Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondria and vascular calcification in chronic kidney disease: Lessons learned from the past to improve future therapy

Chronic kidney disease–mineral and bone disorders (CKD‐MBD) is a common complication of CKD Stages 3–5. Hyperphosphatemia is one of the major metabolic components of CKD‐MBD, frequently resulting in vascular calcification (VC) in advanced‐stage patients. Also, a long duration of renal replacement therapy can cause the worsening of VC, leading to increased cardiovascular morbidity and mortality. Vascular smooth muscle cells play an important role in the development of VC through osteochondrogenic transformation and the apoptotic process. It has been shown that mitochondrial dysfunction is involved with CKD progression, and excessive oxidative stress can aggravate osteoblastic transformation and VC. Currently, novel interventions targeting mitochondrial function and dynamics, in addition to mitochondrial antioxidants, have been studied with the aim of attenuating VC. This review aims to comprehensively summarize and discuss the experimental and clinical reports concerning mitochondrial studies, along with the purpose of interventions that can improve the outcomes of VC among CKD patients.
Three-dimensional remodelling of the cellular energy distribution system during postnatal heart development

The heart meets the high energy demands of constant muscle contraction and calcium cycling primarily through the conversion of fatty acids into adenosine triphosphate (ATP) by a large volume of mitochondria. As such, the spatial relationships among lipid droplets (LDs), mitochondria, the sarcotubular system and the contractile apparatus are critical to the efficient distribution of energy within the cardiomyocyte. However, the connectivity among components of the cardiac cellular energy distribution system during postnatal development remains unclear. Here, we use volume electron microscopy to demonstrate that the sarcomere branches uniting the myofibrillar network occur more than twice as frequently during early postnatal development as in mature cardiomyocytes. Moreover, we show that the mitochondrial networks arranged in parallel to the contractile apparatus are composed of larger, more compact mitochondria with greater connectivity to adjacent mitochondria in mature as compared with early postnatal cardiomyocytes. Finally, we find that connectivity among mitochondria, LDs and the sarcotubular network is greater in developing than in mature muscles. These data suggest that physical connectivity among cellular structures may facilitate the communication needed to coordinate developmental processes within the cardiac muscle cell. This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Sarcomere maturation: function acquisition, molecular mechanism, and interplay with other organelles

During postnatal cardiac development, cardiomyocytes mature and turn into adult ones. Hence, all cellular properties, including morphology, structure, physiology and metabolism, are changed. One of the most important aspects is the contractile apparatus, of which the minimum unit is known as a sarcomere. Sarcomere maturation is evident by enhanced sarcomere alignment, ultrastructural organization and myofibrillar isoform switching. Any maturation process failure may result in cardiomyopathy. Sarcomere function is intricately related to other organelles, and the growing evidence suggests reciprocal regulation of sarcomere and mitochondria on their maturation. Herein, we summarize the molecular mechanism that regulates sarcomere maturation and the interplay between sarcomere and other organelles in cardiomyocyte maturation. This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Ontogeny of cardiomyocytes: ultrastructure optimization to meet the demand for tight communication in excitation–contraction coupling and energy transfer

The ontogeny of the heart describes its development from the fetal to the adult stage. In newborn mammals, blood pressure and thus cardiac performance are relatively low. The cardiomyocytes are thin, and with a central core of mitochondria surrounded by a ring of myofilaments, while the sarcoplasmic reticulum (SR) is sparse. During development, as blood pressure and performance increase, the cardiomyocytes become more packed with structures involved in excitation–contraction (e-c) coupling (SR and myofilaments) and the generation of ATP (mitochondria) to fuel the contraction. In parallel, the e-c coupling relies increasingly on calcium fluxes through the SR, while metabolism relies increasingly on fatty acid oxidation. The development of transverse tubules and SR brings channels and transporters interacting via calcium closer to each other and is crucial for e-c coupling. However, for energy transfer, it may seem counterintuitive that the increased structural density restricts the overall ATP/ADP diffusion. In this review, we discuss how this is because of the organization of all these structures forming modules. Although the overall diffusion across modules is more restricted, the energy transfer within modules is fast. A few studies suggest that in failing hearts this modular design is disrupted, and this may compromise intracellular energy transfer. This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Gas dynamics in interacting disc galaxies. Fuelling of nuclei by induced bars

Des modeles de nuages de gaz en collision dans un potentiel gravitationnel stellaire a n corps sont developpes pour etudier le comportement du gaz interstellaire dans une galaxie a disque en interaction avec une autre. La formation d'une barre dans le disque causee par un effet de maree induit l'effondrement du gaz dans la region du noyau favorisant ainsi l'emergence d'une importante activite galactique
Application based on Hybrid CNN-SVM and PCA-SVM Approaches for Classification of Cocoa Beans

—In our study, we propose a hybrid Convolutional Neural Network with Support Vector Machine (CNN-SVM) and Principal Component Analysis with support vector machine (PCA-SVM) methods for the classification of cocoa beans obtained by the fermentation of beans collected from cocoa pods after harvest. We also use a convolutional neural network (CNN) and support vector machine (SVM) for the classification operation. In the case of the hybrid model, we use a convolutional network as a feature extractor and the SVM is used to perform the classification operation. The use of PCA-SVM allowed for a reduction in image size while maintaining the main features still using the SVM classifier. Radial, linear and polynomial basis function kernels were used with various control parameters for the SVM, and optimizers such as the Stochastic Gradient Descent (SGD) algorithm, Adam, and RMSprop were used for the CNN softmax classifier. The results showed the robustness of the hybrid CNN-SVM model which obtained the best score with a value of 98.32% then the PCA-SVM based model had a score of 97.65% outperforming the standard CNN and SVM classification algorithms. Metrics such as accuracy, recall, F1 score, mean squared error (MSE), and MCC have allowed us to consolidate the results obtained from our different experiments.
Deriving task specific performance from the information processing capacity of a reservoir computer

Abstract In the reservoir computing literature, the information processing capacity is frequently used to characterize the computing capabilities of a reservoir. However, it remains unclear how the information processing capacity connects to the performance on specific tasks. We demonstrate on a set of standard benchmark tasks that the total information processing capacity correlates poorly with task specific performance. Further, we derive an expression for the normalized mean square error of a task as a weighted function of the individual information processing capacities. Mathematically, the derivation requires the task to have the same input distribution as used to calculate the information processing capacities. We test our method on a range of tasks that violate this requirement and find good qualitative agreement between the predicted and the actual errors as long as the task input sequences do not have long autocorrelation times. Our method offers deeper insight into the principles governing reservoir computing performance. It also increases the utility of the evaluation of information processing capacities, which are typically defined on i.i. d. input, even if specific tasks deliver inputs stemming from different distributions. Moreover, it offers the possibility of reducing the experimental cost of optimizing physical reservoirs, such as those implemented in photonic systems.
Rapid Oscillations in Cataclysmic Variables. XVII. 1RXS J070407 + 262501

We present a study of the recently discovered intermediate polar 1RXS J070407 + 262501, distinctive for its large-amplitude pulsed signal at P = 480 s. Radial velocities indicate an orbital period of 0.1821(2) days, and the light curves suggest 0.18208(6) days. Time-series photometry shows a precise spin period of 480.6700(4) s, decreasing at a rate of 0.096(9) ms yr-1 : i.e., on a time scale P / P ˙ = 2.5 × 10 6 yr . The light curves also appear to show a mysterious signal at P = 0.263 days, which could possibly signify the presence of a superhump in this magnetic cataclysmic variable.
Ab initio excited states from the in-medium similarity renormalization group

We give a simple criterion for a Heegaard splitting to yield a Haken manifold. As a consequence, we construct many Haken manifolds, in particular homology spheres, with prescribed properties, namely Heegaard genus, Heegaard distance and Casson invariant. Along the way we give simpler and shorter proofs of the existence of splittings with specified Heegaard distance, originally proven by Ido-Jang-Kobayashi, of the existence of hyperbolic manifolds with prescribed Casson invariant, originally due to Lubotzky-Maher-Wu, and of a result about subsurface projections of disc sets (for which we even get better constants), originally due to Masur-Schleimer.
Metrology Influence on the Cutting Modelisation

High speed machining has been improved thanks to considerable advancement on the tools (optimum geometry, harder materials), on machined materials (increased workability and machining capacity for harder workpieces) and finally on the machines (higher accuracy and power at the high speeds, performances of the numerical control system). However at such loading velocities, the cutting process generates high strain and high-speed strain which cause complex, various and irreversible phenomena in plasticity. These phenomena are comprehended through the complete measurement of the mechanical actions using a six-component dynamometer and flux and temperatures measurements at the tip of the cutting tool. Balanced energy assessments are the starting points of our reflection on the machining modelling. The modelling of these phenomena and the material behaviour under this type of loading requires a suitable theoretical approach. The main points of the strain gradient theory are developed. A theoretical behaviour law adapted to the cutting phenomena is then expressed.
Asymptotic analysis of the Boltzmann equation for dark matter relics in the presence of a running dilaton and space-time defects

The interplay of dilatonic effects in dilaton cosmology and stochastic quantum space-time defects within the framework of string/brane cosmologies is examined. The Boltzmann equation describes the physics of thermal dark-matter-relic abundances in the presence of rolling dilatons. These dilatons affect the coupling of stringy matter to D-particle defects, which are generic in string theory. This coupling leads to an additional source term in the Boltzmann equation. The techniques of asymptotic matching and boundary-layer theory, which were recently applied by two of the authors (CMB and SS) to a Boltzmann equation, are used here to find the detailed asymptotic relic abundances for all ranges of the expectation value of the dilaton field. The phenomenological implications for the search of supersymmetric dark matter in current colliders, such as the LHC, are discussed.
Nutrients Changed the Assembly Processes of Profuse and Rare Microbial Communities in Coals

Abstract Nutrient stimulation is considered effective for improving biogenic coalbed methane production potential. However, our knowledge of the microbial assembly process for profuse and rare microbial communities in coals under nutrient stimulation is still limited. This study collected 16S rRNA gene data from 59 microbial communities in coals for a meta-analysis. Among these communities, 116 genera were identified as profuse taxa, and the remaining 1,637 genera were identified as rare taxa. Nutrient stimulation increased the Chao1 richness of profuse and rare genera and changed the compositions of profuse and rare genera based on nonmetric multidimensional scaling with Bray-Curtis dissimilarities. In addition, many profuse and rare genera belonging to Proteobacteria and Acidobacteria were reduced, whereas those belonging to Euryarchaeota and Firmicutes were increased under nutrient stimulation. Concomitantly, the microbial co-occurrence relationship network was also altered by nutrient addition, and many rare genera mainly belonging to Firmicutes, Bacteroides, and Euryarchaeota also comprised the key microorganisms. In addition, the compositions of most of the profuse and rare genera in communities were driven by stochastic processes, and nutrient stimulation increased the relative contribution of dispersal limitation for both profuse and rare microbial community assemblages and that of variable selection for rare microbial community assemblages. In summary, this study strengthened our knowledge regarding the mechanistic responses of coal microbial diversity and community composition to nutrient stimulation, which are of great importance for understanding the microbial ecology of coals and the sustainability of methane production stimulated by nutrients.
Convolutional Neural Networks with Transfer Learning for Pneumonia Detection

—Pneumonia is a type of acute respiratory infection caused by microbes, and viruses that affect the lungs. Pneumonia is the leading cause of infant mortality in the world, accounting for 81% of deaths in children under five years of age. There are approximately 1.2 million cases of pneumonia in children under five years of age and 180 000 died in 2016. Early detection of pneumonia can help reduce mortality rates. Therefore, this paper presents four convolutional neural network (CNN) models to detect pneumonia from chest X-ray images. CNNs were trained to classify X-ray images into two types: normal and pneumonia, using several convolutional layers. The four models used in this work are pre-trained: VGG16, VGG19, ResNet50, and InceptionV3. The measures that were used for the evaluation of the results are Accuracy, recall, and F1-Score. The models were trained and validated with the dataset. The results showed that the Inceptionv3 model achieved the best performance with 72.9% accuracy, recall 93.7%, and F1-Score 82%. This indicates that CNN models are suitable for detecting pneumonia with high accuracy.
THE VALIDITY AND RELIABILITY OF THE REACTION TIME AND BASKETBALL DEFENSIVE SLIDE SPEED TEST

The aim of the present study was to examine the content validity and reliability of the newly developed Reaction Time and Defensive Slide Test (RTADST). Thirty-six female basketball players were recruited from three professional State Basketball league of Bosnia and Herzegovina clubs (age: 18.81 ± 2.58 years) who completed three separate trials of the RTADST with each trial consisting of fast shuffling movements left and right. Each athlete performed the test 3 times in one day, and repeated testing was conducted the following day at evening basketball sessions. The RTADST relative reliability was evaluated by Cronbach’s alpha and ICC. Cronbach’s alpha coefficient was 0.81 which indicates good reliability. When recommendations from Bucheit et al. (2011) were taken into account, the value of ICC <0.69 indicated poor reliability. Absolute reliability of RTADST was assessed by CV, and its value was 5.3%, which is somewhat above the 5%, or the limit of acceptable reliability. Parameters of relative and absolute reliability after the exclusion of the first trial (familiarization with the test task), were more acceptable. Cronbach’s alpha coefficient was 0.90 and ICC = 0.82 compared to the one from all three trials. Considering absolute reliability, it could be concluded that the test is reliable since the CV value is below 5% (3.9%). Reliability between two days was assessed by ICC, and its value was 0.74, which confirms good reliability. Finally, the RTADST can be considered as a valid test that discriminates female basketball perimeter players and post players in reaction time and basketball defensive slide speed, while conditioning programs for the development of these abilities need to be carried out with a tool such is RTADST for the initial and final evaluation of these abilities.
Bayesian analysis of spatially distorted cosmic signals from Poissonian data

Reconstructing the matter density field from galaxy counts is a problem frequently addressed in current literature. Two main sources of error are shot noise from galaxy counts and insufficient knowledge of the correct galaxy position because of peculiar velocities and redshift measurement uncertainty. Here, we address the reconstruction problem of a Poissonian sampled lognormal density field with velocity distortions in a Bayesian way using a maximum a posteriori method. We test our algorithm on a one-dimensional test case and find significant improvement compared to simple data inversion. In particular, we address the following problems: photometric redshifts, mapping of extended sources in coded mask systems, real space reconstruction from redshift space galaxy distribution and combined analysis of data with different point spread functions.
Microscopic Description of Quantum Lorentz Gas by Complex Spectral Representation of the Liouville-von Neumann Equation: A Limitation of the Boltzmann Approximation

Irreversible processes of one-dimensional quantum perfect Lorentz gas is studied on the basis of the fundamental laws of physics in terms of the complex spectral analysis associated with the resonance state of the Liouville-von Neumann operator. A limitation of the usual phenomenological Boltzmann equation is discussed from this dynamical point of view. For a Wigner distribution function that spreads over moderately small scale comparative to the mean-free-path, we found a shifting motion in space of the distribution that cannot be described by the hydrodynamic approximation of the kinetic equation. The mechanism of the shifting has two completely different origins: one is due to different value of the imaginary part of the eigenvalue of the Liouvillian and predominates in moderately small wavenumber associated to the spatial distribution, while the other is due to the existence of the real part of the eigenvalue associated to a wave propagation and predominates in moderately large wavenumber.
Pion form factor from a contact interaction

The pion has a unique place in the Standard Model. It is a bound-state of a dressed-quark and -antiquark, and also that almost-massless collective excitation which is the Goldstone mode arising from the dynamical breaking of chiral symmetry. This dichotomy can only be understood by merging the study of many-body aspects of the QCD vacuum with the symmetry-preserving analysis of two-body bound-states. Furthermore, the possibility that this dichotomous nature could have wide-ranging effects on pion properties has made the empirical investigation of these properties highly desirable, despite the difficulty in preparing a system that can act as a pion target and the concomitant complexities in the interpretation of the experiments; e.g., [1–4]. A true understanding of the pion is achievable via QCD’s Dyson-Schwinger equations (DSEs) [5]. Key to this is the existence of a nonperturbative symmetrypreserving truncation scheme [6–8], which enables: the connection to be made between dynamical chiral symmetry breaking (DCSB) and the bound-state pion [9]; and the use of experiment to chart QCD’s �-function. The �function’s perturbative evolution is well-known but this new feedback between experiment and nonperturbative theory may provide access to its long-range behaviour. Studying the electromagnetic pion form factor, F em
Bounded Asynchrony: A Biologically Inspired Notion of Concurrency

We introduce {\em bounded asynchrony}, a notion of `concurrency tailored to the modeling of biological cell-cell interactions. Bounded asynchrony is the result of a scheduler that bounds the number of steps that one process get ahead of other processes; this allows the components of a system to move independently while keeping them coupled. Bounded asynchrony accurately reproduces the experimental observations made about certain cell-cell interactions: its constrained nondeterminism captures the variability observed in cells that, although equally potent, assume distinct fates. Cells are not ``scheduled'', but we show that distributed real-time behavior can lead to component interactions that are observationally equivalent to bounded asynchrony; this provides a possible mechanistic explanation for the phenomena observed during cell fate specification. We use model checking to determine cell fates. The nondeterminism of bounded asynchrony causes state explosion during model checking, but partial-order methods are not directly applicable. We present a new algorithm that reduces the number of states that need to be explored: our optimization takes advantage of the bounded-asynchronous progress and the spatially local interactions of components that model cells. Our experiments illustrate that the algorithm leads to substantial savings in model checking.