Miracle-dz/UniFAR-FTUs huggingface dataset:
Interdisciplinarity in Socio-economics, mathematical analysis and predictability of complex systems

In this essay, I attempt to provide supporting evidence as well as some balance for the thesis on `Transforming socio-economics with a new epistemology' presented by Hollingworth and Mueller (2008). First, I review a personal highlight of my own scientific path that illustrates the power of interdisciplinarity as well as unity of the mathematical description of natural and social processes. I also argue against the claim that complex systems are in general `not susceptible to mathematical analysis, but must be understood by letting them evolve over time or with simulation analysis'. Moreover, I present evidence of the limits of the claim that scientists working within Science II do not make predictions about the future because it is too complex. I stress the potentials for a third `Quantum Science' and its associated conceptual and philosophical revolutions, and finally point out some limits of the `new' theory of networks.
J/$\psi$ and $\psi$(2S) production in p-Pb collisions at $\sqrt{s_{NN}}=\mathrm{5.02}$ TeV with ALICE at the LHC

The ALICE Collaboration has studied the inclusive J/$\psi$ and $\psi(\mathrm{2S})$ production in p-Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV, at the CERN LHC. The J/$\psi$ measurement is performed in the $\mu^{+}\mu^{-}$ and in the $e^{+}e^{-}$ decay channels, down to zero $p_{\mathrm{T}}$. The results are in fair agreement with theoretical predictions. The $\psi(\mathrm{2S})$ measurement has also been performed. In particular, a smaller $\psi(\mathrm{2S})$ nuclear modification factor, with respect to the J$/\psi$ one, has been observed.
A Gap in the Spectrum of the Faltings Height

We show that the minimum $h_{\text{min}}$ of the stable Faltings height on elliptic curves found by Deligne is followed by a gap. This means that there is a constant $C >0$ such that for every elliptic curve $E/K$ with everywhere semistable reduction over a number field $K$, we either have $h(E/K)=h_{\text{min}}$ or $h(E/K)\geq h_{\text{min}} +C$. We determine such an absolute constant explicitly. On the contrary, we show that there is no such gap for elliptic curves with unstable reduction.
Early initiation of electrical stimulation paired with range of motion after a volumetric muscle loss injury does not benefit muscle function

What is the central question of this study? First, how does physical rehabilitation influence recovery from traumatic muscle injury? Second, how does physical activity impact the rehabilitation response for skeletal muscle function and whole‐body metabolism? What is the main finding and its importance? The most salient findings were that rehabilitation impaired muscle function and range of motion, while restricting activity mitigated some negative effects but also impacted whole‐body metabolism. These data suggest that first, work must continue to explore treatment parameters, including modality, time, type, duration and intensity, to find the best rehabilitation approaches for volumetric muscle loss injuries; and second, restricting activity acutely might enhance rehabilitation response, but whole‐body co‐morbidities should continue to be considered.
mSep: investigating physiological and immune-metabolic biomarkers in septic and healthy pregnant women to predict feto-maternal immune health – a prospective observational cohort study protocol

Introduction Maternal sepsis remains a leading cause of death in pregnancy. Physiological adaptations to pregnancy obscure early signs of sepsis and can result in delays in recognition and treatment. Identifying biomarkers that can reliably diagnose sepsis will reduce morbidity and mortality and antibiotic overuse. We have previously identified an immune-metabolic biomarker network comprising three pathways with a >99% accuracy for detecting bacterial neonatal sepsis. In this prospective study, we will describe physiological parameters and novel biomarkers in two cohorts—healthy pregnant women and pregnant women with suspected sepsis—with the aim of mapping pathophysiological drivers and evaluating predictive biomarkers for diagnosing maternal sepsis. Methods and analysis Women aged over 18 with an ultrasound-confirmed pregnancy will be recruited to a pilot and two main study cohorts. The pilot will involve blood sample collection from 30 pregnant women undergoing an elective caesarean section. Cohort A will follow 100 healthy pregnant women throughout their pregnancy journey, with collection of blood samples from participants at routine time points in their pregnancy: week 12 ‘booking’, week 28 and during labour. Cohort B will follow 100 pregnant women who present with suspected sepsis in pregnancy or labour and will have at least two blood samples taken during their care pathway. Study blood samples will be collected during routine clinical blood sampling. Detailed medical history and physiological parameters at the time of blood sampling will be recorded, along with the results of routine biochemical tests, including C reactive protein, lactate and white blood cell count. In addition, study blood samples will be processed and analysed for transcriptomic, lipidomic and metabolomic analyses and both qualitative and functional immunophenotyping. Ethics and dissemination Ethical approval has been obtained from the Wales Research Ethics Committee 2 (SPON1752-19, 30 October 2019). Trial registration number NCT05023954.
Role of intratumoral and peritumoral CT radiomics for the prediction of EGFR gene mutation in primary lung cancer

Objectives To determine the added value of combining intratumoral and peritumoral CT radiomics for the prediction of epidermal growth factor receptor (EGFR) gene mutations in primary lung cancer (PLC). Methods This study included 478 patients with PLC (348 adenocarcinomas and 130 other histological types) who underwent surgical resection and EGFR gene testing. Two radiologists performed segmentation of tumors and peritumoral regions using precontrast high-resolution CT images, and 398 radiomic features (212 intra- and 186 peritumoral features) were extracted. The peritumoral region was defined as the lung parenchyma within a distance of 3 mm from the tumor border. Model performance was estimated using Random Forest, a machine-learning algorithm. Results EGFR mutations were found in 162 tumors; 161 adenocarcinomas, and one pleomorphic carcinoma. After exclusion of poorly reproducible and redundant features, 32 radiomic features remained (14 intra- and 18 peritumoral features) and were included in the model building. For predicting EGFR mutations, combining intra- and peritumoral radiomics significantly improved the performance compared to intratumoral radiomics alone (AUC [area under the receiver operating characteristic curve], 0.774 vs 0.730; p < 0.001). Even in adenocarcinomas only, adding peritumoral radiomics significantly increased performance (AUC, 0.687 vs 0.630; p < 0.001). The predictive performance using radiomics and clinical features was significantly higher than that of clinical features alone (AUC, 0.826 vs 0.777; p = 0.005). Conclusions Combining intra- and peritumoral radiomics improves the predictive accuracy of EGFR mutations and could be used to aid in decision-making of whether to perform biopsy for gene tests. Advances in knowledge Adding peritumoral to intratumoral radiomics yields greater accuracy than intratumoral radiomics alone in predicting EGFR mutations and may serve as a non-invasive method of predicting of the gene status in PLC.
Two different types of plasmoids in the plasma sheet: Cluster multisatellite analysis application

The fine magnetic field structure of two successive plasmoids previously reported is investigated by magnetic rotation analysis using four Cluster satellite data. Between these two plasmoids, opposite trends of curvature radius (Rc) variations of the magnetic field lines from the boundary to the inner part are found. The different variations of Rc reflect that the two plasmoids have different magnetic configurations. The electric current density distributions for both plasmoids are found distinct. The By increase and abundant field‐aligned currents in the narrow core region of the first plasmoid indicate that a possible magnetic flux rope (MFR) core exists inside. The results indicate that the first observed plasmoid is of a magnetic loop (ML) type (with possible MFR core) and the second plasmoid is of a magnetic flux rope (MFR) type. The coexistence of ML and MFR in the near‐Earth plasma sheet may imply that multiple X line reconnection can occur by either an antiparallel or a component‐parallel way.
Remyelination varies between and within lesions in multiple sclerosis following bexarotene

In multiple sclerosis chronic demyelination is associated with axonal loss, and ultimately contributes to irreversible progressive disability. Enhancing remyelination may slow, or even reverse, disability. We recently trialled bexarotene versus placebo in 49 people with multiple sclerosis. While the primary MRI outcome was negative, there was converging neurophysiological and MRI evidence of efficacy. Multiple factors influence lesion remyelination. In this study we undertook a systematic exploratory analysis to determine whether treatment response – measured by change in magnetisation transfer ratio – is influenced by location (tissue type and proximity to CSF) or the degree of abnormality (using baseline magnetisation transfer ratio and T1 values).
A Method of Planar-Template- Based Camera Self-Calibration for Single-View

— Camera calibration is an important step in 3D reconstruction. Camera calibration may be classified into two major types: traditional calibration and self-calibration. However, a calibration method in using a checkerboard is intermediate between traditional calibration and self-calibration. A self is proposed based on a square in this paper. Only a square in the planar template, the camera self-calibration can be completed through the single view. The proposed algorithm is that the virtual circle and straight line are established by a square on planar template, and circular points, vanishing points in straight lines and the relation between them are be used, in order to obtain the image of the absolute conic (IAC) and establish the camera intrinsic parameters. To make the calibration template is simpler, as compared with the Zhang Zhengyou’s method. Through real experiments and s experiments, t he experimental results show that this algorithm is feasible and available, and has a certain precision and robustness
Dimension fractale d'attracteurs : cas du modèle de Hogg-Huberman

In this work, we deal with the fractal dimension D of a chaotic attractor which is generated by a bidimensional endomorphism (the Hogg-Huberman model). Using a modiﬁed box-counting method, we study the numerical behavior of D with respect to the number n of points of the considered set.One establishes an important relation D=D(n) which is valid for other dynamical systems.
Lifting with Inner Functions of Polynomial Discrepancy

Lifting theorems are theorems that bound the communication complexity of a composed function f ◦ g n in terms of the query complexity of f and the communication complexity of g . Such theorems constitute a powerful generalization of direct-sum theorems for g , and have seen numerous applications in recent years. We prove a new lifting theorem that works for every two functions f, g such that the discrepancy of g is at most inverse polynomial in the input length of f . Our result is a significant generalization of the known direct-sum theorem for discrepancy, and extends the range of inner functions g for which lifting theorems hold.
Contraband detection based on deep learning

This paper focuses on the detection of contraband scanned by X-ray. Due to the complexity of passenger’s luggage, contraband in X-ray images have the characteristics of small target, fuzzy features and complex background. This paper proposes a scheme based on deep learning to detect the contraband in X-ray images. The paper mainly adopts YOLO (You Only Look Once) algorithm, which regards object detection as a regression task and obtains all information through one neural network, including the probability and bounding boxes. After investigation, the paper uses YOLOv3 algorithm, and the accuracy for the dev set achieves 45.2813 % . The paper also explores two tasks in object detection, one is the number of bounding boxes for every grid in the YOLO algorithm, the other is over-fitting in training neural network.
The Interpretation of Universally Quantified DPs and Singular Definites in Adverbially Quantified Sentences

It is well known that adverbially quantified sentences with singular indefinites as well as ones with bare plurals get readings according to which the quantificational force of the respective DP seems to depend on the quantificational force of the respective Q-adverb. This phenomenon is generally referred to as Quantificational Variability Effect (QVE). Consider the sentences in (1) and (2) below:
Shellability of semigroup rings

Abstract The concepts of Λ-shellability of locally finite posets as well as of extendable sequentially Koszul algebras will be introduced. It will be proved that the divisor poset of a homogeneous semigroup ring is Λ-shellable if and only if the semigroup ring is extendable sequentially Koszul. Examples of extendable sequentially Koszul semigroup rings contain all monomial ASL’s (algebras with straightening laws) and all second squarefree Veronese subrings.
Modelling the Growth of Supermassive Black Holes in Cosmological Simulations

There is strong evidence that supermassive black holes reside in all galaxies that contain a stellar spheroid and their mass is tightly correlated with properties such as stellar bulge mass and velocity dispersion. There are also strong theoretical arguments that feedback from supermassive black holes plays an important role in shaping the high mass end of the galaxy mass function, hence to accurately model galaxies we also need to model the black holes. We present a comparison of two black hole growth models implemented within a large-scale, cosmological SPH simulation including star formation and feedback. One model is a modified Bondi-Hoyle prescription that grows black holes based on the smooth density of local gas, while the other is the recently proposed Accretion Disc Particle (ADP) method. This model swallows baryonic particles that pass within an accretion radius of the black hole and adds them to a subgrid accretion disc. Black holes are then grown by material from this disc. We find that both models can reproduce local scaling relations, although the ADP model is offset from the observed relations at high black hole masses. The total black hole mass density agrees between models to within a factor of three, but both struggle to reproduce the black hole mass function. The simulated mass functions are too steep and underestimate the number of intermediate and high mass black holes. In addition, the ADP model swallows excessive amounts of material at the resolution of large-scale, cosmological simulations producing unrealistically large accretion discs. Future work needs to be performed to improve the black hole mass function within simulations. This should be done through the mass growth and feedback as they are strongly coupled and should not be treated as separate entities.
Chemical abundances of massive stars in Local Group galaxies

The relative abundances of elements in galaxies can provide valuable information on the stellar and chemical evolution of a galaxy. While nebulae can provide abundances for a variety of light elements, stars are the only way to directly determine the abundances of iron-group and s-process and r-process elements in a galaxy. The new 8m and 10m class telescopes and high-efficiency spectrographs now make high-quality spectral observations of bright supergiants possible in dwarf galaxies in the Local Group. We have been concentrating on elemental abundances in the metal-poor dwarf irregular galaxies, NGC 6822, WLM, Sextants A, and GR8. Comparing abundance ratios to those predicted from their star formation histories, determined from color-magnitude diagrams, and comparing those ratios between these galaxies can give us new insights into the evolution of these dwarf irregular galaxies. Iron-group abundances also allow us to examine the metallicities of the stars in these galaxies directly, which affects their inferred mass loss rates and predicted stellar evolution properties.
Expression of vimentin alters cell mechanics, cell-cell adhesion, and gene expression profiles suggesting the induction of a hybrid EMT in human mammary epithelial cells

Vimentin is a Type III intermediate filament (VIF) cytoskeletal protein that regulates the mechanical and migratory behavior of cells. Its expression is considered to be a marker for the epithelial to mesenchymal transition (EMT) that takes place in tumor metastasis. However, the molecular mechanisms regulated by the expression of vimentin in the EMT remain largely unexplored. We created MCF7 epithelial cell lines expressing vimentin from a cumate-inducible promoter to address this question. When vimentin expression was induced in these cells, extensive cytoplasmic VIF networks were assembled accompanied by changes in the organization of the endogenous keratin intermediate filament networks and disruption of desmosomes. Significant reductions in intercellular forces by the cells expressing VIFs were measured by quantitative monolayer traction force and stress microscopy. In contrast, laser trapping micro-rheology revealed that the cytoplasm of MCF7 cells expressing VIFs was stiffer than the uninduced cells. Vimentin expression activated transcription of genes involved in pathways responsible for cell migration and locomotion. Importantly, the EMT related transcription factor TWIST1 was upregulated only in wild type vimentin expressing cells and not in cells expressing a mutant non-polymerized form of vimentin, which only formed unit length filaments (ULF). Taken together, our results suggest that vimentin expression induces a hybrid EMT correlated with the upregulation of genes involved in cell migration.
Characterization of bending balloon actuators

The emerging field of soft robotics often relies on soft actuators powered by pressurized fluids to obtain a variety of movements. Strategic incorporation of soft actuators can greatly increase the degree of freedom of soft robots thereby bestowing them with a range of movements. Balloon actuators are extensively used to achieve various motions such as bending, twisting, and expanding. A detailed understanding of how material properties and architectural designs of balloon actuators influence their motions will greatly enable the application of these soft actuators. In this study, we developed a framework involving experimental and theoretical analyses, including computational analysis, delineating material and geometrical parameters of balloon actuators to their bending motions. Furthermore, we provide a simple analytical model to predict and control the degree of bending of these actuators. The described analytical tool could be used to predict the actuating function of balloon actuators and thereby help generate optimal actuators for functions which require control over the extent and direction of actuation.
Resource efficiency and environmental impact of juglone in Pericarpium Juglandis: A review

Black walnut (Juglans nigra) is considered one of the most valuable plants, with a global production of 3.5 million tons of dried fruit yearly. Throughout the past two millennia, its allelopathic effects have been widely recognized. Black walnuts produce a natural naphthoquinone called juglone, which occurs naturally in all parts of the tree, particularly the green husk, and contributes significantly to the allelopathic effects of black walnut. Except for the fruit’s edible nature, the walnut green husk (Pericarpium Juglandis) has been used for centuries to make wine, natural dyes, and traditional medicines to cure certain diseases. Within the extracts of walnut green husk, 1,4-naphthoquinones, gallic acid, caffeic acid, and quercitrin were separated and characterized. Among these compounds, the major active ingredient with a good application prospect is juglone, which has proven to be a natural chemical compound with anticancer, antitumor, antibacterial, and antiviral activities, especially the strong anticancer activity. Juglone is also an environmentally friendly biological pesticide and herbicide. Certainly, the environmental impact of juglone also needs to be considered. Significant quantities of walnut green husk are currently produced as a byproduct of walnut production; however, its value has not been fully utilized and explored, which raises environmental concerns. This review attempts to: 1) summarize the origin and historical use of walnut and walnut green husk; 2) introduce the structure, biosynthesis pathway, extraction method, biological activity, and potential applications of juglone, as well as its environmental impact assessment.
Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq

Decreases in the costs of high-throughput sequencing technologies have led to continually increasing numbers of livestock RNA-Seq studies in the last decade. Although the number of studies has increased dramatically, most livestock RNA-Seq experiments are limited by cost to a small number of biological replicates. Meta-analysis procedures can be used to integrate and jointly analyze data from multiple independent studies. Meta-analyses increase the sample size, which in turn increase both statistical power and robustness of the results. In this work, we discuss cutting edge approaches to combining results from multiple independent RNA-Seq studies to improve livestock transcriptomics research. We review currently published RNA-Seq meta-analyses in livestock, describe many of the key issues specific to RNA-Seq meta-analysis in livestock species, and discuss future perspectives.
TACI: an ImageJ plugin for 3D calcium imaging analysis

Research in the field of neuroscience has evolved to use complex imaging and computational tools to extract comprehensive information from data sets. Calcium imaging is a widely used technique that requires sophisticated software to obtain reproducible results, but many laboratories struggle to adopt computational methods when updating protocols to meet modern standards. Difficulties arise due to the lack of computational knowledge and paywalls for software. In addition, most calcium imaging analysis approaches ignore motion on the z-axis. Here, we described a workflow to use ImageJ to analyze 3D calcium imaging. We applied TrackMate, an open-source ImageJ plugin, to track neurons in the lateral (x/y) direction, detect regions of interest (ROIs), and extract fluorescence intensities. To track motion on the z-axis, we developed a new ImageJ plugin, TrackMate Analysis of Calcium Imaging (TACI). For neurons appearing on multiple z-positions, maximum fluorescence values were identified to represent neurons’ intensities of corresponding z-stacks. This workflow does not require coding ability, avoids human bias, and increases reproducibility. We validated this workflow using fly larval thermosensitive neurons that displayed movements in all directions during temperature fluctuation and a 3D calcium imaging dataset acquired from the fly brain.