bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids
Authors: Jiao Jinzhen , Wu Jian , Zhou Chuanshe , He Zhixiong , Tan Zhiliang , Wang Min 
Published: January 2024

Abstract
Goats are globally invaluable ruminants that balance food security and environmental impacts, and their commensal microbiome residing in the gastrointestinal tract (GIT) is associated with animal health and productivity. However, the reference genomes and functional repertoires of GIT microbes in goat kids have not been fully elucidated. Herein, we performed a comprehensive landscape survey of the GIT microbiome of goat kids using metagenomic sequencing and binning, spanning a dense sampling regime covering three gastrointestinal compartments spatially and five developmental ages temporally. We recovered 1002 high-quality metagenome-assembled genomes (termed the goat kid GIT microbial catalog [GKGMC]), 618 of which were novel. They encode more than 2.3 million nonredundant proteins, and represent a variety of carbohydrate-degrading enzymes and metabolic gene clusters. The GKGMC-enriched microbial taxa, particularly Sodaliphilus, expanded the microbial tree of life in goat kids. Using this GKGMC, we first deciphered the prevalence of fiber-degrading bacteria for carbohydrate decomposition in the rumen and colon, while the ileal microbiota specialized in the uptake and conversion of simple sugars. Moreover, GIT microorganisms were rapidly assembled after birth, and their carbohydrate metabolic adaptation occurred in three phases of progression. Finally, phytobiotics modified the metabolic cascades of the ileal microbiome, underpinned by the enrichment of Sharpea azabuensis and Olsenella spp. implicated in lactate formation and utilization. This GKGMC reference provides novel insights into the early-life microbial developmental dynamics in distinct compartments, and offers expanded resources for GIT microbiota-related research in goat kids.
Exploring the Impact of Matching E-Training Material to Arabic Dyslexia Type on Learners’ Reading Performance, Satisfaction and Behaviour
Authors: Al-Dawsari Hadeel Mohammed , Hendley Robert 
Published: January 2024

Abstract
Dyslexia is a reading difficulty that can be found everywhere, regardless of a person’s ethnicity or race. The manifestation of dyslexia depends on the structure and orthography of a language. There is a lack of research into Arabic dyslexia, particularly the benefits of adaptive learning in this area. The study presented in this paper aimed to understand the impact on learners’ reading performance, satisfaction and behaviour when matching e-training material with learner attributes. The focus is on learners with short vowel dyslexia. The study was undertaken with 22 female primary school children in Saudi Arabia, all of whom were native Arabic speakers. These children were divided into two groups: a matched group (which included learners with short vowel dyslexia) and a mismatched group (which included learners with vowel dyslexia). An e-training system ‘DysTypeTrain2’ was designed and developed to support the study. A mixed-methods approach was used to collect both quantitative and qualitative data. The quantitative data were collected from (i) pre- and post-test results to calculate the improvement in reading performance and (ii) learner satisfaction scores. The qualitative data were collected from observations of learners’ behaviour. It was found that the learners’ reading performance and satisfaction improved in both experimental conditions (short vowel dyslexia group and vowel dyslexia group), regardless of their Arabic dyslexia type, indicating that the system was effective and the learning process was improved. Further, the learners were happy and excited about the system.
Anti-biofilm and antivirulence activities of 1,2,6-tri-O-galloyl-β-d-glucose against Proteus penneri
Authors: Jiang Huan , Wang Zhennan , Jia Ai-Qun 
Published: January 2024

Abstract

Aims
The present study investigated the anti-virulence and anti-biofilm effects of 1,2,6-tri-O-galloyl-β-d-glucose (TGG), isolated from Camellia nitidissima Chi flowers, on Proteus penneri ALK 1200.

Methods and results
TGG was isolated from C. nitidissima Chi flowers using various chromatographic techniques. The milk plate assay, azocasein assay, and exopolysaccharides (EPS) inhibition assay revealed that TGG effectively inhibited the production of crucial virulence factors, including protease and EPS, in P. penneri ALK 1200. Furthermore, Fourier transform infrared spectroscopic analysis indicated that TGG interfered with the composition of P. penneri ALK 1200’s cellular component, potentially reducing the bacteria’s pathogenicity. In addition, crystal violet assay, scanning electron microscopy, and confocal laser scanning microscopy analysis indicated a significant reduction in biofilm formation following TGG treatment. The swimming and swarming assays also showed that TGG reduced the motility of P. penneri ALK 1200. Furthermore, the quantitative real-time PCR assay demonstrated that TGG down-regulated the expression of positive regulatory genes (hfq and flhD) responsible for motility and biofilm formation, while up-regulating the expression of the negative regulator of the quorum sensing system, bssS, in P. penneri ALK 1200.

Conclusions
TGG displayed potent anti-QS and anti-biofilm activity toward P. penneri ALK 1200.
Right to Privacy and Data Protection Concerns Raised by the Development and Usage of Face Recognition Technologies in the European Union
Authors: Kavoliūnaitė-Ragauskienė Eglė 
Published: January 2024

Abstract
The fast and fragmentedly regulated development of facial recognition technologies and related artificial intelligence poses various challenges to personal privacy, which leads to potential infringements of a wide range of related human rights. This article analyses the threats that the development and use of facial recognition technologies pose to privacy and personal data protection. It discusses the concept of privacy and the protection of personal data, including biometric data, at European Union level, and assesses the proposed new legal framework. It questions whether this is sufficient to protect privacy and ensure personal data protection in the context of the rapid development and increasing usage of facial recognition technologies in public and private sectors.
Piloting delivery of PfSPZ vaccines for malaria through a cryogenic vaccine cold chain to travel and military medicine clinics
Authors: James Eric R , Church L W Preston , Hoffman Stephen L , Richie Thomas L , Robertson Brian D , Hickey Patrick W , Schwartz David J , Logan Patrick T , Asare Theresa D , Jones Macie L , Bay Jeannie L , Roschel Austin K , Pfeiffer Jacqueline L , Acosta Rebecca W , Schiavi Ethan , Acosta Alberto M , Noble Mark , Henkel Thomas , Young Cebrina 
Published: January 2024

Abstract

Background
PfSPZ vaccines comprising Plasmodium falciparum (Pf) sporozoites (SPZ) have demonstrated &gt; 90% protection against variant Pf malaria infections for at least 12 weeks; they are the only vaccines with the level of efficacy necessary to protect travellers. PfSPZ are eukaryotic cells stabilized by cryopreservation and distributed using a cryogenic (below −150 °C) cold chain. The Ebola vaccine and mRNA vaccines against SARS-CoV-2 pioneered uptake of vaccines requiring non-standard ultra-low temperature cold chains. The cryogenic cold chain using liquid nitrogen (LN2) vapour phase (LNVP) cryoshippers, is simpler, more efficient than −80, −20 or 2–8 °C cold chains, and does not use electricity. This study was conducted to evaluate implementation and integration of a cryogenically distributed vaccine at travel and military immunization clinics.

Methods
We conducted sequential 28-day studies evaluating vaccine shipping, storage, maintenance and accession at two US military and two civilian travel health/immunization clinics. In each clinic, personnel were trained in equipment use, procurement and handling of LN2, temperature monitoring and inventory record keeping by in-person or video instruction.

Results
Sites required 2–4 h/person for two persons to assimilate and develop the expertise to manage vaccine storage and LNVP operations. LN2 for recharging cryoshippers was delivered every 1–2 weeks. Vaccine ordering, receipt, storage and inventory control was conducted effectively. Simulated single dose vaccine cryovial retrieval and thawing were performed successfully in different travel clinic settings. Continuous temperature monitoring at each site was maintained with only one short excursion above −150 °C (−145 °C) through shipping, use and reverse logistics. Staff, during and at study conclusion, provided feedback that has been incorporated into our models for cold chain logistics.

Conclusions
These studies demonstrated that the training in delivery, storage, administration and integration of PfSPZ vaccines can be successfully managed in different immunization clinic settings for travellers and military personnel.
Topic modelling literary interviews from The Paris Review
Authors: Greene Derek , O'Sullivan James , O'Reilly Daragh 
Published: January 2024

Abstract
The interview has always proved to be a rich source for those hoping to better understand the figures behind a text, as well as any social contexts and writing practices which might have informed their aesthetic sentiments. Over the past two decades, research into the literary interview has made significant strides, both in terms of how this literary genre is conceptualized and how its emergence and development has been historically traced, the form remains somewhat neglected by literary and cultural theorists and scholars. There is also a remarkable absence of distant readings in this domain. With the rise of the digital humanities, particularly digital literary studies, one would expect more scholars to have used computer-assisted techniques to mine literary interviews, which are, in terms of dataset practicalities, somewhat ideal, semi-structured by nature, and typically available online. Such is the question to which this article attends, taking as its dataset seven decades’ worth of literary interviews from The Paris Review, and ‘topic modelling’ these documents to determine the key themes that dominate such a culturally significant set of materials while also exploring the value of topic modelling to socio-literary criticism.
LAMOST J040901.83+329355.6 – a new Galactic star with Wolf–Rayet characteristics in the transitional stage from post-asymptotic giant branch to central star of a planetary nebula
Authors: Maryeva Olga , Abdulkarimova Aynur , Karpov Sergey , Moiseev Alexei , Oparin Dmitry 
Published: January 2024

ABSTRACT
The similarity in physical conditions in the winds of low-mass post-asymptotic giant branch stars and evolved massive stars leads to the appearance of an interesting phenomenon of spectral mimicry. Because of this, the discovery of every new star with a Wolf–Rayet (WR) spectrum requires a special study of its evolutionary status before it can be included in the list of Galactic WR stars. A couple of years ago, LAMOST J040901.83+323955.6 (hereafter J0409+3239) was selected as a WR star in the LAMOST spectroscopic data base by machine-learning methods. In this work, we investigate its evolutionary status. After analysing the spatial location of J0409+3239  in the Galaxy and its position in the colour–magnitude diagram, we conclude that J0409+3239  is instead a low-mass object displayng the WR phenomenon. Its luminosity is $L*=1000~\rm L_\odot$ and its effective temperature is Teff = 40 000 K. Using new and archival photometric data, we detected irregular variability on time-scales from hours to tens of days with an amplitude of up to ~0.2 mag. A comparison of the spectrum obtained in 2022 with that from 2014 also shows evidence of spectral variability. The absence of a clearly detected circumstellar nebula prevents the classification of J0409+3239  as [WR], namely as the central star of a planetary nebula (CSPN). However, the position of J0409+3239 on the Hertzsprung–Russell diagram suggests that this object  is a low-mass star caught in a rare transitional phase to CSPN. Estimation of the J0409+3239  mass based on evolutionary tracks shows that it is less than $0.9~\rm M_\odot$, and thus that the age of the Galaxy is barely sufficient for the star to have evolved to its current stage.
Neutral carbon in diffuse interstellar medium: abundance matching with H2 for damped Lyman alpha systems at high redshifts
Authors: Balashev S A , Kosenko D N 
Published: January 2024

ABSTRACT
We present a study of C i/H2 relative abundance in the diffuse cold neutral medium (CNM). Using the chemical and thermal balance model, we calculate the dependence of C i/H2 on the main parameters of the medium: hydrogen number density, metallicity, strength of the UV field, and cosmic ray ionization rate (CRIR). We show that the observed relative C i and H2 column densities in damped Lyman alpha systems (DLAs) at high redshifts can be reproduced within our model assuming the typically expected conditions in the diffuse CNM. Using additional observed information on metallicity, H i column density, and excitation of C i fine-structure levels, as well as temperature, we estimated for a wide range metallicities in the CNM at high redshifts that CRIRs are in the range from ∼10−16 to a $\rm few \times 10^{-15}\, \rm s^{-1}$, hydrogen number densities are in the range ∼10−103 cm−3, and the UV field is in the range from 10−2 to a $\rm few \times 10^2$ of the Mathis field. We argue that because the observed quantities used in this work are quite homogeneous and much less affected by radiative transfer effects (in comparison with, for example, the dissociation of HD and UV pumping of H2 rotational levels), our estimates are quite robust against the assumption of the exact geometrical model of the cloud and local sources of the UV field.
Astroconformer: The prospects of analysing stellar light curves with transformer-based deep learning models
Authors: Pan Jia-Shu , Ting Yuan-Sen , Yu Jie 
Published: January 2024

ABSTRACT
Stellar light curves contain valuable information about oscillations and granulation, offering insights into stars’ internal structures and evolutionary states. Traditional asteroseismic techniques, primarily focused on power spectral analysis, often overlook the crucial phase information in these light curves. Addressing this gap, recent machine learning applications, particularly those using Convolutional Neural Networks (CNNs), have made strides in inferring stellar properties from light curves. However, CNNs are limited by their localized feature extraction capabilities. In response, we introduce Astroconformer, a Transformer-based deep learning framework, specifically designed to capture long-range dependencies in stellar light curves. Our empirical analysis centres on estimating surface gravity (log g), using a data set derived from single-quarter Kepler light curves with log g values ranging from 0.2 to 4.4. Astroconformer demonstrates superior performance, achieving a root-mean-square-error (RMSE) of 0.017 dex at log g ≈ 3 in data-rich regimes and up to 0.1 dex in sparser areas. This performance surpasses both K-nearest neighbour models and advanced CNNs. Ablation studies highlight the influence of receptive field size on model effectiveness, with larger fields correlating to improved results. Astroconformer also excels in extracting νmax with high precision. It achieves less than 2 per cent relative median absolute error for 90-d red giant light curves. Notably, the error remains under 3 per cent for 30-d light curves, whose oscillations are undetectable by a conventional pipeline in 30 per cent cases. Furthermore, the attention mechanisms in Astroconformer align closely with the characteristics of stellar oscillations and granulation observed in light curves.
On using the counting method to constrain the anisotropy of kilonova radiation
Authors: Zhang Siqi , Deng Furen , Lu Youjun 
Published: January 2024

ABSTRACT
A large number of binary neutron star (BNS) mergers are expected to be detected by gravitational wave (GW) detectors and the electromagnetic (EM) counterparts (e.g. kilonovae) of a fraction of these mergers may be detected in multibands by large area survey telescopes. For a given number of BNS mergers detected by their GW signals, the expected numbers of their EM counterparts that can be detected by a survey with given selection criteria depend on the kilonova properties, including the anisotropy. In this paper, we investigate whether the anisotropy of kilonova radiation and the kilonova model can be constrained statistically by the counting method, i.e. using the numbers of BNS mergers detected via GW and multiband EM signals. Adopting simple models for the BNS mergers, afterglows, and a simple two (blue and red)-component model for kilonovae, we generate mock samples for GW detected BNS mergers, their associated kilonovae, and afterglows detected in multibands. By assuming some criteria for searching the EM counterparts, we simulate the observations of these EM counterparts and obtain the EM observed samples in different bands. With the numbers of BNS mergers detected by GW detectors and EM survey telescopes in different bands, we show that the anisotropy of kilonova radiation and the kilonova model can be well constrained by using the Bayesian analysis. Our results suggest that the anisotropy of kilonova radiation may be demographically and globally constrained by simply using the detection numbers of BNS mergers by GW detectors and EM survey telescopes in multibands.
Stability of dusty rings in protoplanetary discs
Authors: Chan Kevin , Paardekooper Sijme-Jan 
Published: January 2024

ABSTRACT
Dust rings in protoplanetary discs are often observed in thermal dust emission and could be favourable environments for planet formation. While dust rings readily form in gas pressure maxima, their long-term stability is key to both their observability and potential to assist in planet formation. We investigate the stability of the dust ring generated by interactions of a protoplanetary disc with a Neptune-sized planet and consider its possible long-term evolution using the FARGO3D Multifluid code. We look at the onset of the Rossby Wave Instability (RWI) and compare how the addition of dust in a disc can alter the stability of the gas phase. We find that with the addition of dust, the rings generated by planet–disc interactions are more prone to RWI and can cause the gas phase to become unstable. The instability is shown to occur more easily for higher Stokes number dust, as it accumulates into a more narrow ring which triggers the RWI, while the initial dust fraction plays a more minor role in the stability properties. We show that the dusty RWI generates vortices that collect dust in their cores, which could be sites for further planetesimal formation. We conclude that the addition of dust can cause a ring in a protoplanetary disc to become more prone to instability leading to a different long-term evolution compared to gas-only simulations of the RWI.
On the likely magnesium–iron silicate dusty tails of catastrophically evaporating rocky planets
Authors: Campos Estrada Beatriz , Owen James E , Jankovic Marija R , Wilson Anna , Helling Christiane 
Published: January 2024

ABSTRACT
Catastrophically evaporating rocky planets provide a unique opportunity to study the composition of small planets. The surface composition of these planets can be constrained via modelling their comet-like tails of dust. In this work, we present a new self-consistent model of the dusty tails: we physically model the trajectory of the dust grains after they have left the gaseous outflow, including an on-the-fly calculation of the dust cloud’s optical depth. We model two catastrophically evaporating planets: KIC 1255 b and K2-22 b. For both planets, we find the dust is likely composed of magnesium–iron silicates (olivine and pyroxene), consistent with an Earth-like composition. We constrain the initial dust grain sizes to be ∼ 1.25–1.75 μm and the average (dusty) planetary mass-loss rate to be ∼ 3$\, M_{\oplus } \mathrm{Gyr^{-1}}$. Our model shows that the origin of the leading tail of dust of K2-22 b is likely a combination of the geometry of the outflow and a low radiation pressure force to stellar gravitational force ratio. We find the optical depth of the dust cloud to be a factor of a few in the vicinity of the planet. Our composition constraint supports the recently suggested idea that the dusty outflows of these planets go through a greenhouse effect–nuclear winter cycle, which gives origin to the observed transit depth time variability. Magnesium–iron silicates have the necessary visible-to-infrared opacity ratio to give origin to this cycle in the high mass-loss state.
Cosmology from weak lensing peaks and minima with Subaru Hyper Suprime-Cam Survey first-year data
Authors: Marques Gabriela A , Liu Jia , Shirasaki Masato , Thiele Leander , Grandón Daniela , Huffenberger Kevin M , Cheng Sihao , Harnois-Déraps Joachim , Osato Ken , Coulton William R 
Published: January 2024

ABSTRACT
We present cosmological constraints derived from peak counts, minimum counts, and the angular power spectrum of the Subaru Hyper Suprime-Cam first-year (HSC Y1) weak lensing shear catalogue. Weak lensing peak and minimum counts contain non-Gaussian information and hence are complementary to the conventional two-point statistics in constraining cosmology. In this work, we forward-model the three summary statistics and their dependence on cosmology, using a suite of N-body simulations tailored to the HSC Y1 data. We investigate systematic and astrophysical effects including intrinsic alignments, baryon feedback, multiplicative bias, and photometric redshift uncertainties. We mitigate the impact of these systematics by applying cuts on angular scales, smoothing scales, signal-to-noise ratio bins, and tomographic redshift bins. By combining peaks, minima, and the power spectrum, assuming a flat-ΛCDM model, we obtain $S_{8} \equiv \sigma _8\sqrt{\Omega _m/0.3}= 0.810^{+0.022}_{-0.026}$, a 35 per cent tighter constraint than that obtained from the angular power spectrum alone. Our results are in agreement with other studies using HSC weak lensing shear data, as well as with Planck 2018 cosmology and recent CMB lensing constraints from the Atacama Cosmology Telescope and the South Pole Telescope.
Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN
Authors: Gabre Jonatan L , Merseburger Peter , Claeys Arne , Siaw Joachim , Bekaert Sarah-Lee , Speleman Frank , Hallberg Bengt , Palmer Ruth H , Van den Eynden Jimmy 
Published: January 2024

Abstract
Neuroblastoma (NB) is the most common cancer in infancy with an urgent need for more efficient targeted therapies. The development of novel (combinatorial) treatment strategies relies on extensive explorations of signaling perturbations in neuroblastoma cell lines, using RNA-Seq or other high throughput technologies (e.g. phosphoproteomics). This typically requires dedicated bioinformatics support, which is not always available. Additionally, while data from published studies are highly valuable and raw data (e.g. fastq files) are nowadays released in public repositories, data processing is time-consuming and again difficult without bioinformatics support. To facilitate NB research, more user-friendly and immediately accessible platforms are needed to explore newly generated as well as existing high throughput data. To make this possible, we developed an interactive data centralization and visualization web application, called CLEAN (the Cell Line Explorer web Application of Neuroblastoma data; https://ccgg.ugent.be/shiny/clean/). By focusing on the regulation of the DNA damage response, a therapeutic target of major interest in neuroblastoma, we demonstrate how CLEAN can be used to gain novel mechanistic insights and identify putative drug targets in neuroblastoma.