Miracle-dz/UniFAR-FTUs huggingface dataset:
Linear Dimensionality Reduction

These notes are an overview of some classical linear methods in Multivariate Data Analysis. This is a good old domain, well established since the 60's, and refreshed timely as a key step in statistical learning. It can be presented as part of statistical learning, or as dimensionality reduction with a geometric flavor. Both approaches are tightly linked: it is easier to learn patterns from data in low dimensional spaces than in high-dimensional spaces. It is shown how a diversity of methods and tools boil down to a single core methods, PCA with SVD, such that the efforts to optimize codes for analyzing massive data sets like distributed memory and task-based programming or to improve the efficiency of the algorithms like Randomised SVD can focus on this shared core method, and benefit to all methods.
Superconductivity in the Hexagonal Ternary Phosphide ScIrP

We report the discovery of a bulk superconducting transition at 3.4 K in the ternary phosphide, ScIrP, which crystallizes in a hexagonal ZrNiAl-type structure without spatial inversion symmetry. On the basis of heat capacity data in a zero magnetic field, ScIrP is suggested to be a weakly-coupled Bardeen-Cooper-Schrieffer superconductor. Alternatively, experimental results under magnetic fields indicate that this material is a type-II superconductor with an upper critical field Hc2 at magnetic fields above 5 T at zero temperature. This moderately high Hc2 does not violate the Pauli limit, but it does imply that there is a significant effect from the strong spin-orbit interaction of Ir 5d electrons in the noncentrosymmetric crystal structure. Electronic structure calculations show an interesting feature of ScIrP, where both the Sc 3d and Ir 5d orbitals contribute to the electronic density of states at the Fermi level.
NOISY WEAK-LENSING CONVERGENCE PEAK STATISTICS NEAR CLUSTERS OF GALAXIES AND BEYOND

Taking into account noise from intrinsic ellipticities of source galaxies, in this paper, we study the peak statistics in weak-lensing convergence maps around clusters of galaxies and beyond. We emphasize how the noise peak statistics is affected by the density distribution of nearby clusters, and also how cluster-peak signals are changed by the existence of noise. These are the important aspects to be thoroughly understood in weak-lensing analyses for individual clusters as well as in cosmological applications of weak-lensing cluster statistics. We adopt Gaussian smoothing with the smoothing scale θG = 0.5arcmin in our analyses. It is found that the noise peak distribution near a cluster of galaxies sensitively depends on the density profile of the cluster. For a cored isothermal cluster with the core radius Rc, the inner region with R ⩽ Rc appears noisy containing on average ∼2.4 peaks with ν ⩾ 5 for Rc = 1.7arcmin and the true peak height of the cluster ν = 5.6, where ν denotes the convergence signal-to-noise ratio. For a Navarro–Frenk–White (NFW) cluster of the same mass and the same central ν, the average number of peaks with ν ⩾ 5 within R ⩽ Rc is ∼1.6. Thus a high peak corresponding to the main cluster can be identified more cleanly in the NFW case. In the outer region with Rc < R ⩽ 5Rc, the number of high noise peaks is considerably enhanced in comparison with that of the pure noise case without the nearby cluster. For ν ⩾ 4, depending on the treatment of the mass-sheet degeneracy in weak-lensing analyses, the enhancement factor f is in the range of ∼5 to ∼55 for both clusters as their outer density profiles are similar. The properties of the main-cluster-peak identified in convergence maps are also significantly affected by the presence of noise. Scatters as well as a systematic shift for the peak height are present. The height distribution is peaked at ν ∼ 6.6, rather than at ν = 5.6, corresponding to a shift of Δν ∼ 1, for the isothermal cluster. For the NFW cluster, Δν ∼ 0.8. The existence of noise also causes a location offset for the weak-lensing identified main-cluster-peak with respect to the true center of the cluster. The offset distribution is very broad and extends to R ∼ Rc for the isothermal case. For the NFW cluster, it is relatively narrow and peaked at R ∼ 0.2Rc. We also analyze NFW clusters of different concentrations. It is found that the more centrally concentrated the mass distribution of a cluster is, the less its weak-lensing signal is affected by noise. Incorporating these important effects and the mass function of NFW dark matter halos, we further present a model calculating the statistical abundances of total convergence peaks, true and false ones, over a large field beyond individual clusters. The results are in good agreement with those from numerical simulations. The model then allows us to probe cosmologies with the convergence peaks directly without the need of expensive follow-up observations to differentiate true and false peaks.
: Navigating large collections of text notes in electronic health records for clinical chart review

Before seeing a patient for the first time, healthcare workers will typically conduct a comprehensive clinical chart review of the patient's electronic health record (EHR). Within the diverse documentation pieces included there, text notes are among the most important and thoroughly perused segments for this task; and yet they are among the least supported medium in terms of content navigation and overview. In this work, we delve deeper into the task of clinical chart review from a data visualization perspective and propose a hybrid graphics+text approach via ChartWalk, an interactive tool to support the review of text notes in EHRs. We report on our iterative design process grounded in input provided by a diverse range of healthcare professionals, with steps including: (a) initial requirements distilled from interviews and the literature, (b) an interim evaluation to validate design decisions, and (c) a task-based qualitative evaluation of our final design. We contribute lessons learned to better support the design of tools not only for clinical chart reviews but also other healthcare-related tasks around medical text analysis.
Clinical and patient-reported outcomes of tissue engineering strategies for periodontal and peri-implant reconstruction

Scientific advancements in biomaterials, cellular therapies, and growth factors have brought new therapeutic options for periodontal and peri-implant reconstructive procedures. These tissue engineering strategies involve the enrichment of scaffolds with living cells or signaling molecules and aim at mimicking the cascades of wound healing events and the clinical outcomes of conventional autogenous grafts, without the need for donor tissue. Several tissue engineering strategies have been explored over the years for a variety of clinical scenarios, including periodontal regeneration, treatment of gingival recessions/mucogingival conditions, alveolar ridge preservation, bone augmentation procedures, sinus floor elevation, and peri-implant bone regeneration therapies. The goal of this article was to review the tissue engineering strategies that have been performed for periodontal and peri-implant reconstruction and implant site development, and to evaluate their safety, invasiveness, efficacy, and patient-reported outcomes. A detailed systematic search was conducted to identify eligible randomized controlled trials reporting the outcomes of tissue engineering strategies utilized for the aforementioned indications. A total of 128 trials were ultimately included in this review for a detailed qualitative analysis. Commonly performed tissue engineering strategies involved scaffolds enriched with mesenchymal or somatic cells (cell-based tissue engineering strategies), or more often scaffolds loaded with signaling molecules/growth factors (signaling molecule-based tissue engineering strategies). These approaches were found to be safe when utilized for periodontal and peri-implant reconstruction therapies and implant site development. Tissue engineering strategies demonstrated either similar or superior clinical outcomes than conventional approaches for the treatment of infrabony and furcation defects, alveolar ridge preservation, and sinus floor augmentation. Tissue engineering strategies can promote higher root coverage, keratinized tissue width, and gingival thickness gain than scaffolds alone can, and they can often obtain similar mean root coverage compared with autogenous grafts. There is some evidence suggesting that tissue engineering strategies can have a positive effect on patient morbidity, their preference, esthetics, and quality of life when utilized for the treatment of mucogingival deformities. Similarly, tissue engineering strategies can reduce the invasiveness and complications of autogenous graft-based staged bone augmentation. More studies incorporating patient-reported outcomes are needed to understand the cost-benefits of tissue engineering strategies compared with traditional treatments.
Predicting User Preferences of Dimensionality Reduction Embedding Quality

A plethora of dimensionality reduction techniques have emerged over the past decades, leaving researchers and analysts with a wide variety of choices for reducing their data, all the more so given some techniques come with additional hyper-parametrization (e.g., t-SNE, UMAP, etc.). Recent studies are showing that people often use dimensionality reduction as a black-box regardless of the specific properties the method itself preserves. Hence, evaluating and comparing 2D embeddings is usually qualitatively decided, by setting embeddings side-by-side and letting human judgment decide which embedding is the best. In this work, we propose a quantitative way of evaluating embeddings, that nonetheless places human perception at the center. We run a comparative study, where we ask people to select “good” and “misleading” views between scatterplots of low-dimensional embeddings of image datasets, simulating the way people usually select embeddings. We use the study data as labels for a set of quality metrics for a supervised machine learning model whose purpose is to discover and quantify what exactly people are looking for when deciding between embeddings. With the model as a proxy for human judgments, we use it to rank embeddings on new datasets, explain why they are relevant, and quantify the degree of subjectivity when people select preferred embeddings.
Cadaveric findings of a duplicated superior petrosal sinus

Knowledge of the intracranial dural venous sinuses and their variations is important in the diagnosis and management of many cranial pathologies. We report a unique duplication of the right-sided superior petrosal sinus identified during routine dissection of the skull base. Lateral to this sinus, a separate and more curvilinear superior petrosal sinus left the normally positioned superior petrosal sinus and traveled posteriorly near the foramen spinosum and then turned medially to drain into the normally positioned superior petrosal sinus. Anteriorly, the two sinuses joined together and drained into the cavernous sinus. Posteriorly, the laterally positioned sinus drained into the normally positioned sinus which then traveled in normal fashion along the petrous ridge to end in the transverse sinus. To our knowledge, such a duplication has not been previously reported in the extant medical literature.
The Modernization of Clozapine

Abstract Purpose Although clozapine was Food and Drug Administration (FDA) approved more than 3 decades ago, major barriers and gaps in knowledge continue to prevent its effective and safe use. We review modern-day problems encountered with clozapine in the United States (US). Methods Information surrounding current administrative, clinical, research, and technological gaps or barriers related to clozapine use in the US was reviewed. Findings The history of how clozapine became FDA approved likely contributes to gaps in knowledge. The frequency of safety warnings added to the FDA prescribing information may add to fears about clozapine, as evidence by numerous published survey studies. The clozapine Risk Evaluation and Mitigation Strategy (REMS) program has been modified several times in the last decade, causing access and safety issues for patients, which are discussed. Evidence may suggest that the FDA REMS requirements for hematologic monitoring are too cumbersome, and there may be ability to safely loosen requirements. The COVID-19 pandemic brought forth the ability for extended interval monitoring but also greater awareness of the clozapine-inflammation interaction. Newer guidelines published describe considerations in personalizing clozapine titration based on principles of ethnopsychopharmacology. Emerging technologies to support the use of clozapine are not widely available. Implications Clozapine is a unique life-saving drug but it is underused in the US, despite its established efficacy. The 2021 REMS changes led to significant difficulties for providers and patients. We highlight the importance of the clozapine-inflammation interaction, therapeutic drug monitoring, and the ability for individual care based on patient-specific factors. There is an urgent need for advancing technology used for clozapine monitoring, evaluating barriers created by REMS, and establishing consistent practices throughout the US.
The search for a low-dimensional characterization of a local climate system

Along with the computation of attractor dimension via the Grassberger-Procaccia method and the nearest neighbour algorithm, a variety of phase space tests are used to search for low-dimensional characterization of daily maximum and minimum atmospheric temperature data (ca. 25 000 points each, spanning about a 70-year period). These tests include global and local singular value decompositions, as well as others for uncovering nonlinear correlations among amplitudes of the global singular vectors and for recognizing determinism in a time series. The results show that a low-dimensional characterization of the temperature data is unlikely.
Excited OH+, H2O+, and H3O+ in NGC 4418 and Arp 220

We report on Herschel/PACS observations of absorption lines of OH^+, H_2O^+ and H_3O^+ in NGC 4418 and Arp 220. Excited lines of OH^+ and H_2O^+ with E_(lower) of at least 285 and ~200 K, respectively, are detected in both sources, indicating radiative pumping and location in the high radiation density environment of the nuclear regions. Abundance ratios OH^+/H_2O^+ of 1−2.5 are estimated in the nuclei of both sources. The inferred OH^+ column and abundance relative to H nuclei are (0.5−1) × 10^(16) cm^(-2) and ~ 2 × 10^(-8), respectively. Additionally, in Arp 220, an extended low excitation component around the nuclear region is found to have OH^+/H^2O^+ ~ 5−10. H_3O^+ is detected in both sources with N(H_3O^+) ~ (0.5−2) × 10^(16) cm^(-2), and in Arp 220 the pure inversion, metastable lines indicate a high rotational temperature of ~500 K, indicative of formation pumping and/or hot gas. Simple chemical models favor an ionization sequence dominated by H^+ → O^+ → OH^+ → H_2O^+ → H_3O^+, and we also argue that the H^+ production is most likely dominated by X-ray/cosmic ray ionization. The full set of observations and models leads us to propose that the molecular ions arise in a relatively low density (≳10^4 cm^(-3)) interclump medium, in which case the ionization rate per H nucleus (including secondary ionizations) is ζ > 10^(-13) s^(-1), a lower limit that is several × 10^2 times the highest current rate estimates for Galactic regions. In Arp 220, our lower limit for ζ is compatible with estimates for the cosmic ray energy density inferred previously from the supernova rate and synchrotron radio emission, and also with the expected ionization rate produced by X-rays. In NGC 4418, we argue that X-ray ionization due to an active galactic nucleus is responsible for the molecular ion production.
Antidiabetic effects of nerolidol through promoting insulin receptor signaling in high-fat diet and low dose streptozotocin-induced type 2 diabetic rats

The present study was designed to investigate the antidiabetic effect of nerolidol on high-fat diet and streptozotocin-induced diabetic rats. Type 2 diabetes was induced in animals by feeding them a high-fat diet for 4 weeks and administering a single intraperitoneal dose of streptozotocin (35 mg/kg body weight). Diabetic rats were treated with nerolidol (25 mg/kg BW) for 28 days. Results showed that nerolidol treatment significantly reduced (p < 0.05) the level of elevated glucose, glycosylated hemoglobin and improved (p < 0.05) the body weight and insulin level. Nerolidol also considerably improved (p < 0.05) the carbohydrate metabolic enzyme activities and increased the glycogen storage in the liver of diabetic rats. Increased serum triglycerides, total cholesterol (C), low-density lipoproteins-C and very low-density lipoproteins-C levels were significantly lowered (p < 0.05), while reduction of serum high-density lipoprotein-C was alleviated after administration of nerolidol. In addition, nerolidol attenuated oxidative stress markers by significantly increasing (p < 0.05) the levels of superoxide dismutase, catalase, reduced glutathione, and lowering (p < 0.05) the level of thiobarbituric acid reactive substances, and lipid hydroperoxide. Similarly, nerolidol showed its pharmacological effects against hepatic markers via restoring (p < 0.05) the alleviated level of alanine transaminase, aspartate aminotransferase, and alkaline phosphatase. Finally, it improved insulin-dependent glucose transport in skeletal muscle by enhancing and activating glucose transporter protein-4. These findings confirmed the antidiabetic potential of nerolidol in type 2 diabetic rats. This may be related to a high antioxidant capacity, the restoration of plasma insulin and lipid levels, and the activation of insulin signaling in STZ/HFD-induced diabetic rats.
Shadow of a naked singularity

We analyze the redshift suffered by photons originating from an external source, traversing a collapsing dust cloud and finally being received by an asymptotic observer. In addition, we study the shadow that the collapsing cloud casts on the sky of the asymptotic observer. We find that the resulting redshift and properties of the shadow depend crucially on whether the final outcome of the complete gravitational collapse is a black hole or a naked singularity. In the black hole case, the shadow is due to the high redshift acquired by the photons as they approach the event horizon, implying that their energy is gradually redshifted toward zero within a few crossing times associated with the event horizon radius. In contrast to this, a naked singularity not only absorbs photons originating from the source, but it also emits infinitely redshifted photons with and without angular momenta. This emission introduces an abrupt cutoff in the frequency shift of the photons detected in directions close to the radial one, and it is responsible for the shadow masking the source in the naked singularity case. Furthermore, even though the shadow forms and begins to grow immediately after the observer crosses the Cauchy horizon, it takes many more crossing times than in the black hole case for the source to be occulted from the observer's eyes. We discuss possible implications of our results for testing the weak cosmic censorship hypothesis. Even though at late times the image of the source perceived by the observer looks the same in both cases, the dynamical formation of the shadow and the redshift images has distinct features and time scales in the black hole versus the naked singularity case. For stellar collapse, these time scales seem to be too short to be resolved with existing technology. However, our results may be relevant for the collapse of seeds leading to supermassive black holes.
Lorentzian proper vertex amplitude: Asymptotics

In previous work, the Lorentzian proper vertex amplitude for a spin-foam model of quantum gravity was derived. In the present work, the asymptotics of this amplitude are studied in the semi-classical limit. The starting point of the analysis is an expression for the amplitude as an action integral with action differing from that in the EPRL case by an extra `projector' term which scales linearly with spins only in the asymptotic limit, and is discontinuous on a submanifold of the integration domain. New tools are introduced to generalize stationary phase methods to this case. For the case of boundary data which can be glued to a non-degenerate Lorentzian 4-simplex, the asymptotic limit of the amplitude is shown to equal the single Feynman term, showing that the extra term in the asymptotics of the EPRL amplitude has been eliminated.
Open clusters in Auriga OB2

This research is partially supported by the Spanish Ministerio de Ciencia e Innovacion (MICINN) under grants AYA2012-39364-C02-02 and AYA2015-68012-C2-2-P, and by the Generalitat Valenciana (ACOMP/2014/129). AM acknowledges support from the Generalitat Valenciana through the grant BEST/2015/242 and from the Ministerio de Educacion, Cultura y Deporte through the grant PRX15/00030.
Direct dark matter searches—Test of the Big Bounce Cosmology

We consider the possibility of using dark matter particle's mass and its interaction cross section as a smoking gun signal of the existence of a Big Bounce at the early stage in the evolution of our currently observed universe. A study of dark matter production in the pre-bounce contraction and the post bounce expansion epochs of this universe reveals a new venue for achieving the observed relic abundance of our present universe. Specifically, it predicts a characteristic relation governing a dark matter mass and interaction cross section and a factor of 1/2 in thermally averaged cross section, as compared to the non-thermal production in standard cosmology, is needed for creating enough dark matter particle to satisfy the currently observed relic abundance because dark matter is being created during the pre-bounce contraction, in addition to the post-bounce expansion. As the production rate is lower than the Hubble expansion rate information of the bounce universe evolution is preserved. Therefore once the value of dark matter mass and interaction cross section are obtained by direct detection in laboratories, this alternative route becomes a signature prediction of the bounce universe scenario. This leads us to consider a scalar dark matter candidate, which if it is light, has important implications on dark matter searches.