Miracle-dz/UniFAR-FTUs huggingface dataset:
Model-based clustering for aCGH data using variational EM

DNA copy number alterations (CNAs) are genetic changes that can produce adverse effects in numerous human diseases, including cancer. Copy number variations (of which CNAs are a subset) are a common phenomenon and not much is known about the nature of many of the mutations. By clustering patients according to CNA patterns, we can identify recurrent CNAs and understand molecular heterogeneity. This differs from normal distance-based clustering that doesn’t exploit the sequential structure of the data. Our approach is based on the hmmmix model introduced by [Sha08]. We show how it can be trained with variational methods to achieve better results and make it more flexible. We show how this allows for soft patient clusterings and how it partly addresses the difficult issue of determining the number of clusters to use. We compare the performance of our method with that of [Sha08] using their original benchmark test as well as with synthetic data generated from the hmmmix model itself. We show how our method can be parallelized and adapted to huge datasets.
PHOTOGRAMMETRIC METHODS APPLIED TO THE REPRESENTATION OF CURVE FACADES: AN EXPERIMENT CONDUCED ONTO PALAZZO CARIGNANO IN TURIN

The dealt topic is the representation of a curve building facade; the experiment has been conduced onto the Palazzo Carignano facade in Turin. Facades with a curvilinear plant and a prospect characterized from projections out of the surface cannot be developed on a plan simply developing a cylindrical surface on control points (GPC) and second or third order polynomial rectification. In order to correct perspective deformations of the three-dimensional projections, the classic ortho-photogrammetric method has been used, inserting a polar to Cartesian coordinate transformation into the calculation procedure, following therefore the canonical passages of inner and outer orientation, with the use of a 3d digital model realized through data-acquisition from laserscanner. The used procedure concurs therefore the rigorous verification of the accuracy through the appraisal of the residuals, otherwise not possible using control points to guide a simple deformation, because a little deviation of the control point from the reference surface can cause a wrong deformation of the whole image. The program-module of rectification has been modified, introducing the transformation of polar coordinates (x-axis as curvilinear development, y-axis parallel to the cylinder axis and z-axis in radial sense) in Cartesian coordinates; using the Cartesian coordinates it will be therefore possible to trace the photographic image of an ideal cylindrical development plan. The final photographic mosaic therefore will be characterized from x-axis as development of a circumference arc that concurs to bring back in scale only the ideal surface of the object, the nearer or more distant parts from the axis of the cylinder finding themselves on arc of circumference whose development is smaller or greater than the reference surface. The measure on axis x in fact represents the angle of the polar reference system. The advantages of this type of method consist in obtaining the development of a surface curve also of objects with a 3d development (as it is the usual case in architecture), using data that would be acquired for a traditional architectonic ortho-photogrammetry, but whose final product contributes to represent a curve surface in the most complete way. Moreover the acquired control points can prescind from effective geometry of the object, since the transformation of the projection from orthographic to cylindrical is calculated on the base of outer orientation, an ideal geometry of one or more reference cylinder and a real 3d elevation model.
The role of self-fertilization in plant colony establishment

Increased rates of self-fertilization are often found in plant colonies, but the factors driving the observed higher selfing rates remain unclear. Specifically, the higher selfing rates in colonist populations may be due to 1) source populations with a higher selfing rate being more likely to successfully establish colonies (a filter effect), 2) the in situ evolution of selfing rate or a plastic selfing rate increase rescuing the colony from extinction, 3) selfing rate evolution post establishment. Using individual-based simulations and eco-evo models, we show that under both single and multiple dispersal, colony establishment may often be driven by a filter effect, due to a higher initial selfing rate and lower genetic load, which are correlated since selfing can purge deleterious mutations. Moreover, the role of the filter effect is weaker under multiple dispersal than single dispersal. The evolution of a higher selfing rate is unlikely to contribute directly to colony establishment. Although selfing rate evolution occurs during the colonization process, most of the selfing rate evolution may occur post establishment. Plasticity in selfing rates is more effective in facilitating colony establishment than the evolution of selfing.
A protein hydroxylase couples epithelial membrane biology to 1 nucleolar ribosome biogenesis 2

20 Jumonji-C (JmjC) ribosomal protein hydroxylases are an ancient class of oxygen- and Fe(II)- 21 dependent oxygenases that spawned the wider JmjC family and Histone Lysine Demethylases 22 (KDMs) in eukaryotes. Myc-induced Antigen (MINA) has been implicated in ribosome 23 biogenesis and was assigned as a nucleolar-localized JmjC histidyl hydroxylase of the large
Note on instability of compressible jets and wakes to long-wave disturbances

A two-dimensional jet or wake is observed in a frame of reference moving with the fluid at infinity, so that the velocity w(y) in the x-direction tends to zero as y → ± ∞. The fluid is assumed to be an inviscid perfect gas, to undergo-adiabatic changes, and the local speed of sound to be a function of y such that a(y)→ a∞, as y → ±∞. If the disturbance pressure has the form
Accurate estimation of rare cell type fractions from tissue omics data via hierarchical deconvolution

Bulk transcriptomics in tissue samples reflects the average expression levels across different cell types and is highly influenced by cellular fractions. As such, it is critical to estimate cellular fractions to both deconfound differential expression analyses and infer cell type-specific differential expression. Since experimentally counting cells is infeasible in most tissues and studies, in silico cellular deconvolution methods have been developed as an alternative. However, existing methods are designed for tissues consisting of clearly distinguishable cell types and have difficulties estimating highly correlated or rare cell types. To address this challenge, we propose Hierarchical Deconvolution (HiDecon) that uses single-cell RNA sequencing references and a hierarchical cell type tree, which models the similarities among cell types and cell differentiation relationships, to estimate cellular fractions in bulk data. By coordinating cell fractions across layers of the hierarchical tree, cellular fraction information is passed up and down the tree, which helps correct estimation biases by pooling information across related cell types. The flexible hierarchical tree structure also enables estimating rare cell fractions by splitting the tree to higher resolutions. Through simulations and real data applications with the ground truth of measured cellular fractions, we demonstrate that HiDecon significantly outperforms existing methods and accurately estimates cellular fractions.
Positive definite matrices and Sylvester's criterion

1. William Boyce and Richard DiPrima, Calculus, Wiley, New York, 1988. 2. Constantin Caratheodory, Theory of Functions of a Complex Variable, vol. 1, Chelsea, New York, 1954. 3. __ , Vorlesungen uiber Reele Functionen, Chelsea Publishing Company, New York, 1968. 4. C. H. Edwards, Jr., The Historical Development of the Calculus, Springer-Verlag, New York, 1979. 5. Robert Ellis and Denny Gulick, Calculus with Analytic Geometry, Harcourt Brace Jovanovich, New York, 1978. 6. Philip Gillett, Calculus and Analytic Geometry, third ed., D. C. Heath, Lexington, Mass. , 1988. 7. Judith V. Grabiner, The Origin of Cauchy's Rigorous Calculus, MIT Press, Cambridge, Mass. , 1981. 8. Maurice Heins, Complex Function Theory, Academic Press, New York, 1968. 9. Louis Leithold, The Calculus with Analytic Geometry, fifth ed., Harper and Row, New York, 1986. 10. M. H. Protter and C. B. Morrey, A First Course in Real Analysis, Springer-Verlag, New York, 1977. 11. Edwin Purcell and Dale Varburg, Calculus with Analytic Geometry, fifth ed., Prentice-Hall, Englewood Cliffs, N.J., 1987. 12. Maxwell Rosenlicht, Introduction to Analysis, Scott Foresman, Glenview, Ill. , 1968. 13. Laurence Young, Mathematicians and Their Times, North-Holland, Amsterdam, 1981.
Observateurs itératifs en horizon fini. Application à la reconstruction de données initiales pour des EDP d'évolution

A new iterative algorithm for solving initial data inverse problems from partial observations has been recently proposed in Ramdani, Tucsnak and Weiss (Ramdani et al., 2010). The algorithm, which can be used for finite-dimensional and infinite-dimensional linear systems, is based on the use of two observers (also called Luenberger observers) used iteratively back and forth in time. In this paper, we first present the algorithm in a finite-dimensional context and then generalize it to Partial Differential Equations (PDE). To conclude, the method is applied to the 1D wave equation and numerical results will be given.
A STUDY ON THE EFFECTS OF U.S. EVENTS ON SENTIMENT RELATING TO MINORITY GROUPS ON TWITTER

This is a study on how U.S. national events affect the sentiment relating to different minority groups on Twitter. First, several groups of minorities were identified for examination. Next, the relationship between hashtag usage and Tweet composition relating to various minority groups was investigated. Using the Twitter API and several Python packages, we were able to gather Tweets relating to our areas of interest over the months of June to August 2020. Average Tweet sentiment was determined to see how that sentiment changed before, during, and after selected events. Three metrics were used to draw conclusions from the collected data. These were average sentiment of the Tweets, percentage of Tweets that were “retweets” versus those composed originally, and number of Tweets that were deemed “relevant” by twitter and therefore available for sample. We found that Tweets relating to the Black Lives Matter and related movements decreased in original tweet composition and average sentiment. Overall, this indicated a negative effect on the sentiment relating to Black Lives Matter initiatives during several related events. Tweets relating to the Coronavirus and people of Asian ethnicity did not change in average sentiment and decreased in original tweet composition in relation to the Coronavirus epidemic. Overall, this also indicated a negative effect on the sentiment relating to Asians due to this world event. Finally, Tweets relating to members of the LGBTQ+ community increased average sentiment, and decreased in original tweet composition during the month of June, commonly associated with “Pride Month”. This indicated a positive effect on the sentiment relating to the LGBTQ+ community during this event. We can come to the overarching conclusion that U.S. national events do not have a direct effect on positive or negative sentiment independently, rather that these events cause a change in the sentiment that can be characterized as either more positive or more negative.
The Impact of Large Language Model ChatGPT on Contemporary Productivity

The article discusses the potential impacts of the large language model ChatGPT on social productivity. This includes advances in natural language processing technology, intelligent customer service, automated writing, intelligent education, improved social media, and improved healthcare, among others. However, the development of artificial intelligence may also bring some negative impacts, such as the replacement of human work, issues of safety and privacy, among others. Therefore, how to balance the positive effects of using AI technology and address the potential problems it may bring will be an urgent issue to be solved in future research on large language models
Simulation study of the effect of modelling errors on the solution of inverse cardiac source imaging problem using realistic source patterns

The effect of the modelling errors on the solution of the inverse problem of electrocardiography is investigated. The electrocardiographic signal is simulated using a finite element model of the human torso and realistic source patterns gained with a cellular automaton. Noise is added to simulated measurements and the inverse problem is solved. The modelling errors consist of false conductivity assumptions, changed anisotropy ratio of skeletal muscles and geometric errors. The effect of modelling errors on optimal regularization parameter determination is investigated. The changes in muscle anisotropy and heart position are shown to have the highest effect on reconstructed epicardial potentials. CRESO (Composite REsidual and Smoothing Operator) and L-curve criteria for optimal regularization parameter estimation are compared.
Besov‐Morrey spaces and Triebel‐Lizorkin‐Morrey spaces for nondoubling measures

We define Morrey type Besov‐Triebel spaces with the underlying measure non‐doubling. After defining the function spaces, we investigate boundedness property of some class of the singular integral operators (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Generator for the reciprocals of binary numbers

A quantity which may easily be measured by digital instruments is sometimes the reciprocal of that quantity which it is desired to measure. A serial method is presented by which a number available in binary code can be converted to its reciprocal. The method is one of approximation using linear sections, and it is illustrated by outlining the design of a 2-section system.
Détection et reconstruction des éléments hautes fréquences appliquées au désentrelacement

This article presents a new algorithm for spatial deinterlacing that could easily be integrated in a more complete deinterlacing system, typically a spatio-temporal motion adaptive one. The spatial interpolation part often fails to reconstruct close to horizontal lines with a proper continuity, leading to highly visible artifacts. Our system preserves the structure continuity taking into account that the misinterpolated points usually correspond to local value extrema. The processing is based on chained lists and connected graph construction. The new interpolation method is restricted to such structures, for the rest of the image, a proper traditional directional spatial interpolation gives satisfactory results already. Although the number of pixels affected by the extrema interpolation is relatively small, the overall image quality is subjectively well improved. Moreover, our solution allows to gain back one of the major advantages of motion compensation methods, without having to afford their complexity cost.
Integrated modified rectangular loop slot antenna on substrate lenses for millimeter- and submillimeter-wave frequencies mixer applications

A coplanar waveguide (CPW)-fed rectangular-loop slot antenna with built-in tuning and DC-return capabilities on extended hemispherical lenses is examined. The proposed configuration is scalable up to the submillimeter-wave frequencies. For designing and analyzing the impedance characteristics of the proposed antenna, a multilayer method of moments (MoM) solver has been developed based on the mixed potential integral equation (MPIE) formulation. The corresponding patterns through the lens are obtained using geometrical optics and the surface equivalence principle. Three models have been simulated and one of them has been built and tested at 65 GHz. The integrated antenna exhibits tuning capability, rotationally symmetric patterns, high directivity, good Gaussian coupling efficiency, and a reasonable bandwidth. In addition, computed results agree well with measurements and are used to characterize the input impedance and pattern behavior of the antenna.
Simulation on light refocusing through a highly scattering turbid medium using circular Gaussian distribution model

Abstract. We present a simulation method for studying turbid media in the optical field based on circular Gaussian distribution (CGD) model, by which the transmission matrix, representing the modulation of a turbid medium on the amplitude and the phase of incident light, can be generated directly and efficiently. As an application example, light refocusing through a turbid medium is realized employing the CGD model approach, combining with wavefront–phase modulation technique and Fresnel diffraction theory, which is applied to describe the light propagation between optical elements of the entire system. Simulation results based on this approach agree well with theoretical analysis for light refocusing, which can validate the feasibility of CGD model. This work can be used for exploring the potential applications of turbid media in the optical field further, especially for developing new microscopic imaging technologies beyond the diffraction limit.
Probabilistic Approach To Determination Of Internal Heat Gains In Office Building For Peak Load Calculations

We propose a methodology for determining internal heat gains in workspace for peak cooling/heating load calculations. First, we collected measurement data of the lighting and plug loads in workspaces in Japan and analyzed these data. The investigation results show that internal heat gains remain relatively flat during work hours for each space, but their magnitudes vary considerably from space to space. Time-averaged heat gains during work hours conform to a lognormal distribution if those spaces are approximately the same size in floor area. Next, we present a methodology to determine the value of heat gains at specified frequencies of occurrence for each space. We present detailed procedures to calculate the probabilistic distributions with the Markov chain Monte Carlo method in conjunction with the Bayesian approach and analyze the calculation results by using the measured data. Finally, we discuss the applicability of the proposed stochastic approach.
Superparamagnetic nanoparticles for the treatment of periodontal disease

Periodontal diseases are prevalent worldwide and are linked to numerous other health conditions due to dysbiosis and chronic inflammatory state. Most periodontal diseases are caused by pathogenic bacteria that colonize dental tissues in the form of biofilm. Eradication of bacterial biofilms can be difficult to achieve due to the complex architecture of the teeth and gums which complicates the removal. Orthodontic wires and dental devices introduce additional hurdles to the adequate removal of biofilms by traditional methods since mechanical disruption via direct contact with toothbrush bristles, floss, and abrasive toothpaste is limited. Magnetically activated nanoparticles (NPs), specifically iron oxide nanoparticles (IONPs) that can be functionalized as antimicrobial particles and remotely controlled by magnetic fields, are of interest for oral biofilm eradication. We present data in multi-species bacterial cultures, established biofilms, human gingival keratinocytes, and human gingival fibroblast cells alone and in the presence of multispecies biofilm co-cultures to determine the safest, most efficacious IONP size ranges and treatment concentrations of active magnetic NPs for removal of dental biofilms. We report enhanced efficacy for IONPs coated with alginate vs. dextran, and small sizes (~8 nm vs. >20 nm in size) appear to exhibit enhanced antimicrobial efficacy. Human gingival keratinocyte (TIGK) cells in co-culture with treated and untreated multispecies biofilms in an in-vitro periodontitis model also exhibited a trend of reduced inflammatory markers in wells with IONP-treated biofilms.
Reproduction of plane wave sound fields

The problem of reproducing a desired sound field in space, not just at a number of discrete points, but over a continuous two‐dimensional area, is investigated. In theory, any sound field can be reconstructed perfectly in a given region by using a continuous monopole/dipole layer, but this is obviously not possible in practice. This paper attempts to give some quantitative measures of the extent to which a given sound field can be reproduced by using a number of discrete monopole sources. Some of the physical limitations that apply to any sound reproduction system are illustrated by studying a simple model. The desired sound field is a plane wave, the sources are ideal monopoles in a free field, and the optimal source accelerations are calculated using the traditional least‐squares method. All calculations are undertaken in the frequency domain, and three different loudspeaker arrangements are studied. The results clearly demonstrate that the quality of the reproduced sound field is mainly determined by t.
FREE VIBRATION OF SYMMETRICALLY LAMINATED SKEW PLATES

Abstract A Ritz approach, developed for the analysis of the vibration of thin, laminated, rectangular plates, is extended to apply to symmetrically laminated, composite, skew plates. There is relatively little information available on the vibration of such skew plates, despite their increasing use in the aerospace industry. A convergence study and comparisons with results available from the literature indicate that the approach presented is reliable and accurate. A fairly extensive set of numerical results is given in graphical form, illustrating the influence of different lamination lay-ups, skew angles and edge conditions on the natural frequencies and nodal patterns of a selection of plates.
Vertical Differencing of the Primitive Equations Based on the Charney–Phillips Grid in Hybrid &sigma–p Vertical Coordinates

Abstract Two types of vertical grids are used for atmospheric models: the Lorenz grid (L grid) and the Charney–Phillips grid (CP grid). Although the CP grid is the standard grid for quasigenstrophic models, it is not widely used in the primitive equation models because it is easier with the L grid to maintain some of the integral properties of the continuous system. In this paper, problems with the L grid are pointed out that are due to the existence of an extra degree of freedom in the vertical distribution of the temperature (and the potential temperature). Then a vertical differencing of the primitive equations based on the CP grid is presented, while most of the advantages of the L grid in a hybrid σ–p vertical coordinate are maintained. The discrete hydrostatic equation is constructed in such a way that it is free from the vertical computational mode in the thermal field. Also, the vertical advection of the potential temperature in the discrete thermodynamic equation is constructed in such a way that.