bluuebunny/crossref_metadata_2025_split huggingface dataset:
S8.5c MLST genotyping and phylogenetics of AD-hybrids
Authors: Cogliati Massimo , Chen Min , Xu Jianping , Hitchcock Megan , Chung June Kwon , Yang Dong-Hoon , Rickerts Volker , Ollivier Marie Desnos , Silva Joao Inacio , Meyer Wieland , Florek Magdalena , Nawrot Urszula , Escandon Patricia , Puime Andrés , Roger Frederic , Bertout Sébastien 
Published: September 2022

Abstract

S8.5 Genotyping of Cryptococcus neoformans and C. gattii, September 23, 2022, 3:00 PM - 4:30 PM

Objectives
In a previous study a set of new molecular-type specific primers were designed to apply the standard ISHAM consensus multi-locus sequence typing (MLST) scheme to Cryptococcus neoformans AD hybrids. In the present study, we report the preliminary results of the investigation by MLST of a large number of AD hybrids with the aim to identify the circulating genotypes, their phylogenesis, and population genetics.

Methods
A total of 50 AD-hybrid isolates from different parts of the world and from different sources were genotyped by MLST. Minimum spanning trees using GoeBurst algorithm were generated by comparing hybrid genotypes and by comparing separately either allele-A and allele-D portions of the hybrid genotypes to the haplotypes recorded in the MLST global database.

Results
Analysis identified 32 hybrid genotypes grouped in three distinct main clusters (CC12, CC21, and CC30) including 12 isolates each. Both CC12 and CC21 clusters included isolates from different countries and continents but the former grouped only isolates with mating type aADalpha whereas the latter those with mating type alphaADa. Cluster CC30 included only isolates from Ivory Coasts. Heterozygous allelic combinations in each of the seven MLST loci presented two or three combinations more frequent than the other ones. In some isolates, one or more alleles were not amplified after multiple attempts, and therefore, they were considered as lacking. A total of 22 MLST profiles were identified by analyzing separately the allele-A combinations of the hybrids. Comparison with all MLST profiles of VNI, VNII, and VNB included in the MLST global database showed that the allele-A portion of the hybrid genotypes was grouped in few VNI or VNB clusters. In none of the investigated hybrids, the allele-A portion originated from VNII genotypes. Similarly, when the MLST profile of allele-D portion of hybrids was compared to all VNIV genotypes present in the global MLST database, few clusters were identified but, in this case, mostly originated from genotypes not yet found among VNIV haplotypes.

Conclusions
These preliminary results suggest that the AD hybrids here investigated originated from the mating of A haploids very common in both clinical and environmental isolates and D haploids that are not circulating at present or are very rare. Therefore, it is likely that hybrids originated in the environment where VNIV genotypic diversity is higher and suitable AD combinations can occur. Sequencing of further AD hybrids is in progress to confirm these results.
S9.2d Directed evolution of voriconazole resistance in Aspergillus fumigatus identifies novel mutations responsible for triazole resistance
Authors: Handelman Mariana , Kandil Amar Abo , Shadkchan Yona , Osherov Nir 
Published: September 2022

Abstract

S9.2 Azole resistance in Aspergillus fumiagatus: how hot is your hotspot?, September 23, 2022, 4:45 PM - 6:15 PM
Aspergillus fumigatus is the leading invasive mold pathogens in humans. The first line of treatment for invasive A. fumigatus infections are the triazole antifungals that inhibit Erg11/Cyp51 lanosterol demethylase activity, blocking ergosterol biosynthesis.

In recent years, triazole resistance of A. fumigatus has been increasingly reported, both as a result of widespread agricultural use of fungicidal triazoles and long-term treatment in patients with chronic aspergillosis. To date, the most common triazole resistance mechanisms in A. fumigatus are alterations in the erg11A/cyp51A gene or promoter, followed by overexpression of efflux pumps and mutations in hmg1, encoding HMG-CoA reductase. To identify novel triazole resistance mechanisms, we passaged A. fumigatus wild type and cyp51A-null strains under increasing concentrations of voriconazole (0.25 μg/ml-20 μg/ml) to generate resistant strains. Resistant isolates were whole-genome sequenced and compared with untreated controls. We identified known cyp51A and cyp51B mutations, and novel mutations in HMG1 and in previously uncharacterized genes in the ergosterol biosynthesis pathway as well as several efflux pumps. We identified at which stage of evolution each of the mutations occurred as well as their contribution to the resistance phenotype by re-introduction, alone and in combination, into the susceptible parental strain. Our study identified novel genes conferring triazole resistance and helps outline the complex stepwise evolutionary paths by which A. fumigatus develops resistance.
S9.4a Ocular infections by melanized fungi Curvularia lunata and Lasiodiplodia theobromae: Antifungal susceptibility and clinical outcome
Authors: Mitra Sanchita , Garg Prashant , Murthy Somasheila , Dave Vivek Pravin 
Published: September 2022

Abstract

S9.4 Free oral presentations (late breaking), September 23, 2022, 4:45 PM - 6:15 PM

Purpose
To report antifungal susceptibility and clinical correlations in melanized fungal isolates of Curvularia lunata and Lasiodiplodia theobromae from ocular infections.

Methods
Antifungal susceptibility testing was performed by broth microdilution testing, following Clinical and Laboratory Standard Institute guidelines, of 17 C. lunata and 13 L. theobromae isolates from monomicrobial infections of microbial keratitis or fungal endophthalmitis patients. Isolates resistant to ≥2 classes of antifungals were considered as multidrug-resistant (MDR). The panel of antifungals tested were amphotericin B, natamycin, voriconazole, ketoconazole, fluconazole, itraconazole, posaconazole, and caspofungin.

Results
Voriconazole showed the highest susceptibility (83.3% isolates) followed by natamycin (80%), fluconazole (80%), itraconazole (76.7%), ketoconazole (70%), posaconazole, and caspofungin (66.7% each) and lastly amphotericin B (63.3%). For treatment, all patients received topical natamycin, and few received additional oral ketoconazole or intraocular voriconazole. MDR isolates led to the poorer clinical outcomes (P=.015) in patients. But natamycin resistance alone did not show unfavorable outcomes (P=.28), though this was the most frequent drug used topically in fungal ocular infections.

Conclusion
Melanized fungi causing ocular infections have varying susceptibility to different antifungal agents. Most effective drug as seen in vitro in our study, was voriconazole. Significant resistance to amphotericin B, which is the most common antifungal used in intravitreal injections, was noted. MDR isolates overall, had poorer clinical outcomes.
S9.4c Diverse environmental inputs mediate changes in β-glucan exposure at the Candida albicans cell surface thereby influencing tissue colonisation during systemic infection
Authors: Pradhan Arnab , Ma Qinxi , Hickey Emer , Avelar Gabriela , Larcombe Daniel , Bain Judith , Childers Delma , Dambuza Ivy , Leaves Ian , de Assis Leandro Jose , Netea Mihai , Brown Gordon , Erwig Lars , Gow Neil A. R. , Brown Alistair J. P. 
Published: September 2022

Abstract

S9.4 Free oral presentations (late breaking), September 23, 2022, 4:45 PM - 6:15 PM

Candida albicans adaptation to host niches affects the exposure of key pathogen-associated molecular patterns (PAMPs) on its cell surface and, consequently, the detection of C. albicans cells by the immune system. Focusing on β-(1,3)-glucan, we screened for host inputs that influence the exposure of this immune-stimulatory PAMP on the C. albicans cell surface. We used a combination of fluorescent microscopy, flow cytometry, and cytokine assays, and then analyzed certain conditions in more detail using transmission electron microscopy and time-lapse video microscopy of C. albicans-phagocyte interactions. We found that some nutrients, micronutrient limitation, stresses, and antifungal drugs trigger β-glucan masking, whereas other inputs, such as nitrogen sources and quorum sensing molecules, exert limited effects on β-glucan exposure. In particular, host- or bacterial-derived L-lactate, hypoxia, or iron limitation induce β-glucan masking, and this leads to attenuation of phagocytic responses [Nature Micro 2, 16 238; mBio 9, e01318-18; Nature Comms 10, 5315]. Lactate signals through Gpr1 to activate Crz1 in a calcineurin-independent manner, whereas hypoxia signals via mitochondrial ROS, and iron limitation signals through Ftr1 and Sef1. β-glucan masking also depends upon downstream signaling via the cAMP-PKA pathway. We conclude that C. albicans has evolved to exploit a range of specific host-derived signals to modulate the exposure of a major PAMP at its cell surface in an attempt to evade phagocytic uptake. Using barcode-sequencing in direct competition assays in vivo, we showed that preadaptation to specific β-glucan masking signals affects the ability of this fungus to colonize particular tissues during systemic infection in a murine model. This reinforces the view that β-glucan masking promotes C. albicans infection.
S9.4d Main reservoirs of Trichophyton mentagrophytes Type V in Iran
Authors: Nikkholgh Sivash , Pchelin Ivan , Mahmoudabadi Ali Zarei , Shabanzadeh-Bardar Mahbubeh , Gharaghani Maral , Sharifzadeh Aghil , Mohammadi Rasoul , Noripour-Sisakht Sadegh , Katiraee Farzad , Rezaei-matehkolaei Ali 
Published: September 2022

Abstract

S9.4 Skin mycoses and microbiome, September 23, 2022, 4:45 PM - 6:15 PM

Objectives
Dermatophytosis in livestock receives attention because of its contagiousness, high treatment costs, and lack of control programs. Compared with cattle, mycological aspects of dermatophytosis in sheep and goats have been studied less frequently. Dermatophytosis in these animals (small ruminants) may lead to serious economic losses due to the negative impact on the growth of involved animals, as well as their milk and meat production. Recent studies showed that the old Trichophyton verrucosum var. verrucosum (which is known to have some African and Asiatic sheep as its reservoirs) is currently synonymous with T. mentagrophytes Type V, the most common genotype of T. mentagrophytes isolated from Iranian patients. But the animal reservoirs of this genotype are not well known in Iran and in this investigation, we aimed to determine them.

Methods
A total of 678 skin and hair samples from animals including sheep (n = 190), cows (n = 79), goats (n = 9), camels (n = 20), stray and domestic cats (n = 195), stray and pet dogs (n = 146), horses (n = 27), foxes (n = 2), hedgehogs (n = 2), and poultries (n = 8) were subjected to direct microscopy and culture on Mycobiotic agar. Most animals had skin lesions, though some stray cats and dogs were asymptomatic. Molecular identification of dermatophyte cultures was done by ITS-rDNA RFLP. To confirm the RFLP identification, 59 representative isolates from all studied animal species were subjected to ITS-rDNA sequencing. The likelihood for isolation of a specific species or genotype with regard to the type of infected animal was determined using the chi-square test.

Results
We obtained 334 dermatophyte cultures. ITS-RFLP and ITS region sequencing revealed the species T. verrucosum (n = 62; all from cows), T. mentagrophytes Type V (sheep = 95; goat = 6; cat = 1; horse = 2), T. mentagrophytes Type II* (cat = 2), T. mentagrophytes Type VII (dog = 2), Microsporum canis (cats, n = 94; dogs, n = 55; cow, n = 1; horse, n = 1), T. quinckeanum (fox, n = 1), Nannizzia gypsea (cats, n = 5; dogs, n = 4; cow, n = 1; horse, n = 1), and N. fulva (cow, n = 1). No dermatophytes were isolated from camels, hedgehogs, and poultries. There was a statistically significant difference in the isolation rate of T. mentagrophytes Type V between sampled animals meaning that with a high probability it is isolated from sheep and goats.

Conclusion
Purposive sampling from suspected animals confirmed that sheep are the main animal reservoir of T. mentagrophytes Type V, at least in Iran. Further international sequence-based investigations can test our conclusion.
Constraints on the extragalactic magnetic field strength from blazar spectra based on 145 months of Fermi-LAT observations
Authors: Podlesnyi E I , Dzhatdoev T A , Galkin V I 
Published: September 2022

ABSTRACT
Properties of the extragalactic magnetic field (EGMF) outside of clusters and filaments of the large-scale structure are essentially unknown. The EGMF could be probed with γ-ray observations of distant (redshift z &gt; 0.1) blazars. TeV γ-rays from these sources are strongly absorbed on extragalactic background light photons; secondary electrons and positrons produce cascade γ-rays with the observable flux dependent on EGMF parameters. We put constraints on the EGMF strength using 145 months of Fermi-LAT observations of the blazars 1ES 1218+304, 1ES 1101−232, and 1ES 0347−121, and imaging atmospheric Cherenkov telescope observations of the same sources. We perform a series of full direct Monte Carlo simulations of intergalactic electromagnetic cascades with the elmag 3.01 code and construct a model of the observable spectra inside the point spread functions of the observing instruments for a range of EGMF strengths. We compare the observed spectra with the models for various values of the EGMF strength B and calculate the exclusion statistical significance for every value of B. We find that the values of the EGMF strength B ≤ 10−17 G are excluded at a high level of the statistical significance Z &gt; 4σ for all the four options of the intrinsic spectral shape considered (power law, power law with exponential cutoff, log-parabola, and log-parabola with exponential cutoff). The value of B = 10−16 G is not excluded; it is still a viable option of the EGMF strength. These results were obtained for the case of steady sources.
The merger and assembly histories of Milky Way- and M31-like galaxies with TNG50: disc survival through mergers
Authors: Sotillo-Ramos Diego , Pillepich Annalisa , Donnari Martina , Nelson Dylan , Eisert Lukas , Rodriguez-Gomez Vicente , Joshi Gandhali , Vogelsberger Mark , Hernquist Lars 
Published: September 2022

ABSTRACT
We analyse the merger and assembly histories of Milky Way (MW) and Andromeda (M31)-like galaxies to quantify how, and how often, disc galaxies of this mass can survive recent major mergers (stellar mass ratio ≥ 1:4). For this, we use the cosmological magneto-hydrodynamical simulation TNG50 and identify 198 analog galaxies, selected based on their z = 0 stellar mass ($10^{10.5-11.2}\, \rm {M}_{\odot }$), discy stellar morphology and local environment. First, major mergers are common: 85 per cent (168) of MW/M31-like galaxies in TNG50 have undergone at least one major merger across their lifetime. In fact, 31 galaxies (16 per cent) have undergone a recent major merger, i.e. in the last 5 Gyr. The gas available during the merger suffices to either induce starbursts at pericentric passages or to sustain prolonged star formation after coalescence: in roughly half of the cases, the pre-existing stellar disc is destroyed because of the merger but reforms thanks to star formation. Moreover, higher merger mass ratios are more likely to destroy the stellar discs. In comparison to those with more ancient massive mergers, MW/M31-like galaxies with recent major mergers have, on average, somewhat thicker stellar discs, more massive and somewhat shallower stellar haloes, larger stellar ex situ mass fractions, but similarly massive kinematically defined bulges. All this is qualitatively consistent with the different observed properties of the Galaxy and Andromeda and with the constraints on their most recent major mergers, 8–11 and 2 Gyr ago, respectively. According to contemporary cosmological simulations, a recent quiet merger history is not a pre-requisite for obtaining a relatively thin stellar disc at z = 0.
Properties beyond mass for unresolved haloes across redshift and cosmology using correlations with local halo environment
Authors: Ramakrishnan Sujatha , Velmani Premvijay 
Published: September 2022

ABSTRACT
The structural and dynamic properties of the dark matter haloes, though an important ingredient in understanding large-scale structure formation, require more conservative particle resolution than those required by halo mass alone in a simulation. This reduces the parameter space of the simulations, more severely for high redshift and large-volume mocks, which are required by the next-generation large-sky surveys. Here, we incorporate redshift and cosmology dependence into an algorithm that assigns accurate halo properties such as concentration, spin, velocity, and spatial distribution to the subresolution haloes in a simulation. By focusing on getting the right correlations with halo mass and local tidal anisotropy α measured at 4 × halo radius, our method will also recover the correlations of these small-scale structural properties with the large-scale environment, i.e. the halo assembly bias at all scales greater than 5 × halo radius. We find that the distribution of halo properties is universal with redshift and cosmology. By applying the algorithm to a large-volume simulation $(600\, h^{-1}\, {\rm Mpc})^3$, we can access the 30–500 particle haloes, thus gaining an order of magnitude in halo mass and two to three orders of magnitude in number density at z = 2–4. This technique reduces the cost of mocks required for the estimation of covariance matrices, weak lensing studies, or any large-scale clustering analysis with less massive haloes.
The SAMI–Fornax Dwarfs Survey – II. The Stellar Mass Fundamental Plane and the dark matter fraction of dwarf galaxies
Authors: Eftekhari F Sara , Peletier Reynier F , Scott Nicholas , Mieske Steffen , Bland-Hawthorn Joss , Bryant Julia J , Cantiello Michele , Croom Scott M , Drinkwater Michael J , Falcón-Barroso Jésus , Hilker Michael , Iodice Enrichetta , Napolitano Nicola R , Spavone Marilena , Valentijn Edwin A , van de Ven Glenn , Venhola Aku 
Published: September 2022

ABSTRACT
We explore the kinematic scaling relations of 38 dwarf galaxies in the Fornax Cluster using observations from the SAMI integral field spectrograph. We focus on the Fundamental Plane (FP), defined by the physical properties of the objects (scale length, surface brightness, and velocity dispersion) and the Stellar Mass (Fundamental) Plane, where surface brightness is replaced by stellar mass, and investigate their dynamical-to-stellar-mass ratio. We confirm earlier results that the Fornax dEs are significantly offset above the FP defined by massive, hot stellar systems. For the Stellar Mass (Fundamental) Plane, which shows much lower scatter, we find that young and old dwarf galaxies lie at about the same distance from the plane, all with comparable scatter. We introduce the perpendicular deviation of dwarf galaxies from the Stellar Mass Plane defined by giant early-types as a robust estimate of their DM fraction, and find that the faintest dwarfs are systematically offset above the plane, implying that they have a higher dark matter fraction. This result is confirmed when estimating the dynamical mass of our dEs using a virial mass estimator, tracing the onset of dark matter domination in low mass stellar systems. We find that the position of our galaxies on the Stellar Mass FP agrees with the galaxies in the Local Group. This seems to imply that the processes determining the position of dwarf galaxies on the FP depend on the environment in the same way, whether the galaxy is situated in the Local Group or in the Fornax Cluster.
FastChem 2
: an improved computer program to determine the gas-phase chemical equilibrium composition for arbitrary element distributions
Authors: Stock Joachim W , Kitzmann Daniel , Patzer A Beate C 
Published: September 2022

ABSTRACT
The computation of complex neutral/ionized chemical equilibrium compositions is invaluable to obtain scientific insights of, for example, the atmospheres of extrasolar planets and cool stars. We present FastChem 2 , a new version of the established semi-analytical thermochemical equilibrium code FastChem. Whereas the original version is limited to atmospheres containing a significant amount of hydrogen, FastChem 2 is also applicable to chemical mixtures dominated by any other species, such as CO2 or N2. The new c++ code and an optional python module are publicly available under the GPLv3 license. The program is backward compatible so that the previous version can be easily substituted. We updated the thermochemical data base by adding HNC, FeH, TiH, Ca−, and some organic molecules. In total 523 species are now in the thermochemical data base including 28 chemical elements. The user can reduce the total number of species to, for example, increase the computation performance or can add further species if the thermochemical data are available. The program is validated against its previous version and extensively tested over an extended pressure–temperature grid with pressures ranging from $10^{-13}$ up to $10^3\, \mathrm{bar}$ and temperatures between $100$ and $6000\, \mathrm{K}$. FastChem 2 is successfully applied to a number of different scenarios including nitrogen-, carbon-, and oxygen-dominated atmospheres and test cases without hydrogen and helium. Averaged over the extended pressure–temperature grid FastChem 2 is up to 50 times faster than the previous version and is also applicable to situations not treatable with version 1.
Do periods of decayless kink oscillations of solar coronal loops depend on noise?
Authors: Nakariakov Valery M , Kolotkov Dmitrii Y , Zhong Sihui 
Published: September 2022

ABSTRACT
Decayless kink oscillations of solar coronal loops are studied in terms of a low-dimensional model based on a randomly driven Rayleigh oscillator with coefficients experiencing random fluctuations. The model considers kink oscillations as natural modes of coronal loops, decaying by linear resonant absorption. The damping is counteracted by random motions of the loop footpoints and the interaction of the loop with external quasi-steady flows with random fluctuations. In other words, the model combines the self-oscillatory and randomly driven mechanisms for the decayless behaviour. The random signals are taken to be of the stationary red noise nature. In the noiseless case, the model has an asymptotically stationary oscillatory solution, i.e. a kink self-oscillation. It is established that the kink oscillation period is practically independent of noise. This finding justifies the seismological estimations of the kink and Alfvén speeds, and the magnetic field in an oscillating loop by kink oscillations, based on the observed oscillation period. The oscillatory patterns are found to be almost harmonic. Noisy fluctuations of external flows modulate the amplitude of the almost monochromatic oscillatory pattern symmetrically, while random motions of the loop footpoints cause antisymmetric amplitude modulation. Such modulations are also consistent with the observed behaviour.