bluuebunny/crossref_metadata_2025_split huggingface dataset:
A complete characterization of minima of the spectral abscissa and rightmost roots of second-order systems with input delay
Authors: Michiels Wim , Niculescu Silviu-Iulian , Boussaada Islam 
Published: June 2023

Abstract
The numerical minimization of the spectral abscissa function of linear time-invariant time-delay systems, an established approach to compute stabilizing controllers with a fixed structure, often gives rise to minima characterized by active characteristic roots with multiplicity higher than one. At the same time, recent theoretical results reveal situations where the so-called multiplicity induced dominancy property holds, i.e., a sufficiently high multiplicity implies that the root is dominant. Using an integrative approach, combining analytical characterizations, computation of characteristic roots and numerical optimization, a complete characterization of the stabilizability of second-order systems with input delays is provided, for both state feedback and delayed output feedback. The level sets of the minimal achievable spectral abscissa are also characterized. These results shed light on the complex relations between (configurations involving) multiple roots, the property of being dominant roots and the property of corresponding to (local/global) minimizers of the spectral abscissa function.
A model for analysis of antibiotic usage in low-income settings
Authors: Rockwood Neesha , Mani Uma , Ranawaka Sarith , Gunarathna Sathika , Sivaganesh Sivasuriya 
Published: June 2023

Abstract

Objectives
Quantification of antibiotic usage is an important component of antimicrobial stewardship programmes. We aimed to estimate institutional antibiotic usage and costs using methodology and metrics applicable to low-income settings without electronic health records.

Methods
The DDD per 100 patient-days (DDDs/100 PDs) of antibiotics used in a calendar year was calculated retrospectively from ward registers and inpatient drug records in general surgical wards of a tertiary hospital. The antibiotics were categorized using the Access, Watch, Reserve classification. The annual expenditure on antibiotics was estimated from price lists of the state medication procurer.

Results
Annual usage of IV co-amoxiclav, cefuroxime and metronidazole was significantly higher than other antibiotics and certain wards showed outlier use of the same. The IV formulations of co-amoxiclav (5-fold), metronidazole (3-fold) and ciprofloxacin (2-fold) were used in excess of the oral formulation. Proportionate antibiotic usage based on the AWaRe category did not vary significantly between wards. Two wards were outliers for annual expenditure/100 PDs. IV clindamycin and meropenem combined accounted for 43.8% of expenditure on antibiotics.

Conclusions
This study demonstrated intra-institutional variations of annual antibiotic usage and related costs. The metric DDD/100 PDs and the methodology used here are suitable for intra- and inter-institutional analyses of antibiotic usage, particularly in low-income settings.
Emerging insights into ethnic-specific TP53 germline variants
Authors: Fischer Nicholas W , Ma Yu-Heng Vivian , Gariépy Jean 
Published: June 2023

Abstract
The recent expansion of human genomics repositories has facilitated the discovery of novel TP53 variants in populations of different ethnic origins. Interpreting TP53 variants is a major clinical challenge because they are functionally diverse, confer highly variable predisposition to cancer (including elusive low-penetrance alleles), and interact with genetic modifiers that alter tumor susceptibility. Here, we discuss how a cancer risk continuum may relate to germline TP53 mutations on the basis of our current review of genotype–phenotype studies and an integrative analysis combining functional and sequencing datasets. Our study reveals that each ancestry contains a distinct TP53 variant landscape defined by enriched ethnic-specific alleles. In particular, the discovery and characterization of suspected low-penetrance ethnic-specific variants with unique functional consequences, including P47S (African), G334R (Ashkenazi Jewish), and rs78378222 (Icelandic), may provide new insights in terms of managing cancer risk and the efficacy of therapy. Additionally, our analysis highlights infrequent variants linked to milder cancer phenotypes in various published reports that may be underdiagnosed and require further investigation, including D49H in East Asians and R181H in Europeans. Overall, the sequencing and projected functions of TP53 variants arising within ethnic populations and their interplay with modifiers, as well as the emergence of CRISPR screens and AI tools, are now rapidly improving our understanding of the cancer susceptibility spectrum, leading toward more accurate and personalized cancer risk assessments.
Arabidopsis flippase ALA3 is required for adjustment of early subcellular trafficking in plant response to osmotic stress
Authors: Pukyšová Vendula , Sans Sánchez Adrià , Rudolf Jiří , Nodzyński Tomasz , Zwiewka Marta 
Published: June 2023

Abstract
To compensate for their sessile lifestyle, plants developed several responses to exogenous changes. One of the previously investigated and not yet fully understood adaptations occurs at the level of early subcellular trafficking, which needs to be rapidly adjusted to maintain cellular homeostasis and membrane integrity under osmotic stress conditions. To form a vesicle, the membrane needs to be deformed, which is ensured by multiple factors, including the activity of specific membrane proteins, such as flippases from the family of P4-ATPases. The membrane pumps actively translocate phospholipids from the exoplasmic/luminal to the cytoplasmic membrane leaflet to generate curvature, which might be coupled with recruitment of proteins involved in vesicle formation at specific sites of the donor membrane. We show that lack of the AMINOPHOSPHOLIPID ATPASE3 (ALA3) flippase activity caused defects at the plasma membrane and trans-Golgi network, resulting in altered endocytosis and secretion, processes relying on vesicle formation and movement. The mentioned cellular defects were translated into decreased intracellular trafficking flexibility failing to adjust the root growth on osmotic stress-eliciting media. In conclusion, we show that ALA3 cooperates with ARF-GEF BIG5/BEN1 and ARF1A1C/BEX1 in a similar regulatory pathway to vesicle formation, and together they are important for plant adaptation to osmotic stress.
CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES: their evolution, structure, and roles in stress response and development
Authors: Zeiner Adam , Colina Francisco J , Citterico Matteo , Wrzaczek Michael 
Published: June 2023

Abstract
Plant-specific receptor-like protein kinases (RLKs) are central components for sensing the extracellular microenvironment. CYSTEINE-RICH RLKs (CRKs) are members of one of the biggest RLK subgroups. Their physiological and molecular roles have only begun to be elucidated, but recent studies highlight the diverse types of proteins interacting with CRKs, as well as the localization of CRKs and their lateral organization within the plasma membrane. Originally the DOMAIN OF UNKNOWN FUNCTION 26 (DUF26)-containing extracellular region of the CRKs was proposed to act as a redox sensor, but the potential activating post-translational modification or ligands perceived remain elusive. Here, we summarize recent progress in the analysis of CRK evolution, molecular function, and role in plant development, abiotic stress responses, plant immunity, and symbiosis. The currently available information on CRKs and related proteins suggests that the CRKs are central regulators of plant signaling pathways. However, more research using classical methods and interdisciplinary approaches in various plant model species, as well as structural analyses, will not only enhance our understanding of the molecular function of CRKs, but also elucidate the contribution of other cellular components in CRK-mediated signaling pathways.
Stellar clustering and the kinematics of stars around Collinder 121 using Gaia DR3
Authors: Fleming Graham D , Kirk Jason M , Ward-Thompson Derek 
Published: June 2023

ABSTRACT
We study the region around Collinder 121 (Cr 121) using newly available 6D data from the Gaia DR3 catalogue. Situated in the third quadrant, near the Galactic plane, Collinder 121 lies in the region of Canis Major centred around (l, b) ≈(236°, −10°). Previous studies have suggested that the stellar associations in this region comprise an OB association (CMa OB2) lying at about 740 pc with a more distant open cluster (Cr 121) at approximately 1170 pc. Despite these studies, the precise nature of Collinder 121 remains uncertain. This study investigates the region bounded by the box (l, b) = (225°–245°, 0.00° to −20.00°) to a depth of 700 pc from 500 to 1200 pc which fully encompasses the region discussed in the literature. Using Gaia DR3 data, we do not find associations at the distances given in the literature. Instead, using the hdbscan machine learning algorithm, we find a major association of OB stars centred around 803 pc. Within this association we find four smaller subgroups that may be indicative of a larger association and which are located at a mean distance of 827 pc. Proper motion studies find coherence between these four subgroups and show a distinctive east-to-west increase in the size of the velocity vectors which supports contemporary studies that show similar trends in OB populations in Cygnus and within the Carina spiral Arm. Therefore, we hypothesize that Cr 121 and CMa OB2 are the same cluster, consistent with the 1977 study by Hoogerwerf.
Properties and observables of massive galaxies in self-interacting dark matter cosmologies
Authors: Mastromarino Claudio , Despali Giulia , Moscardini Lauro , Robertson Andrew , Meneghetti Massimo , Maturi Matteo 
Published: June 2023

ABSTRACT
We use hydrodynamic cosmological simulations to test the differences between cold and self-interacting dark matter models (CDM and SIDM) in the mass range of massive galaxies (1012 &lt; M200/M⊙ h−1 &lt; 1013.5). We consider two SIDM models: one with constant cross-section $\sigma /m_{\chi } = 1\, \mathrm{cm^2 \, g^{-1}}$ and one where the cross-section is velocity-dependent. Despite a weak trend in mass, we find that with the inclusion of baryons the differences between SIDM and CDM density profiles observed in the dark-matter-only case are almost erased. We also search for signatures of SIDM in the distribution of strong lensing Einstein radii and find that the distributions derived from CDM and SIDM hydro runs are both comparable to observational samples of strong lenses. We find that, looking at the total matter distribution, the interplay between self-interactions and baryons can greatly reduce the expected differences between CDM and SIDM models at this mass scale, making the discrimination between these DM models challenging. However, looking at the dark matter/baryonic fractions in the inner region of the haloes we show that the deviations of SIDM from CDM can still be found considering these components separately. These results highlight that one of the most promising paths to discriminate between CDM and SIDM is to focus on techniques able to distinguish between the dark matter and baryonic components in galaxies and clusters.
Prospects of additional contribution at optical-NIR band of EBL in the light of VHE spectra
Authors: Mankuzhiyil Nijil , Persic Massimo , Franceschini Alberto 
Published: June 2023

ABSTRACT
The extragalactic background light (EBL) that spans the ultraviolet-infrared (UV-IR) band originates from direct and dust-reprocessed starlight integrated over the history of the Universe. EBL measurements are very challenging due to foreground emission like the zodiacal light and interplanetary dust emission. Indeed, some optical/NIR (near infrared) direct measurements overpredict EBL models based on galaxy counts. On the other hand, there is some debate on possible additional components of the optical-NIR photon density, e.g. population-III stars, axion-photon decay, direct collapse of black holes, intrahalo light, etc. Owing to the absorption of very high energy (VHE) gamma-rays by interaction with EBL photons, we study the prospects of accommodating an additional population of EBL sources in the optical-NIR band on top of the standard galaxy-count–based component. To this aim we use 105 VHE spectra of 37 blazars with known redshifts, 0.03 &lt; z &lt; 0.94. We correct the observed spectra for absorption by our model EBL. By requiring the intrinsic spectra to be non-concave and with a VHE spectral index &gt;1.5, we estimate, at different wavelengths, upper limits to the additional low-energy photon fields that would contribute to the absorption of gamma-rays. Considering these limits, we suggest that there is room for photons from Pop III stars and axion-like particle annihilation. However, these additional hypothetical photon fields are bound to fall significantly below direct published EBL measurements by several instruments, and therefore, our limits are either in tension or even inconsistent with such measurements.
The imprint of galaxy mergers on satellite planes in a cosmological context
Authors: Kanehisa Kosuke Jamie , Pawlowski Marcel S , Müller Oliver 
Published: June 2023

ABSTRACT
Flattened and kinematically correlated planes of dwarf satellite galaxies have been observed in the Local Volume. The slinging out of satellites during host galaxy mergers has been suggested as a formation mechanism for these peculiar structures. We statistically examined the impact of major mergers on present-time satellite systems for the first time in a full cosmological context using the IllustrisTNG suite of hydrodynamic simulations. Mergers with mass ratios above 1/3 generally have a negligible or adverse impact on the phase-space correlation of observationally motivated satellites. Even high angular momentum mergers are inefficient at slinging satellites outward due to the extended nature of simulated satellite distributions. Furthermore, any potential merger imprint is partially washed out by post-merger accretion of satellites, while satellites bound to the merging haloes since the merger’s beginning are disrupted and stripped of mass – minimizing the merger’s influence on the present-time distribution of the most massive satellites after $2{\!-\!}5\, \mathrm{Gyr}$. Constraining our sample to satellites bound to their host throughout the full duration of their system’s last merger, we recover no particular improvement in their phase-space correlation. Instead, such participant satellites experience a contraction of their radial distribution during and after the merger, resulting in smaller absolute plane heights (but comparable axial ratios). Overall, major mergers do not appear to form correlated planes in a statistical sample. Mergers that efficiently transfer their angular momentum to satellite distributions can marginally enhance their phase-space correlation, but cannot form highly flattened and orbitally coherent configurations as observed in our local Universe.
Hidden cooling flows in clusters of galaxies – III. Accretion on to the central black hole
Authors: Fabian A C , Sanders J S , Ferland G J , McNamara B R , Pinto C , Walker S A 
Published: June 2023

ABSTRACT
Recently, we have uncovered hidden cooling flows (HCFs) in the X-ray spectra of the central brightest galaxies of 11 clusters, 1 group, and 2 elliptical galaxies. Here, we report such flows in a further 15 objects, consisting of 8 clusters, 3 groups, 3 ellipticals, and 1 Red Nugget. The mass cooling rates are about $1\hbox{$\hbox{$\rm \, {\rm M}_{\odot }$}{\rm \, yr}^{-1}\, $}$ in the ellipticals, 2 to $20\hbox{$\hbox{$\rm \, {\rm M}_{\odot }$}{\rm \, yr}^{-1}\, $}$ in the groups, and 20 to $100\hbox{$\hbox{$\rm \, {\rm M}_{\odot }$}{\rm \, yr}^{-1}\, $}$ in regular clusters. The Red Nugget, MRK 1216, has an HCF of $10\hbox{$\hbox{$\rm \, {\rm M}_{\odot }$}{\rm \, yr}^{-1}\, $}$. We review the fate of the cooled gas and investigate how some of it might accrete on to the central black hole. The gas is likely to be very cold and to have fragmented into low-mass stars and smaller objects before being swallowed whole, with little luminous output. If such a scenario is correct and operates at a few $\hbox{$\hbox{$\rm \, {\rm M}_{\odot }$}{\rm \, yr}^{-1}\, $}$ then such objects may host the fastest growing black holes in the low-redshift Universe. We briefly discuss the relevance of HCF to the growth of early galaxies and black holes.
Generation of high circular polarization of interstellar Lyman α radiation triggering biological homochirality
Authors: Fukushima Hajime , Yajima Hidenobu , Umemura Masayuki 
Published: June 2023

ABSTRACT
The homochirality of biological molecules on Earth is a long-standing mystery regarding the origin of life. Circularly polarized ultraviolet (UV) light could induce the enantiomeric excess of biological molecules in the interstellar medium, leading to the homochirality on Earth. By performing 3D radiation transfer simulations with multiple scattering processes in interstellar dusty slabs, we study the generation of the circular polarization (CP) of UV light at Lyα ($\lambda = 0.1216~{\rm \mu m}$) as well as at near-infrared (NIR, $\lambda = 2.14~{\rm \mu m}$) wavelengths. Our simulations show that the distributions of CP exhibit a symmetric quadrupole pattern, regardless of wavelength and viewing angle. The CP degree of scattered light from a dusty slab composed of aligned grains is ∼15 per cent for Lyα and ∼3 per cent at NIR wavelengths in the case of oblate grains with an Mathis-Rumpl-Nordsieck size distribution. We find that the CP degree of Lyα is well correlated with that in the NIR regardless of viewing angle, whilst being a factor of ∼5 higher. Thus, a high CP of Lyα is expected at sites where NIR CP is detected. We suggest that such circularly polarized Lyα may initiate the enantiomeric excess of biological molecules in space.
Probing the hot circumgalactic medium of external galaxies in X-ray absorption II: a luminous spiral galaxy at z ≈ 0.225
Authors: Mathur Smita , Das Sanskriti , Gupta Anjali , Krongold Yair 
Published: June 2023

ABSTRACT
The circumgalactic medium (CGM) is the most massive baryonic component of a spiral galaxy, shock heated to about 106 K for an $\rm L^{\star }$ galaxy. The CGM of the Milky Way has been well-characterized through X-ray absorption line spectroscopy. However, the paucity of bright background sources makes it challenging to probe the CGM of external galaxies. Previously, using broad O vi absorption as a signpost, we successfully detected the CGM of one galaxy in X-rays. Here we report on the detection of the O vii K α absorption line at the redshift of a spiral galaxy at z ≈ 0.225, using 1.2 Ms of Chandra observations. This is a robust detection, clearly showing the presence of the hot gas. The mass in the hot phase is at least an order of magnitude larger than that in the cooler phases detected in the UV. The presence of hot gas 116 h−1 kpc from the centre of this galaxy provides credence to the existence of the extended CGM of the Milky Way. There has been a report of the detection of O vii absorption from the warm-hot intergalactic medium in this sightline, using stacking analysis on older data set. We argue that the absorption line is from the CGM of the z ≈ 0.225 galaxy instead.
On the nature of the planet-powered transient event ZTF SLRN-2020
Authors: Soker Noam 
Published: June 2023

ABSTRACT
The Red Nova ZTF SLRN-2020 is the third transient event with properties that are compatible with the merger of a planet with a main-sequence (or close to) star on a dynamical time-scale. While the two first transient events occurred in young stellar objects, ZTF SLRN-2020 occurred in an old system. None the less, I show that the three star–planet intermediate luminosity optical transients (ILOTs, also termed Red Novae) occupy the same area in the energy–time diagram of ILOTs. Based on models for ILOTs that are power by stellar binary interaction, I suggest that the planet in ZTF SLRN-2020 launched jets at about its escape speed before it was engulfed by the star. Interestingly, the escape speed from the planet is similar to the orbital speed of the planet. This leads to an outflow with a very low terminal velocity, much below the escape velocity from the star, and in concentration around ≈45° to the equatorial plane. As well, the planet might have lost back some of the accreted mass just before engulfment, forming an accretion disc around the star. This disc might have launched jets during the main outburst of the event. The jets form a bipolar expanding nebula.
Analysis of Genome-Wide Mutational Dependence in Naturally Evolving Mycobacterium tuberculosis Populations
Authors: Green Anna G , Vargas Roger , Marin Maximillian G , Freschi Luca , Xie Jiaqi , Farhat Maha R 
Published: June 2023

Abstract
Pathogenic microorganisms are in a perpetual struggle for survival in changing host environments, where host pressures necessitate changes in pathogen virulence, antibiotic resistance, or transmissibility. The genetic basis of phenotypic adaptation by pathogens is difficult to study in vivo. In this work, we develop a phylogenetic method to detect genetic dependencies that promote pathogen adaptation using 31,428 in vivo sampled Mycobacterium tuberculosis genomes, a globally prevalent bacterial pathogen with increasing levels of antibiotic resistance. We find that dependencies between mutations are enriched in antigenic and antibiotic resistance functions and discover 23 mutations that potentiate the development of antibiotic resistance. Between 11% and 92% of resistant strains harbor a dependent mutation acquired after a resistance-conferring variant. We demonstrate the pervasiveness of genetic dependency in adaptation of naturally evolving populations and the utility of the proposed computational approach.
Independent Recruitment of Different Types of Phospholipases A2 to the Venoms of Caenophidian Snakes: The Rise of PLA2-IIE within Pseudoboini (Dipsadidae)
Authors: Bayona-Serrano Juan David , Grazziotin Felipe Gobi , Salazar-Valenzuela David , Valente Richard H , Nachtigall Pedro Gabriel , Colombini Monica , Moura-da-Silva Ana , Junqueira-de-Azevedo Inacio Loiola Meirelles 
Published: June 2023

AbstractSnake venoms harbor a wide and diverse array of enzymatic and nonenzymatic toxic components, allowing them to exert myriad effects on their prey. However, they appear to trend toward a few optimal compositional scaffolds, dominated by four major toxin classes: SVMPs, SVSPs, 3FTxs, and PLA2s. Nevertheless, the latter appears to be restricted to vipers and elapids, as it has never been reported as a major venom component in rear-fanged species. Here, by investigating the original transcriptomes from 19 species distributed in eight genera from the Pseudoboini tribe (Dipsadidae: Xenodontinae) and screening among seven additional tribes of Dipsadidae and three additional families of advanced snakes, we discovered that a novel type of venom PLA2, resembling a PLA2-IIE, has been recruited to the venom of some species of the Pseudoboini tribe, where it is a major component. Proteomic and functional analyses of these venoms further indicate that these PLA2s play a relevant role in the venoms from this tribe. Moreover, we reconstructed the phylogeny of PLA2s across different snake groups and show that different types of these toxins have been recruited in at least five independent events in caenophidian snakes. Additionally, we present the first compositional profiling of Pseudoboini venoms. Our results demonstrate how relevant phenotypic traits are convergently recruited by different means and from homologous and nonhomologous genes in phylogenetically and ecologically divergent snake groups, possibly optimizing venom composition to overcome diverse adaptative landscapes.