bluuebunny/crossref_metadata_2025 huggingface dataset:
Inqasm: InQuIR compiler to NetQASM
Authors: Vázquez-Pérez Jorge , Cardama F. Javier , Piñeiro César , Pichel Juan C. , Pena Tomás F. , Gómez Andrés
Published: January 2025

Quantum computing is a rapidly evolving field, with almost every aspect open to change or improvement. This includes moving from using a single quantum processing unit to interconnecting multiple quantum processing units (or several of them), establishing a new paradigm called distributed quantum computing and increasing the overall computing capability. Some research is already underway in this area to prepare the ground for an eventual architecture with these characteristics. This is the case of InQuIR (Nishio and Wakizaka in arXiv:2302.00267 2023) and NetQASM (Dahlberg et al in QST 7:035023 2022), two languages developed for distributed quantum computing. This paper presents the development of the InQASM compiler with the aim of translating code from the InQuIR language to NetQASM, establishing a compilation stack for the new distributed paradigm. An example of this compilation and a simulation of the compiled code are shown to showcase it.
E2CNN: entity-type-enriched cascaded neural network for Chinese financial relation extraction
Authors: Li Mengfan , Shi Xuanhua , Qiao Chenqi , Huang Xiao , Wang Weihao , Wan Yao , Zhang Teng , Jin Hai
Published: January 2025

Knowledge Graphs (KGs) are pivotal for effectively organizing and managing structured information across various applications. Financial KGs have been successfully employed in advancing applications such as audit, anti-fraud, and anti-money laundering. Despite their success, the construction of Chinese financial KGs has seen limited research due to the complex semantics. A significant challenge is the overlap triples problem, where entities feature in multiple relations within a sentence, hampering extraction accuracy–more than 39% of the triples in Chinese datasets exhibit the overlap triples. To address this, we propose the Entity-type-Enriched Cascaded Neural Network (E2CNN), leveraging special tokens for entity boundaries and types. E2CNN ensures consistency in entity types and excludes specific relations, mitigating overlap triple problems and enhancing relation extraction. Besides, we introduce the available Chinese financial dataset FinCorpus.CN, annotated from annual reports of 2,000 companies, containing 48,389 entities and 23,368 triples. Experimental results on the DUIE dataset and FinCorpus.CN underscore E2CNN’s superiority over state-of-the-art models.
Genomic profiling at a single center cracks the code in inborn errors of immunity
Authors: Andriano Alessandro , Desantis Vanessa , Marasco Carolina , Marzollo Antonio , Bresolin Silvia , Resta Nicoletta , Di Marzo Lucia , Pappagallo Fabrizio , Mascolo Antonella , Caradonna Ingrid Catalina , D’Amore Simona , Vacca Angelo , Solimando Antonio Giovanni
Published: January 2025

Inborn errors of immunity (IEI) entail a diverse group of disorders resulting from hereditary or de novo mutations in single genes, leading to immune dysregulation. This study explores the clinical utility of next-generation sequencing (NGS) techniques in diagnosing monogenic immune defects. Eight patients attending the immunodeficiency clinic and with unclassified antibody deficiency were included in the analysis. Clinical records, immune characteristics, and family histories were reviewed, and a target gene panel (TGP) sequencing was performed to identify pathogenic variants. TGPs identified seven variants in TNFRSF13B (TACI), CARMIL2, STAT1, STAT3, and ORAI1 genes. These findings provided definitive diagnoses and proper prognostic assessment. Patients exhibited a wide range of clinical manifestations, including recurrent infections, autoimmune cytopenias, and organ-specific complications. The genetic diversity observed highlights the importance of genetic testing in diagnosing IEIs and tailoring treatments. This study underscores the role of TGPs in diagnosing IEIs, revealing significant genetic heterogeneity and phenotypic variability. They offer a precise tool for identifying underlying genetic defects, facilitating personalized medicine approaches, and eventually improving patient outcomes. The findings emphasize the need for comprehensive genetic testing to uncover novel pathogenic variants, enhancing our understanding of immune system dysfunction. NGS is a critical tool for the management of IEI, enabling precise diagnosis and personalized treatment strategies. Despite resource limitations, the progressive affordability is likely to expand its clinical utility, ultimately improving patient care and advancing the field of immunology. In the meantime, accurate phenotypic assessment is essential for resource optimization and case prioritization.
Archaeological Ethnography of Indigenous Heritage Rights: Emergent Realities around the Petroglyph of the ‘Chiqui’ in Amaicha del Valle (NW Argentina)
Authors: Orlandi Francesco
Published: January 2025

This article aims to contribute to an ethical and post-disciplinary reflection in indigenous and postcolonial archaeologies. Adopting the relational perspective of political ontology unravels the complexities behind the seemingly superficial conflicts over the interpretation of a piece of rock art and the failed implementation of the solar energy project in the Indigenous Community Amaicha del Valle. The juxtaposition of state-authorised and place-based narratives and political actions brings to the fore conflicting perspectives of heritage, rights and indigeneity. Through ethnohistorical and early archaeological accounts from the Calchaquí Valleys, the research reveals the epistemic disavowal of Indigenous histories and lifeworlds as the Argentine state established its national sovereignty and development models between the late nineteenth and mid-twentieth centuries. The case study also draws on archaeological ethnography to highlight generative spaces of knowledge and articulation across divergence and materiality, and that conflicting heritage ontologies can generate new cultural-political forms that diverge from the established consensus.
Re-scaling images using a SVD-based approach
Authors: Motylinski M. , Plater A. J. , Higham J. E.
Published: January 2025

There are many instances in computer science where computational operations must be performed on matrices of different sizes. In the field of machine learning, particularly when interpreting images, it is often necessary to resize and re-scale images to achieve higher resolutions. While there are various methods for this, they typically involve fitting a simple linear or cubic model to scale the image. The singular value decomposition (SVD) is a powerful tool for dimension reduction and projection. Our proposed state-of-the-art method leverages the capabilities of SVD to create a technique for re-scaling images. This method is primarily based on modifications of the eigenvectors derived from SVD. Previous work has shown that by editing only these Eigenvectors, it is possible to minimize error propagation through the images. When applied to several well-known image processing tasks, it is possible to scale an image with reduced error compared to the current state-of-the-art methods. Additionally, we show that our method can improve the results of machine learning approaches.
In Situ Neutron Diffraction Study of Strain Evolution and Load Partitioning During Elevated Temperature Tensile Test in HIP-Treated Electron Beam Powder Bed Fusion Manufactured Ti-6Al-4V
Authors: Pandian K. , Neikter M. , Ekh M. , Harjo S. , Kawasaki T. , Woracek R. , Hansson T. , Pederson R.
Published: January 2025

To manufacture almost fully dense components, electron beam powder bed fusion of Ti-6Al-4V is typically combined with post-heat treatment, such as hot isostatic pressing (HIP). The standard HIP treatment performed at 920°C and 100 MPa for 2 h results in coarsening of the microstructure and impacting the yield strength. A low-temperature HIP treatment performed at 800°C and 200 MPa for 2 h resulted in limited coarsening and comparable yield strength to as-built material. A coarser microstructure is detrimental to tensile properties. Tensile testing at different temperatures revealed that thermal activation of different slip systems could possibly affect the elongation behavior, demanding additional investigation. Performing in situ neutron time of flight diffraction during tensile testing provides data to analyze strain evolution and load partitioning in the crystal lattice, which includes the slip planes. A two-phase elastic–plastic self-consistent model has been used to analyze and compare the experimental results. The lattice strain evolution results indicated that the basal slip {0 0 0 2} was activated at 20°C while the pyramidal slip {1 0 

$$\overline{1 }$$

1
¯

 1} was first activated during loading at 350°C. Load partitioning results showed that the β phase endures higher stresses than the α phase in the plastic regime.
Associations Between Lead and Cadmium Exposure and Subclinical Cardiovascular Disease in U.S. Adults
Authors: Liu Lin , Xu Aimin , Cheung Bernard M. Y.
Published: January 2025

The impact of lead and cadmium exposure on subclinical cardiovascular disease (CVD), indicated by elevated high-sensitivity cardiac troponin (hs-cTnT) and N-terminal pro b-type natriuretic peptide (NT-proBNP) remains uncertain. We analyzed data from participants aged 20 and older, without overt CVD, in the National Health and Nutrition Examination Survey (NHANES; 1999–2004). Elevated lead and cadmium levels were defined as 3.5 μg/dL and 1.0 μg/L (inductively coupled plasma mass spectrometry) and 3.8 μg/dL and 0.9 μg/L (atomic absorption spectrometry), respectively. Elevated hs-cTnT was ≥ 19 ng/L, and elevated NT-proBNP was ≥ 125 pg/mL. Multivariate logistic regression estimated the odds ratios (OR) and 95% confidence intervals (CI) for elevated biomarkers. Among 10,197 participants (mean age 48.8 years; 50.3% female), 5.3% had elevated hs-cTnT and 19.4% had elevated NT-proBNP. Elevated blood lead was associated with increased ORs for elevated hs-cTnT (OR 1.45, 95% CI 1.15–1.84) and NT-proBNP (OR 1.66, 95% CI 1.40–1.97). The corresponding ORs (95% CI) for elevated blood cadmium were 1.33 (1.02, 1.74) and 1.39 (1.18, 1.65). The effect of elevated blood lead on NT-proBNP was particularly pronounced among non-Hispanic Blacks (OR [95% CI], 3.26 [2.24, 4.74]) compared to Mexican Americans (1.46 [0.99, 2.17]) and non-Hispanic Whites (1.31 [1.02, 1.68]) and was stronger in individuals with impaired kidney function (OR [95% CI], 2.31 [1.43, 3.75]) compared to those with normal kidney function (1.44 [1.18, 1.75]). This study first reveals the association between lead and cadmium exposure and subclinical CVD, underscoring the need for targeted preventive measures to reduce cardiovascular risk and improve health outcomes.
AAV Capsid Modification and Its Influence on Viral Protein Stoichiometry and Packaging Fitness: Current Understandings and Future Direction
Authors: Dogbey Dennis Makafui , Barth Stefan
Published: January 2025

The field of gene therapy has witnessed significant advancements in the utilization of Adeno-associated virus (AAV) owing to its inherent biological advantages. Targeted AAV vectors are generated through genetic or chemical modification of the capsid for user-directed purposes. However, this process can result in imbalances in viral protein sequence homogeneity, stoichiometry, and functional transduction vector units, thereby introducing new challenges. This mini review focuses on the ongoing efforts to develop targeted vectors, which inadvertently present unsolicited obstacles for clinical application and provided perspectives on future directions.
Porn Use and Sexting in Health Science Students: A Transversal Descriptive Study
Authors: Martínez-Fernández María Cristina , García-Fernández Rubén , Granado-Soto Mirena , Martín-Vázquez Cristian , Bermejo-Martínez David , Liébana-Presa Cristina
Published: January 2025

Pornography consumption among young people through smart devices, along with the practice of sexting, is on the rise. However, it is not known exactly how these variables relate to the sexual education received by this population. This study analyses pornography consumption patterns and the relationship between pornography, sexting, and affective-sexual education in Health Sciences university students. A quantitative, descriptive, cross-sectional, and analytical study was carried out with data collected from 311 students from the Faculty of Health Sciences of a regional campus of a Spanish public university. The following questionnaires were collected through an online platform: Survey on pornography consumption among university students and Sexting Behaviour Scale. The average age of the first contact with pornography is 14.5 years old. Men are greater pornography consumers than women, and this consumption occurs online with the purpose of stimulating masturbation. Sexting is a practice carried out by the majority of those surveyed, with women receiving most of this type of messages and men being the main senders. Although more than half of the sample had received affective-sexual education, it was found to be deficient, as it did not meet the desired expectations. There is a noticeable relationship between the male gender and pornography consumption, with men being the largest consumers. People who consume pornography more frequently also show greater use of sexting. In view of these data, it is very relevant to implement and evaluate comprehensive sexuality education programs adapted to the needs of the population.
Developing a novel model for predicting overall survival in late-onset colon adenocarcinoma patients based on LODDS: a study based on the SEER database and external validation
Authors: Chen Chen , Xia Heng-Bo , Yuan Wei-Wei , Zhou Meng-Ci , Zhang Xue , Xu A.-Man
Published: January 2025

Aim

To construct a predictive model based on the LODDS stage established for patients with late-onset colon adenocarcinoma to enhance survival stratification.

Methods

Late-onset colon adenocarcinoma data were obtained from the public database. After determining the optimal LODDS truncation value for the training set via X-tile software, we created a new staging system by integrating the T stage and M stage. Nomograms of the prognostic model were created after Cox analyses identified independent risk factors for overall survival (OS) and cause-specific survival (CSS) and were validated internally and externally. The efficacy of the nomograms was assessed by calibration, time-dependent area under the curve (AUC) and decision curve analysis (DCA). Finally, the prognoses of the patients were compared by plotting survival curves on the basis of risk scores.

Results

A total of 103,291 and 100 patients with late-onset colon adenocarcinoma (50–80 years old) were screened from the Surveillance, Epidemiology, and End Results (SEER) and The Cancer Genome Atlas (TCGA) databases, respectively. Cox regression analysis revealed independent risk factors for OS and CSS, including age, gender, race, size, LODDS stage, PLN stage, LNR stage, and TNM stage. A comparison of the four models constructed on the basis of different stages revealed that the model constructed with the LODDS stage had the minimum AIC (Akaike information criterion), maximum C-index (concordance index) and time-dependent AUC. Nomograms based on the LODDS stage were constructed and successfully validated for accuracy and clinical utility.

Conclusion

For patients with late-onset colon adenocarcinoma, LODDS may achieve optimal predictive performance. Furthermore, compared to the 8th edition of the AJCC classification system, the nomogram based on LODDS stage may demonstrate superior survival prediction capabilities.
In this current wildfire crisis, acknowledge widespread suffering
Authors: Newman Thacker Fiona E. , Uyttewaal Kathleen , Quiñones Tomás , Leemans Rik , Hannah Bethany , Stoof Cathelijne R.
Published: January 2025

With climate change causing more extreme weather events globally, climate scientists have argued that societies have three options: mitigation, adaptation or suffering. In recent years, devastating wildfires have caused significant suffering, yet the extent of this suffering has not been defined. To encapsulate this suffering, we determined impacts and effects of extreme wildfires through two systematic literature reviews. Six common themes of wildfire suffering emerged: environmental, social, physical, mental, cultural and resource suffering. These themes varied in scale: from local to regional; from individuals to communities; and from ecosystems to landscapes. We then applied these themes in the Las Maquinas (Chile) and Fort McMurray (Canada) wildfires. This highlighted several adaptation strategies that can reduce suffering, however our exploration indicates these strategies must address social and ecological factors. This analysis concludes that suffering from wildfires is diverse and widespread, and that significant engagement with adaptation strategies is needed if this is going to decrease.
Exploring Marine Cloud Brightening with a Reduced Complexity Model
Authors: Khan Muhammad Mueed , Runyan Christopher , Bashir Shahzad , Amjad Abdul Basit
Published: January 2025

Throughout the industrial period, anthropogenic aerosols have likely offset approximately one-third of the warming caused by greenhouse gases. Marine cloud brightening aims to capitalize on one aspect of this phenomenon to potentially mitigate global warming by enhancing cloud reflectivity through adjustments in cloud droplet concentration. This study employs a simplified yet comprehensive modeling framework, integrating an open-source parcel model for aerosol activation, a radiation transport model based on commercial computational fluid dynamics code, and assimilated meteorological data. The reduced complexity model addresses the challenges of rapid radiation transfer calculations while managing uncertainties in aerosol–cloud-radiation (ACR) parameterizations. Despite using an uncoupled ACR mechanism and omitting feedback between clouds and aerosols, our results closely align with observations, validating the robustness of our assumptions and methodology. This demonstrates that even simplified models, supported by parcel modeling and observational constraints, can achieve accurate radiation transfer calculations comparable to advanced climate models. We analyze how variations in droplets size and concentration affect cloud albedo for geoengineering applications. Optimal droplet sizes, typically within the 20–35-µm range, significantly increase cloud albedo by approximately 28%–57% across our test cases. We find that droplets transmit about 29% more solar radiation than droplets. Effective albedo changes require injection concentrations exceeding background levels by around 30%, diminishing as concentrations approach ambient levels. Considerations must also be given to the spray pattern of droplet injections, as effective deployment can influence cloud thickness and subsequently impact cloud albedo. This research provides insights into the feasibility and effectiveness of using a reduced complexity model for marine cloud brightening with frontal cyclone and stratus cumulus clouds, and emphasizes the need to also consider background droplets size and concentration than just meteorological conditions.
Integration of on-board monitoring data into infrastructure management for effective decision-making in railway maintenance
Authors: Yan Tzu-Hao , Hoelzl Cyprien , Corman Francesco , Dertimanis Vasilis , Chatzi Eleni
Published: January 2025

Railway infrastructure is a crucial asset for the mobility of people and goods. The increased traffic frequency imposes higher loads and speeds, leading to accelerated infrastructure degradation. Asset managers require timely information regarding the current (diagnosis) and future (prognosis) condition of their assets to make informed decisions on maintenance and renewal actions. In recent years, in-service vehicles equipped with on-board monitoring (OBM) measuring devices, such as accelerometers, have been introduced on railroad networks, traversing the network almost daily. This article explores the application of state-of-the-art OBM-based track quality indicators for railway infrastructure condition assessment and prediction, primarily under the prism of track geometry quality. The results highlight the similarities and advantages of applying track quality indicators generated from OBM measurements (high frequency and relatively lower accuracy data) compared to those generated from higher precision, yet temporally sparser, data collected by traditional track recording vehicles (TRVs) for infrastructure management purposes. The findings demonstrate the performance of the two approaches, further revealing the value of OBM information for monitoring the track status degradation process. This work makes a case for the advantageous use of OBM data for railway infrastructure management, and attempts to aid understanding in the application of OBM techniques for engineers and operators.
Supporting Literacy Assessment in West Africa: Using State-of-the-Art Speech Models to Assess Oral Reading Fluency
Authors: Henkel Owen , Horne-Robinson Hannah , Hills Libby , Roberts Bill , McGrane Josh
Published: January 2025

This paper reports on a set of three recent experiments utilizing large-scale speech models to assess the oral reading fluency (ORF) of students in Ghana. While ORF is a well-established measure of foundational literacy, assessing it typically requires one-on-one sessions between a student and a trained rater, a process that is time-consuming and costly. Automating the assessment of ORF could support better literacy instruction, particularly in education contexts where formative assessment is uncommon due to large class sizes and limited resources. This research is among the first to examine the use of the most recent versions of large-scale speech models for ORF assessment in the Global South.We find that the best performing model, Whisper V2, with no additional fine-tuning, produces transcriptions of Ghanaian students reading aloud with a Word Error Rate of 10.3. When these transcriptions are used to produce fully automated ORF scores, they closely align with scores generated by expert human raters, with a correlation coefficient of 0.98. These results were achieved on a representative dataset (i.e., students with regional accents, recordings taken in actual classrooms), using a free and publicly available speech with no additional fine-tuning. This model’s strong performance on real-world classroom data, combined with its accessibility and simplified implementation, suggests potential for scaling ORF assessment in lower-resource, linguistically diverse educational contexts.
Semiparametric Latent Topic Modeling on Consumer-Generated Corpora
Authors: Dayta Dominic B. , Barrios Erniel B.
Published: January 2025

Common methods used for topic modeling have generally suffered problems of overfitting, leading to diminished predictive performance, as well as a weakness towards reconstructing sparse topic structures that involve only a few critical words to aid in interpretation. Considering the text typically contained in customer feedback, this paper proposes a semiparametric topic model utilizing a two-step approach: (1) makes use of nonnegative matrix factorization to recover topic distributions based on word co-occurrences and; (2) use semiparametric regression to identify factors driving the expression of particular topics in the documents given additional auxiliary information such as location, time of writing, and other features of the author. This approach provides a generative model that can be useful for predicting topics in new documents based on these auxiliary variables, and is demonstrated to accurately identify topics even for documents limited in length or size of vocabulary. In an application to real customer feedback, the topics provided by our model are shown to be as interpretable and useful for downstream analysis tasks as with those produced by current legacy methods.
Compassion-Focused Therapy Groups in Secondary Care Adult Mental Health Services: A Service Evaluation
Authors: Vivolo Marco , Ardeman Gabriel , Ford Catherine
Published: January 2025

Preliminary research highlights the potential benefits of compassion-focused therapy (CFT) groups for individuals with severe and enduring mental health difficulties (MHD) and high levels of self-criticism. This service evaluation aimed to assess whether attendance at CFT groups run by two adult community mental health teams (CMHTs) was associated with improvements in compassion, depression, anxiety, and self-esteem. A mixed-method design was employed. Quantitative and qualitative patient-reported routine outcome measures (PROMs) and experience feedback were obtained from 12 service users and analyzed using a reliable change index clinically significant change metrics, and frequency and content analyses. The most common, significant improvements indicated were found for self-compassion and self-kindness, and, to a lesser extent, in levels of anxiety and depression. Service users described the groups as enjoyable and useful, and valued the relational safety of the group and specific CFT techniques and concepts, requesting more sessions and visual materials. This service evaluation found that CFT group interventions can represent an acceptable alternative to individual treatment, though results need to be interpreted with caution due to the small sample size and use of different measures at each site.
(Semi-)automatic Extraction of Urban Planning Rules in French for Better Management of Land Artificialization
Authors: Koptelov Maksim , Holveck Margaux , Cremilleux Bruno , Reynaud Justine , Roche Mathieu , Teisseire Maguelonne
Published: January 2025

Land artificialization is a significant modern concern, as it is irreversible, diminishes agriculturally suitable land and causes environmental problems. Our project, Hérelles, aims to address this challenge by developing a framework for land artificialization management. In this framework, we associate urban planning rules in text form with clusters extracted from time series of satellite images. To achieve this, it is crucial to understand the planning rules with two key objectives: (1) to verify if the constraints derived from the rules are verifiable on satellite images and (2) to use these constraints to guide the labelling (or semantization) of clusters. The first step in this process involves the automatic extraction of rules from urban planning documents written in the French language. To solve this problem, we propose a method based on the multilabel classification of textual segments and their subsequent summarization. This method includes a special format for representing segments, in which each segment has a title and a subtitle. We then propose a cascade approach to address the hierarchy of class labels. Additionally, we develop several text augmentation techniques for French texts that can improve prediction results. Finally, we reformulate classified segments into concise text portions containing necessary elements for expert rule construction. We adapt an approach based on Abstract Meaning Representation (AMR) graphs to generate these portions in the French language and conduct a comparative analysis with ChatGPT. We experimentally demonstrate that the resulting framework correctly classifies each type of segment with more than 90% accuracy. Furthermore, our results indicate that ChatGPT outperforms the AMR-based approach, leading to a discussion of the advantages and limitations of both methods.
The Pluralistic Frameworks of Ibn Rushd and Abdullahi Ahmed An-Na'im
Authors: Omar Ayesha
Published: January 2025

The purpose of this Element is to analyse the assiduous attempts of two Islamic political thinkers-the 12th century Andalusian philosopher Ibn Rushd and the contemporary Sudanese reformist Abdullahi Ahmed An-Na'im-to theorise Islamic politics through an approach the author refers to as 'pluralistic frameworks'. A pluralistic framework, is a systematic mediation of Islamic ethics and politics that incorporates extra-Islamic traditions of thought from diverse sources. Pluralistic frameworks selectively and self-consciously enable dialogue, synthesis, and hybridity and seek to maintain a distinct conception of Islamic ethics that concords with a preferred set of political arguments. They enable reflexivity within the ethical purview of Islam and with an awareness of the normativity of sharī'a.Both Ibn Rushd and An-Na'im reconcile sharī'a in two very different ways, but to a common end; Ibn Rushd lays out a method of harmonisation with Greek thought, while An-Na'im resorts to the radical subversion of sharia under liberal thought.
Aristotle on Accidental Causation
Authors: Huismann Tyler
Published: January 2025

In this major new study, Tyler Huismann connects Aristotle's natural philosophy to modern theories of causation and provides fresh interpretations of classic issues. He links two of the most important notions in Aristotle's philosophy, accidents and causes, and using the concept of accidental causation as a guide, argues for ground-breaking proposals on some of the most foundational areas of Aristotle's thought: the relation between substances and accidents, the nature of efficient causation, the workings of 'qua,' the possibility of uncaused events, and the role of accidental causation in the natural world. Structured around close readings of Aristotle's Physics and Metaphysics and informed by contemporary theories of causation, Huismann's book offers students an accessible treatment of some of Aristotle's core texts, and provides specialists with a series of provocative interpretations.
Canonical heights for abelian group actions of maximal dynamical rank
Authors: Hu Fei , Zhong Guolei
Published: January 2025

Let X be a smooth projective variety of dimension

$n\geq 2$

and

$G\cong \mathbf {Z}^{n-1}$

a free abelian group of automorphisms of X over

$\overline {\mathbf {Q}}$

. Suppose that G is of positive entropy. We construct a canonical height function

$\widehat {h}_G$

associated with G, corresponding to a nef and big

$\mathbf {R}$

-divisor, satisfying the Northcott property. By characterizing the zero locus of

$\widehat {h}_G$

, we prove the Kawaguchi–Silverman conjecture for each element of G. As for other applications, we determine the height counting function for non-periodic points and show that X satisfies potential density.
The Maya Enlightenment: Towards a Post-Postclassic
Authors: Kratimenos Panos
Published: January 2025

While increased focus in recent decades has been paid to conceptions of time in archaeological interpretation, comparably less attention has been afforded to the way in which we ourselves conceive of time in the construction of chronologies to periodize the past. In this paper, I focus on the tripartite chronology utilized by scholars of the Precolumbian Maya as a case study to explore the potential of a critical approach to archaeological chronologies and periodizations. By examining the chronology's origins and the intellectual histories which underpin it, I demonstrate that the issues at stake are more than questions of temporal accuracy but, rather, matters of reflexivity. Through a process of ‘sublimation’, problematic assumptions and mentalities upon which periodizations were originally constructed are obscured in contemporary usage, leading to the perpetuation of outdated tropes and a conceptual path dependency in narratives of the past. Conversely, appreciating the arbitrary nature of chronological demarcations and treating such frameworks as negotiable and open to revision is a powerful tool in opening up new interpretive possibilities to the narration of the past.
Impact of Climate Change on the Dynamics of the Southern Senegal Upwelling Center
Authors: Ndoye S. , Echevin V. , Mignot J. , Capet X.
Published: January 2025

The Canary current upwelling System (CCS) is one the most productive marine ecosystems. CMIP5 simulations under the RCP8.5 scenario for the end of the 21st century project a modest upwelling‐favorable wind decrease over the CCS southern outpost, that is, the southern senegalese upwelling center (SSUC). We explore the coastal‐scale physical manifestations of climate change in the SSUC through dynamical downscaling of projected changes from nine CMIP5 models selected for their realistic representation of present‐day thermohaline structure. We find that coastal upwelling reduction due to wind changes is projected to be aggravated by geostrophic/pressure adjustments related, in large part, to changes in upper ocean stratification. The reduction could reach 25% of present‐day upwelling rates. The intensity of the poleward boundary current offshore of the SSUC is projected to decrease. Together with upper ocean warming this opens vast possibilities of ecological evolutions with large impact on neighboring societies.
Effects of Monsoon‐Driven Currents on Copepods in the Northeastern South China Sea
Authors: Liu Yuan , Ren Yuzheng , Li Kaizhi , Tan Yehui , Liu Hui , Ke Zhixin , Liu Jiaxing , Li Gang , Liang Junce
Published: January 2025

The northeastern South China sea (NESCS) is characterized by highly dynamic currents regulated by monsoonal variability. To understand the responses of copepods to local currents, two cruises were conducted in the NESCS during the 2015/16 El Niño event in summer and winter. In the shelf waters off the NESCS, coastal upwelling (CU) occurs in summer and the southward China Coastal Current (CCC) happens in winter. The intrusion of Kuroshio Current (KC), which extends from the basin to the slope‐shelf, was observed with in situ observations and remote sensing in both summer and winter. The individual‐size‐based community structure of copepods varied with seasons, areas, and depths, and was characterized by an increase in large‐sized taxa from the shelf to basin, and from upper to deep water. This size‐based distribution pattern is more pronounced during winter. The species‐based copepod community structure was altered by increased KC intrusion, which was associated with high species diversity, and relatively low abundance and carbon biomass, and greater network stability of copepod community in winter than in summer through the network invulnerability test. The CU in summer and the CCC in winter shaped the copepod community structure different from the KC, shown by a low species number, and a high abundance and biomass of copepods. Temora turbinata, Calanus sinicus and Lucicutia flavicornis were effective indicators for the occurrence of the CU, CCC, and KC, respectively, in the NESCS. This study highlights the importance of quantifying the responses of copepods to the ocean currents at a species level.
Energetically Consistent Eddy‐Diffusivity Mass‐Flux Convective Schemes: 1. Theory and Models
Authors: Perrot M. , Lemarié F. , Dubos T.
Published: January 2025

This paper presents a self‐contained derivation, from first principles, of a convective vertical mixing scheme based on the Eddy‐Diffusivity Mass‐Flux (EDMF) approach. This type of closure separates vertical turbulent fluxes into two components: an eddy‐diffusivity (ED) which accounts for local small‐scale mixing in a nearly isotropic environment, and a mass‐flux (MF) transport term, which represents the non‐local transport driven by vertically coherent plumes. Using the multi‐fluid averaging underlying the MF concept, we review consistent energy budgets between resolved and subgrid scales for seawater and dry atmosphere, in anelastic and Boussinesq frameworks. We demonstrate that when using an EDMF scheme, closed energy budgets can be recovered if: (a) bulk production terms of turbulent kinetic energy (TKE) by shear buoyancy include MF contributions; (b) boundary conditions are consistent with EDMF, to avoid spurious energy fluxes at the boundary. Furthermore, we show that lateral mixing, due to either entrainment or detrainment induces a net production of TKE via the shear term, with enhanced production under increased horizontal drag. We also provide constraints on boundary conditions to ensure mathematical consistency. Throughout the theoretical development, we maintain transparency regarding underlying assumptions. In a companion paper (Perrot and Lemarié (2024, https://hal.science/hal‐04666049); hereafter Part II) we assess the validity of these hypotheses, and analyze the sensitivity of the scheme to modeling choices against Large Eddy Simulations (LES) and observational data on oceanic convection. Part II also details an energy‐conserving discretization and quantifies energy biases in inconsistent formulations.
RECQL4 requires PARP1 for recruitment to DNA damage, and PARG dePARylation facilitates its associated role in end joining
Authors: Hussain Mansoor , Khadka Prabhat , Pekhale Komal , Kulikowicz Tomasz , Gray Samuel , May Alfred , Croteau Deborah L. , Bohr Vilhelm A.
Published: January 2025

RecQ helicases, highly conserved proteins with pivotal roles in DNA replication, DNA repair and homologous recombination, are crucial for maintaining genomic integrity. Mutations in RECQL4 have been associated with various human diseases, including Rothmund–Thomson syndrome. RECQL4 is involved in regulating major DNA repair pathways, such as homologous recombination and nonhomologous end joining (NHEJ). RECQL4 has more prominent single-strand DNA annealing activity than helicase activity. Its ability to promote DNA damage repair and the precise role of its DNA annealing activity in DNA repair are unclear. Here we demonstrate that PARP1 interacts with RECQL4, increasing its single-stranded DNA strand annealing activity. PARP1 specifically promoted RECQL4 PARylation at both its N- and C-terminal regions, promoting RECQL4 recruitment to DNA double-strand breaks (DSBs). Inhibition or depletion of PARP1 significantly diminished RECQL4 recruitment and occupancy at specific DSB sites on chromosomes. After DNA damage, PARG dePARylated RECQL4 and stimulated its end-joining activity. RECQL4 actively displaced replication protein A from single-stranded DNA, promoting microhomology annealing in vitro. Furthermore, depletion of PARP1 or RECQL4 substantially impacted classical-NHEJ- and alternative-NHEJ-mediated DSB repair. Consequently, the combined activities of PARP1, PARG and RECQL4 modulate DNA repair.
Quantification and optimization of platinum–molybdenum carbide interfacial sites to enhance low-temperature water-gas shift reaction
Authors: Li Ruiying , Shang Jingyuan , Wang Fei , Lu Qing , Yan Hao , Tuo Yongxiao , Liu Yibin , Feng Xiang , Chen Xiaobo , Chen De , Yang Chaohe
Published: January 2025

Pt/α-MoC1-x catalysts exhibit exceptional activity in low-temperature water-gas shift reactions. However, quantitatively identifying and fine-tuning the active sites has remained a significant challenge. In this study, we reveal that fully exposed monolayer Pt nanoclusters on molybdenum carbides demonstrate mass activity that exceeds that of bulk molybdenum carbide catalysts by one to two orders of magnitude at 100–200 °C for low-temperature water-gas shift reactions. This advancement is driven by the precise quantification and elucidation of active sites along the Pt-molybdenum carbide interfacial perimeter. By combining sacrificial CO adsorption per Pt atom, Density Functional Theory calculations, and CO chemisorption measurements, we establish a direct correlation between the monolayer Pt nanocluster size and the number of interfacial perimeters on Pt/α-MoC1-x catalysts. In this work, these findings provide key insights into the active site configuration of Pt/α-MoC1-x catalysts and open pathways for innovative catalyst design, with the interfacial perimeter identified as a crucial factor in enhancing catalytic performance.
The architecture of the human default mode network explored through cytoarchitecture, wiring and signal flow
Authors: Paquola Casey , Garber Margaret , Frässle Stefan , Royer Jessica , Zhou Yigu , Tavakol Shahin , Rodriguez-Cruces Raul , Cabalo Donna Gift , Valk Sofie , Eickhoff Simon B. , Margulies Daniel S. , Evans Alan , Amunts Katrin , Jefferies Elizabeth , Smallwood Jonathan , Bernhardt Boris C.
Published: January 2025

The default mode network (DMN) is implicated in many aspects of complex thought and behavior. Here, we leverage postmortem histology and in vivo neuroimaging to characterize the anatomy of the DMN to better understand its role in information processing and cortical communication. Our results show that the DMN is cytoarchitecturally heterogenous, containing cytoarchitectural types that are variably specialized for unimodal, heteromodal and memory-related processing. Studying diffusion-based structural connectivity in combination with cytoarchitecture, we found the DMN contains regions receptive to input from sensory cortex and a core that is relatively insulated from environmental input. Finally, analysis of signal flow with effective connectivity models showed that the DMN is unique amongst cortical networks in balancing its output across the levels of sensory hierarchies. Together, our study establishes an anatomical foundation from which accounts of the broad role the DMN plays in human brain function and cognition can be developed.
Bias-corrected serum creatinine from UK Biobank electronic medical records generates an important data resource for kidney function trajectories
Authors: Gorski Mathias , Wiegrebe Simon , Burkhardt Ralph , Behr Merle , Küchenhoff Helmut , Stark Klaus J. , Böger Carsten A. , Heid Iris M.
Published: January 2025

Loss of kidney function is a substantial personal and public health burden. Kidney function is typically assessed as estimated glomerular filtration rate (eGFR) based on serum creatinine. UK Biobank provides serum creatinine measurements from study center assessments (SC, n = 425,147 baseline, n = 15,314 with follow-up) and emerging electronic Medical Records (eMR, “GP-clinical”) present a promising resource to augment this data longitudinally. However, it is unclear whether eMR-based and SC-based creatinine values can be used jointly for research on eGFR decline. When comparing eMR-based with SC-based creatinine by calendar year (n = 70,231), we found a year-specific multiplicative bias for eMR-based creatinine that decreased over time (factor 0.84 for 2007, 0.97 for 2013). Deriving eGFR based on SC- and bias-corrected eMR-creatinine yielded 454,907 individuals with ≥ 1eGFR assessment (2,102,174 assessments). This included 206,063 individuals with ≥ 2 assessments over up to 60.2 years (median 6.00 assessments, median time = 8.7 years), where we also obtained eMR-based information on kidney disease or renal replacement therapy. We found an annual eGFR decline of 0.11 (95%-CI = 0.10–0.12) versus 1.04 mL/min/1.73m2/year (95%-CI = 1.03–1.05) without and with bias-correction, the latter being in line with literature. In summary, our bias-corrected eMR-based creatinine values enabled a 4-fold increased number of eGFR assessments in UK Biobank suitable for kidney function research.
Ginsenoside Rd protects against acute liver injury by regulating the autophagy NLRP3 inflammasome pathway
Authors: Zhong Xiaomei , Sun Yibin , Lin Yanxiang , Deng Shan , Wang Huan , Zhou Xian , Lu Jinjian , Zheng Yanfang , Luo Ruoyin , Huang Mingqing , Song Jianyuan
Published: January 2025

Ginsenoside Rd (Rd) is a bioactive compound predominantly found in Panax ginseng C.A. Meyer and Panax notoginseng (Burkill) F.H. Chen ex C.H. Chow, both species belonging to genus Panax in the Araliaceae family. However, its hepatic protective effect against acute liver injury and related mechanistic action remain unexplored. To investigate the protective effect of Rd against thioacetamide (TAA)-induced acute liver injury and assess its underlying regulatory mechanisms related to autophagy and inflammation. Forty-eight 8 weeks old C57BL/6 mice were treated with saline (control or model group), Rd (12.5 mg/kg, 25 mg/kg or 50 mg/kg), and diammonium glycyrrhizinate (DG, 30 mg/kg) for three days. Then the mice were stimulated with TAA to establish acute liver injury model, excluding the control group. HSC-T6 cells were treated with Rd at concentrations of 2.5, 5, or 10 µM, for 12 h with or without Lipopolysaccharide (LPS) stimulation at 100 ng/mL. Immunofluorescence staining, qPCR and Western blot were employed to analyze the expressions of genes and proteins associated with inflammation and autophagy. To validate the role of Rd in regulating autophagy and inflammation, the autophagy inducers, rapamycin and GSK621, were utilised in reverse validation experiments in cells. Rd exhibited significant hepatic protective effects in mice by reducing the serum levels of Aspartate aminotransferase (AST), Alanine aminotransferase (ALT), Glutathione S-transferase (GST) and Lactate dehydrogenase (LDH) with acute liver injury. It exhibited strong anti-inflammatory effect by reducing inflammation associated protein, such as cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS), nod-like receptor protein 3 (NLRP3), associated speck-like protein containing a CARD (ASC), interleukin-18 (IL-18) and interleukin-1β(IL-1β) proteins and the mRNA expression levels of COX-2, Tumor Necrosis Factor α (TNF α), interleukin-6 (IL-6) and iNOS were decreased in liver tissue. And Rd inhibited LPS-induced inflammation by reducing the expression of COX-2 and NLRP3 in HSC-T6 cells. Moreover, not only in vivo but also in vitro, Rd downregulated the expression of LC3II, Beclin1, phosphorylation-AMP-activated protein kinase (p-AMPK), phosphorylation-ULK1 (p-ULK1) and upregulated the expression of p62 and phosphorylation-mechanistic target of rapamycin (p-mTOR) to suppress autophagy via the AMPK/mTOR/ULK1 pathway. Finally, the inhibitory effects of Rd on autophagy and inflammation in HSC-T6 cells were partially blocked by rapamycin and GSK621. Rd is a promising therapeutic agent to protect liver against TAA-induced acute liver injury by regulating the autophagy-NLRP3 inflammasome pathway.
Deep learning enhances the prediction of HLA class I-presented CD8+ T cell epitopes in foreign pathogens
Authors: Wohlwend Jeremy , Nathan Anusha , Shalon Nitan , Crain Charles R. , Tano-Menka Rhoda , Goldberg Benjamin , Richards Emma , Gaiha Gaurav D. , Barzilay Regina
Published: January 2025

Accurate in silico determination of CD8+ T cell epitopes would greatly enhance T cell-based vaccine development, but current prediction models are not reliably successful. Here, motivated by recent successes applying machine learning to complex biology, we curated a dataset of 651,237 unique human leukocyte antigen class I (HLA-I) ligands and developed MUNIS, a deep learning model that identifies peptides presented by HLA-I alleles. MUNIS shows improved performance compared with existing models in predicting peptide presentation and CD8+ T cell epitope immunodominance hierarchies. Moreover, application of MUNIS to proteins from Epstein–Barr virus led to successful identification of both established and novel HLA-I epitopes which were experimentally validated by in vitro HLA-I-peptide stability and T cell immunogenicity assays. MUNIS performs comparably to an experimental stability assay in terms of immunogenicity prediction, suggesting that deep learning can reduce experimental burden and accelerate identification of CD8+ T cell epitopes for rapid T cell vaccine development.