bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression
Authors: Nassiri Isar , Kwok Andrew J , Bhandari Aneesha , Bull Katherine R , Garner Lucy C , Klenerman Paul , Webber Caleb , Parkkinen Laura , Lee Angela W , Wu Yanxia , Fairfax Benjamin , Knight Julian C , Buck David , Piazza Paolo 
Published: June 2024

Abstract

Motivation
Pooled designs for single-cell RNA sequencing, where many cells from distinct samples are processed jointly, offer increased throughput and reduced batch variation. This study describes expression-aware demultiplexing (EAD), a computational method that employs differential co-expression patterns between individuals to demultiplex pooled samples without any extra experimental steps.

Results
We use synthetic sample pools and show that the top interindividual differentially co-expressed genes provide a distinct cluster of cells per individual, significantly enriching the regulation of metabolism. Our application of EAD to samples of six isogenic inbred mice demonstrated that controlling genetic and environmental effects can solve interindividual variations related to metabolic pathways. We utilized 30 samples from both sepsis and healthy individuals in six batches to assess the performance of classification approaches. The results indicate that combining genetic and EAD results can enhance the accuracy of assignments (Min. 0.94, Mean 0.98, Max. 1). The results were enhanced by an average of 1.4% when EAD and barcoding techniques were combined (Min. 1.25%, Median 1.33%, Max. 1.74%). Furthermore, we demonstrate that interindividual differential co-expression analysis within the same cell type can be used to identify cells from the same donor in different activation states. By analysing single-nuclei transcriptome profiles from the brain, we demonstrate that our method can be applied to nonimmune cells.

Availability and implementation
EAD workflow is available at https://isarnassiri.github.io/scDIV/ as an R package called scDIV (acronym for single-cell RNA-sequencing data demultiplexing using interindividual variations).
Racially Minoritised Young People’s Experiences of Navigating COVID-19 Challenges: A Community Cultural Wealth Perspective
Authors: Bernard Claudia , Gupta Anna , Lakhanpaul Monica , Sharma Anita , Peres Teresa 
Published: June 2024

Abstract
This article explores the impact of the coronavirus disease 2019 (COVID-19) pandemic on racially minoritised children and young people. It draws on a study that investigated the factors that impacted the well-being and resilience of Black and Asian children and young people in the UK during the pandemic. The study employed a qualitative approach using semi-structured interviews and focus groups with Black and Asian children aged twelve to nineteen years, to explore their perspectives of the contributing factors that impacted the health, well-being and the coping strategies and support they were able to draw upon to navigate challenges. The thematic analysis highlighted themes of: (1) Support and well-being and (2) coping strategies and resilience to understand the layered elements of multiple intersecting identities and inequities. The findings revealed insights into the intersection of multiple disadvantages, namely economic stressors, food poverty, digital inequality, disrupted education and disproportionate losses that impacted family functioning, peer-to-peer support, friendships and social connection. Through the lens of community cultural wealth, this article seeks to examine key factors that need to be foregrounded when lived experiences are rooted in the cumulative effects of multiple intersecting inequalities. The findings provide insights into the challenges exacerbated by structural inequalities and racial disparities that disproportionately impacted youth experiences.
The neural representation of body part concepts
Authors: Mazurchuk Stephen , Fernandino Leonardo , Tong Jia-Qing , Conant Lisa L , Binder Jeffrey R 
Published: June 2024

Abstract
Neuropsychological and neuroimaging studies provide evidence for a degree of category-related organization of conceptual knowledge in the brain. Some of this evidence indicates that body part concepts are distinctly represented from other categories; yet, the neural correlates and mechanisms underlying these dissociations are unclear. We expand on the limited prior data by measuring functional magnetic resonance imaging responses induced by body part words and performing a series of analyses investigating the cortical representation of this semantic category. Across voxel-level contrasts, pattern classification, representational similarity analysis, and vertex-wise encoding analyses, we find converging evidence that the posterior middle temporal gyrus, the supramarginal gyrus, and the ventral premotor cortex in the left hemisphere play important roles in the preferential representation of this category compared to other concrete objects.
EUKARYOME: the rRNA gene reference database for identification of all eukaryotes
Authors: Tedersoo Leho , Hosseyni Moghaddam Mahdieh S , Mikryukov Vladimir , Hakimzadeh Ali , Bahram Mohammad , Nilsson R Henrik , Yatsiuk Iryna , Geisen Stefan , Schwelm Arne , Piwosz Kasia , Prous Marko , Sildever Sirje , Chmolowska Dominika , Rueckert Sonja , Skaloud Pavel , Laas Peeter , Tines Marco , Jung Jae-Ho , Choi Ji Hye , Alkahtani Saad , Anslan Sten 
Published: June 2024

Abstract
Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers—ITS1, ITS2, 18S V4–V5 and 28S D1–D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding—a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.
Rapid adaptation of the rainbow trout intestinal microbiota to the use of a high-starch 100% plant-based diet
Authors: Defaix Raphaël , Lokesh Jep , Calo Jessica , Biasutti Sandra , Surget Anne , Terrier Frédéric , Soengas José Luis , Panserat Stéphane , Ricaud Karine 
Published: June 2024

Abstract
Short-term adaptation of the microbiota could promote nutrient degradation and the host health. While numerous studies are currently undertaking feeding trials using sustainable diets for the aquaculture industry, the extent to which the microbiota adapts to these novel diets is poorly described. The incorporation of carbohydrates (CHO) within a 100% plant-based diet could offer a novel, cost-effective energy source that is readily available, potentially replacing the protein component in the diets. In this study, we investigated the short-term (3 weeks) effects of a high CHO, 100% plant-based diet on the mucosal and digesta associated microbiota diversity and composition, as well as several metabolic parameters in rainbow trout. We highlighted that the mucosa is dominated by Mycoplasma (44.86%). While the diets did not have significant effects on the main phyla (Proteobacteria, Firmicutes, and Actinobacteria), after 3 weeks, a lower abundance of Bacillus genus, and higher abundances of four lactic-acid bacteria were demonstrated in digesta. In addition, no post-prandial hyperglycemia was observed with high carbohydrate intake. These results provide evidence for the rapid adaptation of the gut microbiota and host metabolism to high CHO in combination with 100% plant ingredients in rainbow trout.
COVID-19 Stress and Cognitive Disparities in Black, MENA, and White Older Adults
Authors: Ajrouch Kristine J , Zahodne Laura B , Brauer Simon , Tarraf Wassim , Antonucci Toni C 
Published: June 2024

Abstract

Background and Objectives
Population aging has led to an increased interest in cognitive health and, in particular, the role that stress plays in cognitive disparities. This paper extends previous work by characterizing coronavirus disease 2019 (COVID-19) stress type prevalence and its association with cognitive health in metro-Detroit among Black, Middle Eastern/Arab (MENA), and White older adults.

Research Design and Methods
Data come from a regionally representative sample of adults aged 65+ in metro-Detroit (N = 600; MENA n = 199; Black n = 205; White n = 196). We used generalized linear models to compare groups on sociodemographic, objective stress, and social stress indicators. Multiple group structural equation models evaluated whether COVID-19 stress predicted cognitive health and whether that association varied across racial/ethnic groups.

Results
MENA and Black older adults reported higher levels of objective stress than Whites. There were no racial/ethnic group differences in social stress. More objective stress was associated with better cognitive health, and more social stress was associated with worse cognitive health. The positive effect of objective stress was especially apparent for White older adults.

Discussion and Implications
Though it appears that minority stress was not exacerbated in the context of pandemic stress, links between greater objective stress and better cognitive health apparent among White older adults were not evident among MENA or Black older adults. Broadening health disparities research by including underrepresented populations allows us to elevate scientific knowledge by clarifying what is universal and what is unique about the stress process.
Numerical prediction of the aerodynamics and aeroacoustics of a 25 kW horizontal axis wind turbine
Authors: Wang Wen-Yu , Ferng Yuh-Ming 
Published: June 2024

Abstract
In this study, low-frequency-based numerical methods were used to predict the noise radiating from rotating horizontal axis wind turbine (HAWT) blades. The flow parameters in the vicinity of blade surfaces, which are required for the Ffowcs Williams–Hawkings (FW–H) equation, were calculated using ANSYS FLUENT. The numerical model was verified against the experimental results from the National Renewable Energy Laboratory Phase VI wind turbine blades. The coupling analysis was integrated with four Reynolds-averaged Navier–Stokes turbulence models and FW–H equation under various boundary conditions. The standard k-ε, SST k-ω and V2f turbulence models produced results in agreement with the available experimental pressure coefficient and relative velocity distribution data in the flow fields. Under the verification of aeroacoustic results, the SST k-ω turbulence model was more consistent with the large eddy simulation data. An Institute of Nuclear Energy Research 25-kW HAWT was employed to predict noise frequency distribution at nine points on the tower on the windward and leeward sides under different operating conditions. Noise frequency distributions on the windward and leeward sides exhibited slight differences, whereas those on the left and right sides of the tower were different because of wind-shear influence. Under operating conditions, the decibels of the low-frequency noise at 0–200 Hz were ∼25–40 dB, and the noise frequency distributions on the windward and leeward sides were similar. With increasing distance, the decibel number of the monitoring point ∼25 m away dropped to 0 dB. For the noise prediction in Case 2 (wind speed = 12 m/s, pitches = 18°), the decibel number at 50 m was ∼25 dB and was ∼15 dB at 70 m. In Case 3 (wind speed = 18 m/s, pitches = 33°), the decibel number at 50 m was ∼30 dB and was ∼20 dB at 70 m. The peak amplitude of the noise was inversely proportional to the increasing distance from the tower but proportional to the wind and rotational speeds.
Quasi-isotropic UV emission in the ULX NGC 1313 X–1
Authors: Gúrpide A , Castro Segura N 
Published: June 2024

ABSTRACT
A major prediction of most super-Eddington accretion theories is the presence of anisotropic emission from supercritical discs, but the degree of anisotropy and its dependence on energy remain poorly constrained observationally. A key breakthrough allowing to test such predictions was the discovery of high-excitation photoionized nebulae around ultraluminous X-ray sources (ULXs). We present efforts to tackle the degree of anisotropy of the ultraviolet/extreme ultraviolet (UV/EUV) emission in super-Eddington accretion flows by studying the emission-line nebula around the archetypical ULX NGC 1313 X–1. We first take advantage of the extensive wealth of optical/near-UV and X-ray data from Hubble Space Telescope, XMM–Newton, Swift X-ray telescope, and NuSTAR observatories to perform multiband, state-resolved spectroscopy of the source to constrain the spectral energy distribution (SED) along the line of sight. We then compare spatially resolved cloudy predictions using the observed line-of-sight SED with the nebular line ratios to assess whether the nebula ‘sees’ the same SED as observed along the line of sight. We show that to reproduce the line ratios in the surrounding nebula, the photoionizing SED must be a factor of ≈4 dimmer in UV emission than along the line of sight. Such nearly iosotropic UV emission may be attributed to the quasi-spherical emission from the wind photosphere. We also discuss the apparent dichotomy in the observational properties of emission-line nebulae around soft and hard ULXs, and suggest that only differences in mass-transfer rates can account for the EUV/X-ray spectral differences, as opposed to inclination effects. Finally, our multiband spectroscopy suggests that the optical/near-UV emission is not dominated by the companion star.
CO in the Draco nebula: the atomic–molecular transition
Authors: Bieging John H , Kong Shuo 
Published: June 2024

ABSTRACT
This paper presents maps of the J=2-1 transition of CO towards the Draco nebula intermediate-velocity cloud (IVC). The maps cover 8500 square arcmin with a velocity resolution of 0.33 km s$^{-1}$ and angular resolution of 38 ${\rm arcsec}$, or 0.11 pc at the cloud distance of 600 pc. The mapped area includes all the emission detected by the Herschel satellite with 250 $\mu$m intensity &gt;5 MJy sr−1. Previously published observations of the far-infrared (far-IR) emission and the 21 cm line of HI are used to derive the column density distribution of H$_2$ and the abundance ratio CO/H$_2$, as well as the distribution of the molecular fraction of hydrogen, which approaches 90 per cent over much of the brighter parts of the nebula. The CO emission is highly clumpy and closely resembles the structures seen in far-IR images. The kinematics of the CO show supersonic motions between clumps but near-thermal to trans-sonic motions within clumps, consistent with model predictions that the scale length for dissipation of supersonic turbulence should be $\sim 0.1$ pc, mediated by kinematic viscosity and/or ambipolar diffusion. Different parts of the nebula show evidence for a spread of molecular formation time-scales of a few 10$^5$ yr, comparable with the dynamical time-scale of the infalling gas. The IVC will likely merge with the Galactic interstellar medium in $\sim 10^7$ yr, and the densest clumps may form an unbound cluster of low-mass stars.
TOI-2374 b and TOI-3071 b: two metal-rich sub-Saturns well within the Neptunian desert
Authors: Hacker Alejandro , Díaz Rodrigo F , Armstrong David J , Fernández Fernández Jorge , Müller Simon , Delgado-Mena Elisa , Sousa Sérgio G , Adibekyan Vardan , Stassun Keivan G , Collins Karen A , Yee Samuel W , Bayliss Daniel , Bieryla Allyson , Bouchy François , Butler R Paul , Crane Jeffrey D , Dumusque Xavier , Hartman Joel D , Helled Ravit , Jenkins Jon , Keniger Marcelo Aron F , Lewis Hannah , Lillo-Box Jorge , Lund Michael B , Nielsen Louise D , Osborn Ares , Osip David , Paegert Martin , Radford Don J , Santos Nuno C , Seager Sara , Shectman Stephen A , Srdoc Gregor , Strøm Paul A , Tan Thiam-Guan , Teske Johanna K , Vezie Michael , Watanabe David , Watkins Cristilyn N , Wheatley Peter J , Winn Joshua N , Wohler Bill , Ziegler Carl 
Published: June 2024

ABSTRACT
We report the discovery of two transiting planets detected by the Transiting Exoplanet Survey Satellite (TESS), TOI-2374 b and TOI-3071 b, orbiting a K5V and an F8V star, respectively, with periods of 4.31 and 1.27 d, respectively. We confirm and characterize these two planets with a variety of ground-based and follow-up observations, including photometry, precise radial velocity monitoring and high-resolution imaging. The planetary and orbital parameters were derived from a joint analysis of the radial velocities and photometric data. We found that the two planets have masses of (57 ± 4) M⊕ or (0.18 ± 0.01) MJ, and (68 ± 4) M⊕ or (0.21 ± 0.01) MJ, respectively, and they have radii of (6.8 ± 0.3) R⊕ or (0.61 ± 0.03) RJ and (7.2 ± 0.5) R⊕ or (0.64 ± 0.05) RJ, respectively. These parameters correspond to sub-Saturns within the Neptunian desert, both planets being hot and highly irradiated, with Teq ≈ 745 K and Teq ≈ 1812 K, respectively, assuming a Bond albedo of 0.5. TOI-3071 b has the hottest equilibrium temperature of all known planets with masses between 10 and 300 M⊕ and radii less than 1.5 RJ. By applying gas giant evolution models we found that both planets, especially TOI-3071 b, are very metal-rich. This challenges standard formation models which generally predict lower heavy-element masses for planets with similar characteristics. We studied the evolution of the planets’ atmospheres under photoevaporation and concluded that both are stable against evaporation due to their large masses and likely high metallicities in their gaseous envelopes.
A unified accretion disc model for supermassive black holes in galaxy formation simulations: method and implementation
Authors: Koudmani Sophie , Somerville Rachel S , Sijacki Debora , Bourne Martin A , Jiang Yan-Fei , Profit Kasar 
Published: June 2024

ABSTRACT
It is well established that supermassive black hole (SMBH) feedback is crucial for regulating the evolution of massive, if not all, galaxies. However, modelling the interplay between SMBHs and their host galaxies is challenging due to the vast dynamic range. Previous simulations have utilized simple subgrid models for SMBH accretion, while recent advancements track the properties of the unresolved accretion disc, usually based on the thin α-disc model. However, this neglects accretion in the radiatively inefficient regime, expected to occur through a thick disc for a significant portion of an SMBH’s lifetime. To address this, we present a novel ‘unified’ accretion disc model for SMBHs, harnessing results from the analytical advection-dominated inflow–outflow solution (ADIOS) model and state-of-the-art general relativistic (radiation-)magnetohydrodynamics (GR(R)MHD) simulations. Going from low to high Eddington ratios, our model transitions from an ADIOS flow to a thin α-disc via a truncated disc, incorporating self-consistently SMBH spin evolution due to Lense–Thirring precession. Utilizing the moving mesh code arepo, we perform simulations of single and binary SMBHs within gaseous discs to validate our model and assess its impact. The disc state significantly affects observable luminosities, and we predict markedly different electromagnetic counterparts in SMBH binaries. Crucially, the assumed disc model shapes SMBH spin magnitudes and orientations, parameters that gravitational wave observatories like LISA and IPTA are poised to constrain. Our simulations emphasize the importance of accurately modelling SMBH accretion discs and spin evolution, as they modulate the available accretion power, profoundly shaping the interaction between SMBHs and their host galaxies.
Spatial clustering of gravitational wave sources with k-nearest neighbour distributions
Authors: Gupta Kaustubh Rajesh , Banerjee Arka 
Published: June 2024

ABSTRACT
We present a framework to quantify the clustering of gravitational wave (GW) transient sources and measure their spatial cross-correlation with the large-scale structure (LSS) of the universe using the k-nearest neighbour (kNN) formalism. As a first application, we measure the nearest neighbour distributions of 53 suitably selected binary black hole (BBH) mergers detected in the first three observation runs of LIGO–Virgo–KAGRA and cross-correlate these sources with $\sim 1.7 \times 10^7$ galaxies and quasars from the WISE$\times$ SuperCOSMOS all-sky catalogue. To determine the significance of the clustering signal while accounting for observational systematics in the GW data, we create 135 realizations of mock BBHs that are statistically similar to the observed BBHs but spatially unclustered. We find no evidence for spatial clustering or cross-correlation with LSS in the data and conclude that the present sky localization and number of detections are insufficient to get a statistically significant clustering signal. Looking forwards, the statistically large number of detections and the significant improvements in sky localizations expected from future observing runs of LIGO (including LIGO India) and the next generation of GW detectors will enable measurement of the BBH–LSS cross-correlation and open a new window into cosmology.
Significance of eGFR and proteinuria for cardiovascular disease in individuals beyond 85 years of age
Authors: Azegami Tatsuhiko , Kaneko Hidehiro , Okada Akira , Suzuki Yuta , Fujiu Katsuhito , Morita Hiroyuki , Takeda Norifumi , Takeda Norihiko , Fukui Akira , Yokoo Takashi , Node Koichi , Yasunaga Hideo , Nangaku Masaomi , Hayashi Kaori 
Published: June 2024

ABSTRACT

Background
There are limited data on how advancing age influences prediction of cardiovascular disease (CVD) risk based on the estimated glomerular filtration rate (eGFR) and proteinuria, especially in older adults, including those aged ≥85 years old. This study aimed to clarify the association of eGFR and proteinuria with CVD outcomes and the impact of age on this association.

Methods
The distribution of eGFR and urine protein in Japan was assessed retrospectively using real-world administrative claims and health checkup data collected between April 2014 and November 2022. We investigated the associations of these two parameters with the incidence of CVD, with an emphasis on the impact of aging.

Results
We assessed 1 829 020 individuals for distribution of eGFR and proteinuria; after excluding those with known CVD, their association with CVD risk was examined in 1 040 101 individuals aged ≥40 years. The prevalence of impaired kidney function (eGFR &lt;60 mL/min/1.73 m2) increased with age, being 0.7%, 9.2%, 21.9%, 40.2% and 60.2% at the ages of 18–39, 40–64, 65–74, 75–84 and ≥85 years, respectively (P for trend &lt;.001); similarly, the proportion with positive proteinuria increased with age, being 2.7%, 4.3%, 5.6%, 9.2% and 15.8%, respectively (P for trend &lt;.001). Both eGFR and urine protein were identified to be independent risk factors for CVD. Hazard ratios for CVD increased significantly when eGFR was &lt;45 mL/min/1.73 m2 at the ages of 40–64, 65–74 and 75–84 years and &lt;30 mL/min/1.73 m2 at ≥85 years, while proteinuria remained significantly associated with a high CVD risk regardless of age. These findings were consistent even when analyzed separately by sex.

Conclusions
This study identified eGFR and urine dipstick proteinuria to be independent risk factors for CVD, even among individuals aged ≥85 years. However, the contribution of eGFR to the CVD risk was attenuated by aging, whereas proteinuria remained less affected by advancing age.