritraumatic severity of TI correlated between . 40 and . 65 with post-assault effects on memory, including memory of the assault and memory of the immobility, the two memory-based self-concept measures of self-blame and event centrality, and post-assault anxiety and depression. The correlations with TI were much higher than other peritraumatic characteristics commonly used to predict and describe posttraumatic effects in assaults and other traumas. The results suggest that TI should be considered for a broader, more biologically based and ecologically valid understanding of the effects of trauma on memory and memory-based reactions.
Equilibrium statistics of channel-confined DNA

This thesis is devoted to the study of DNA molecules in nanochannels. In the last ten years, a large number of studies have been conducted wherein DNA molecules were confined to channels with a width of about 100 nm. These studies are motivated both by biotechnical applications, and by the potential for using nanochannels as a model system for studying the physics of confined DNA. The results of this thesis increase our understanding of the equilibrium statistics of such channel-confined DNA. The results can be divided into three parts. In the first, we derive novel predictions for the extension statistics of channel-confined polymers. Specifically, we map out a phase diagram of scaling regimes for a polymer in a rectangular channel. Further, in an important special case known as the extended de Gennes regime, we show that the configurational statistics are equivalent to those of a one-dimensional model known as the weakly self-avoiding random walk. Exact results for that model yield rigorous predictions for the confined polymer. In the second part we report experimental measurements of the extension statistics of confined DNA. We find that the measurements agree very well with theoretical predictions, except at low ionic strengths. Finally, the third part of the thesis concerns the melting of DNA, i.e. the partial disassociation of its two strands at elevated temperatures. We solve a simple model of DNA melting and show that, within this model, channel confinement makes the transition to the molten state less abrupt, despite the fact that the order of the phase transition is unchanged by confinement.
Foundations and guidelines for high‐quality three‐dimensional models using photogrammetry: A technical note on the future of neuroanatomy education

Hands‐on dissections using cadaveric tissues for neuroanatomical education are not easily available in many educational institutions due to financial, safety, and ethical factors. Supplementary pedagogical tools, for instance, 3D models of anatomical specimens acquired with photogrammetry are an efficient alternative to democratize the 3D anatomical data. The aim of this study was to describe a technical guideline for acquiring realistic 3D anatomic models with photogrammetry and to improve the teaching and learning process in neuroanatomy. Seven specimens with different sizes, cadaveric tissues, and textures were used to demonstrate the step‐by‐step instructions for specimen preparation, photogrammetry setup, post‐processing, and display of the 3D model. The photogrammetry scanning consists of three cameras arranged vertically facing the specimen to be scanned. In order to optimize the scanning process and the acquisition of optimal images, high‐quality 3D models require complex and challenging adjustments in the positioning of the specimens within the scanner, as well as adjustments of the turntable, custom specimen holders, cameras, lighting, computer hardware, and its software. MeshLab® software was used for editing the 3D model before exporting it to MedReality® (Thyng, Chicago, IL) and SketchFab® (Epic, Cary, NC) platforms. Both allow manipulation of the models using various angles and magnifications and are easily accessed using mobile, immersive, and personal computer devices free of charge for viewers. Photogrammetry scans offer a 360° view of the 3D models ubiquitously accessible on any device independent of operating system and should be considered as a tool to optimize and democratize the teaching of neuroanatomy.
Peak movement and impact characteristics of different training methods in professional rugby union

ABSTRACT The purpose of this study was to compare the peak periods (1- to 6-minute epochs) for three different training methods (game-based training – GBT; small-sided games – SSG; and conditioning training – CT) in elite male rugby union (RU) players. The peak movement (m·min−1) and impact (impact·min−1) characteristics of 42 players during in-season training were assessed. When comparing between training methods, SSG drills produced the greatest peak movement characteristics for all time epochs (1-minute average peak periods – SSG 195 m·min−1, GBT 160 m·min−1, and CT 144 m·min−1). The peak impact characteristics performed during training were 1–2 impact·min−1 for a 1-minute period and then decreased as the time period increased for all training methods. The greatest distribution of training time occurred at 30–39% (SSG and CT) and 40–49% (GBT) of peak movement intensity, with less than 5% of training performed at or above 80% peak intensity across all drill types. Findings from the current study show that the peak movement periods (m·min−1) in RU training from all three training methods match or exceed those which are previously reported in peak gameplay, yet their ability to replicate peak impact characteristics is questionable.
Translating measurement into practice: Brazilian norms for depressive symptom assessment with the Patient Health Questionnaire (PHQ-9)

Objectives: To provide practical norms for measuring depressive symptoms with the Patient Health Questionnaire 9 (PHQ-9) in Brazil through a state-of-the-art psychometrics analysis. Methods: We used a large representative dataset from the 2019 Brazilian National Health Survey (Pesquisa Nacional de Saúde – 2019), which included 90,846 Brazilian citizens. To assess scale structure, we assessed a unidimensional model using confirmatory factor analysis. Item response theory was used to characterize the distribution of depressive symptoms. Summed- and mean-based PHQ-9 scores were then linked using item response theory-based scores in generalized additive models. Finally, percentiles, T scores, and a newly developed score, called the decimal score (D score), were generated to describe PHQ-9 norms for the Brazilian population. Results: Confirmatory factor analysis revealed a good fit to the unidimensional model, being invariant to age and sex. Item response theory captured item-level information about the latent trait (reliable from 1 to 3 SDs above the mean). Brazilian norms were presented using summed scores, T scores, and D scores. Conclusion: This is the first study to determine Brazilian norms for the PHQ-9 among a large representative sample using robust psychometric tools. More precise PHQ-9 scores are now available and may be widely used in primary and specialized clinical care settings.
Widespread gene flow following range expansion in Anna's Hummingbird

Anthropogenic changes have altered the historical distributions of many North American taxa. As environments shift, ecological and evolutionary processes can combine in complex ways to either stimulate or inhibit range expansion. Here, we examined the role of evolution in a rapid range expansion whose ecological context has been well‐documented, Anna's Hummingbird (Calypte anna). Previous studies have suggested that the C. anna range expansion is the result of an ecological release facilitated by human‐mediated environmental changes, where access to new food sources have allowed further filling of the abiotic niche. We examined the role of gene flow and adaptation during range expansion from their native California breeding range, north into Canada and east into New Mexico and Texas, USA. Using low coverage whole genome sequencing we found high genetic diversity, low divergence, and little evidence of selection on the northern and eastern expansion fronts. Additionally, there are no clear barriers to gene flow across the native and expanded range. The lack of selective signals between core and expanded ranges could reflect (i) an absence of novel selection pressure in the expanded range (supporting the ecological release hypothesis), (ii) swamping of adaptive variation due to high gene flow, or (iii) limitations of genome scans for detecting small shifts in allele frequencies across many loci. Nevertheless, our results provide an example where strong selection is not apparent during a rapid, contemporary range shift.
Histograms of MAD Tracking Results

Two Fortran programs are described that process MAD tracking output for 10 4 or more particles, and produce histograms. The loshst program produces histograms of the particle losses by turn and by position along the orbit. The trkhst program computes means and standard deviations of the particle positions in 6D phase space and the emittances in all three directions, and produces histograms of the particle distributions at the end of the MAD tracking run.
Cost-effectiveness of CT perfusion for the detection of large vessel occlusion acute ischemic stroke followed by endovascular treatment: A model-based health economic evaluation study

Background: CT perfusion (CTP) has been suggested to increase the rate of large vessel occlusion (LVO) detection in patients suspected of acute ischemic stroke (AIS) if used in addition to a standard diagnostic imaging regime of CT angiography (CTA) and non-contrast CT (NCCT). The aim of this study was to estimate the costs and health effects of additional CTP for endovascular treatment (EVT)-eligible occlusion detection using model-based analyses. Methods: In this Dutch, nationwide retrospective cohort study with model-based health economic evaluation, data from 701 EVT-treated patients with available CTP results were included (January 2018 - March 2022; trialregister.nl:NL7974). We compared a cohort undergoing NCCT, CTA, and CTP (NCCT+CTA+CTP) with a generated counterfactual where NCCT and CTA (NCCT+CTA) were used for LVO detection. The NCCT+CTA strategy was simulated using diagnostic accuracy values and EVT effects from the literature. A Markov model was used to simulate 10-year follow-up. We adopted a healthcare payer perspective for costs in euros and health gains in quality-adjusted life years (QALYs). The primary outcome was the net monetary benefit (NMB) at a willingness to pay of 80,000 Euro, secondary outcomes were the difference between LVO detection strategies in QALYs (dQALY) and costs (dCosts). Results: We included 701 patients (median age:72 IQR:[62-81]) years). Per LVO patient, CTP-based occlusion detection resulted in cost savings (dCosts median:-2671 IQR:[-4721;-731] Euro), a health gain (dQALY median:0.073 IQR:[0.044;0.104]), and a positive NMB (median:8436 IQR:[5565;11876]) per LVO patient. Conclusion: Adding CTP to NCCT and CTA for EVT-eligible LVO detection resulted in cost savings and health gains.
Costs of digital adherence technologies for tuberculosis treatment support

Digital adherence technologies (DATs) are increasingly used for tuberculosis (TB) adherence support, but information about their costs remains limited. We used microcosting to estimate health system costs (in 2022 US dollars) of 99DOTS pill sleeves and video-observed treatment (VOT), implemented in demonstration projects during 2018-21. Local cost estimates for standard directly observed treatment (DOT) were also obtained. The estimated per-person costs of 99DOTS for drug-sensitive (DS-) TB were $98, $106, and $174 in Bangladesh (n=719), the Philippines (n=396), and Tanzania (n=976) respectively. The estimated per-person costs of VOT were $1 154, $304, $457, and $661 in Haiti (n=87 DS-TB), Moldova (n=173 DS-TB), Moldova (n=135 drug-resistant [DR]-TB) and the Philippines (n=110 DR-TB) respectively. Health system costs of 99DOTS may be similar to or cheaper than standard DOT. VOT is considerably more expensive; labor cost offsets and/or economies of scale may yield savings relative to standard DOT in some settings.
Linear stability of monopolar vortices over isolated topography

Abstract The linear instability of circular vortices over isolated topography in a homogeneous and inviscid fluid is examined for the shallow-water and quasi-geostrophic models in the $f$-plane. The eigenvalue problem associated with azimuthal disturbances is derived for arbitrary axisymmetric topographies, either submarine mountains or valleys. Amended Rayleigh and Fjørtoft theorems with topographic effects are given for barotropic instability, obtaining necessary criteria for instability when the potential vorticity gradient is zero somewhere in the domain. The onset of centrifugal instability is also discussed by deriving the Rayleigh circulation theorem with topography. The barotropic instability theorems are applied to a wide family of nonlinear, quasi-geostrophic solutions of circular vortices over axisymmetric topographic features. Flow instability depends mainly on the vortex/topography configuration, as well as on the vortex size in comparison with the width of the topography. It is found that anticyclones/mountains and cyclones/valleys may be unstable. In contrast, cyclone/mountain and anticyclone/valley configurations are stable. These statements are validated with two numerical methods. First, the generalised eigenvalue problem is solved to obtain the wavenumber of the fastest-growing perturbations. Second, the evolution of the vortices is simulated numerically to detect the development of linear perturbations. The numerical results show that for unstable vortices over narrow topographies, the fastest growth rate corresponds to mode $1$, which subsequently forms asymmetric dipolar structures. Over wide topographies, the fastest perturbations are mainly modes $1$ and $2$, depending on the topographic features.
Some Comments on the Relation Between Reliability and Statistical Power

Several articles have discussed the curious fact that a difference score with zero reliability can nonetheless allow a powerful test of change. This statistical legerde main should not be overemphasized for three reasons. First, although the reliability of the difference score may be unrelated to power, the reliabilities of the var iables used to create the difference scores are directly related to the power of the test. Second, with what some will regard as additional legerdemain, it is possi ble to define reliability in the context of a difference score in such a way that power is a direct function of reliability. The third and most serious objection to the conclusion that the reliability of a difference score is unimportant is that the underlying statistical model used in its derivation is rarely appropriate for psycho logical data. Index terms: control of individual dif ferences, difference scores, reliability, reliability of the marginal distribution, statistical power, within- group reliabilities.
Pelican — a Time of Flight Cold Neutron Polarization Analysis Spectrometer at OPAL

Pelican, a direct-geometry multi-purpose cold-neutron spectrometer, combines state-of-the-art monochromators and Fermi chopper systems to perform inelastic and quasi-elastic neutron scattering on a variety of materials (powder, polycrystal, single crystal, glass and liquid), covering fields of physics, chemistry and biology. The provision of cryogenic vacuum from sample to detector decreases background to a minimum level. A polarized incident beam is realized by supermirror polarizer and polarization analysis will be achieved by 3He polarization filter. The instrument is designed to accommodate various sample environments including high magnetic fields, and low and high temperatures. Pelican is the first neutron spectrometer having a moveable high-vacuum Aluminium chamber and a full polarization analysis system.
Geometry of space, physics and analysis

In the days of the Greek geometers, plane and Euclidean geometry were reasonably adequate to describe most observations. The Greek scholars were convinced that the earth is round and were able to measure the diameter of the earth and its distance to the sun based on plane geometry. The Chinese scholars also measured the distance of the earth to the heaven using similar ideas. But even then, Archimedes had already started to investigate infinite processes to understand geometric figures that could not be described by Euclidean geometry alone. Calculations of volumes of many different geometric figures started the investigation of integral calculus, as was also proposed by ancient Chinese mathematicians. Not long afterwards, in the process of measuring the movement of celestial bodies, the ancient Indians
Aesthetic Experience in the Green Areas of a Brazilian City: An Eco-Phenomenological Approach to Environmental Education

Abstract:This study investigated the sensory responses of 20 students and a geography teacher in their contact with the green areas around their school in Curitiba, Brazil in 2019. With a theoretical framework of eco-phenomenological and sensory ethnographical references, the study used three data gathering techniques: participant observation, administering a questionnaire, and walking ethnography. Review of the data revealed three categories for analysis: phenomenological deconstruction and reconstruction, slow pedagogy, and the education of attention. The results indicate that the urban context is a rich scenario offering various possibilities for awakening interest in environmental education.