bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of image quality on galaxy merger identification with deep learning
Authors: Bickley Robert W , Wilkinson Scott , Ferreira Leonardo , Ellison Sara L , Bottrell Connor , Jyoti Debarpita 
Published: September 2024

ABSTRACT
Studies have shown that the morphologies of galaxies are substantially transformed following coalescence after a merger, but post-mergers are notoriously difficult to identify, especially in imaging that is shallow or low resolution. We train convolutional neural networks (CNNs) to identify simulated post-merger galaxies in a range of image qualities, modelled after five real surveys: the Sloan Digital Sky Survey (SDSS), the Dark Energy Camera Legacy Survey (DECaLS), the Canada–France Imaging Survey (CFIS), the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP), and the Legacy Survey of Space and Time (LSST). Holding constant all variables other than imaging quality, we present the performance of the CNNs on reserved test set data for each image quality. The success of CNNs on a given data set is found to be sensitive to both imaging depth and resolution. We find that post-merger recovery generally increases with depth, but that limiting 5$\sigma$ point-source depths in excess of $\sim 25$ mag, similar to what is achieved in CFIS, are only marginally beneficial. Finally, we present the results of a cross-survey inference experiment, and find that CNNs trained on a given image quality can sometimes be applied to different imaging data to good effect. The work presented here therefore represents a useful reference for the application of CNNs for merger searches in both current and future imaging surveys.
Badminton birdie-like aerodynamic alignment of drifting dust grains by subsonic gaseous flows in protoplanetary discs
Authors: Lin Zhe-Yu Daniel , Li Zhi-Yun , Yang Haifeng , Looney Leslie W , Stephens Ian W , Fernández-López Manuel , Harrison Rachel E 
Published: September 2024

ABSTRACT
Recent (sub)millimetre polarization observations of protoplanetary discs reveal toroidally aligned, effectively prolate dust grains large enough (at least $\sim 100$$\mu$m) to efficiently scatter millimetre light. The alignment mechanism for these grains remains unclear. We explore the possibility that gas drag aligns grains through gas–dust relative motion when the grain’s centre of mass is offset from its geometric centre, analogous to a badminton birdie’s alignment in flight. A simple grain model of two non-identical spheres illustrates how a grain undergoes damped oscillations from flow-induced restoring torques which align its geometric centre in the flow direction relative to its centre of mass. Assuming specular reflection and subsonic flow, we derive an analytical equation of motion for spheroids where the centre of mass can be shifted away from the spheroid’s geometric centre. We show that a prolate or an oblate grain can be aligned with the long axis parallel to the gas flow when the centre of mass is shifted along that axis. Both scenarios can explain the required effectively prolate grains inferred from observations. Application to a simple disc model shows that the alignment time-scales are shorter than or comparable to the orbital time. The grain alignment direction in a disc depends on the disc (sub-)structure and grain Stokes number (St) with azimuthal alignment for large St grains in sub-Keplerian smooth gas discs and for small St grains near the gas pressure extrema, such as rings and gaps.
KiDS-1000 and DES-Y1 combined: cosmology from peak count statistics
Authors: Harnois-Déraps Joachim , Heydenreich Sven , Giblin Benjamin , Martinet Nicolas , Tröster Tilman , Asgari Marika , Burger Pierre , Castro Tiago , Dolag Klaus , Heymans Catherine , Hildebrandt Hendrik , Joachimi Benjamin , Wright Angus H 
Published: September 2024

ABSTRACT
We analyse the fourth data release of the Kilo Degree Survey (KiDS-1000) and extract cosmological parameter constraints based on the cosmic shear peak count statistics. Peaks are identified in aperture mass maps in which the filter is maximally sensitive to angular scales in the range 2–4 arcmin, probing deep into the non-linear regime of structure formation. We interpret our results with a simulation-based inference pipeline, sampling over a broad wCDM prior volume and marginalizing over uncertainties on shape calibration, photometric redshift distribution, intrinsic alignment, and baryonic feedback. Our measurements constrain the structure growth parameter and the amplitude of the non-linear intrinsic alignment model to $\Sigma _8 \equiv \sigma _8\left[\Omega _{\rm m}/0.3\right]^{0.60}=0.765^{+0.030}_{-0.030}$ and $A_{\rm IA}= 0.71^{+0.42}_{-0.42}$, respectively, in agreement with previous KiDS-1000 results based on two-point shear statistics. These results are robust against modelling of the non-linear physics, different scale cuts, and selections of tomographic bins. The posterior is also consistent with that from the Dark Energy Survey Year-1 peak count analysis presented in Harnois-Déraps et al., and hence we jointly analyse both surveys with a common pipeline. We obtain $\Sigma _8^{\rm joint} \equiv \sigma _8\left[\Omega _{\rm m}/0.3\right]^{0.57}=0.759^{+0.020}_{-0.017}$, in agreement with the PlanckwCDM results. The shear-CMB tension on this parameter increases to $3.1\sigma$ when forcing $w=-1.0$, and to $4.1\sigma$ if comparing instead with $S_{8,\Lambda {\rm CDM}}^{\rm joint} = 0.736^{+0.016}_{-0.018}$, one of the tightest constraints to date on this quantity. Residual biases in the photometric redshifts of the DES-Y1 data and in the modelling of small scales physics could lower this tension, however it is robust against other systematics. Limits in the accuracy of our emulator prevent us from constraining $\Omega _{\rm m}$.
Enhanced Golden Gate Assembly: evaluating overhang strength for improved ligation efficiency
Authors: Strzelecki Patryk , Joly Nicolas , Hébraud Pascal , Hoffmann Elise , Cech Grzegorz M , Kloska Anna , Busi Florent , Grange Wilfried 
Published: September 2024

Abstract
Molecular cloning, a routine yet essential technique, relies heavily on efficient ligation, which can be significantly improved using Golden Gate Assembly (GGA). A key component of GGA is the use of type IIS enzymes, which uniquely cleave downstream of their recognition sequences to generate various overhangs, including non-palindromic ones. Recent advancements in GGA include the development of newly engineered enzymes with enhanced activity. Additionally, high-throughput GGA assays, which allow for the simultaneous study of all possible overhangs, have identified optimal GGA substrates with high efficiencies and fidelities, greatly facilitating the design of complex assemblies. Interestingly, these assays reveal unexpected correlations between ligation efficiencies and overhang stabilities. One hypothesis for this observation is that newly hydrolyzed DNA fragments with strong overhangs can readily re-ligate, thereby slowing down the overall process. In this paper, we employ a combination of gel electrophoresis and numerical calculations to test this hypothesis, ultimately determining that it does not hold true under the conditions established by conventional GGA assays. Using an assembly of 10 fragments, we demonstrate that strong overhangs yield higher GGA efficiency, while weak overhangs result in lower efficiency. These findings enable us to propose optimal overhangs for efficient GGA assays, significantly increasing yield.
StableMate: a statistical method to select stable predictors in omics data
Authors: Deng Yidi , Mao Jiadong , Choi Jarny , Lê Cao Kim-Anh 
Published: September 2024

Abstract
Identifying statistical associations between biological variables is crucial to understanding molecular mechanisms. Most association studies are based on correlation or linear regression analyses, but the identified associations often lack reproducibility and interpretability due to the complexity and variability of omics datasets, making it difficult to translate associations into meaningful biological hypotheses. We developed StableMate, a regression framework, to address these challenges through a process of variable selection across heterogeneous datasets. Given datasets from different environments, such as experimental batches, StableMate selects environment-agnostic (stable) and environment-specific predictors in predicting the response of interest. Stable predictors represent robust functional dependencies with the response, and can be used to build regression models that make generalizable predictions in unseen environments. We applied StableMate to (i) RNA sequencing data of breast cancer to discover genes that consistently predict estrogen receptor expression across disease status; (ii) metagenomics data to identify microbial signatures that show persistent association with colon cancer across study cohorts; and (iii) single-cell RNA sequencing data of glioblastoma to discern signature genes associated with the development of pro-tumour microglia regardless of cell location. Our case studies demonstrate that StableMate is adaptable to regression and classification analyses and achieves comprehensive characterization of biological systems for different omics data types.
scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison
Authors: Ferrena Alexander , Zheng Xiang Yu , Jackson Kevyn , Hoang Bang , Morrow Bernice E , Zheng Deyou 
Published: September 2024

Abstract
Single-cell transcriptomics profiling has increasingly been used to evaluate cross-group (or condition) differences in cell population and cell-type gene expression. This often leads to large datasets with complex experimental designs that need advanced comparative analysis. Concurrently, bioinformatics software and analytic approaches also become more diverse and constantly undergo improvement. Thus, there is an increased need for automated and standardized data processing and analysis pipelines, which should be efficient and flexible too. To address these, we develop the single-cell Differential Analysis and Processing Pipeline (scDAPP), a R-based workflow for comparative analysis of single cell (or nucleus) transcriptomic data between two or more groups and at the levels of single cells or ‘pseudobulking’ samples. The pipeline automates many steps of pre-processing using data-learnt parameters, uses previously benchmarked software, and generates comprehensive intermediate data and final results that are valuable for both beginners and experts of scRNA-seq analysis. Moreover, the analytic reports, augmented by extensive data visualization, increase the transparency of computational analysis and parameter choices, while facilitate users to go seamlessly from raw data to biological interpretation. scDAPP is freely available under the MIT license, with source code, documentation and sample data at the GitHub (https://github.com/bioinfoDZ/scDAPP).
Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation
Authors: Xiong Yingying , Lu Zhuoer , Shao Yuyin , Meng Peiyi , Wang Guoli , Zhou Xinwen , Yao Jun , Bao Huimin , Lu Haojie 
Published: September 2024

ABSTRACT
Protein glycosylation, the most universal post-translational modification, is thought to play a crucial role in regulating multiple essential cellular processes. However, the low abundance of glycoproteins and the heterogeneity of glycans complicate their comprehensive analysis. Here, we develop a rapid and large-scale glycopeptide enrichment strategy via bioorthogonal ligation and trypsin cleavage. The enrichment process is performed in one tube to minimize sample loss and time costs. This method combines convenience and practicality, identifying over 900 O-GlcNAc sites from a 500 μg sample. Surprisingly, it allows simultaneous identification of N-glycosites, O-GlcNAc sites, O-GalNAc sites and N-glycans via a two-step enzymatic release strategy. Combined with quantitative analysis, it reveals the distinct O-GlcNAcylation patterns in different compartments during oxidative stress. In summary, our study offers a convenient and robust tool for glycoproteome and glycome profiling, facilitating in-depth analysis to elucidate the biological functions of glycosylation.
Microbes Causing Spinal Epidural Infection in Patients Who Use Drugs
Authors: Pralea Alexander , Has Phinnara , Auld Dianne , Mermel Leonard A 
Published: September 2024

Abstract

Background
The incidence of spine infections has increased due to the surge in injection drug use driven by the opioid epidemic. Few recent studies have evaluated the microbiology of spinal epidural infections among people who inject drugs compared to the microbiology of such infections among the general population.

Methods
We performed a retrospective chart review to identify patients with a spinal epidural abscess or phlegmon unrelated to recent spine surgery between 2015 and 2023.

Results
Of 346 initial records, 277 met inclusion criteria for demographic analyses. Of the 229 patients with microbiologic results, details regarding possible drug use were available in 227 patients. Patients with no documented history of drug use were categorized as non-PWUD, while patients who use drugs (PWUD) were separated based on whether drug use was active or not. Patients with prior histories of injection or noninjection drug use were categorized as nonactive PWUD, while those with injection or snorting drug use reported in the past 3 months were categorized as active PWUD. Thirty-nine percent of patients with spinal epidural infection had substance use disorder. Most patients with monomicrobial cultures were infected with gram-positive, aerobic bacteria (86%). Active PWUD were more likely to have methicillin-resistant Staphylococcus aureus compared to non-PWUD (36% vs 13%, respectively, P = .002). Nonactive PWUD were more likely to have non–Escherichia coli gram-negative bacterial infections than non-PWUD (18% and 4.4%, respectively, P = .01).

Conclusions
More than 1 in 3 patients with a spinal epidural infection unrelated to recent surgery had substance use disorder. These patients are more likely to have infections due to MRSA and gram-negative bacteria other than E coli such as Serratia marcescens.
Healthcare resource utilization and associated cost in patients with metastatic non-small cell lung cancer treated in the immunotherapy era
Authors: Apter Lior , Sharman Moser Sarah , Gazit Sivan , Chodick Gabriel , Hoshen Moshe , Greenberg Dan , Siegelmann-Danieli Nava 
Published: September 2024

Abstract

Background
Treatment approach for metastatic non-small cell lung cancer (mNSCLC) has revolutionized in the recent decade with the introduction of immunotherapy and targeted medications in first-line (1L) therapy. We present real-world data on clinical outcomes and direct healthcare resource utilization (HCRU) and cost in a 2.7-million-member Israeli health provider.

Patients and methods
Newly diagnosed mNSCLC patients between January 2017 and December 2020 were categorized by 1L treatment: platinum-based chemotherapy, targeted therapy, or immunotherapy. HCRU and costs were calculated based on the Ministry of Health Prices and were assessed at a minimum of 6 months’ follow-up (cutoff: 30 June 2021).

Results
A total of 886 patients were included in the study: 40.6% female, median age 68 years (IQR 61-74), 24.3% never smokers, 80.6% with adenocarcinoma, and 54% with a 0-1 performance status. The median follow-up was 27.12 months (95% CI, 24.7-29.6) and the median duration of first-line (1L) treatment was 2.3 months for platinum-based chemotherapy (n = 177), 12.3 months for targeted therapy (n = 255), and 4.8 months for immunotherapy (n = 463). The median overall survival was 9.09, 27.68, and 12.46 months, respectively. Total 1L costs were driven by radiotherapy for platinum-based chemotherapy and medication for targeted therapy or immunotherapy. Total costs for deceased patients over the entire follow-up were €121 155, €129 458, and €110 716, respectively.

Conclusion
The treatment of mNSCLC carries a high economic burden, primarily driven by first-line therapy, especially with targeted and immune therapies. Further studies are needed to evaluate the impact of innovative treatments on the disease management costs of mNSCLC.
Race-Making Festivities in Brandenburg-Prussia, 1652–1750
Authors: Bevilacqua Alexander 
Published: September 2024

Abstract
The four generations of Hohenzollern rulers who transformed the electorate of Brandenburg into the kingdom of Prussia — a regional player into a great power — all employed Black men at their courts and in their armies. Through court performance, including processions and tournaments, as well as through artistic commissions, the Brandenburgian rulers adapted existing traditions of representing and displaying human difference and hierarchy for their own ends. As the only member of the Holy Roman Empire to join the Atlantic slave trade, Brandenburg had a particular commitment to staging its global aspirations, both during its slave-trading venture and after it failed. Brandenburg-Prussia’s belated rise exhibits with particular clarity the importance to early modern statecraft not just of foreign enterprise but of its courtly representations. Through the display and representation of Black people in performance and art, the rulers of Brandenburg participated in forms of ‘race-making’ that altered the perception not only of sub-Saharan Africans but of the princely lineage as well.
Clinical characteristics influencing timing of cerebral palsy diagnosis in neonatal follow-up
Authors: Journault Marina M , Leijser Lara M , McLeod Scott A , Tang Selphee , Fiedrich Elsa , Moe Amanda M , Benlamri Amina A 
Published: September 2024

Abstract

Objectives
To describe clinical characteristics influencing the timing of cerebral palsy (CP) diagnosis in a traditional neonatal follow-up clinic (NFC) setting.

Methods
Retrospective observational cohort study involving preterm infants, born &lt;29 weeks gestation and/or birthweight &lt;1000 g between January 2005 and December 2014, with CP and followed in Calgary’s NFC. Infant data were collected, including demographics, perinatal and neonatal parameters, cranial ultrasound (cUS) results, co-occurring conditions, and CP characteristics (timing of suspicion and diagnosis, type, topography, distribution, and Gross Motor Function Classification System [GMFCS] level). This cohort was divided into two groups, early (diagnosed &lt;19 months corrected age [CA]) and late (diagnosed ≥19 months CA), based on the median age of CP diagnosis, and characteristics were compared.

Results
A total of 99 infants met the inclusion criteria. Median age at first CP suspicion was 9 months CA (interquartile range [IQR] 14) and median age at diagnosis was 19 months CA (IQR 17), with median time lag from suspicion to diagnosis of 6 months (IQR 12). CP characteristics associated with diagnosis at an earlier age included higher GMFCS level, mixed type (compared to spastic only), and upper and lower extremities involvement. Infant characteristics, severity of cUS results, and co-occurring conditions were not different between early and late groups.

Conclusions
CP diagnosis timing is affected by GMFCS level, motor type, and distribution. Especially in infants with CP involving less motor impairment, there is a prolonged delay between CP suspicion and formal diagnosis. This gap may be amenable to quality improvement initiatives aimed at targeted implementation of early assessment tools.
Berezinskii–Kosterlitz–Thouless Transition of the Two-Dimensional XY Model on the Honeycomb Lattice
Authors: Jiang Fu-Jiun 
Published: September 2024

Abstract
The Berezinskii–Kosterlitz–Thouless (BKT) transition of the two-dimensional $XY$ model on the honeycomb lattice is investigated using both the techniques of Neural network (NN) and Monte Carlo simulations. It is demonstrated in the literature that, with certain plausible assumptions, the associated critical temperature $T_{\text{BKT,H}}$ is found to be ${1}/{\sqrt{2}}$ exactly. Surprisingly, the value of $T_{\text{BKT,H}}$ obtained from our NN calculations is 0.572(3), which deviates significantly from ${1}/{\sqrt{2}}$. In addition, based on the helicity modulus, the $T_{\text{BKT,H}}$ determined is 0.576(4), agreeing well with that resulting from the NN estimation. It will be interesting to carry out a more detailed analytic calculation to obtain a theoretical value consistent with the numerical result reached here.
Health literacy of rheumatology patients in three clinics in Australia and its association with sociodemographic and clinical characteristics
Authors: Tsai Ted Yi-Eng , Podgorski Alexander , Al-Heilfi Anmar , Hassett Geraldine , Gorelik Alexandra , Buchbinder Rachelle , Gibson Kathryn 
Published: September 2024

Abstract

Objectives
To describe and compare health literacy (HL) using contrasting instruments of Rapid Estimate of Adult Literacy in Medicine (REALM) and the Health Literacy Questionnaire (HLQ) in patients attending three Australian rheumatology clinics and their associations with sociodemographic and clinical characteristics.

Methods
We conducted a cross-sectional study of rheumatology patients at Liverpool (Sydney) and Canberra public hospital clinics and a private Liverpool clinic using the REALM test and HLQ sociodemographic and clinical questionnaires. One-way analysis of variance and multivariate ordinal and binary logistic regressions were used to examine the association between HL and sociodemographic and clinical factors.

Results
A total of 278 people participated (111 Liverpool public, 112 private, 55 Canberra public clinic). Compared with Canberra, Liverpool patients were older, non-native English speakers, had less than a tertiary education and were more likely to have comorbidities. A total of 40% of Liverpool public, 29% of private and 13% of Canberra patients had suboptimal REALM HL scores (P &lt; 0.05). Lower REALM scores were associated with male gender, &lt;10 years of education, being born outside Australia/New Zealand and English as a secondary language, but was not associated with clinical characteristics. All nine HLQ domain scores did not differ across sites despite intergroup comparisons as stratified by REALM bands. Completing 10 years of schooling was associated with better scores in three HLQ scales: ‘Navigating the healthcare system’ (P = 0.009), ‘Ability to find information’ (P &lt; 0.001) and ‘Reading and understanding information’ (P &lt; 0.001).

Conclusion
Patient HL as measured by the REALM differed across sites, explained by differences in gender distribution, country of birth, English as the primary language and years of education. HL as measured by the HLQ did not differ across sites and was more informative for understanding differing patient HL needs.