Miracle-dz/UniFAR-FTUs huggingface dataset:
Near-infrared (Fe II) and Pa Beta imaging and spectroscopy of Arp 220

We have imaged the ultraluminous infrared galaxy Arp 220 in light of the near-infrared [Fe II] 1.257 μm and Paβ lines, and have obtained spectra in the J- and H-band atmospheric windows. Arp 220 is a strong source of [Fe II] and Paβ emission, with luminosities of 1.3 x 10^(41) and 9.2 x 10^(40) ergs s^(-1), respectively. The [Fe II] and Paβ emission are both extended over the central 2"-3", but with different morphologies. The Paβ line is strongly peaked at the position of the western nucleus seen at 2.2 μm (Graham et al. 1990) with a fainter "spur" in the direction of the eastern nucleus. The [Fe II] emission line shows a weak peak at the western nucleus along with diffuse emission extending to the east, but with no indication of a secondary maximum. The [Fe II] is more extended in the north-south direction than the Paβ line. Nearly 75% of the detected [Fe II] emission is spatially resolved. The overall [Fe II]-to-Paβ line flux ratio in Arp 220 is consistent with that seen over similar spatial scales in Seyfert 2 galaxies, yet larger than what is measured in galaxies with nuclear starbursts. The [Fe II]-to-Paβ line flux ratio is spatially variable being approximately 0.8 at the position of the western nucleus and approximately 2.0 at radii of up to 500 pc. We suggest that the extended [Fe II] emission is produced through the interaction of fast shocks with ambient gas in the ISM at the base of the outflowing, supernovae-driven superwind mapped by Heckman et al. (1987). The bolometric luminosity of the starburst required to power this wind is estimated to be at least 2 x 10^(11) L_☉. If the spatially unresolved [Fe II] emission is produced via a large number of supernova remnants, the implied rate is ~0.6 yr^(-1). The overall luminosity of such a starburst could account for a large fraction (1/2-1/3) of the Arp 220 energy budget, but the large deficit of ionizing photons (as counted by the Paβ luminosity) requires that the starburst be rapidly declining and/or have a low upper mass cutoff. Alternatively, dust may effectively compete with the gas for ionizing photons, or much of the ionizing radiation may escape through "holes" in the ISM. It is also possible that a buried AGN produces a large fraction of the unresolved [Fe II] and Paβ emission. We briefly discuss these possibilities in light of these new imaging and spectroscopic data.
Learning cell-specific networks from dynamical single cell data

Cell dynamics and biological function are governed by changing patterns of gene expression. Intricate gene interaction networks orchestrate these changes. Inferring these interactions from data is a notoriously diﬀicult inverse problem. The majority of existing network inference methods work at the population level. They construct static representations of gene regulatory networks, and they do not naturally allow us to infer differences in gene regulation across heterogeneous cell populations. Here we build upon recent dynamical inference methods that model single cell dynamics using Markov processes, which leads to an information-theoretic approach, locaTE, which employs the localised transfer entropy to infer cell-specific, causal gene regulatory networks. LocaTE uses high-resolution estimates of dynamics and geometry of the cellular gene expression manifold to inform inference of regulatory interactions. We find that this approach is superior to static inference methods, often by a significant margin. We demonstrate that factor analysis can give detailed insights into the inferred cell-specific GRNs. In application to three experimental datasets, we demonstrate superior performance and additional insights compared to stancard static GRN inference methods. For example, we recover key transcription factors and regulatory interactions driving mouse primitive endoderm formation, pancreatic development, and haematopoiesis. For both simulated and experimental data, we find that locaTE provides a powerful, eﬀicient and scalable network inference method that allows us to distil cell-specific networks from single cell data.
Function projective synchronization of a new hyperchaotic system

The function projective synchronization of a new four-dimensional hyperchaotic system is studied.First,the dynamics of the system are investigated by hyperchaotic attractor and time response diagrams.Synchronization of the system with fully unknown parameters is realized by function projective controller,and identification laws are designed for all unknown parameters.Numerical simulations show the effectiveness and feasibility of the theoretical analysis and numerical computation.
Controlled natural language with temporal features

A controlled natural language (CNLs) is a fragment of a given natural language that is computer processable. Initially created to serve as a tool for teaching non-native speakers of a given natural language, controlled natural languages have more recently served as an interface between natural languages and formal languages. Many CNLs with different base languages have been defined over the past two decades. These controlled languages have very varied domains of application such as software and hardware specification , ontology authoring and editing, air traffic control etc. Controlled natural languages have gradually gained some level popularity in the real world. From a survey of existing CNLs, we observe the lack of a controlled natural language able to parse temporal expressions. In order to be able to provide correct syntactic structures and corresponding semantic interpretations for these temporal expressions, we consider thousands of generated sentences analyzing the various tense, aspect, aspectual class and temporal modifier configuration. We also analyze sentence extracts from the Brown corpus. From which we are able to define semantic interpretations for the various temporal modifiers of interest, taking into consideration how these interpretations are affected by the sentence tense and aspect and aspectual class configuration. From this analysis we are able to provide syntactic rules defined with context free grammars. Natural languages are known to be very robust, representing it with a context free grammar therefore would require consideration of factors other than syntactic categories. In order to be able to cater for these other syntactic restrictions such as tense and number agreement, we assign parameters to each terminal and non-terminal symbol in our grammar. We can therefore define rules to satisfy these syntactic restrictions using assigned parameters before the production rules are being applied. We apply Montague semantics to these syntactic rules which enables us generate semantic interpretations from the syntactic structures for sentences in our language.
Analysis of microstrip antennas using neural networks

This paper presents the application of non-linear neural optimization networks to the analysis of arbitrarily shaped microstrip patch antennas with a very general bianisotropic grounded slab. A neural network approach is presented to solve in a new and efficient way the integral equation which describes, from the electromagnetic point of view the planar integrated structure.
Bone vascularization and bone micro-architecture characterizations according to the μCT resolution

Trabecular bone and its micro-architecture are of prime importance for health. Changes of bone micro-architecture are linked to different pathological situations like osteoporosis and begin now to be understood. In a previous paper [12], we started to investigate the relationships between bone and vessels and proposed some indices of characterization for the vessels issued from those used for the bone. Our main objective in this paper is to qualify the classical values used for bone as well as those we proposed for vessels according to different acquisition parameters and for several thresholding methods used to separate bone vessels and background. This study is also based on vessels perfusion by a contrast agent (barium sulfate mixed with gelatin) before euthanasia on rats. Femurs and tibias as well as mandibles were removed after rat’s death and were imaged by microCT (Skyscan 1272, Bruker, Belgium) with a resolution ranging from 18 to 3μm. The so obtained images were analyzed with various softwares (NRecon Reconstruction, CtAn, and CtVox from Bruker) in order to calculate bone and vessels micro-architecture parameters (density of bone/blood within the volume), and to know if the results both for bone and vascular micro-architecture are constant along the chosen pixel resolution. The result is clearly negative. We found a very different characterization both for bone and vessels with the 3μm acquisition. Tibia and mandibles bones were also used to show results that can be visually assessed. The largest portions of the vascular tree are orthogonal to the obtained slices of the bone. Therefore, the contrast agent appears as cylinders of various sizes.
Artefact Indicator for Flow‐based Temporal Interpolation of Power Doppler Ultrasound

Power Doppler ultrasound is a sonography technique to detect and visualise blood circulation. Its acquired image sequences suffer from poor temporal resolution and artefacts caused by aliasing, noise, large displacements, shearings or out‐of‐plane movements. These pitfalls distort flow fields and have unforeseen consequences on flow‐based temporal interpolations. We propose a method to detect artefacts caused by such distorted flow fields and to improve the visual quality by replacing regions with detected artefacts by locally better results. This is demonstrated on real data.
A finite strain gradient theory for viscoplasticity by means of micromorphic regularization

Stretching of polycarbonate films leads to the formation of shear bands in the necking zone [1]. Standard viscoplastic material models render mesh size dependent results, which requires a mathematical regularization. To this end, we present a finite strain gradient theory for a viscoplastic, isotropic material model where we extend the model presented in [2] to a micromorphic model by introducing a new micromorphic variable as an additional degree of freedom with its first gradient [3, 4]. The variable here has the meaning of a micro plastic strain, and is coupled with the macro plastic by a micro penalty term, forcing the macro‐plastic strain to be close to the micro‐plastic strain for the targeted shear band regularization effect. We have implemented the model equations as a three dimensional initial boundary value problem in an in house FE‐tool, to simulate different geometries with different thickness and to compare it the experimental tests. The analysis is performed for a uniaxial tensile geometry as well as for a biaxial tensile geometry. The numerical examples show the ability of the model to regularize the shear bands and solve the problem of localization.
Semi-rational evolution of a recombinant DNA polymerase for modified nucleotide incorporation efficiency

Engineering improved B-family DNA polymerases to incorporate 3′-O-modified nucleotide reversible terminators is limited by an insufficient understanding of the structural determinants that define polymerization efficiency. To explore the key mechanism for unnatural nucleotide incorporation, we engineered a B-family DNA polymerase from Thermococcus Kodakaraenis (KOD pol) by using semi-rational design strategies. We first scanned the active pocket of KOD pol through site-directed saturation mutagenesis and combinatorial mutations and identified a variant Mut_C2 containing five mutation sites (D141A, E143A, L408I, Y409A, A485E) using a high-throughput microwell-based screening method. Mut_C2 demonstrated high catalytic efficiency in incorporating 3’-O-azidomethyl-dATP labeled with a Cy3 dye, whereas the wild-type KOD pol failed to incorporate it. Computational simulations were then conducted towards the DNA binding region of KOD pol to predict additional mutations with enhanced catalytic activity, which were subsequently experimentally verified. By a stepwise combinatorial mutagenesis approach, we obtained an eleven-mutation variant, named Mut_E10 by introducing additional mutations to the Mut_C2 variant. Mut_E10, which carried six specific mutations (S383T, Y384F, V389I, V589H, T676K, and V680M) within the DNA-binding region, demonstrated over 20-fold improvement in kinetic efficiency as compared to Mut_C2. In addition, Mut_E10 demonstrated satisfactory performance in two different sequencing platforms (BGISEQ-500 and MGISEQ-2000), indicating its potential for commercialization. Our study demonstrates that an effective enhancement in its catalytic efficiency towards modified nucleotides can be achieved efficiently through combinatorial mutagenesis of residues in the active site and DNA binding region of DNA polymerase. These findings contribute to a comprehensive understanding of the mechanisms that underlie the incorporation of modified nucleotides by DNA polymerase. The beneficial mutation sites, as well as the nucleotide incorporation mechanism identified in this study, can provide valuable guidance for the engineering of other B-family DNA polymerases.
The RBPome of influenza A virus mRNA reveals a role for TDP-43 in viral replication

Recent technical advances have significantly improved our understanding of the RNA-binding protein (RBP) repertoire present within eukaryotic cells, with a particular focus on the RBPs that interact with cellular polyadenylated mRNAs. However, recent studies utilising the same technologies have begun to tease apart the RBP interactome of viral mRNAs, notably SARS-CoV-2, revealing both similarities and differences between the RBP profiles of viral and cellular mRNAs. Herein, we comprehensively identified the RBPs that associate with the NP mRNA of an influenza A virus. Moreover, we provide evidence that the viral polymerase is essential for the recruitment of RPBs to viral mRNAs through direct polymerase-RBP interactions during transcription. We show that loss of TDP-43, which associates with the viral mRNAs, results in lower levels of viral mRNAs within infected cells, and a decreased yield of infectious viral particles. Overall, our results uncover an important role for TDP-43 in the influenza A virus replication cycle via a direct interaction with viral mRNAs, and point to a role of the viral polymerase in orchestrating the assembly of viral mRNPs.
Trustworthy Wireless Personal Area Networks

In the Internet of Things (IoT), everyday objects are equipped with the ability to compute and communicate. These smart things have invaded the lives of everyday people, being constantly carried or worn on our bodies, and entering into our homes, our healthcare, and beyond. This has given rise to wireless networks of smart, connected, always-on, personal things that are constantly around us, and have unfettered access to our most personal data as well as all of the other devices that we own and encounter throughout our day. It should, therefore, come as no surprise that our personal devices and data are frequent targets of ever-present threats. Securing these devices and networks, however, is challenging. In this dissertation, we outline three critical problems in the context of Wireless Personal Area Networks (WPANs) and present our solutions to these problems. First, I present our Trusted I/O solution (BASTION-SGX) for protecting sensitive user data transferred between wirelessly connected (Bluetooth) devices. This work shows how in-transit data can be protected from privileged threats, such as a compromised OS, on commodity systems. I present insights into the Bluetooth architecture, Intel’s Software Guard Extensions (SGX), and how a Trusted I/O solution can be engineered on commodity devices equipped with SGX. Second, I present our work on Amulet and how we successfully built a wear-
Temporal genome-wide fitness analysis of Mycobacterium marinum during infection reveals genetic requirement for virulence and survival in amoebae and microglial cells

Tuberculosis remains the most pervasive infectious disease and the recent emergence of multiple or even fully drug-resistant strains increases the risk and emphasizes the need for more efficient and better drug treatments. A key feature of mycobacteria pathogenesis is the metabolic switch during infection and expression of virulence genes is often adapted to specific infection conditions. This study aims to identify genes that are involved in the establishment and maintenance of the infection. To answer these questions, we have applied Transposon Sequencing (Tn-Seq) in M. marinum, an unbiased genome-wide strategy that combines saturation insertional mutagenesis and high throughput sequencing. This approach allowed us to precisely identify the localization and relative abundance of insertions in pools of Tn mutants. The essentiality and fitness cost, in terms of growth advantage and disadvantage of over 105 mutants were quantitatively compared between in vitro and different stages of infection in two evolutionary distinct hosts, D. discoideum and BV2 microglial cells. We found that 57% of TA sites in the M. marinum genome were disrupted and that 568 genes (10.2%) are essential for M. marinum, which is comparable to previous Tn-Seq studies on M. tuberculosis. The major pathways involved in the survival of M. marinum during infection of D. discoideum were related to vitamin metabolism, the esx-1 operon, as well as the mce1 operon.
MIL Cell – A tool for multi-scale simulation of yeast replication and prion transmission

The single celled baker’s yeast, Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, with the three most prominent examples being [URE3] formed from the Ure2 protein (a regulator of nitrogen catabolism), [PSI+] formed from the Sup35 protein (a yeast translation termination release factor) and [PIN+] formed from the Rnq1 protein (of as yet unknown function). In a laboratory environment, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i.) Spontaneous nucleation of the prion within the yeast cell, and (ii.) Receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost from a yeast due to (i) Dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) Preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool, called MIL-CELL, for modelling these four general processes using a multiscale approach that is able to describe both spatial and kinetic aspects of the yeast life cycle and the amyloid- prion behavior. The yeast growth cycle is considered in two stages, a mature yeast that is competent to bud (M), and a daughter yeast (D) defined as a fully grown and detached bud. In the virtual plate experiment each transition in yeast growth is stochastically regulated, according to temporal and spatial characteristics, in a manner able to incorporate concepts of confluent growth. Between the relatively coarse time-points used for the particle level description, a set of differential equations, describing the nucleation, growth, fragmentation and clumping of amyloid fibrils, is solved numerically, for each individual yeast cell. Distribution of amyloid between the mother and the daughter is carried out by solving a set of kinetic partition equations between mother and the newly forming (and still attached) daughter during the yeast budding stage. In this paper we describe the workings of the model, the assumptions upon which it is based and some interesting simulation results that pertain to wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL (Monitoring Induction and Loss of prions in Cells) is provided as a stand-alone graphical user interface-based executable program for free download with the paper (supplementary section). MIL-CELL download: https://drive.google. com/drive/folders/1xNBSL_2sGNkyXfYLYUyXjyM9ibGAcQUL? usp=sharing
Involvement of the putative metal efflux protein YbeX in ribosomal metabolism

YbeX of Escherichia coli, a member of CorC protein family, is a putative Co2+/ Mg2+ efflux factor. Here, we describe several ΔybeX phenotypes and report an involvement of YbeX in ribosomal metabolism. E. coli lacking ybeX has a longer lag phase on outgrowth from the stationary phase. This phenotype is heterogeneous at the individual cell level and can be rescued by supplementing the growth media with magnesium. ΔybeX strain is sensitive to elevated growth temperatures and to several ribosome-targeting antibiotics, which have a common ability to induce the cold shock response in E. coli. ΔybeX cells accumulate distinct 16S rRNA degradation intermediates present in both 30S particles and 70S ribosomes. We propose that a function of YbeX is maintaining the magnesium homeostasis in the cell, which is needed for proper ribosomal assembly.
Fever-like temperature impacts on Staphylococcus aureus and Pseudomonas aeruginosa interaction, physiology, and virulence both in vitro and in vivo

Background Staphylococcus aureus and Pseudomonas aeruginosa cause a wide variety of bacterial infections and coinfections, showing a complex interaction that involves the production of different metabolites and metabolic changes. Temperature is a key factor for bacterial survival and virulence and within the host, bacteria could be exposed to an increment in temperature during fever development. We analyzed the previously unexplored effect of fever-like temperatures (39°C) on S. aureus USA300 and P. aeruginosa PAO1 microaerobic mono- and co-cultures compared with 37°C, by using RNAseq and physiological assays including in-vivo experiments. Results In general terms both temperature and co-culturing had a strong impact on both PA and SA with the exception of the temperature response of monocultured PA. We studied metabolic and virulence changes on both species. Altered metabolic features at 39°C included arginine biosynthesis and the periplasmic glucose oxidation in S. aureus and P. aeruginosa monocultures respectively. When PA co-cultures were exposed at 39°C they upregulated ethanol oxidation related genes along with an increment in organic acid accumulation. Regarding virulence factors, monocultured SA showed an increase in the mRNA expression of the agr operon and hld, pmsα and pmsβ genes at 39°C. Supported by mRNA data, we performed physiological experiments and detected and increment in hemolysis, staphylxantin production and a decrease in biofilm formation at 39°C. On the side of PA monocultures, we observed increase in extracellular lipase and protease and biofilm formation at 39°C along with a decrease in motility in correlation with changes observed at mRNA abundance. Additionally, we assessed host-pathogen interaction both in-vitro and in-vivo. S. aureus monocultured at 39°C showed a decrease in cellular invasion and an increase in IL-8 -but not in IL-6- production by A549 cell line. PA also decreased its cellular invasion when monocultured at 39°C and did not induce any change in IL-8 or IL-6 production. PA strongly increased cellular invasion when co-cultured at 37°C and 39°C. Finally, we observed increased lethality in mice intranasally inoculated with S. aureus monocultures pre-incubated at 39°C and even higher levels when inoculated with co-cultures. The bacterial burden for P. aeruginosa was higher in liver when the mice were infected with co-cultures previously incubated at 39°C comparing with 37°C. Conclusion Our results highlight a relevant change in the virulence of bacterial opportunistic pathogens exposed to fever-like temperatures in presence of competitors, opening new questions related to bacteria-bacteria and host-pathogen interactions and coevolution.