bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intellectual disability services in European countries
Authors: Courtenay Ken , Dekker-Couchman Romanie , Attavar Rajnish 
Published: November 2023

Abstract
In European countries, people with intellectual disability live in a range of social systems shaped by culture and attitudes. They have experienced many changes over the centuries, often with little control over their impacts. Culture impacts attitudes towards people with intellectual disability, affecting the quality of education and healthcare that they receive. Deinstitutionalisation across Europe has not been uniform and depends on political will and financial support. The European Union has implemented policies supported by funding to effect changes to more inclusive education and healthcare. Training of health and social care professionals in the needs of people with intellectual disability is essential to ensure that progress continues in enhancing the quality of people’s lives.
Development and validation of a colorimetric antifungal susceptibility testing method for the dimorphic fungus Talaromyces marneffei
Authors: Thu Nguyen Thi Mai , Borda Hannah , Vitsupakorn Shawin , Reddy Kaushik Sreerama , Kasmani Navsin , Barwatt Joseph , Schwartz Ilan S , Giamberardino Charles , Perfect John R , Hoa Ngo Thi , Le Thuy 
Published: November 2023

Abstract
Antifungal drug resistance is an emerging cause of treatment failure in invasive fungal infections, and antifungal susceptibility testing (AFST) may inform treatment decisions. Currently, there are no established AFST guidelines for Talaromyces marneffei (Tm) or other dimorphic fungi. We developed a colorimetric AFST method using a fluorescent redox indicator alamarBlue, which changes from blue to pink in proportion to cellular metabolic activity. We determined the optimal time for alamarBlue addition to be 24 h post-inoculation and for MIC reading to be 72 h post-inoculation. Our method allows three ways to determine minimum inhibitory concentration (MIC): visual inspection of color change, optical density, and fluorescence intensity. We validated the assay by determining the MICs for seven antifungals against 32 Tm clinical isolates and assessed the essential agreement (EA) and inter-rater reliability between our alamarBlue and the Clinical Laboratory Standard Institute (CLSI) broth microdilution methods. The MIC ranges (from low to high) were: 0.008–0.025 μg/ml for itraconazole, 0.004–0.13 μg/ml for voriconazole, 0.03–0.13 μg/ml for posaconazole, 0.06–0.5 µg/ml for flucytosine, 0.5–1 µg/ml for amphotericin B, 0.5–4 µg/ml for caspofungin, and 0.5–16 µg/ml for fluconazole. The EAs were 100% between all three MIC readouts of the alamarBlue method, and 94%–100% between the alamarBlue and CLSI methods. Our alamarBlue method had substantially higher inter-rater agreement and offers a more reliable method that can be standardized across laboratories in both high- and low-resource settings compared to the established CLSI methodology.
Globular clusters contribute to the nuclear star clusters and galaxy centre γ-ray excess, moderated by galaxy assembly history
Authors: Gao Yuan , Li Hui , Zhang Xiaojia , Su Meng , Ng Stephen Chi Yung 
Published: November 2023

ABSTRACT
Two unresolved questions at galaxy centres, namely the formation of the nuclear star cluster (NSC) and the origin of the γ-ray excess in the Milky Way (MW) and Andromeda (M31), are both related to the formation and evolution of globular clusters (GCs). They migrate towards the galaxy centre due to dynamical friction, and get tidally disrupted to release the stellar mass content including millisecond pulsars (MSPs), which contribute to the NSC and γ-ray excess. In this study, we propose a semi-analytical model of GC formation and evolution that utilizes the Illustris cosmological simulation to accurately capture the formation epochs of GCs and simulate their subsequent evolution. Our analysis confirms that our GC properties at z = 0 are consistent with observations, and our model naturally explains the formation of a massive NSC in a galaxy similar to the MW and M31. We also find a remarkable similarity in our model prediction with the γ-ray excess signal in the MW. However, our predictions fall short by approximately an order of magnitude in M31, indicating distinct origins for the two γ-ray excesses. Meanwhile, we utilize the catalogue of Illustris haloes to investigate the influence of galaxy assembly history. We find that the earlier a galaxy is assembled, the heavier and spatially more concentrated its GC system behaves at z = 0. This results in a larger NSC mass and brighter γ-ray emission from deposited MSPs.
Quality flags for GSP-Phot Gaia DR3 astrophysical parameters with machine learning: effective temperatures case study
Authors: Avdeeva Aleksandra S , Kovaleva Dana A , Malkov Oleg Yu , Zhao Gang 
Published: November 2023

ABSTRACT
Gaia Data Release 3 (DR3) provides extensive information on the astrophysical properties of stars, such as effective temperature, surface gravity, metallicity, and luminosity, for over 470 million objects. However, as Gaia’s stellar parameters in GSP-Phot module are derived through model-dependent methods and indirect measurements, it can lead to additional systematic errors in the derived parameters. In this study, we compare GSP-Phot effective temperature estimates with two high-resolution and high signal-to-noise spectroscopic catalogues: APOGEE DR17 and GALAH DR3, aiming to assess the reliability of Gaia’s temperatures. We introduce an approach to distinguish good-quality Gaia DR3 effective temperatures using machine-learning methods such as XGBoost, CatBoost, and LightGBM. The models create quality flags, which can help one to distinguish good-quality GSP-Phot effective temperatures. We test our models on three independent data sets, including PASTEL, a compilation of spectroscopically derived stellar parameters from different high-resolution studies. The results of the test suggest that with these models, it is possible to filter effective temperatures as accurate as 250 K with ∼90 per cent precision even in complex regions, such as the Galactic plane. Consequently, the models developed herein offer a valuable quality assessment tool for GSP-Phot effective temperatures in Gaia DR3. The data set with flags for all GSP-Phot effective temperature estimates, is publicly available, as are the models themselves.
Scaling relations for globular cluster systems in early-type galaxies – III. The inner flattening of the radial distributions
Authors: Caso Juan Pablo , Ennis Ana Inés , De Bórtoli Bruno Javier 
Published: November 2023

ABSTRACT
The current properties of globular cluster systems (GCSs) in the nearby Universe are a consequence of an evolutionary history ruled by accretion and disruption processes. The analysis of scaling relations for GCSs is crucial for understanding the relevance of different physical processes involved in their origin and subsequent survival. In this work, radial profiles are calculated for a sample of GCSs associated with nearby massive galaxies. This is supplemented with results from our previous papers, achieving a total sample of 53 GCSs with radial profiles homogeneously calculated, and spanning more than two orders of magnitude in stellar mass of the host galaxy. Scaling relations involving different parameters of the GCSs are obtained for the entire sample, and their significance in terms of different scenarios is considered. Finally, the results are analysed in the literature context.
Low-mass bursty galaxies in JADES efficiently produce ionizing photons and could represent the main drivers of reionization
Authors: Simmonds C , Tacchella S , Hainline K , Johnson B D , McClymont W , Robertson B , Saxena A , Sun F , Witten C , Baker W M , Bhatawdekar R , Boyett K , Bunker A J , Charlot S , Curtis-Lake E , Egami E , Eisenstein D J , Hausen R , Maiolino R , Maseda M V , Scholtz J , Williams C C , Willott C , Witstok J 
Published: November 2023

ABSTRACT
We use deep imaging from the JWST Advanced Deep Extragalactic Survey (JADES) to study the evolution of the ionizing photon production efficiency, ξion. We estimate ξion for a sample of 677 galaxies at z ∼ 4–9 using NIRCam (Near-Infrared Camera) photometry. Specifically, combinations of the medium and wide bands F335M–F356W and F410M–F444W to constrain emission lines that trace ξion: Hα and [O iii]. Additionally, we use the spectral energy distribution fitting code prospector to fit all available photometry and infer galaxy properties. The flux measurements obtained via photometry are consistent with FRESCO (First Reionisation Epoch Spectroscopic Complete Survey) and NIRSpec-derived fluxes. Moreover, the emission-line-inferred measurements are consistent with the prospector estimates. We also confirm the observed ξion trend with redshift and MUV, and find: log ξion(z, MUV) = (0.05 ± 0.02)z + (0.11 ± 0.02)MUV + (27.33 ± 0.37). We use prospector to investigate correlations of ξion with other galaxy properties. We see a clear correlation between ξion and burstiness in the star formation history of galaxies, given by the ratio of recent to older star formation, where burstiness is more prevalent at lower stellar masses. We also convolve our ξion relations with luminosity functions from the literature, and constant escape fractions of 10 per cent and 20 per cent, to place constraints on the cosmic ionizing photon budget. By combining our results, we find that if our sample is representative of the faint low-mass galaxy population, galaxies with bursty star formation are efficient enough in producing ionizing photons and could be responsible for the reionization of the Universe.
The magnetized and thermally unstable tails of jellyfish galaxies
Authors: Sparre Martin , Pfrommer Christoph , Puchwein Ewald 
Published: November 2023

ABSTRACT
Jellyfish galaxies are promising laboratories for studying radiative cooling and magnetic fields in multiphase gas flows. Their long, dense tails are observed to be magnetized, and they extend up to 100 kpc into the intracluster medium (ICM), suggesting that their gas is thermally unstable so that the cold gas mass grows with time rather than being fully dissolved in the hot wind as a result of hydrodynamical interface instabilities. In this paper, we use the arepo code to perform magnetohydrodynamical windtunnel simulations of a jellyfish galaxy experiencing ram-pressure stripping by interacting with an ICM wind. The ICM density, temperature and velocity that the galaxy encounters are time-dependent and comparable to what a real jellyfish galaxy experiences while orbiting the ICM. In simulations with a turbulent magnetized wind, we reproduce observations, which show that the magnetic field is aligned with the jellyfish tails. During the galaxy infall into the cluster with a near edge-on geometry, the gas flow in the tail is fountain-like, implying preferential stripping of gas where the rotational velocity vectors add up with the ram pressure while fall-back occurs in the opposite case. Hence, the tail velocity shows a memory of the rotation pattern of the disc. At the time of the nearest cluster passage, ram-pressure stripping is so strong that the fountain flow is destroyed and instead the tail is dominated by the removal of gas. We show that gas in the tail is very fragmentative, which is a prediction of shattering due to radiative cooling.
The merger of hard binaries in globular clusters as the primary channel for the formation of second-generation stars
Authors: Kravtsov Valery , Dib Sami , Calderón Francisco A 
Published: November 2023

ABSTRACT
We have recently presented observational evidence which suggests that the origin of the second-generation (G2) stars in globular clusters (GCs) is due to the binary-mediated collision of primordial (G1) low-mass main-sequence (MS) stars. This mechanism avoids both the mass budget problem and the need of external gas for dilution. Here, we report on another piece of evidence supporting this scenario: (1) the fraction of MS binaries is proportional to the fraction of G1 stars in GCs and, at the same time, (2) the smaller the fraction of G1 stars is, the more deficient binaries of higher mass ratio (q&gt;0.7) are. They are, on average, harder than their smaller mass-ratio counterparts due to higher binding energy at a given primary mass. Then (2) implies that (1) is due to the merging/collisions of hard binaries rather than to their disruption. These new results complemented by the present-day data on binaries lead to the following conclusions: (i) the mass-ratio distribution of binaries, particularly short-period ones, with low-mass primaries, MP &lt; 1.5 M⊙, is strongly peaked close to q=1.0, whereas (ii) dynamical processes at high stellar density tend to destroy softer binaries and make hard (nearly) twin binaries to become even harder and favour their mergers and collisions. G2 stars formed this way gain mass that virtually doubles the primary one, 2MP, at which the number of G1 stars is approximately five times smaller than at MP according to the slope of a Milky Way-like initial mass function at MMS &lt; 1.0 M⊙.
High-energy neutrinos from merging stellar-mass black holes in active galactic nuclei accretion disc
Authors: Zhu Jin-Ping 
Published: November 2023

ABSTRACT
A population of binary stellar-mass black hole (BBH) mergers are believed to occur embedded in the accretion disc of active galactic nuclei (AGNs). In this Letter, we demonstrate that the jets from these BBH mergers can propagate collimatedly within the disc atmosphere along with a forward shock and a reverse shock forming at the jet head. Efficient proton acceleration by these shocks is usually expected before the breakout, leading to the production of TeV−PeV neutrinos through interactions between these protons and electron-radiating photons via photon–meson production. AGN BBH mergers occurring in the outer regions of the disc are more likely to produce more powerful neutrino bursts. Taking the host AGN properties of the potential GW190521 electromagnetic (EM) counterpart as an example, one expects ≳1 neutrino events detectable by IceCube if the jet is on-axis and the radial location of the merger is R ≳ 105Rg, where Rg is the gravitational radius of the supermassive BH. Neutrino bursts from AGN BBH mergers could be detected by IceCube following the observation of gravitational waves (GWs), serving as precursor signals before the detection of EM breakout signals. AGN BBH mergers are potential target sources for future joint GW, neutrino, and EM multi-messenger observations.
Alternative Clinical Training During the First Year of COVID-19 Pandemic: Students’ Experience
Authors: Lee Juyoung , Moonier Emma , Heiderscheit Annie 
Published: November 2023

Abstract
The COVID-19 pandemic ushered in widespread restrictions that impacted clinical and academic settings. These restrictions required music therapy educators to not only shift their teaching platform but to find methods to engage students in the continued development of their clinical practice skills through practicum experiences while clinical sites were closed. To provide alternative practicum experiences, three music therapy faculty at a major metropolitan private university offered Telehealth Practica (THP) for undergraduate and graduate students in the first year of the pandemic. Music therapy faculty facilitated individual or group sessions with 10 clients to provide ongoing practicum experiences for students over the course of two semesters. Twenty-two students participated in five focus group interviews to share their experiences of THP. Using a thematic analysis, 14 themes were identified, and through further latent analysis, five attributes of the THP model: accessibility, usefulness, uniqueness, limitation, and potential were developed. THP offered students a new and novel learning opportunity that is not experienced in traditional in-person practicum, and they identified this as a valuable and unique training option. THP experience highlighted the need to develop student competencies and skills related to the use of technology for telehealth delivery, as telehealth has become a new norm and will be one of the ways health professionals continue to provide services in the future.
Reactivation of the G1 enhancer landscape underlies core circuitry addiction to SWI/SNF
Authors: Cermakova Katerina , Tao Ling , Dejmek Milan , Sala Michal , Montierth Matthew D , Chan Yuen San , Patel Ivanshi , Chambers Courtney , Loeza Cabrera Mario , Hoffman Dane , Parchem Ronald J , Wang Wenyi , Nencka Radim , Barbieri Eveline , Hodges H Courtney 
Published: November 2023

Abstract
Several cancer core regulatory circuitries (CRCs) depend on the sustained generation of DNA accessibility by SWI/SNF chromatin remodelers. However, the window when SWI/SNF is acutely essential in these settings has not been identified. Here we used neuroblastoma (NB) cells to model and dissect the relationship between cell-cycle progression and SWI/SNF ATPase activity. We find that SWI/SNF inactivation impairs coordinated occupancy of non-pioneer CRC members at enhancers within 1 hour, rapidly breaking their autoregulation. By precisely timing inhibitor treatment following synchronization, we show that SWI/SNF is dispensable for survival in S and G2/M, but becomes acutely essential only during G1 phase. We furthermore developed a new approach to analyze the oscillating patterns of genome-wide DNA accessibility across the cell cycle, which revealed that SWI/SNF-dependent CRC binding sites are enriched at enhancers with peak accessibility during G1 phase, where they activate genes involved in cell-cycle progression. SWI/SNF inhibition strongly impairs G1-S transition and potentiates the ability of retinoids used clinically to induce cell-cycle exit. Similar cell-cycle effects in diverse SWI/SNF-addicted settings highlight G1-S transition as a common cause of SWI/SNF dependency. Our results illustrate that deeper knowledge of the temporal patterns of enhancer-related dependencies may aid the rational targeting of addicted cancers.
ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome
Authors: Hirsch Pascal , Tagirdzhanov Azat , Kushnareva Aleksandra , Olkhovskii Ilia , Graf Simon , Schmartz Georges P , Hegemann Julian D , Bozhüyük Kenan A J , Müller Rolf , Keller Andreas , Gurevich Alexey 
Published: November 2023

Abstract
The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.
Ionic liquid-caged nucleic acids enable active folding-based molecular recognition with hydrolysis resistance
Authors: Kang Byunghwa , Park Soyeon V , Oh Seung Soo 
Published: November 2023

Abstract
Beyond storage and transmission of genetic information in cellular life, nucleic acids can perform diverse interesting functions, including specific target recognition and biochemical reaction acceleration; the versatile biopolymers, however, are acutely vulnerable to hydrolysis-driven degradation. Here, we demonstrate that the cage effect of choline dihydrogen phosphate permits active folding of nucleic acids like water, but prevents their phosphodiester hydrolysis unlike water. The choline-based ionic liquid not only serves as a universal inhibitor of nucleases, exceptionally extending half-lives of nucleic acids up to 6 500 000 times, but highly useful tasks of nucleic acids (e.g. mRNA detection of molecular beacons, ligand recognition of aptamers, and transesterification reaction of ribozymes) can be also conducted with well-conserved affinities and specificities. As liberated from the function loss and degradation risk, the presence of undesired and unknown nucleases does not undermine desired molecular functions of nucleic acids without hydrolysis artifacts even in nuclease cocktails and human saliva.
Single-cell transcriptomics reveals long noncoding RNAs associated with tumor biology and the microenvironment in pancreatic cancer
Authors: Dang Ha X , Saha Debanjan , Jayasinghe Reyka , Zhao Sidi , Coonrod Emily , Mudd Jacqueline , Goedegebuure S Peter , Fields Ryan , Ding Li , Maher Christopher A 
Published: November 2023

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is highly heterogeneous and lethal. Long noncoding RNAs (lncRNAs) are an important class of genes regulating tumorigenesis and progression. Prior bulk transcriptomic studies in PDAC have revealed the dysregulation of lncRNAs but lack single-cell resolution to distinguish lncRNAs in tumor-intrinsic biology and the tumor microenvironment (TME). We analyzed single-cell transcriptome data from 73 multiregion samples in 21 PDAC patients to evaluate lncRNAs associated with intratumoral heterogeneity and the TME in PDAC. We found 111 cell-specific lncRNAs that reflected tumor, immune and stromal cell contributions, associated with outcomes, and validated across orthogonal datasets. Single-cell analysis of tumor cells revealed lncRNAs associated with TP53 mutations and FOLFIRINOX treatment that were obscured in bulk tumor analysis. Lastly, tumor subcluster analysis revealed widespread intratumor heterogeneity and intratumoral lncRNAs associated with cancer hallmarks and tumor processes such as angiogenesis, epithelial–mesenchymal transition, metabolism and immune signaling. Intratumoral subclusters and lncRNAs were validated across six datasets and showed clinically relevant associations with patient outcomes. Our study provides the first comprehensive assessment of the lncRNA landscape in PDAC using single-cell transcriptomic data and can serve as a resource, PDACLncDB (accessible at https://www.maherlab.com/pdaclncdb-overview), to guide future functional studies.
Head and Neck Squamous Cell Carcinoma of Unknown Primary: A Diagnostic Work-Up
Authors: Manoharan Meenakkshy , Kalman Noah S , Rabinowits Guilherme 
Published: November 2023

Abstract
The current work-up of the primary tumor site of a head and neck squamous cell carcinoma of unknown primary is not standardized and results in several time-consuming procedures that delay treatment initiation. This article seeks to consolidate contemporary strategies used to identify the primary tumor site of an unknown primary head and neck squamous cell carcinoma and offer recommendations based on current literature review.