Miracle-dz/UniFAR-FTUs huggingface dataset:
Model Reduction in Classical Molecular Dynamics

This thesis explores different routes to model reduction in the context of classical molecular dynamics. Adopting a reductionist's point of view, our main concern is the sound causal explanation of observable macroscopic properties, e.g., activation energies or dynamical stability of conformations in terms of the microscopic physical model. Notwithstanding computational aspects, the difficulty lies in the sheer complexity of the microscopic models with their vastly different spatial and temporal scales. Roughly speaking, reduced modelling comes in two varieties: elimination of specific (e.g., fast) degrees of freedom from the original model, or parametrization of certain simplified models. The first approach is usually referred to as "mode reduction", whereas the latter is often termed "remodelling". In this thesis we mainly focus on mode reduction, since sticking to the original microscopic model means to keep as much of the problem's physics as possible. (The microscopic models are based on profound physical and chemical knowledge, both theoretical considerations and experimental data, which constitutes their empirical adequacy and predictive power.) In doing so, we extend and refine available methods of mode reduction such as averaging or projection operator techniques and set them in context with one another. Nevertheless we also allude to aspects of parametrized models.
Predictors of large cell transformation in patients with Sezary Syndrome—A retrospective analysis

Background Large cell transformation (LCT) of Sezary Syndrome (SS) is a rare phenomenon. To date, there are no rigorous studies identifying risk factors for its development. Objectives Here, we seek to characterize the clinicopathologic risk factors that predispose patients with SS to develop LCT. Methods We retrospectively evaluated all SS patient records available in the Michigan Medicine Cancer Registry from 2010–2021. Clinical and pathologic variables were compared between groups. The Kaplan-Meier method and log-rank test were used to assess overall survival. Results Of 28 SS patients identified, eight patients experienced LCT, and 20 did not (NLCT). Peak lactate dehydrogenase (LDH) before LCT (p = 0.0012), maximum total body surface area (TBSA) involvement before LCT (p = 0.0114), absolute CD8+ cell count measured on flow cytometry at diagnosis of SS (p = 0.0455) and at the most recent blood draw (p = 0.00736), and ulceration on biopsy (p = 0.0034) were significant clinicopathologic variables identified between the SS patients that developed LCT versus those that did not. Conclusions Maximum TBSA involvement, peak LDH, presence of ulceration, and decreased levels of CD8+ cells in the peripheral blood may predict the development of LCT in patients with SS.
Off-Center Ignition in Type Ia Supernovae. I. Initial Evolution and Implications for Delayed Detonation

The explosion of a carbon-oxygen white dwarf as a Type Ia supernova is known to be sensitive to the manner in which the burning is ignited. Studies of the presupernova evolution suggest asymmetric, off-center ignition, and here we explore its consequences in two- (2D) and three-dimensional (3D) simulations. Compared with centrally ignited models, one-sided ignitions initially burn less and release less energy. For the distributions of ignition points studied, ignition within two hemispheres typically leads to the unbinding of the white dwarf, while ignition within a small fraction of one hemisphere does not. We also examine the spreading of the blast over the surface of the white dwarf that occurs as the first plumes of burning erupt from the star. In particular, our studies test whether the collision of strong compressional waves can trigger a detonation on the far side of the star as has been suggested by Plewa and coworkers. The maximum temperature reached in these collisions is sensitive to how much burning and expansion has already gone on, and to the dimensionality of the calculation. Although detonations are sometimes observed in 2D models, none ever happens in the corresponding 3D calculations. Collisions between the expansion fronts of multiple bubbles also seem, in the usual case, unable to ignite a detonation. "Gravitationally confined detonation" is therefore not a robust mechanism for the explosion. Detonation may still be possible in these models, however, either following a pulsation or by spontaneous detonation if the turbulent energy is high enough.
Electromagnetic control of the collective radiations with three-photon blockade

We study properties of collective radiations of coherently driven two three-level ladder-type atoms trapped in a single-mode cavity. Using the electromagnetically induced transparency technique, we show that the three-photon blockade effect can be observed and the properties of collective radiations are strongly dependent on the phase between two atoms. In the case of in-phase radiations, the frequency range to realize the three-photon blockade can be broadened as the control field increases. However, in the regime of the three-photon blockade, the property of collective radiations changes from hyperradiance to subradiance. In the case of out-of-phase radiations, hyperradiance accompanied with the three-photon blockade can be observed. The results presented in this paper show that our scheme is an attractive candidate to generate antibunched photon pairs and control the properties of collective radiations.
Closed Form Approximations for the Trajectories of the Three Body Problem

The problem of describing the free motions of three gravitating bodies under each others gravitational influence is one of the oldest of unsolved problems of classical mechanics. Henry Poincare proved in his dictum that due to the nature of the instabilities involved in the problem, it could not be solved. Yet closed form approximations for the problem can be found and it is on these lines that we will explore the problem. It will be shown that closed form approximations for the associated trajectories can be found.
Trends in the Extracorporeal Membrane Oxygenation Literature: A Bibliometric Analysis in the COVID-19 Era.

Extracorporeal Membrane Oxygenation (ECMO) was first used in the 1970s. Its use is increasingly common in critical care and perioperative settings and has gained newfound prominence during COVID-19. To guide future research, we conducted a bibliometric analysis of ECMO literature. Thomson Reuters Web of Science was searched to March 7, 2021. Articles were ranked by total number of citations. Data was extracted from the 100 most cited papers relevant to ECMO for study design, topic, author, year, and institution. Journal impact factor for 2019 and Eigenfactor scores were also recorded. Our search retrieved a total of 18,802 articles. Median number of citations for the top 100 articles was 220 (range 157-1,819). These were published in 34 journals, with first authors originating from 15 countries. The Annals of Thoracic Surgery had the highest number of articles (n = 9) while Lancet publications had the most citations (n = 3,191). Use of ECMO was most commonly observed in cardiogenic shock or acute respiratory distress syndrome. United States had the greatest article output (n = 49). With 10 publications, 2013 was the most prolific year. Using linear regression, when controlled for time since publication, there was no statistically significant relationship between 2019 journal impact factor and number of article citations (p = .09). Top articles in the ECMO literature are of considerable impact and quality. As the United States produced the bulk of the prominent evidence base, and most data were regarding respiratory issues, outsized advances in ECMO may be possible within the United States during the COVID-19 era.
A Volcanic Hydrogen Habitable Zone

The classical habitable zone (HZ) is the circular region around a star in which liquid water could exist on the surface of a rocky planet. The outer edge of the traditional N2–CO2–H2O HZ extends out to nearly ∼1.7 au in our solar system, beyond which condensation and scattering by CO2 outstrips its greenhouse capacity. Here, we show that volcanic outgassing of atmospheric H2 can extend the outer edge of the HZ to ∼2.4 au in our solar system. This wider volcanic-hydrogen HZ (N2–CO2–H2O–H2) can be sustained as long as volcanic H2 output offsets its escape from the top of the atmosphere. We use a single-column radiative-convective climate model to compute the HZ limits of this volcanic hydrogen HZ for hydrogen concentrations between 1% and 50%, assuming diffusion-limited atmospheric escape. At a hydrogen concentration of 50%, the effective stellar flux required to support the outer edge decreases by ∼35%–60% for M–A stars. The corresponding orbital distances increase by ∼30%–60%. The inner edge of this HZ only moves out ∼0.1%–4% relative to the classical HZ because H2 warming is reduced in dense H2O atmospheres. The atmospheric scale heights of such volcanic H2 atmospheres near the outer edge of the HZ also increase, facilitating remote detection of atmospheric signatures.
Finite-sized rigid spheres in turbulent Taylor–Couette flow: effect on the overall drag

We report on the modification of drag by neutrally buoyant spherical finite-sized particles in highly turbulent Taylor–Couette (TC) flow. These particles are used to disentangle the effects of size, deformability and volume fraction on the drag, and are contrasted to the drag in bubbly TC flow. From global torque measurements, we find that rigid spheres hardly decrease or increase the torque needed to drive the system. The size of the particles under investigation has a marginal effect on the drag, with smaller diameter particles showing only slightly lower drag. Increase of the particle volume fraction shows a net drag increase. However, this increase is much smaller than can be explained by the increase in apparent viscosity due to the particles. The increase in drag for increasing particle volume fraction is corroborated by performing laser Doppler anemometry, where we find that the turbulent velocity fluctuations also increase with increasing volume fraction. In contrast to rigid spheres, for bubbles, the effective drag reduction also increases with increasing Reynolds number. Bubbles are also much more effective in reducing the overall drag.
Spin interference in silicon one-dimensional rings

We present the first findings of the spin transistor effect in the Rashba gate-controlled ring embedded in the p-type self-assembled silicon quantum well that is prepared on the n-type Si (100) surface. The coherence and phase sensitivity of the spin-dependent transport of holes are studied by varying the value of the external magnetic field and the top gate voltage that are applied perpendicularly to the plane of the double-slit ring and revealed by the Aharonov-Bohm (AB) and Aharonov-Casher (AC) conductance oscillations, respectively. Firstly, the amplitude and phase sensitivity of the 0.7. (2e2/h) feature of the hole quantum conductance staircase revealed by the quantum point contact inserted in the one of the arms of the double-slit ring are found to result from the interplay of the spontaneous spin polarization and the Rashba spin-orbit interaction (SOI). Secondly, the values of the AC conductance oscillations caused by the Rashba SOI are found to take the fractional form with both the plateaus and steps as a function of the top gate voltage.
Ultra-Widefield OCT Angiography

Optical Coherence Tomography Angiography (OCTA), a functional extension of OCT, has the potential to replace most invasive fluorescein angiography (FA) exams in ophthalmology. So far, OCTA’s field of view is however still lacking behind fluorescence fundus photography techniques. This is problematic, because many retinal diseases manifest at an early stage by changes of the peripheral retinal capillary network. It is therefore desirable to expand OCTA’s field of view to match that of ultra-widefield fundus cameras. We present a custom developed clinical high-speed swept-source OCT (SS-OCT) system operating at an acquisition rate 8–16 times faster than today’s state-of-the-art commercially available OCTA devices. Its speed allows us to capture ultra-wide fields of view of up to 90 degrees with an unprecedented sampling density and hence extraordinary resolution by merging two single shot scans with 60 degrees in diameter. To further enhance the visual appearance of the angiograms, we developed for the first time a three-dimensional deep learning based algorithm for denoising volumetric OCTA data sets. We showcase its imaging performance and clinical usability by presenting images of patients suffering from diabetic retinopathy.
Statistical speed of quantum states: Generalized quantum Fisher information and Schatten speed

We analyze families of measures for the quantum statistical speed which include as special cases the quantum Fisher information, the trace velocity, i.e., the quantum statistical speed obtained from the trace distance, and more general quantifiers obtained from the family of Schatten norms. These measures quantify the statistical speed under generic quantum evolutions and are obtained by maximizing classical measures over all possible quantum measurements. We discuss general properties, optimal measurements and upper bounds on the speed of separable states. We further provide a physical interpretation for the trace velocity by linking it to an analogue of the quantum Cram\'{e}r-Rao bound for median-unbiased quantum phase estimation.
Developmental effects of constitutive mTORC1 hyperactivity and environmental enrichment on structural synaptic plasticity and behaviour in a rat model of autism spectrum disorder

Autism spectrum disorder (ASD) is a neurodevelopmental condition causing a range of social and communication impairments. Although the role of multiple genes and environmental factors has been reported, the effects of the interplay between genes and environment on the onset and progression of the disease remains elusive. We housed wild‐type (Tsc2+/+) and tuberous sclerosis 2 deficient (Tsc2+/−) Eker rats (ASD model) in individually ventilated cages or enriched conditions and conducted a series of behavioural tests followed by the histochemical analysis of dendritic spines and plasticity in three age groups (days 45, 90 and 365). The elevated plus‐maze test revealed a reduction of anxiety by enrichment, whereas the mobility of young and adult Eker rats in the open field was lower compared to the wild type. In the social interaction test, an enriched environment reduced social contact in the youngest group and increased anogenital exploration in 90‐ and 365‐day‐old rats. Self‐grooming was increased by environmental enrichment in young and adult rats and decreased in aged Eker rats. Dendritic spine counts revealed an increased spine density in the cingulate gyrus in adult Ekers irrespective of housing conditions, whereas spine density in hippocampal pyramidal neurons was comparable across all genotypes and groups. Morphometric analysis of dendritic spines revealed age‐related changes in spine morphology and density, which were responsive to animal genotype and environment. Taken together, our findings suggest that under TSC2 haploinsufficiency and mTORC1 hyperactivity, the expression of behavioural signs and neuroplasticity in Eker rats can be differentially influenced by the developmental stage and environment.
Explicit solutions of one-dimensional total variation problem

This work deals with denosing of a one-dimensional signal corrupted by additive white Gaussian noise. A common way to solve the problem is to utilize the total variation (TV) method. Basically, the TV regularization minimizes a functional consisting of the sum of fidelity and regularization terms. We derive explicit solutions of the one-dimensional TV regularization problem that help us to restore noisy signals with a direct, non-iterative algorithm. Computer simulation results are provided to illustrate the performance of the proposed algorithm for restoration of noisy signals.
Critical current density and resistivity of MgB2 films

The high resistivity of many bulk and film samples of MgB2 is most readily explained by the suggestion that only a fraction of the cross-sectional area of the samples is effectively carrying current. Hence, the supercurrent (Jc) in such samples will be limited by the same area factor, arising for example from porosity or from insulating oxides present at the grain boundaries. We suggest that a correlation should exist, Jc∝1/Δρ300–50 K, where Δρ300–50 K is the change in the apparent resistivity from 300 to 50 K. We report measurements of ρ(T) and Jc for a number of films made by hybrid physical-chemical vapor deposition which demonstrate this correlation, although the “reduced effective area” argument alone is not sufficient. We suggest that this argument can also apply to many polycrystalline bulk and wire samples of MgB2.
Probing the physicochemical characteristics of carrot sauce during storage

Globally, the prevalence of vit-A deficiency disorders i.e., xerophthalmia and nyctalopia is increasing especially in teenagers due to lifestyle shifts and undernutrition. This research was designed to develop carrot-supplemented tomato sauce to overcome vit-A deficiency and its related disorders. The carrot sauce was formulated with the addition of 50, 60, and 70% carrot pulp in tomato paste. The prepared sauce samples were tested for physical and biochemical changes in beta carotene (BC), lycopene, viscosity, pH, total soluble solids, titratable acidity, total plate count, and sensory parameters for 12 weeks. A non-significant effect of storage on BC, lycopene, and total soluble solids was observed. The total plate count, acidity, pH, and viscosity were influenced significantly. Sauce containing 60% of the carrot paste showed good sensory characteristics and 42.39 μg/g BC for the whole period of storage. It is concluded that carrot sauce can be used as tomato ketchup replacers to boost the overall quality of life by fighting against vit-A deficiency disorders.
Multi-second magnetic coherence in a single domain spinor Bose–Einstein condensate

We describe a compact, robust and versatile system for studying the macroscopic spin dynamics in a spinor Bose–Einstein condensate. Condensates of 87 Rb are produced by all-optical evaporation in a 1560 nm optical dipole trap, using a non-standard loading sequence that employs an ancillary 1529 nm beam for partial compensation of the strong differential light-shift induced by the dipole trap itself. We use near-resonant Faraday rotation probing to non-destructively track the condensate magnetization, and demonstrate few-Larmor-cycle tracking with no detectable degradation of the spin polarization. In the ferromagnetic F = 1 ground state, we observe the spin orientation between atoms in the condensate is preserved, such that they precess all together like one large spin in the presence of a magnetic field. We characterize this dynamics in terms of the single-shot magnetic coherence times  1 and  2 * , and observe them to be of several seconds, limited only by the residence time of the atoms in the trap. At the densities used, this residence is restricted only by one-body losses set by the vacuum conditions.
Cutting the second order chords during mitral valve repair

The chordae tendinae connect the papillary muscles (PMs) to the mitral valve. While the first‐order chordae serve to secure the leaflets to maintain valve closure and prevent mitral valve prolapse, the second‐order chordae are believed to play a role in maintaining normal left ventricle size and geometry. The PMs, from where the chordae tendinae originate, function as shock absorbers that compensate for the geometric changes of the left ventricular wall. The second‐order chordae connect the PMs to both trigons under tension. The tension distributed towards the second‐order chordae has been demonstrate to be more than threefold that in their first‐order counterpart. Cutting the second‐order chordae puts all the tension on the first‐order chordae, which are then closer to their rupture point. However, it has been experimentally demonstrated that the tension at which the first‐order chordae break is 6.8 newtons (N), by far higher than the maximal tension reached, that is 0.4 N. Even if the clinical reports have been favorable, the importance of cutting the second‐order chordae to recover curvature of the anterior leaflet and increase the coaptation length between the mitral valve leaflets has been slowly absorbed by the surgical world. Nevertheless, there are progressive demonstrations that chordal tethering affects the anterior leaflet not only in secondary, but also in primary mitral regurgitation, having a not negligible role in the long‐term outcome of mitral repair.
Treatment Response to Tumor Necrosis Factor Inhibitors and Methotrexate Monotherapy in Adults With Juvenile Idiopathic Arthritis: Data From NOR-DMARD

Objective To compare the effectiveness of tumor necrosis factor inhibitors (TNFi) ± comedication and methotrexate (MTX) monotherapy between patients with adult juvenile idiopathic arthritis (JIA) and patients with rheumatoid arthritis (RA). Methods Adult patients with JIA and RA were identified from the Norwegian Antirheumatic Drug Register (NOR-DMARD) register. Disease activity measurements at baseline, 3, 6, and 12 months were compared between patients with JIA and RA starting (1) TNFi and (2) MTX monotherapy, using age- and gender-weighted analyses. We calculated differences between JIA and RA in mean changes in Disease Activity Score in 28 joints (DAS28), Clinical Disease Activity Index (CDAI), and Simplified Disease Activity Index (SDAI), among other disease activity measures. DAS28, CDAI, SDAI, and American College of Rheumatology (ACR)/European Alliance of Associations for Rheumatology (EULAR) remission rates at 3, 6, and 12 months, as well as 6- and 12-month Lund Efficacy Index (LUNDEX)-corrected rates, were calculated. Results We identified 478 patients with JIA (TNFi/MTX monotherapy, n = 358/120) and 4637 patients with RA (TNFi/MTX monotherapy, n = 2292/2345). Patients with JIA had lower baseline disease activity compared to patients with RA across treatment groups. After baseline disease activity adjustment, there were no significant differences in disease activity change from baseline to 3, 6, and 12-months of follow-up between patients with JIA and RA for either treatment group. Twelve-month remission rates were similar between groups based on DAS28 (TNFi: JIA 55.2%, RA 49.5%; MTX monotherapy: JIA 45.3%, RA 41.2%) and ACR/EULAR remission criteria (TNFi: JIA 20.4%, RA 20%; MTX monotherapy: JIA 17%, RA 12.7%). Median drug survival (yrs) was similar for JIA and RA in both treatment groups (TNFi: JIA 1.2, RA 1.4; MTX monotherapy: JIA 1.3, RA 1.6). Conclusion TNFi and MTX monotherapy are effective in adult JIA, with similar effectiveness to that shown in RA.