bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling the migratory patterns of scarlet flycatchers using citizen science databases
Authors: Thibaudier Julian , Lopes Leonardo Esteves , Cunha Filipe C. R. 
Published: January 2025

Abstract
The migratory patterns of many Neotropical bird species remain largely unknown. Numerous logistic challenges prevent such studies, from research costs, often prohibitively expensive to Neotropical research institutions, to equipment weight limitations. Therefore, it is paramount to explore new possibilities in the field of migratory bird research such as the abundant records from citizen science platforms. In this study, we investigated the spatial and temporal migratory patterns of the scarlet flycatcher Pyrocephalus rubinus using two citizen science platforms: eBird and WikiAves, which provided 40,837 records of the species. Our findings indicated that scarlet flycatchers arrive at the wintering grounds in central-western Brazil, central-eastern Bolivia, and eastern Peru around May and June. We also found that scarlet flycatchers arrive at breeding grounds in central and eastern Argentina, southern Brazil, and Uruguay between August and October, where it stays in the months thereafter (November, December, January). The year-round records of the species in northern Argentina and southern Paraguay deserve further studies. Understanding migratory patterns is imperative for predicting population dynamics and climate influence on the breeding biology of these species in the face of a rapidly changing world.
Regulating Restraint: Legal Oversight of Seclusion in Canadian Forensic Psychiatric Hospitals
Authors: Perryman Benjamin 
Published: January 2025

AbstractProlonged solitary confinement is inconsistent with international minimum rules for the treatment of prisoners and may constitute cruel, inhuman, or degrading treatment. In a series of recent cases, appellate courts in Canada have curtailed the use of prolonged solitary confinement in prisons on the basis that such detention is “grossly disproportionate” and “cruel and unusual.” But these judgments in the penal context have not resulted in comparable regulation of seclusion in forensic psychiatric hospitals. Seclusion in these contexts is often comparable to solitary confinement in prison and carries with it the same serious risks of lasting harm. This article comparatively reviews the legislative and policy framework that regulates the use of seclusion in different provinces in Canada. The article argues that case law on prolonged solitary confinement in the penal context has application to the forensic psychiatric context and that a failure to more closely regulate the use of seclusion may render this type of mental health legislation and treatment unconstitutional.
Donna Elvira and the Dark Places of the Heart
Authors: BANDY DORIAN 
Published: January 2025

AbstractDespite the density of scholarly engagement with Mozart’s operas, Donna Elvira’s aria ‘Mi tradì quell’alma ingrata’, composed for the 1788 Viennese production of Don Giovanni, has received little sustained, critical attention. Yet this oversight is unjustified, particularly considering the aria’s many stylistic elements that expand beyond the musical language of the original Prague Don Giovanni, and which therefore show Mozart not only deepening Elvira’s characterization but probing new compositional horizons. This article undertakes a thorough, analytic examination of ‘Mi tradì’, focusing especially on its evocation of Elvira’s subjectivity and self-consciousness, and paying particular attention to formal rhetoric and topical reference, both of which, by suggesting affinities with genres such as variation and the free fantasia, move the aria significantly beyond the expressive world often associated with Mozart’s vocal writing. The article closes with brief speculations on the relationship between ‘Mi tradì’ and the composer’s career aspirations in the late 1780s.
Racial disparities in timing and outcomes for patients undergoing staged single ventricle palliation: a single institution report
Authors: Beshish Asaad G. , Adamson Marissa , Brady Maximilian , Menon Ambika , Qian Joshua , Golloshi Klevi , Cote Olivia , Gathoo Asmita , Zinyandu Tawanda , Nayi Pranay , Ferguson M. Eric , John Mohan , Shaw Fawwaz R. , Deshpande Shriprasad R. , Maher Kevin O. 
Published: January 2025

AbstractBackground:Racial disparities in healthcare have been well documented in the United States. We hypothesise that there will be a racial variance in different clinical variables in single-ventricle patients through stages of palliation.Materials and Methods:Retrospective single-centre study stratified all single-ventricle patients who reached stage 2 palliation by race: Black and White. Other races were excluded. Demographic and clinical characteristics were compared, alongside follow-up survival data. Primary outcomes were progression to Fontan and overall survival.Results:Among 526 patients, 325 (61.8%) were White, and 201 (38.2%) were Black. Median age at stage 2 palliation was 150 days for White and 165 for Black patients (p = 0.005), with similar weights. Black patients exhibited higher median cardiopulmonary bypass times (87 vs. 74 minutes, p = 0.001) and a greater frequency of genetic syndromes (30.1% vs. 22.1%, p = 0.044). No significant differences were observed in outcomes between groups from stage 2 to stage 3, pre-stage 3 cardiac catheterisation variables, or perioperative outcomes. Multivariable regression analysis identified hypoplastic pulmonary arteries as the risk factor for mortality after stage 2. Survival analysis showed no difference in survival by race; however, occurrence of combined cardiovascular event was significantly higher in Black race.Conclusions:Significant racial disparities exist among single-ventricle patients regarding the timing of stage 2 palliation, cardiopulmonary bypass duration, and frequency of genetic syndromes. Black race was a risk factor for sub-optimal long-term outcome, although perioperative mortality was similar. These race-related factors warrant further studies to improve our understanding of the impact of race on outcomes.
Peat Depth and Carbon Storage of the Hudson Bay Lowlands, Canada
Authors: Li Yiyao , Han Daorui , Rogers Cheryl A. , Finkelstein Sarah A. , Hararuk Oleksandra , Waddington James M. , Barreto Carlos , McLaughlin James W. , Snider James , Gonsamo Alemu 
Published: January 2025

AbstractThe Hudson Bay Lowlands (HBL) are recognized as the second largest peatland complex in the world. Due to variability in peat thickness across a large and heterogeneous landscape, the existing carbon (C) storage estimates for the HBL may contain large uncertainty. Here, we use geospatial variables that are associated with HBL peat formation, age, accumulation, and occurrence to understand the driving factors for peat depth variability and map peat depth and C storage at 30 m spatial resolution. The estimated average peat depth of HBL is 184(±48) cm with 90% of values falling between 89 and 264 cm. Based on the spatially explicit peat depth, the HBL total C storage is estimated to be 30(±6) Pg. Distance to the coastline is the most important indicator of peat depth where the depth increases with distance further away from Hudson Bay coastline, confirming that the time since peat formation is closely related to peat depth.
Permafrost Response in Northern High‐Latitude Regions to 1.5°C Warming and Overshoot Scenarios Achieved via Solar Radiation Modification
Authors: Ji Duoying , Cui Min , Chen Yangxin , Dai Yongjiu 
Published: January 2025

AbstractThe thawing of carbon‐rich northern high‐latitude permafrost might unleash irreversible changes in the Earth's climate system. Previous studies have suggested that solar radiation modification (SRM) can significantly slow the degradation of permafrost, potentially restoring its extent and soil carbon stocks to levels comparable to those under equivalent global warming caused by greenhouse gas increases alone. However, this study identifies that the efficacy of SRM in mitigating permafrost degradation is contingent upon the warming trajectory and the timing of SRM intervention. Employing SRM to keep global warming at a maximum of 1.5°C can substantially reduce permafrost degradation; however, simulations suggest that by 2300, approximately half of the permafrost area reduction and one‐third of the carbon losses expected under the high‐emissions SSP5‐8.5 scenario would still take place. By employing SRM to achieve a return to 1.5°C warming stabilization levels after a temperature overshoot, it is possible to effectively restore the permafrost area. However, the lost permafrost carbon cannot be regained. Additionally, the soil carbon within permafrost regions displays contrasting trends between the phases of overshoot and subsequent stabilization. Our simulations show that achieving the 1.5°C warming target after a 4°C temperature overshoot could necessitate up to 7% increase in SRM application due to permafrost carbon release. Moreover, perturbed parameter ensemble simulations indicate that the key parameter influencing the uncertainty of soil carbon losses in permafrost regions under 1.5°C warming and overshoot scenarios is distinct from that under the SSP5‐8.5 scenario.
Evolution of Basal Force Fluctuations and Seismic Signals of Granular Flows and Their Proxy: Insights From Laboratory Flume Experiments
Authors: Li Wei , Wang Dongpo , Doi Issei , Wang Gonghui , Zhang Zhen , Yan Shuaixing , He Siming 
Published: January 2025

AbstractThe forces exerted by geophysical granular flows on Earth's surface, and the resulting seismic signals, can be used to monitor natural geohazards and understand their dynamic evolution and characteristics. Substantial research has focused on linking basal force fluctuations and seismic signals to granular flow dynamics. However, the mechanisms behind the generation and evolution of seismic signals remain incompletely understood. In this study, we conducted laboratory flume experiments to gain insights into the evolution and characteristics of basal force fluctuations and seismic signals and explored their relationship with the macroscopic properties of granular flows. Our results show that the shear and normal components of basal force fluctuations exhibit different behavior during flow evolution, which are related to variations in flow velocity fluctuations. As the granular flow moves downstream, shear basal force fluctuations decrease due to weakening velocity fluctuations, whereas normal force fluctuations increase. Similar to basal force fluctuations, seismic signals follow a generalized Pareto distribution. Basal force fluctuations and seismic signals are strongly nonlinearly related to the bulk flow properties, indicating that thicker, denser and faster flows generate stronger basal force fluctuations and more intense seismic signals. However, particle size significantly influences this relationship. We demonstrate that the inertial number, characterizing the macroscopic rheological properties of granular flows, can unify basal force fluctuations and seismic signals across different particle sizes, exhibiting a negative correlation on the temporal scale. This implies that the macroscopic rheological behavior of granular flows may provide critical insights into the mechanisms of generation and evolution of seismic signals.
Acoustic frequency comb generation on a composite diamond/silicon microcantilever in ambient air
Authors: Zhao Zhixin , Li Yanyan , Zhang Wangyang , Luo Wenyao , Liu Duo 
Published: January 2025

Abstract
Acoustic frequency combs (AFCs) contain equidistant coherent signals with unconventional possibilities on metrology. Previously, implementation of AFCs on mechanical microresonators with large air damping loss is difficult, which restricted their atmospheric applications. In this work, we explore the potentials of a composite diamond/silicon microcantilever for parametric generation of AFCs in ambient air. We discover that the diamond layer provides a viable route to reduce the linewidth of the primary flexural mode, yielding a 7.1-times increase of the quality factor. We develop a parametric driving scheme that enables generation of AFCs through injection locking and sequential nonlinear dynamic transitions involving subharmonic synchronization (Arnold tongue), and chaotic dynamics. Ultimately, we realize AFCs with a frequency range extending 800 kHz in the air. This work advances the understanding of AFCs and provides a viable route towards their applications in ambient air for high precision metrology.
Human ACE2 transgenic pigs are susceptible to SARS-CoV-2 and develop COVID-19-like disease
Authors: Chau Long Fung , Lillico Simon , Opriessnig Tanja , Blake Rosemary , Tardy Luc , Lee Chen-Hsuin , Maxwell Scott , Warren Claire , Thornton Elizabeth , Mclaughlin Catherine L. , McLachlan Gerry , Tait-Burkard Christine , Fletcher Sarah , Anderson Stephen , Brown Sharon , Gibbard Louise , Tzelos Thomas , MacMillan-Christensen Dawn , Baillie J. Kenneth , Dorward David A. , Griffiths David J. , Grey Finn 
Published: January 2025

Abstract
Animal models that accurately reflect COVID-19 are vital for understanding mechanisms of disease and advancing development of improved vaccines and therapeutics. Pigs are increasingly recognized as valuable models for human disease due to their genetic, anatomical, physiological, and immunological similarities to humans, and they present a more ethically viable alternative to non-human primates. However, pigs are not susceptible to SARS-CoV-2 infection which limits their utility as a model. To address this, we have developed transgenic pigs expressing human ACE2 that are susceptible to SARS-CoV-2 infection. Following challenge, clinical signs consistent with COVID-19, including fever, coughing and respiratory distress were observed, with virus replication detected in the nasal turbinates, trachea and lungs up to the study endpoint, seven days post-infection. Notably, examination of tissues revealed immunopathology in the lungs consistent with histological changes observed in fatal human COVID-19 cases. This study establishes human ACE2 transgenic pigs as a large animal model that accurately reflects many aspects of COVID-19 disease.
MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model
Authors: Jeong Yunhee , Gerhäuser Clarissa , Sauter Guido , Schlomm Thorsten , Rohr Karl , Lutsik Pavlo 
Published: January 2025

Abstract
DNA methylation (DNAm) is a key epigenetic mark that shows profound alterations in cancer. Read-level methylomes enable more in-depth analyses, due to their broad genomic coverage and preservation of rare cell-type signals, compared to summarized data such as 450K/EPIC microarrays. Here, we propose MethylBERT, a Transformer-based model for read-level methylation pattern classification. MethylBERT identifies tumour-derived sequence reads based on their methylation patterns and local genomic sequence, and estimates tumour cell fractions within bulk samples. In our evaluation, MethylBERT outperforms existing deconvolution methods and demonstrates high accuracy regardless of methylation pattern complexity, read length and read coverage. Moreover, we show its applicability to cell-type deconvolution as well as non-invasive early cancer diagnostics using liquid biopsy samples. MethylBERT represents a significant advancement in read-level methylome analysis and enables accurate tumour purity estimation. The broad applicability of MethylBERT will enhance studies on both tumour and non-cancerous bulk methylomes.
Robust quantum spin liquid state in the presence of giant magnetic isotope effect in D3LiIr2O6
Authors: Takayama T. , Gibbs A. S. , Kitagawa K. , Matsumoto Y. , Ishii K. , Kato A. , Takano R. , Bette S. , Dinnebier R. , Takagi H. 
Published: January 2025

Abstract
The deuterium isotope effect on the honeycomb iridate H3LiIr2O6, a quantum spin-orbit-entangled liquid, was examined by synthesizing D3LiIr2O6. The structural refinements indicate the different character of the interlayer OH and OD bonds, which results in a giant isotope effect on the magnetic interactions; the antiferromagnetic Curie-Weiss temperature |θ
CW| of D3LiIr2O6 increases to ~ 170 K from ~ 100 K of H3LiIr2O6. Nevertheless, the quantum liquid state is robust against the deuterium isotope exchange in contrast to the theoretical prediction that the Kitaev spin liquid is stable only for a limited phase space of magnetic interactions. The bond- and site disorders associated with disordered OD(H) bonds, in combination with Kitaev physics, may play a role in realizing the quantum liquid state.
Functionally-informed fine-mapping identifies genetic variants linking increased CHD1L expression and HIV restriction in monocytes
Authors: Tough Riley H. , McLaren Paul J. ,   The International Collaboration for the Genomics of HIV
Published: January 2025

Abstract
Human Immunodeficiency Virus Type 1 (HIV) set-point viral load is a strong predictor of disease progression and transmission risk. A recent genome-wide association study in individuals of African ancestries identified a region on chromosome 1 significantly associated with decreased HIV set-point viral load. Knockout of the closest gene, CHD1L, enhanced HIV replication in vitro in myeloid cells. However, it remains unclear if HIV spVL associated variants are associated with CHD1L gene expression changes. Here we apply a heuristic fine-mapping approach to prioritize combinations of variants that explain the majority of set-point viral load variance and identify variants likely driving the association. We assess the combined impact of these variants on CHD1L regulation using publicly available sequencing studies, and test the relationship between CHD1L expression and set-point viral load using imputed CHD1L expression from monocytes. Taken together, this work characterizes genetically regulated CHD1L expression and further expands our knowledge of CHD1L-mediated HIV restriction in monocytes.
Comparison of 1D and 3D volume measurement techniques in NF2-associated vestibular schwannoma monitoring
Authors: Gugel Isabel , Aboutaha Nuran , Pfluegler Bianca , Ernemann Ulrike , Schuhmann Martin Ulrich , Tatagiba Marcos , Grimm Florian 
Published: January 2025

Abstract
To compare 1D (linear) tumor volume calculations and classification systems with 3D-segmented volumetric analysis (SVA), focusing specifically on their effectiveness in the evaluation and management of NF2-associated vestibular schwannomas (VS). VS were clinically followed every 6 months with cranial, thin-sliced (< 3 mm) MRI. We retrospectively reviewed and used T1-weighted post-contrast enhanced (gadolinium) images for both SVA and linear measurements. 3D-SVA was performed manually or combined with semiautomated segmentation by using axial planes. The maximum linear dimensions (MLD) were determined in three dimensions (anteroposterior, transverse, and craniocaudal planes) using axial and coronal planes. The MLD was cubed (MLD3), and orthogonal analysis (OA) was derived to establish comparability with the SVA. The Hannover and Koos classification was used to depict the size ratio in each MRI and tumor. A linear regression model was performed to compare 1D/classification systems to SVA, and the percentage deviation change of MLD3 and OA to SVA was established using a one-way multivariate variance analysis. 2586 SVA and 10344 linear measurements were performed in a cohort of 149 NF2 patients and 292 associated VS. All measurement techniques (MLD3, OA, KOOS, and Hannover) significantly (and strongly, r2 > 0.5) correlated with SVA (p < 0.001). The OA showed an even stronger positive correlation than the MLD3 to SVA. Smaller classified tumors (T1/T2, K1/K2) exhibited a low-moderate positive correlation (r2 = 0.23–0.44) compared to medium-sized (T3, K2/3) and large tumors (T4, K4; r2 = 0.54–0.76). Pre- and postoperative MLD3 and OA statistically significantly predict SVA (p < 0.001), but the postoperative correlation was weaker, particularly for MLD3 to SVA values. All analyses showed a large scatter range. In the percentage deviation analysis of MLD3 and OA from SVA, small tumors (K1/K2, T1/T2) were overestimated. Compared to the SVA, the MLD3 and especially the OA are a time-saving alternative for monitoring the tumor volume of NF2-associated VS. However, the scatter range in small/surgically reduced tumors is enormous. For this reason, they are not recommended for monitoring off-label therapy with Bevacizumab or for treatment decisions depending on a precise assessment of tumor volume and growth. Developing deep learning-based volume determinations in the future is essential to reduce SVA’s time intensity.
Sociodemographic factors associated with dental students knowledge and attitudes regarding disinfection as a control measure to reduce the spread of COVID-19
Authors: Silva-Robles Geanella , Briceño-Vergel Gissela , Aroste-Andía Rosa , Hernández-Huamaní Emily , Ladera-Castañeda Marysela , Castro-Rojas Miriam , Gavilán-Chávez Percy , Cervantes-Ganoza Luis , Cayo-Rojas César 
Published: January 2025

Abstract
Despite maintaining a lower mortality rate and greater control of victims infected by COVID-19, the world’s population and science are still confronted with this coronavirus. Therefore, the aim was to assess the association between sociodemographic factors and the level of knowledge and attitudes of dental students regarding disinfection as a control measure to reduce the spread of COVID-19. This cross-sectional study evaluated 503 dental students from the capital city and one Peruvian province between February and June 2022. A validated 13-item questionnaire was used. A Poisson regression model with robust variance was used to evaluate the influence of the variables sex, age, year of study, marital status, place of origin, death of a family member due to COVID-19, and history of COVID-19, with the level of knowledge and attitudes of the dental students, considering a significance level of p < 0.05. Of the total participants, 14.3% showed sufficient knowledge, and 89.3% showed positive attitudes regarding disinfection as a control measure to reduce the spread of COVID-19. Furthermore, those from the capital city were 52% less likely to have sufficient knowledge regarding disinfection as a control measure to reduce the spread of COVID-19, compared to those from the province (APR = 0.48; 95% CI: 0.31–0.75). Moreover, none of the variables considered in this study were significantly associated with attitudes toward this topic (p > 0.05). A minority of dental students presented sufficient knowledge, while the majority presented positive attitudes regarding disinfection as a control measure to reduce the spread of COVID-19. In addition, being from the capital city was a limiting factor for sufficient knowledge. The variables sex, age, year of study, marital status, place of origin, death of a family member due to COVID-19, and history of COVID-19 were not influential factors for positive attitudes on this topic.