Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypic flux: The role of physiology in explaining the conundrum of bacterial persistence amid phage attack

Abstract Bacteriophages, the viruses of bacteria, have been studied for over a century. They were not only instrumental in laying the foundations of molecular biology, but they are also likely to play crucial roles in shaping our biosphere and may offer a solution to the control of drug-resistant bacterial infections. However, it remains challenging to predict the conditions for bacterial eradication by phage predation, sometimes even under well-defined laboratory conditions, and, most curiously, if the majority of surviving cells are genetically phage-susceptible. Here, I propose that even clonal phage and bacterial populations are generally in a state of continuous ‘phenotypic flux’, which is caused by transient and nongenetic variation in phage and bacterial physiology. Phenotypic flux can shape phage infection dynamics by reducing the force of infection to an extent that allows for coexistence between phages and susceptible bacteria. Understanding the mechanisms and impact of phenotypic flux may be key to providing a complete picture of phage–bacteria coexistence. I review the empirical evidence for phenotypic variation in phage and bacterial physiology together with the ways they have been modeled and discuss the potential implications of phenotypic flux for ecological and evolutionary dynamics between phages and bacteria, as well as for phage therapy.
Cefmetazole Resistance Mechanism for Escherichia Coli Including ESBL-Producing Strains

Purpose Cefmetazole (CMZ), a cephamycin antibiotic, is primarily used as a definitive therapy for Extended Spectrum β-Lactamase (ESBL)-producing Escherichia coli infections. However, the mechanism of CMZ resistance in E. coli is still unknown. To elucidate the resistance mechanism and to determine combined drugs for prevention of resistance acquisition. Methods Clinical isolates of 14 ESBL-producing E. coli and non-producing 12 isolates were used in in vitro testing of CMZ resistance acquisition. After 10-day of CMZ exposure (1st subculture), these strains were incubated in an antibacterial-free medium for 14-day. These strains were again exposed to CMZ for 10-day (2nd subculture) and confirmed for changes in MIC. For each strain detected after 1st subculture, each mRNA expression level of porin, chromosomal ampC, and drug-efflux pump was measured using real-time RT-PCR. Relebactam (REL) has the potency to recover antimicrobial activity against carbapenem-resistant Enterobacterales that has porin deficiency. REL was added to the CMZ dilution series, and MIC changes and those of porin were confirmed. Results Of these 26 strains, 15 strains (57.7%) acquired resistance after 1st subculture, but after passage culture on the antibacterial-free medium, 11 strains recovered susceptibility. These 11 strains showed resistance after 2nd subculture. The expression levels of ompF and ompC were significantly decreased in these strains (P<0.05). When REL was added, all strains suppressed resistance acquisition after 1st subculture. The mechanism was the activation of ompF. Conclusion Our results showed that the mRNA expression levels of genes encoding porin were decreased in the strains that acquired resistance due to CMZ exposure, and that ompF and ompC in particular were thought to be involved in the acquisition of resistance. The CMZ acquisition of resistance was also suppressed by the concomitant use of REL and actually suppressed the decrease in mRNA expression in ompF. It was confirmed that porin reactivated by REL.
Probing Particle Physics from Top Down with Cosmic Strings

Making use of the wealth of new observational data coming from the sky it is possible to constrain particle physics theories beyond the Standard Model. One way to do this is illustrated in this article: a subset of theories admits cosmic string solutions, topologically stable matter field configurations. In these models, a network of cosmic strings inevitably forms in the early universe and persists to the present time. The gravitational effects of these strings leads to cosmological signatures which could be visible in current and future data. The magnitude of these signatures increases as the energy scale of the new physics involved in cosmic string formation increases. Thus, searching for cosmological signatures of strings is a way to probe particle physics model "from top down", as opposed to "from bottom up" as is done using data from accelerators such as the Large Hadron Collider. Different ways of searching for cosmic strings are illustrated in this article. They include Cosmic Microwave Background temperature and polarization anisotropy maps, Large Scale Structure optical and infrared surveys, and 21cm intensity maps.
BlackCAT: A catalogue of stellar-mass black holes in X-ray transients

During the last ~50 years, the population of black hole candidates in X-ray binaries has increased considerably with 59 Galactic objects detected in transient low-mass X-ray binaries, plus a few in persistent systems (including ~5 extragalactic binaries). We collect near-infrared, optical and X-ray information spread over hundreds of references in order to study the population of black holes in X-ray transients as a whole. We present the most updated catalogue of black hole transients, which contains X-ray, optical and near-infrared observations together with their astrometric and dynamical properties. It provides new useful information in both statistical and observational parameters providing a thorough and complete overview of the black hole population in the Milky Way. Analysing the distances and spatial distribution of the observed systems, we estimate a total population of ~1300 Galactic black hole transients. This means that we have already discovered less than ~5% of the total Galactic distribution. The complete version of this catalogue will be continuously updated online and in the Virtual Observatory, including finding charts and data in other wavelengths.
Working in the digital economy: A systematic review of the impact of work from home arrangements on personal and organizational performance and productivity

Work-from-home has become an increasingly adopted practice globally. Given the emergence of the COVID-19 pandemic, such arrangements have risen substantially in a short timeframe. Work-from-home has been associated with several physical and mental health outcomes. This relationship has been supported by previous research; however, these health and safety issues often receive little resources and attention from business perspectives compared to organizational and worker performance and productivity. Therefore, aligning work-from-home practices with business goals may help catalyze awareness from decision makers and serve to effectively implement work-from-home policies. We conducted a review to synthesize current knowledge on the impact of work-from-home arrangements on personal and organizational performance and productivity. Four large databases including Scopus, PubMed, PsychInfo, and Business Source Complete were systematically searched. Through a two-step screening process, we selected and extracted data from 37 relevant articles. Key search terms surrounded two core concepts: work-from-home and productivity/performance. Of the articles published prior to the COVID-19 pandemic, 79% (n = 19) demonstrated that work-from-home increased productivity and performance whereas 21% (n = 5) showed mixed or no effects. Of the articles published during the pandemic, 23% (n = 3) showed positive effects, 38% (n = 5) revealed mixed results, and 38% (n = 5) showed negative effects. Findings suggest that non-mandatory work-from-home arrangements can have positive impacts on productivity and performance. When work-from-home becomes mandatory and full-time, or external factors (i.e., COVID-19 pandemic) are at play, the overall impacts are less positive and can be detrimental to productivity and performance. Results will help foster an understanding of the impact of work-from-home on productivity and performance and inform the development of organizational strategies to create an effective, resilient, and inclusive work-from-home workplace by helping to effectively implement work-from-home policies that are aligned with business goals.
Attention Shifts to More Complex Structures With Experience

Our environments are saturated with learnable information. What determines which of this information is prioritized for limited attentional resources? Although previous studies suggest that learners prefer medium-complexity information, here we argue that what counts as medium should change as someone learns an input’s structure. Specifically, we examined the hypothesis that attention is directed toward more complicated structures as learners gain more experience with the environment. College students watched four simultaneous streams of information that varied in complexity. RTs to intermittent search trials (Experiment 1, N = 75) and eye tracking (Experiment 2, N = 45) indexed where participants attended during the experiment. Using two participant- and trial-specific measures of complexity, we demonstrated that participants attended to increasingly complex streams over time. Individual differences in structure learning also predicted attention allocation, with better learners attending to complex structures earlier in learning, suggesting that the ability to prioritize different information over time is related to learning success.
Cross modality fusion for modality-specific lung tumor segmentation in PET-CT images

Although positron emission tomography-computed tomography (PET-CT) images have been widely used, it is still challenging to accurately segment the lung tumor. The respiration, movement and imaging modality lead to large modality discrepancy of the lung tumors between PET images and CT images. To overcome these difficulties, a novel network is designed to simultaneously obtain the corresponding lung tumors of PET images and CT images. The proposed network can fuse the complementary information and preserve modality-specific features of PET images and CT images. Due to the complementarity between PET images and CT images, the two modality images should be fused for automatic lung tumor segmentation. Therefore, cross modality decoding blocks are designed to extract modality-specific features of PET images and CT images with the constraints of the other modality. The edge consistency loss is also designed to solve the problem of blurred boundaries of PET images and CT images. The proposed method is tested on 126 PET-CT images with non-small cell lung cancer, and Dice similarity coefficient scores of lung tumor segmentation reach 75.66 ± 19.42 in CT images and 79.85 ± 16.76 in PET images, respectively. Extensive comparisons with state-of-the-art lung tumor segmentation methods have also been performed to demonstrate the superiority of the proposed network.
Dual instantons in antimembranes theory

We introduce two ansatzs for the 3-form potential of Euclidean 11d supergravity on skew-whiffed AdS{sub 4}xS{sup 7} background which results in two scalar modes with m{sup 2}=-2 on AdS{sub 4}. Being conformally coupled with a quartic interaction, it is possible to find the exact solutions of the scalar equation on this background. These modes turn out to be invariant under the SU(4) subgroup of the SO(8) isometry group, whereas there are no corresponding SU(4) singlet Bogomol'nyi-Prasad-Sommerfeld operators of dimensions one or two on the boundary theory constructed by Aharony, Bergman, Jafferis, and Maldacena. Noticing the interchange of 8{sub s} and 8{sub c} representations under skew-whiffing in the bulk, we propose the theory of antimembranes should similarly be obtained from Aharony, Bergman, Jafferis, and Maldacena's theory by swapping these representations. In particular, this enables us to identify the dual boundary operators of the two scalar modes. We deform the boundary theory by the dual operators and examine the fermionic field equations, and compare the solutions of the deformed theory with those of the bulk.
Unraveling schizophrenia replicable functional connectivity disruption patterns across sites

Functional connectivity (FC) disruption is a remarkable characteristic of schizophrenia. However, heterogeneous patterns reported across sites severely hindered its clinical generalization. Based on qualified nodal‐based FC of 340 schizophrenia patients (SZ) and 348 normal controls (NC) acquired from seven different scanners, this study compared four commonly used site‐effect correction methods in removing the site‐related heterogeneities, and then tried to cluster the abnormal FCs into several replicable and independent disrupted subnets across sites, related them to clinical symptoms, and evaluated their potentials in schizophrenia classification. Among the four site‐related heterogeneity correction methods, ComBat harmonization (F1 score: 0.806 ± 0.145) achieved the overall best balance between sensitivity and false discovery rate in unraveling the aberrant FCs of schizophrenia in the local and public data sets. Hierarchical clustering analysis identified three replicable FC disruption subnets across the local and public data sets: hypo‐connectivity within sensory areas (Net1), hypo‐connectivity within thalamus, striatum, and ventral attention network (Net2), and hyper‐connectivity between thalamus and sensory processing system (Net3). Notably, the derived composite FC within Net1 was negatively correlated with hostility and disorientation in the public validation set (p < .05). Finally, the three subnet‐specific composite FCs (Best area under the receiver operating characteristic curve [AUC] = 0.728) can robustly and meaningfully discriminate the SZ from NC with comparable performance with the full identified FCs features (best AUC = 0.765) in the out‐of‐sample public data set (Z = −1.583, p = .114). In conclusion, ComBat harmonization was most robust in detecting aberrant connectivity for schizophrenia. Besides, the three subnet‐specific composite FC measures might be replicable neuroimaging markers for schizophrenia.
Analytical models of X-shape magnetic fields in galactic halos

Context. External spiral galaxies seen edge-on exhibit X-shape magnetic fields in their halos. Whether the halo of our own Galaxy also hosts an X-shape magnetic field is still an open question. Aims. We would like to provide the necessary analytical tools to test the hypothesis of an X-shape magnetic field in the Galactic halo. Methods. We propose a general method to derive analytical models of divergence-free magnetic fields whose field lines are assigned a specific shape. We then utilize our method to obtain four particular models of X-shape magnetic fields in galactic halos. In passing, we also derive two particular models of predominantly horizontal magnetic fields in galactic disks. All our field models have spiraling field lines with spatially varying pitch angle. Results. Our four halo field models do indeed lead to X patterns in synthetic synchrotron polarization maps. Their precise topologies can all be explained by the action of a wind blowing outward from the galactic disk or from the galactic center. In practice, our field models may be used for fitting purposes or as inputs to various theoretical problems.
Review and Consultations of Canadian Financial Education Programs for Individuals with Disabilities

Background. Individuals or persons who live with a disability (PWD) can experience unique financial occupation challenges. Financial education programs can address some challenges. Purpose. The aim of this study was to describe and critically appraise current financial education programs for PWD in Canada. Method. This environmental scan framed by scoping review methods included a critical appraisal of Canadian programs’ online content and provider consultations. Researchers used four search methods to identify programs, interviewed service providers from four Canadian programs, and thematically analyzed interview transcripts. Findings. Researchers identified 134 programs; 50 (37.3%) included services. The online content of only 26 (19%) programs explicitly addressed accessibility; 106 (79%) programs’ content was at least college reading level. The qualitative results include three themes: (a) individualized approach, (b) “getting the word out”, and (c) service growth. Implications. There are financial education programs specific to PWD in Canada. Accessibility, individualization, advocacy, and development are needed.
Fibred toric varieties in toric hyperk\"{a}hler varieties

We introduce the fibred toric varieties as equivariant $\mathbb{C}P^r$ bundles over lower dimensional toric varieties. An equivalent characterization is that the natural morphisms on them degenerate to bundle projections in the context of variation of toric varieties as GIT quotients. Our main observation is that these fibred toric varieties also arise naturally in the variation of hyperk\"{a}hler varieties, namely, the fibred toric varieties are contained in the exceptional sets of the hyperk\"{a}hler natural morphisms and the Mukai flops.
Roles of the Microbiota of the Female Reproductive Tract in Gynecological and Reproductive Health

The microbiome of the female reproductive tract defies the convention that high biodiversity is a hallmark of an optimal ecosystem. Although not universally true, a homogeneous vaginal microbiome composed of species of Lactobacillus is generally associated with health, whereas vaginal microbiomes consisting of other taxa are generally associated with dysbiosis and a higher risk of disease. SUMMARY The microbiome of the female reproductive tract defies the convention that high biodiversity is a hallmark of an optimal ecosystem. Although not universally true, a homogeneous vaginal microbiome composed of species of Lactobacillus is generally associated with health, whereas vaginal microbiomes consisting of other taxa are generally associated with dysbiosis and a higher risk of disease. The past decade has seen a rapid advancement in our understanding of these unique biosystems. Of particular interest, substantial effort has been devoted to deciphering how members of the microbiome of the female reproductive tract impact pregnancy, with a focus on adverse outcomes, including but not limited to preterm birth. Herein, we review recent research efforts that are revealing the mechanisms by which these microorganisms of the female reproductive tract influence gynecologic and reproductive health of the female reproductive tract.
Principal component analysis-based inversion of effective temperatures for late-type stars

We show how the range of application of the principal component analysis-based inversion method of Paletou et al. (2015) can be extended to late-type stars data. Besides being an extension of its original application domain, for FGK stars, we also used synthetic spectra for our learning database. We discuss our results on effective temperatures against previous evaluations made available from Vizier and Simbad services at CDS.
Adiabatic solution of Dirac equation of "graphinos" in an intense electromagnetic field and emission of high order harmonics near the Dirac points

We obtain a class of adiabatic solutions of Dirac equation for the charged massless relativistic quasi-particles that arise from the low-energy excitations \cite{foot-1} in a 2D graphene sheet, interacting with an electromagnetic field. The analytic solutions obtained are useful for {\it non-perturbative} investigation of processes in intense laser fields. As a first example we employ them to predict copious emissions of high order harmonics by THz lasers interacting with the occupied states of graphinos in the vicinity of the degenerate Dirac points. The relative intensity of the emitted harmonics is seen to decrease by only about two orders of magnitude from the 3rd to the 81st harmonic order, and is characterized by two phenomena of "revival" and "plateau" formation in the middle and the far end of the spectrum calculated. A preliminary comparison is made for harmonic emission from 2D graphene that reveals a qualitatively different spectrum in the latter case showing a sharp cutoff at an order $n_{cutoff} = \frac{\omega_B}{\omega}$ where $\omega_B=eF_0b/\hbar$ is the so-called Bloch frequency.
Modified viscosity in accretion disks - Application to Galactic black hole binaries, intermediate mass black holes, and active galactic nuclei

Black holes surrounded by accretion disks are present in the Universe in different scales of masses, from microquasars up to the Active Galactic Nuclei. The current picture of the accretion disk theory remains still ad hoc, due the complexity of the magnetic field action. In addition, the accretion disks at high Eddington rates can be radiation-pressure dominated and, according to some of the heating prescriptions, thermally unstable. The observational verification of their resulting variability patterns may shed the light on both the role of radiation pressure and magnetic field in the accretion process. We compute the structure and time evolution of an accretion disk. We supplement this model with a modified viscosity prescription, which can to some extent describe the magnetization of the disk. We study the results for a large grid of models and derive conclusions separately for different scales of black hole masses. We show the dependences between the flare, or outburst, duration, its amplitude and period, on the accretion rate and viscosity scaling. We present the results for the three grids of models, designed for different black hole systems. We show that if the heating rate in the accretion disk grows more rapidly with the total pressure and temperature, the instability results in the longer, and sharper flares. In general, we find that the disks around the supermassive black holes are more radiation-pressure dominated and present relatively brighter bursts. Our method can also be used as an independent tool for the black hole mass determination, which we confront now for the intermediate black hole in the source HLX-1. For both the microquasars and Ultraluminous X-ray sources, we reproduce their observed lighcurves. We also compare the duration times of the model outbursts with the ages and bolometric luminosities of AGN.