bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semiparametric Latent Topic Modeling on Consumer-Generated Corpora
Authors: Dayta Dominic B. , Barrios Erniel B. 
Published: January 2025

Abstract
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

Abstract
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

Abstract
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.
Canonical heights for abelian group actions of maximal dynamical rank
Authors: Hu Fei , Zhong Guolei 
Published: January 2025

Abstract
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

Abstract
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

AbstractThe 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

AbstractThe 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

AbstractThis 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
National climate strategies show inequalities in global development of carbon dioxide geological storage
Authors: Alcalde Juan , Johnson Gareth , Roberts Jennifer J. 
Published: January 2025

Abstract
Carbon dioxide geological storage (CGS) is considered critical for limiting global average temperature rise to below 1.5 °C by mitigating fossil industrial emissions and delivering permanent Carbon Dioxide Removals. Here we examine the role of CGS in long-term national emission reduction strategies submitted to the UNFCCC under the Paris Agreement. We find that a third of countries plan to develop CGS for emissions mitigation only, and a third for both emissions mitigation and carbon removals, but no countries plan on CGS for carbon removals alone. Neither the presence or performance of CGS maturity assessments correspond to CGS plans. Climate strategies of high income countries with high historic oil and gas production show firmest commitment to CGS. These countries already have multiple advantages for implementing and benefiting from CGS, which raises inequalities and sensitivities that must be carefully considered when designing carbon market and climate finance policies and frameworks for CGS development.