Miracle-dz/UniFAR-FTUs huggingface dataset:
A mesoscale model intercomparison

Abstract An intercomparison of four mesoscale numerical prediction models that could lead to the selection of a model for use in the theater of operations by United States Air Force (USAF) meteorological personnel is described. Mesoscale numerical prediction models have matured, and recent advances in computer hardware make this a realizable objective. Two studies were launched to determine if a mesoscale model could be used operationally in theater and to select the model that produced the best forecast under simulated operational conditions. Of prime concern was not whether the model could produce reliable forecasts in data-rich areas, but how well the models operated and thus produced forecasts in data-sparse areas. The first study did an overall review of the available mesoscale numerical weather prediction models resulting in a general ranking of the models by expected forecast ability and operational maturity. At the conclusion of this study it became apparent that a more in-depth analysis was neede.
Spectra of $(H_1,H_2)-$combined subdivision graph of a graph

In this paper, we define a ternary graph operation which generalizes the construction of subdivision graph, $R-$graph, central graph. Also, it generalizes the construction of overlay graph (Marius Somodi et al., 2017), and consequently, $Q-$graph, total graph, and quasitotal graph. We denote this new graph by $[S(G)]^{H_1}_{H_2}$, where $G$ is a graph and, $H_1$ and $H_2$ are suitable graphs corresponding to $G$. Further, we define several new unary graph operations which becomes particular cases of this construction. We determine the Adjacency and Laplacian spectrum of $[S(G)]^{H_1}_{H_2}$ for some classes of graphs $G$, $H_1$ and $H_2$. As applications, these results enable us to compute the number of spanning trees and Kirchhoff index of these graphs.
Bounds on the Jensen Gap, and Implications for Mean-Concentrated Distributions

This paper gives upper and lower bounds on the gap in Jensen's inequality, i.e., the difference between the expected value of a function of a random variable and the value of the function at the expected value of the random variable. The bounds depend only on growth properties of the function and specific moments of the random variable. The bounds are particularly useful for distributions that are concentrated around the mean, a commonly occurring scenario.
Application of combined CRISPR screening for genetic and chemical-genetic interaction profiling in Mycobacterium tuberculosis

CRISPR screening, including CRISPR interference (CRISPRi) and CRISPR-knockout (CRISPR-KO) screening, has become a powerful technology in the genetic screening of eukaryotes. In contrast with eukaryotes, CRISPR-KO screening has not yet been applied to functional genomics studies in bacteria. Here, we constructed genome-scale CRISPR-KO and also CRISPRi libraries in Mycobacterium tuberculosis (Mtb). We first examined these libraries to identify genes essential for Mtb viability. Subsequent screening identified dozens of genes associated with resistance/susceptibility to the antitubercular drug bedaquiline (BDQ). Genetic and chemical validation of the screening results suggested that it provided a valuable resource to investigate mechanisms of action underlying the effects of BDQ and to identify chemical-genetic synergies that can be used to optimize tuberculosis therapy. In summary, our results demonstrate the potential for efficient genome-wide CRISPR-KO screening in bacteria and establish a combined CRISPR screening approach for high-throughput investigation of genetic and chemical-genetic interactions in Mtb.
On the Reynolds time-averaged equations and the long-time behavior of Leray–Hopf weak solutions, with applications to ensemble averages

We consider the three dimensional incompressible Navier–Stokes equations with a non stationary source term , chosen in a suitable space. We prove the existence of global Leray–Hopf weak solutions and also that it is possible to characterize (up to sub-sequences) their long-time averages, which satisfy the Reynolds averaged equations, involving the additional Reynolds stress. Moreover, we show that the turbulent dissipation is bounded by the sum of the Reynolds stress work and the external turbulent fluxes, without any additional assumption, other than that of using Leray–Hopf weak solutions. Finally, in the last section we consider ensemble averages of solutions, associated to a set of different forces and we prove that the fluctuations continue to have a dissipative effect on the mean flow.
Graded C*-algebras, Graded K-theory, And Twisted P-graph C*-algebras

We develop methods for computing graded K-theory of C*-algebras as defined in terms of Kasparov theory. We establish graded versions of Pimsner's six-term sequences for graded Hilbert bimodules whose left action is injective and by compacts, and a graded Pimsner-Voiculescu sequence. We introduce the notion of a twisted P-graph C*-algebra and establish connections with graded C*-algebras. Specifically, we show how a functor from a P-graph into the group of order two determines a grading of the associated C*-algebra. We apply our graded version of Pimsner's exact sequence to compute the graded K-theory of a graph C*-algebra carrying such a grading.
A new restart procedure for combinatorial optimization and its convergence

We propose a new iterative procedure to optimize the restart for meta-heuristic algorithms to solve combinatorial optimization, which uses independent algorithm executions. The new procedure consists of either adding new executions or extending along time the existing ones. This is done on the basis of a criterion that uses a surrogate of the algorithm failure probability, where the optimal solution is replaced by the best so far one. Therefore, it can be applied in practice. We prove that, with probability one, the restart time of the proposed procedure approaches, as the number of iterations diverges, the optimal value that minimizes the expected time to find the solution. We apply the proposed restart procedure to several Traveling Salesman Problem instances with hundreds or thousands of cities. As basic algorithm, we used different versions of an Ant Colony Optimization algorithm. We compare the results from the restart procedure with those from the basic algorithm. This is done by considering the failure probability of the two approaches for equal computation cost. This comparison showed a significant gain when applying the proposed restart procedure, whose failure probability is several orders of magnitude lower.
Growing in Suffering: The Curvilinear Relationship Between Prolonged Grief and Post-traumatic Growth of Recently Bereaved Individual During the COVID-19 Pandemic

The outbreak of the COVID-19 pandemic brought new challenges to mourning and growth of bereaved. The purpose is to explore the relationship between the prolonged grief (PG) symptoms and the post-traumatic growth (PTG) of recently bereaved people during the COVID-19 period, and the mediating role of meaning making. 305 participants were recruited to complete the Posttraumatic Growth Inventory, Inventory of Complicated Grief, and Integration of Stressful Life Experiences Scale. Hierarchical multiple regression analyses and Medcurve in SPSS were adapted to test the hypotheses. The results revealed that there was a curvilinear relationship between PG and PTG and meaning making had a completely mediating effect on this relationship. Different intervention goals - whether alleviating distress or cultivating growth – should be set up according to the level of grief for recently bereaved individuals during COVID-19. More attention should be paid to the role of meaning making in the future clinical practice.
Pathogenicity and virulence of malaria: Sticky problems and tricky solutions

ABSTRACT Infections with Plasmodium falciparum and Plasmodium vivax cause over 600,000 deaths each year, concentrated in Africa and in young children, but much of the world’s population remain at risk of infection. In this article, we review the latest developments in the immunogenicity and pathogenesis of malaria, with a particular focus on P. falciparum, the leading malaria killer. Pathogenic factors include parasite-derived toxins and variant surface antigens on infected erythrocytes that mediate sequestration in the deep vasculature. Host response to parasite toxins and to variant antigens is an important determinant of disease severity. Understanding how parasites sequester, and how antibody to variant antigens could prevent sequestration, may lead to new approaches to treat and prevent disease. Difficulties in malaria diagnosis, drug resistance, and specific challenges of treating P. vivax pose challenges to malaria elimination, but vaccines and other preventive strategies may offer improved disease control.
Self-adjoint local boundary problems on compact surfaces. II. Family index

The paper presents a first step towards a family index theorem for classical self-adjoint boundary value problems. We address here the simplest non-trivial case of manifolds with boundary, namely the case of two-dimensional manifolds. The first result of the paper is an index theorem for families of first order self-adjoint elliptic differential operators with local boundary conditions, parametrized by points of a compact topological space $X$. We compute the $K^1(X)$-valued index in terms of the topological data over the boundary. The second result is the universality of the index: we show that the index is a universal additive homotopy invariant for such families, if the vanishing on families of invertible operators is required.
New relations between $G_2$-geometries in dimensions 5 and 7

There are two well-known parabolic split $G_2$-geometries in dimension five, $(2,3,5)$-distributions and $G_2$-contact structures. Here we link these two geometries with yet another $G_2$-related contact structure, which lives on a seven-manifold. We present a natural geometric construction of a Lie contact structure on a seven-dimensional bundle over a five-manifold endowed with a $(2,3,5)$-distribution. For a class of distributions the induced Lie contact structure is constructed explicitly and we determine its symmetries. We further study the relation between the canonical normal Cartan connections associated with the two structures. In particular, we show that the Cartan holonomy of the induced Lie contact structure reduces to $G_2$. Moreover, the curved orbit decomposition associated with a $\mathrm{G}_2$-reduced Lie contact structure on a seven-manifold is discussed. It is shown that in a neighbourhood of each point on the open curved orbit the structure descends to a $(2,3,5)$-distribution on a local leaf space, provided an additional curvature condition is satisfied. The closed orbit carries an induced $G_2$-contact structure.
Weighted infinitesimal unitary bialgebras on matrix algebras and weighted associative Yang-Baxter equations.

We equip a matrix algebra with a weighted infinitesimal unitary bialgebraic structure, via a construction of a suitable coproduct. Furthermore, an infinitesimal unitary Hopf algebra, under the view of Aguiar, is constructed on a matrix algebra. By exploring the relationship between weighted infinitesimal bialgebras and pre-Lie algebras, we construct a pre-Lie algebraic structure and then a new Lie algebraic structure on a matrix algebra. We also introduce the weighted associative Yang-Baxter equations (AYBEs) and obtain the relationship between solutions of weighted AYBEs and weighted infinitesimal unitary bialgebras. We give a bijection between the solutions of the associative Yang-Baxter equation of weight $\lambda$ and Rota-Baxter operators of weight $-\lambda$ on matrix algebras. As a consequence, weighted quasitriangular infinitesimal unitary bialgebras are constructed, which generalize the results studied by Aguiar. Finally, We show that any weighted quasitriangular infinitesimal unitary bialgebra can be made into a dendriform algebra.
The Hopf monoid of Megagreedoids

We introduce megagreedoids, which generalize polymatroids, megamatroids, and greedoids. We define a quasisymmetric function invariant for a megagreedoid, and show that it has a positive expansion in the basis of fundamental quasisymmetric functions. Our proof involves lexicographic shellability. We also show that megagreedoids form a Hopf monoid. A running example is a megagreedoid associated to a rooted connected graph, and the resulting generalization of the chromatic symmetric function.
Implications of time and space factors related with youth substance use prevention: a conceptual review and case study of the Icelandic Prevention Model being implemented in the context of the COVID-19 pandemic

ABSTRACT Purpose: This research examines the implementation of the Icelandic Prevention Model (IPM) in Canada to identify opportunities revealed by the COVID-19 pandemic to re-design our social eco-system to promote wellbeing. This paper has two objectives: 1) to provide a conceptual review of research that applies the bioecological model to youth substance use prevention with a focus on the concepts of time and physical space use and 2) to describe a case study that examines the implementation of the IPM in Canada within the context of the COVID-19 pandemic. Method: Study data were collected through semi-structured qualitative interviews with key stakeholders involved in implementing the IPM. Results: Findings are organized within three over-arching themes derived from a thematic analysis: 1) Issues that influence time and space use patterns and youth substance use, 2) Family and community cohesion and influences on developmental context and time use and 3) Opportunities presented by the pandemic that can promote youth wellbeing. Conclusion: We apply the findings to research on the IPM as well as the pandemic to examine opportunities that may support primary prevention and overall youth wellbeing. We use the concepts of time and space as a foundation to discuss implications for policy and practice going forward.
Variations in the application of equine prosthetic laryngoplasty: A survey of 128 equine surgeons

Abstract Objective To document variations in the application of equine prosthetic laryngoplasty among equine surgeons. Study design Cross‐sectional survey. Sample population Six hundred and seventy‐eight equine surgeons performing prosthetic laryngoplasty. Methods An online questionnaire was sent to equine surgeons, including diplomates of the American College of Veterinary Surgeons and European College of Veterinary Surgeons. Questions focused on participant profile, surgical technique, antimicrobial therapy, and concurrent procedures. Descriptive statistical analysis was performed on the survey output. Results Complete responses were received from 128/678 individuals, mostly from experienced surgeons. Most participants used 2 prostheses (106/128, 82.8%) and a single loop was the most common method used to anchor the prosthesis in the cricoid (95/128, 74.2%) and arytenoid (125/128, 97.7%) cartilages. Use of general anesthesia was common, although 46/128 (35.9%) participants now performed most laryngoplasty surgery with standing sedation. The material used as a prosthesis varied among surgeons, although participants typically aimed to achieve grade 2 intraoperative arytenoid abduction. Participants most commonly administered perioperative systemic antimicrobial therapy for 1‐3 days (57/128, 44.5%) and 48/128 (37.5%) used local antimicrobial therapy. Conclusion Most surgeons performed laryngoplasty with 2 prostheses, a single loop construct at the muscular process of the arytenoid cartilage and systemic antimicrobial therapy. There was variation in the preferred method of surgical restraint, prosthesis material selection, and use of local antimicrobial therapy. Clinical significance Long‐established techniques remain popular in clinical practice despite evidence that variations offer advantages, particularly in relation to biomechanics. Other factors are also likely to influence technique selection in a clinical context.
Histogram matching for the calibration of kNN stem volume estimates

The k-nearest neighbours (kNN) methods have been used successfully in many countries for the production of spatially comprehensive raster databases of forest attributes, made from the combination of National Forest Inventory (NFI) and satellite data. In Sweden, country-wide kNN estimates of forest variables have been produced to represent the forest condition in the years 2000 and 2005 by using a combination of Système Pour l'Observation de la Terre 5 (SPOT 5) satellite data and field data from the Swedish NFI. The resulting products are wall-to-wall raster maps with estimates of total stem volume, stem volume per tree species, tree height and stand age and a 25 × 25 m2 pixel resolution. However, probability-based kNN stem volume estimates tend to have a suppressed variation range as large values are usually underestimated and small values are overestimated. One way to handle this problem is to calibrate the kNN stem volume estimates to the reference distribution of stem volume observations by histogram matching (HM) for a defined geographic area. In this study, we have tested HM for the calibration of kNN total stem volume raster maps to the reference distribution captured by a forest inventory (FI) from 106 stands in Strömsjöliden, in the north of Sweden. The available field FI data set comprises 1084 circular plots, divided into a reference data set and an evaluation data set of total stem volume observations. The reference data set was used for the creation of a cumulative frequency histogram of total stem volume and the evaluation data set was used to assess the accuracy of volume estimates, before and after HM. The HM adjusted the cumulative distribution of the kNN data set to the distribution of the reference observations and resulted in a distribution of kNN estimates of total stem volume, which corresponded closely to that of the evaluation data set. The results show that the variation range of the kNN stem volume estimates can be extended by HM both on the pixel and stand levels. The extension of the range of estimates towards the range provided by the field observations allows improvement of kNN volume estimation for use in forest management planning based on stand-level analysis, given that the reference stem volume distribution can be estimated accurately, for example, using field data from NFI.
Neuromorphic Engineering: In Memory of Misha Mahowald

Abstract We review the coevolution of hardware and software dedicated to neuromorphic systems. From modest beginnings, these disciplines have become central to the larger field of computation. In the process, their biological foundations become more relevant, and their realizations increasingly overlap. We identify opportunities for significant steps forward in both the near and more distant future.
Non-convex regularization of bilinear and quadratic inverse problems by tensorial lifting

Considering the question: how non-linear may a non-linear operator be in order to extend the linear regularization theory, we introduce the class of dilinear mappings, which covers linear, bilinear, and quadratic operators between spaces. The corresponding dilinear inverse problems cover blind deconvolution, deautoconvolution, parallel imaging in MRI, and the phase retrieval problem. Based on the universal property of the tensor product, the central idea is here to lift the non-linear mappings to linear representatives on a suitable topological tensor space. At the same time, we extend the class of usually convex regularization functionals to the class of diconvex functionals, which are likewise defined by a tensorial lifting. Generalizing the concepts of subgradients and distances from convex analysis to the new framework, we analyse the novel class of dilinear inverse problems with non-convex regularization terms and establish convergence rates with respect to a generalized distance under similar conditions than in the linear setting. Considering the deautoconvolution problem as specific application, we derive satisfiable source conditions and validate the theoretical convergence rates numerically.
Asthma exacerbations: the genes behind the scenes.

The clinical and socioeconomic burden of asthma exacerbations (AEs) represents a major public health problem. In the last four years, there has been an increase in ethnic diversity in candidate-gene and genome-wide association studies (GWAS) of AEs, which in the latter case has led to the identification of novel genes and underlying pathobiological processes. Pharmacogenomics, admixture mapping analyses, and the combination of multiple "omic" layers have contributed to prioritizing genomic regions of interest and/or understanding the functional consequences of genetic variation. Despite this, the field still lags behind the genomics of asthma, where a vast compendium of genetic approaches has been used (e.g., gene-environment interactions, next-generation sequencing, or polygenic risk scores). Furthermore, the roles of the DNA methylome and histone modifications in AEs have been scarcely investigated, and microRNA findings remain to be validated in independent studies. Likewise, the most recent transcriptomic studies highlight the importance of host-airway microbiome interaction in the modulation of AEs risk. Leveraging -omics and deep-phenotyping data from sub-types or homogenous subgroups of patients will be crucial to overcome the inherent heterogeneity of AEs, and boost the identification of potential therapeutic targets and the implementation of precision medicine in clinical practice for AEs.
Metabolomics of asthma, COPD, and asthma-COPD overlap: an overview

Abstract The two common progressive lung diseases, asthma and chronic obstructive pulmonary disease (COPD), are the leading causes of morbidity and mortality worldwide. Asthma-COPD overlap, referred to as ACO, is another complex pulmonary disease that manifests itself with features of both asthma and COPD. The disease has no clear diagnostic or therapeutic guidelines, thereby making both diagnosis and treatment challenging. Though a number of studies on ACO have been documented, gaps in knowledge regarding the pathophysiologic mechanism of this disorder exist. Addressing this issue is an urgent need for improved diagnostic and therapeutic management of the disease. Metabolomics, an increasingly popular technique, reveals the pathogenesis of complex diseases and holds promise in biomarker discovery. This comprehensive narrative review, comprising 99 original research articles in the last five years (2017–2022), summarizes the scientific advances in terms of metabolic alterations in patients with asthma, COPD, and ACO. The analytical tools, nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), and liquid chromatography-mass spectrometry (LC-MS), commonly used to study the expression of the metabolome, are discussed. Challenges frequently encountered during metabolite identification and quality assessment are highlighted. Bridging the gap between phenotype and metabotype is envisioned in the future.