bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplex real-time PCR for skin fungal infections: The diagnostic reliability in a one-year non-interventional study
Authors: Trovato Laura , Calvo Maddalena , Domina Maria , De Pasquale Rocco , Scalia Guido , Oliveri Salvatore 
Published: September 2023

Abstract
The skin fungal infection diagnostic workflow currently includes microscopic and culture-based methods as the gold standard. Recent published data described the possible limitations of these conventional techniques documenting the possibility of reducing response time intervals. The present study reports an evaluation of the DermaGenius® (DG) multiplex kit (PathoNostics) for rapid C. albicans and dermatophytes identification directly from skin samples. The investigations involved 90 specimens that underwent DNA extraction and amplification simultaneously to microscopic and culture methods. According to current guidelines, we defined a dermatophytic skin infection as the simultaneous presence of clinical evidence of skin lesions and positive results for dermatophyte elements from microscopy and/or cultures. The collected data remarked on the advantages of the molecular assay, especially in terms of sensitivity and rapidity. A statistical evaluation analysed a comparison between conventional and innovative diagnostic methods. The sensitivity, specificity, positive predictive value, and negative predictive value of DG-PCR in the cutaneous dermatophytosis were, respectively, 94.7%, 78.8%, 88.5%, and 89.6%. Based on our experience, the molecular technique could represent a diagnostic confirmation in the case of previous antifungal treatment, little biological material available, or urgent clinical conditions.
Antifungal susceptibility profiles of Cryptococcus neoformans strains clinically isolated from non-HIV-infected patients in Nagasaki, Japan
Authors: Ashizawa Nobuyuki , Takazono Takahiro , Ito Yuya , Nakada Nana , Hirayama Tatsuro , Takeda Kazuaki , Ide Shotaro , Iwanaga Naoki , Tashiro Masato , Hosogaya Naoki , Yanagihara Katsunori , Mukae Hiroshi , Izumikawa Koichi 
Published: September 2023

Abstract
Data on antifungal susceptibility of Cryptococcus neoformans are limited in Japan. A total of 89 C. neoformans strains isolated from 83 non-human immunodeficiency virus-infected patients with cryptococcosis between 1997 and 2021 in Nagasaki, Japan, were investigated. Using the reference method M27-Ed4 by the Clinical and Laboratory Standards Institute, the minimum inhibitory concentration for 90% of isolates of fluconazole, itraconazole, voriconazole, amphotericin B, and flucytosine were 4, 0.125, 0.06, 0.5, and 4 µg/ml, respectively, which were below the reported epidemiological cutoff values, without any detectable non-wild-type strains. Our findings imply no increasing trend of antifungal-resistant C. neoformans in Nagasaki, Japan.
A sub-pc BBH system in SDSS J1609+1756 through optical QPOs in ZTF light curves
Authors: Zhang XueGuang 
Published: September 2023

ABSTRACT
Optical quasi-periodic oscillations (QPOs) are the most preferred signs of sub-pc binary black hole (BBH) systems in active galactic nucleus (AGN). In this manuscript, robust optical QPOs are reported in quasar SDSS J1609+1756 at z = 0.347. In order to detect reliable optical QPOs, four different methods are applied to analyse the 4.45 yr-long Zwicky Transient Facility (ZTF) g/r/i-band light curves of SDSS J1609+1756, direct fitting results by sine function, generalized Lomb–Scargle periodogram, autocross correlation function, and weighted wavelet Z-transform method. The four different methods can lead to well determined reliable optical QPOs with periodicities ∼340 d with confidence levels higher than 5σ, to guarantee the robustness of the optical QPOs in SDSS J1609+1756. Meanwhile, based on simulated light curves through continuous autoregressive process to trace intrinsic AGN activities, confidence level higher than 3σ can be confirmed that the optical QPOs are not misdetected in intrinsic AGN activities, reconfirming the robust optical QPOs and strongly indicating a central sub-pc BBH system in SDSS J1609+1756. Furthermore, based on apparent redshifted shoulders in broad Balmer emission lines in SDSS J1609+1756, space separation of the expected central BBH system can be estimated to be smaller than 107 ± 60 light-days, accepted upper limit of total BH mass ∼(1.03 ± 0.22) × 108 M⊙. Therefore, to detect and report BBH system expected optical QPOs with periodicities around 1 yr is efficiently practicable through ZTF light curves, and combining with peculiar broad-line emission features, further clues should be given on space separations of BBH systems in broad-line AGN in the near future.
Non-LTE abundance analysis of A-B stars with low rotational velocities – II. Do A-B stars with normal abundances exist?
Authors: Romanovskaya A M , Ryabchikova T A , Pakhomov Yu V , Korotin S A , Sitnova T M 
Published: September 2023

ABSTRACT
We present chemical composition and fundamental parameters (the effective temperature, surface gravity, and radius) for four sharp-lined A-type stars γ Gem (HD 41705), o Peg (HD 214994), θ Vir (HD 114330), and ν Cap (HD 193432). Our analysis is based on a self-consistent model fitting of high-resolution spectra and spectrophotometric observations over a wide wavelength range. We refined the fundamental parameters of the stars with the sme (Spectroscopy Made Easy) package and verified their accuracy by comparing with the spectral energy distribution and hydrogen line profiles. We found Teff/log g = 9190 ± 130 K/3.56 ± 0.08, 9600 ± 50 K/3.81 ± 0.04, 9600 ± 140 K/3.61 ± 0.12, and 10200 ± 220 K/3.88 ± 0.08 for γ Gem, o Peg, θ Vir, and ν Cap, respectively. Our detailed abundance analysis employs a hybrid technique for spectrum synthesis based on classical model atmospheres calculated in local thermodynamic equilibrium (LTE) assumption together with the non-LTE (NLTE) line formation for 18 of 26 investigated species. Comparison of the abundance patterns observed in A stars of different types (normal A, Am, and Ap) with similar fundamental parameters reveals significant abundance diversity that cannot be explained by the current mechanisms of abundance peculiarity formation in stellar atmospheres. We found a rise of the heavy element (Zn, Sr, Y, Zr, and Ba) abundance excess up to +1 dex with Teff increasing from 7200 to 10 000 K, with a further decrease down to solar value at Teff = 13 000 K, indicating that stars with solar element abundances can be found among late B-type stars.
An HST survey of 33 T8 to Y1 brown dwarfs: NIR photometry and multiplicity of the coldest isolated objects
Authors: Fontanive Clémence , Bedin Luigi R , De Furio Matthew , Biller Beth , Anderson Jay , Bonavita Mariangela , Allers Katelyn , Pantoja Blake 
Published: September 2023

ABSTRACT
We present results from a Hubble Space Telescope imaging search for low-mass binary and planetary companions to 33 nearby brown dwarfs with spectral types of T8–Y1. Our survey provides new photometric information for these faint systems, from which we obtained model-derived luminosities, masses, and temperatures. Despite achieving a deep sensitivity to faint companions beyond 0.2–0.5 arcsec, down to mass ratios of 0.4–0.7 outside ∼5 au, we find no companions to our substellar primaries. From our derived survey completeness, we place an upper limit of $f \lt 4.9~{{\ \rm per\ cent}}$ at the 1σ level (&lt;13.0 per cent at the 2σ level) on the binary frequency of these objects over the separation range 1–1000 au and for mass ratios above q = 0.4. Our results confirm that companions are extremely rare around the lowest mass and coldest isolated brown dwarfs, continuing the marginal trend of decreasing binary fraction with primary mass observed throughout the stellar and substellar regimes. These findings support the idea that if a significant population of binaries exist around such low-mass objects, it should lie primarily below 2–3 au separations, with a true peak possibly located at even tighter orbital separations for Y dwarfs.
The common fundamental plane of X-ray emissions from pulsars and magnetars in quiescence
Authors: Chu Che-Yen , Chang Hsiang-Kuang 
Published: September 2023

ABSTRACT
Magnetars are a unique class of neutron stars characterized by their incredibly strong magnetic fields. Unlike normal pulsars whose X-ray emission was driven by rotational energy loss, magnetars exhibit distinct X-ray emissions thought to be driven by their strong magnetic fields. Here, we present the results of magnetar X-ray spectra analysis in their quiescent state. In the sample studied in this paper, spectra of 17 magnetars can be fitted well with a model consisting of a power-law and a blackbody component. We found that the luminosity of the power-law component can be described by a function of blackbody temperature and emission-region radius. The same relation was seen in pulsars whose X-ray emission mechanism is thought to be different. The fact that these magnetars and pulsars share a common fundamental plane in the space spanned by non-thermal X-ray luminosity, surface temperature, and the radius of the thermally emitting region presents both challenges and hints to theoretical models for a complete comprehension of the magnetospheric emissions from these two classes of neutron stars.
Unveiling the accretion scenario of BH-ULXs using XMM–Newton observations
Authors: Majumder Seshadri , Das Santabrata , Agrawal Vivek K , Nandi Anuj 
Published: September 2023

ABSTRACT
We present a comprehensive spectrotemporal analysis of five ultraluminous X-ray sources (ULXs) with central object likely being a black hole, using archival XMM–Newton observations. These sources, namely NGC1313 X−1, NGC5408 X-1, NGC6946 X−1, M82 X−1, and IC342 X−1, reveal short-term variability with fractional variance of 1.42$-27.28~{{\ \rm per\ cent}}\, $ and exhibit Quasi-periodic Oscillations (QPOs) with frequency νQPO ∼ 8−667 mHz. Long-term evolution of ULXs energy spectra (0.3–10 keV; excluding M82 X−1) are described satisfactorily with a model combination that comprises a thermal Comptonization component (nthComp, yielding Γnth ∼ 1.48–2.65, kTe ∼ 1.62–3.76 keV, τ ∼ 8–20, y-par∼1.16–6.24) along with a standard disc component (diskbb, kTin ∼ 0.16–0.54 keV). We find that these ULXs generally demonstrate anticorrelation between disc luminosity and inner disc temperature as $L_{\rm disc} \propto T_{\rm in}^\alpha$, where α = −3.58 ± 0.04 for NGC1313 X−1 and IC342 X−1, α = −8.93 ± 0.11 for NGC6946 X−1, and α = −10.31 ± 0.10 for NGC5408 X−1. We also obtain a linear correlation between bolometric luminosity Lbol and Γnth that indicates spectral softening of the sources when Lbol increases. We observe that in presence of QPO, Comptonized seed photon fraction varies in between $\sim 5-20~{{\ \rm per\ cent}}\, $, while the Comptonized flux contribution (50$-90~{{\ \rm per\ cent}}\, $) dominates over disc flux. Utilizing νQPO and Lbol, we constrain ULXs mass by varying their spin (ak) and accretion rate ($\dot{m}$). We find that NGC6946 X−1 and NGC5408 X−1 seem to accrete at sub-Eddington accretion rate provided their central sources are rapidly rotating, whereas IC342 X−1 and NGC1313 X−1 can accrete in sub/super-Eddington limit irrespective to their spin values.
Dark matter induced stellar oscillations
Authors: Sakstein Jeremy , Saltas Ippocratis D 
Published: September 2023

ABSTRACT
It has been hypothesized that dark matter is comprised of ultra-light bosons whose collective phenomena can be described as a scalar field undergoing coherent oscillations. Examples include axion and fuzzy dark matter models. In this ultra-light dark matter (ULDM) scenario, the harmonic variation in the field’s energy–momentum tensor sources an oscillating component of the gravitational potential that we show can resonantly excite stellar oscillations. A mathematical framework for predicting the amplitude of these oscillations is developed, which reveals that ULDM predominantly excites p-modes of degree l = 1. An investigation of resonantly excited solar oscillations is presented, from which we conclude that dark matter induced oscillations of the Sun are likely undetectable. We discuss prospects for constraining ULDM using other stellar objects.
Synchrotron X-rays reveal the modes of Fe binding and trace metal storage in the brown algae Laminaria digitata and Ectocarpus siliculosus
Authors: Mijovilovich Ana , Cloetens Peter , Lanzirotti Antonio , Newville Matt , Wellenreuther Gerd , Kumari Puja , Katsaros Christos , Carrano Carl J , Küpper Hendrik , Küpper Frithjof C 
Published: September 2023

Abstract
Iron is accumulated symplastically in kelp in a non-ferritin core that seems to be a general feature of brown algae. Microprobe studies show that Fe binding depends on tissue type.
The sea is generally an iron-poor environment and brown algae were recognized in recent years for having a unique, ferritin-free iron storage system. Kelp (Laminaria digitata) and the filamentous brown alga Ectocarpus siliculosus were investigated using X-ray microprobe imaging and nanoprobe X-ray fluorescence tomography to explore the localization of iron, arsenic, strontium, and zinc, and micro-X-ray absorption near-edge structure (μXANES) to study Fe binding. Fe distribution in frozen hydrated environmental samples of both algae shows higher accumulation in the cortex with symplastic subcellular localization. This should be seen in the context of recent ultrastructural insight by cryofixation–freeze substitution that found a new type of cisternae that may have a storage function but differs from the apoplastic Fe accumulation found by conventional chemical fixation. Zn distribution co-localizes with Fe in E. siliculosus, whereas it is chiefly located in the L. digitata medulla, which is similar to As and Sr. Both As and Sr are mostly found at the cell wall of both algae. XANES spectra indicate that Fe in L. digitata is stored in a mineral non-ferritin core, due to the lack of ferritin-encoding genes. We show that the L. digitata cortex contains mostly a ferritin-like mineral, while the meristoderm may include an additional component.
High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase
Authors: Jensen Drake , Ruiz Manzano Ana , Rector Maxwell , Tomko Eric J , Record M Thomas , Galburt Eric A 
Published: September 2023

Abstract
The first step in gene expression is the transcription of DNA sequences into RNA. Regulation at the level of transcription leads to changes in steady-state concentrations of RNA transcripts, affecting the flux of downstream functions and ultimately cellular phenotypes. Changes in transcript levels are routinely followed in cellular contexts via genome-wide sequencing techniques. However, in vitro mechanistic studies of transcription have lagged with respect to throughput. Here, we describe the use of a real-time, fluorescent-aptamer-based method to quantitate steady-state transcription rates of the Mycobacterium tuberculosis RNA polymerase. We present clear controls to show that the assay specifically reports on promoter-dependent, full-length RNA transcription rates that are in good agreement with the kinetics determined by gel-resolved, α-32P NTP incorporation experiments. We illustrate how the time-dependent changes in fluorescence can be used to measure regulatory effects of nucleotide concentrations and identity, RNAP and DNA concentrations, transcription factors, and antibiotics. Our data showcase the ability to easily perform hundreds of parallel steady-state measurements across varying conditions with high precision and reproducibility to facilitate the study of the molecular mechanisms of bacterial transcription.
Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery
Authors: Liu Ze , Wang Justin , Shi Yi , Yee Brian A , Terrey Markus , Zhang Qian , Lee Jenq-Chang , Lin Kuo-I , Wang Andrew H-J , Ackerman Susan L , Yeo Gene W , Cui Haissi , Yang Xiang-Lei 
Published: September 2023

Abstract
Translational readthrough of UGA stop codons by selenocysteine-specific tRNA (tRNASec) enables the synthesis of selenoproteins. Seryl-tRNA synthetase (SerRS) charges tRNASec with serine, which is modified into selenocysteine and delivered to the ribosome by a designated elongation factor (eEFSec in eukaryotes). Here we found that components of the human selenocysteine incorporation machinery (SerRS, tRNASec, and eEFSec) also increased translational readthrough of non-selenocysteine genes, including VEGFA, to create C-terminally extended isoforms. SerRS recognizes target mRNAs through a stem-loop structure that resembles the variable loop of its cognate tRNAs. This function of SerRS depends on both its enzymatic activity and a vertebrate-specific domain. Through eCLIP-seq, we identified additional SerRS-interacting mRNAs as potential readthrough genes. Moreover, SerRS overexpression was sufficient to reverse premature termination caused by a pathogenic nonsense mutation. Our findings expand the repertoire of selenoprotein biosynthesis machinery and suggest an avenue for therapeutic targeting of nonsense mutations using endogenous factors.
Short-range end resection requires ATAD5-mediated PCNA unloading for faithful homologous recombination
Authors: Park Su Hyung , Kim Namwoo , Kang Nalae , Ryu Eunjin , Lee Eun A , Ra Jae Sun , Gartner Anton , Kang Sukhyun , Myung Kyungjae , Lee Kyoo-young 
Published: September 2023

Abstract
Homologous recombination (HR) requires bidirectional end resection initiated by a nick formed close to a DNA double-strand break (DSB), dysregulation favoring error-prone DNA end-joining pathways. Here we investigate the role of the ATAD5, a PCNA unloading protein, in short-range end resection, long-range resection not being affected by ATAD5 deficiency. Rapid PCNA loading onto DNA at DSB sites depends on the RFC PCNA loader complex and MRE11-RAD50-NBS1 nuclease complexes bound to CtIP. Based on our cytological analyses and on an in vitro system for short-range end resection, we propose that PCNA unloading by ATAD5 is required for the completion of short-range resection. Hampering PCNA unloading also leads to failure to remove the KU70/80 complex from the termini of DSBs hindering DNA repair synthesis and the completion of HR. In line with this model, ATAD5-depleted cells are defective for HR, show increased sensitivity to camptothecin, a drug forming protein-DNA adducts, and an augmented dependency on end-joining pathways. Our study highlights the importance of PCNA regulation at DSB for proper end resection and HR.
Evaluation and management of enuresis in the general paediatric setting
Authors: Harris James , Lipson Alisa , Dos Santos Joana 
Published: September 2023

Abstract
Assessing enuresis involves distinguishing monosymptomatic from non-monosymptomatic for this common paediatric problem, and identifying concomitant comorbidities. Addressing co-occurring factors concurrently ensures the best opportunity for a satisfactory outcome. Treatment begins with patient and family education on the natural history of enuresis and practical behavioural guidance. Evidence to support particular interventions is limited, and children and families should be involved when choosing appropriate therapy. Enuresis alarms and desmopressin are treatment options when more active intervention is desired. Clinical refinements and combined treatment modalities are emerging.
1 Youth Experiencing Homelessness Presenting to an Urban Paediatric Emergency Department: A Descriptive Study
Authors: Lachance-Soulard Amelie , Harrison Megan , Reid Sarah 
Published: September 2023

Abstract

Background
Youth experiencing homelessness (YEH) have high rates of both mental and physical health concerns. This population faces multiple barriers in accessing care, resulting in unaddressed needs and reliance on Emergency Departments (ED). In Canada, the use of the paediatric ED by YEH has not been well described, and there is no data exploring the effects of the COVID-19 pandemic lockdown on ED attendance by this population.

Objectives
This study aims: 1) To review the frequency/nature of the presentations to the paediatric ED by YEH; 2) To compare pre- and post-COVID-19 data.

Design/Methods
Medical records were searched for ED encounters where a patient identified a youth shelter as their address and/or had terms documented such as “homeless”, during two time periods: pre-COVID-19 (May 1, 2018–March 15, 2020) and post-COVID-19 lockdown (March 16, 2021–Jan 31, 2022). Pertinent details of the encounters were documented, including chief complaint (CC). Descriptive statistics were used, as well as comparative analysis of the two time periods.

Results
A total of 1103 encounters were included. Over the total 45-month study time period, CCs were split between mental health-related (n=562, 50.9%) and physical health-related presentations (n=541, 49%). Of the mental health CCs, 396 (70.4%) were documented as “depression/overdose/suicidal/self-harm”. The most common CCs related to physical health were injuries (n=127, 23.4%), and pain (n=126, 23.2%).
YEH most commonly attended the paediatric ED between 17:00-00:00 (n=504, 45%), and were triaged as CTAS 3/urgent (n = 676, 61.2%). Of those who completed an Ask Suicide-Screening Questionnaire (ASQ) (n=303), 45.8% (n=139) had an acute positive screen/imminent risk identified.
The most common principal diagnoses documented at disposition were related to injuries/assault/pain (n= 224, 20%), and suicide attempt/self-harm (n=196, 17.7%). Of the 166 outpatient referrals made at discharge from ED, 105 (63%) were to mental health/psychiatry.
While overall there were fewer ED encounters for this population “post COVID-lockdown” (n=465) as compared to “pre-COVID” (n=638) (p-value &lt;0.05), there was a significant reduction in mental health-related CCs (pre-COVID n=365, post-COVID n=197; p-value &lt;0.05), with no significant reduction in physical-related CCs after the pandemic lockdown (pre-COVID, n=273, n=268).

Conclusion
YEH utilize the paediatric ED for both their mental and physical healthcare and frequently report suicide risk. The findings that lower attendance to the paediatric ED for mental health-related concerns followed the pandemic lockdown, while physical health encounters remained steady, may reflect increased barriers to care or novel methods of mental health care delivery post-pandemic.