bluuebunny/crossref_metadata_2025_split huggingface dataset:
Psychotic experiences and disorders in adolescents and young adults with borderline intellectual functioning and intellectual disabilities: evidence from a population-based birth cohort in the United Kingdom
Authors: Dardani Christina , Underwood Jack , Jones Hannah , Rammos Alexandros , Sullivan Sarah , Hull Laura , Khandaker Golam , Zammit Stan , Rai Dheeraj , Madley-Dowd Paul 
Published: February 2025

Abstract

Background
Individuals with borderline intellectual functioning and intellectual disabilities (intellectual impairment) may be at increased risk of psychosis. However, studies have been limited by small and selected samples. Moreover, the role of early life trauma, a key risk factor for psychosis, in the associations is unknown.

Methods
Using data from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort, we investigated the associations between intellectual impairment, psychotic disorders, and psychotic experiences, and assessed the mediating role of trauma in childhood. Individuals with intellectual impairment were identified using a multisource measure utilizing indicators from ALSPAC combined with health and administrative records. Psychotic disorder diagnoses were extracted through linkage to primary care records. Psychotic experiences were assessed at ages 18 and 24 using the semi-structured Psychosis-Like Symptoms interview (PLIKSi). Trauma between ages 5 and 11 was assessed with questionnaires and interviews administered to children and parents at multiple ages. Multiple imputation was performed to mitigate bias due to missing data.

Results
The maximum sample after multiple imputation was 9,407. We found associations between intellectual impairment and psychotic disorders (OR = 4.57; 95%CI: 1.56–13.39). Evidence was weaker in the case of psychotic experiences (OR = 1.63; 95%CI: 0.93–2.84). There was some evidence suggesting a mediating role of trauma in the associations between intellectual impairment and psychotic experiences (OR = 1.09; 95%CI: 1.03–1.15). Complete records analyses yielded comparable estimates.

Conclusions
Intellectual impairment is associated with psychotic disorders and experiences in adulthood. Research into the contribution of trauma could shape intervention strategies for psychotic disorders in this population.
Incorporating control inputs in continuous-time Gaussian process state estimation for robotics
Authors: Lilge Sven , Barfoot Timothy D. 
Published: February 2025

Abstract
Continuous-time batch state estimation using Gaussian processes is an efficient approach to estimate the trajectories of robots over time. In the past, relatively simple physics-motivated priors have been considered for such approaches, using assumptions such as constant velocity or acceleration. This paper presents an approach to incorporating exogenous control inputs, such as velocity or acceleration commands, into the continuous Gaussian process state estimation framework. It is shown that this approach generalizes across different domains in robotics, making it applicable to both the estimation of continuous-time trajectories for mobile robots and the estimation of quasi-static continuum-robot shapes. Results show that incorporating control inputs leads to more informed priors, potentially requiring less measurements and estimation nodes to obtain accurate estimates. This makes the approach particularly useful in situations in which limited sensing is available. For example, in a mobile robot localization experiment with sparse landmark distance measurements and frequent odometry control inputs, our approach provides accurate trajectory estimates with root-mean-square errors around 3-4 cm and 4-5 degrees, even with time intervals up to five seconds between discrete estimation nodes, which significantly reduces computation time.
A Hybrid Model Coupling Data and Hydraulic Transient Laws for Water Distribution Systems
Authors: Yan Hexiang , Li Shixun , Tian Wenchong , Wang Jiaying , Li Fei , Duan Huanfeng , Tao Tao , Xin Kunlun 
Published: February 2025

AbstractThe physics‐informed neural network (PINN) method has been applied to solve water hammer equations in pipeline systems due to its ability of seamlessly integrate measurement data with conservation laws, offering advantages over traditional numerical method. However, existing PINN approaches require multiple neural networks to construct composite models for complex water distribution systems (WDS). This situation treats nodal information as boundary condition or labeled data during training, leading to a weaker robustness and a high demand for data. To address these issues, a hybrid water hammer model based on eXtended Physics‐Informed Neural Networks for WDS (WDS‐XPINN) is developed in this study. Unlike the standard PINN, WDS‐XPINN incorporates the nodal mechanistic model directly into the loss function, enabling to synchronously train a unified neural network jointly through sparse augmented measurement data for pipeline system. Additionally, an adaptive weights method is introduced to improve model robustness by balancing the contributions of flowrates and pressures. The proposed WDS‐XPINN is evaluated in two case studies: a series pipeline system with different operational events and noise perturbation, as well as a topological structure with looped and branched pipe. According to the simulation results and uncertainty analysis, the WDS‐XPINN model demonstrates its excellent capacity of modeling fluid transient accurately in pipeline system, even without exact operational conditions or true pipe parameters.
Constraining Soil Hydrothermal CO2 Degassing Across the Changbaishan Volcanic Area: Insights From 13C‐14C Perspective
Authors: Wang Linan , Zhong Jun , Zhang Mao‐Liang , Liu Guo‐Ming , Li Si‐Liang , Xu Sheng 
Published: February 2025

AbstractSoil hydrothermal CO2 represents important forms of diffuse degassing in volcanic areas, but the corresponding CO2 output remains unclear. Herein, we investigated geochemical features of soil gas, that is, soil gas components, carbon isotopic compositions of soil CO2 (δ13C‐CO2 and Δ14C‐CO2), and soil CO2 fluxes in the Changbaishan volcanic area (CHV). The geochemical characteristics of soil gas in diffuse degassing structures differed significantly from those in volcano‐affected structures. Specifically, soil CO2 concentrations were up to 2.5 × 105 ppm, with δ13C‐CO2 values ranging from −6.2‰ to −1.6‰ and Δ14C‐CO2 values spanning from −996‰ to −845‰, showing significant hydrothermal CO2 signatures. The isotopic mixing model was constructed to estimate the contribution of hydrothermal, biogenic, and atmospheric CO2 to soil CO2. The results showed that soil CO2 in diffuse degassing structures was predominantly derived from hydrothermal CO2, while soil CO2 in the volcano‐affected structures was mainly derived from biogenic CO2. Combined with the soil CO2 fluxes, it was concluded that the hydrothermal CO2 output through soil degassing was 5.83 × 104 t yr−1 in CHV, significantly lower than previous estimates. We found that hydrothermal CO2 release in CHV exceeded the CO2 consumption through silicate weathering, thereby acting as the carbon source. We also estimated the hydrothermal soil CO2 output from global volcanoes based on literature‐published values from 80‐degassing volcanoes, which was ∼150 Mt yr−1. Our results highlighted the importance of conducting 13C‐14C investigations in global volcanic areas to replenish the database of hydrothermal CO2 output in different forms and subsequently evaluate their climatic implications.
Crustal Structure Beneath the Namche Barwa Massif, Eastern Himalayan Syntaxis: Evidence of Magma Underplating?
Authors: Cheng Siyuan , Shen Xuzhang , Li Lun , Wang Wentian , Gao Rui , Liu Mian , Li Haifeng 
Published: February 2025

AbstractThe Namche Barwa massif (NBM) in the Eastern Himalayan Syntaxis (EHS) hosts some of the most active Cenozoic crustal deformation, magmatism, metamorphism, and extreme topographic relief on earth. The crust‐mantle dynamics responsible for the tectono‐magmatism in the NBM remains debated. We image the detailed crustal structures under the NBM using the recordings of a dense seismic array of 400 3‐component node geophones and 4,290 P‐wave receiver functions (PRFs). Our results show a wide range of negative seismic phases in the middle and lower crust and weak Moho signal in the northern part of the NBM, under the Yarlung‐Zangbo River (YZR). The upper crustal discontinuities show “hut” shape structures, and these features were validated with the forward simulation and PRFs from three broadband seismic stations in the region. These crustal structures indicate the presence of magma underplating in the upper mantle under the NBM.
GP73-mediated secretion of PKM2 and GP73 promotes angiogenesis and M2-like macrophage polarization in hepatocellular carcinoma
Authors: Wang Shujie , Zhang Tongjia , Zhou Yue , Jiao Zitao , Lu Kejia , Liu Xinyi , Jiang Wei , Yang Zhe , Li Hui , Zhang Xiaowei 
Published: February 2025

Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors. Abnormally high expression of Golgi protein 73 (GP73) and pyruvate kinase M2 (PKM2) is intimately associated with HCC progression. However, as secreted proteins, the role of their extracellular secretions in HCC progression remains unclear. Here, we demonstrated that the expression of extracellular GP73 was positively correlated with extracellular PKM2. GP73 interacted with PKM2 to promote SUMO1 modification of PKM2, which in turn enhanced the interaction of GP73 and PKM2. This process continuously promoted the transfer of PKM2 from the cytoplasm to the membrane in HCC cells, and finally secretion. Extracellular PKM2 and GP73 synergistically promoted angiogenesis and polarization of M2-type macrophages, thereby leading to malignant progression and sorafenib resistance in HCC. Sorafenib combined with shikonin, a specific inhibitor of PKM2, has a strong anti-tumor effect. This study reveals the role of GP73 in enhancing PKM2 and GP73 secretion in promoting HCC progression, providing a theoretical basis and drug targets for HCC therapy.
TMEM45A enhances palbociclib resistance and cellular glycolysis by activating AKT/mTOR signaling pathway in HR+ breast cancer
Authors: Chen Cui , Chen Zehong , Zhao Jinze , Wen Xinyun , Yao Hanming , Weng Zijin , Xiong Huiping , Zheng Zongheng , Wu Juekun 
Published: February 2025

Abstract
Palbociclib, a CDK4/6 inhibitor, plays a crucial role in the treatment of HR+ breast cancer. However, resistance to palbociclib is a significant concern that merits further investigation. Our investigation identifies TMEM45A as a potential driver of palbociclib resistance and its association with increased cellular glycolysis. We demonstrate that TMEM45A is highly expressed in palbociclib-resistant breast cancer (BRCA) cells, correlating with enhanced tumor progression. Silencing TMEM45A enhances sensitivity to palbociclib, promotes cell cycle arrest and apoptosis, and inhibits the proliferation of BRCA cells. Moreover, attenuation of TMEM45A expression reduces cancer aggressiveness by decreasing the expression of EMT and glycolysis-related proteins. Subsequent gene set enrichment analysis (GSEA) confirms that TMEM45A activates the AKT/mTOR signaling pathway, which is integral to cell cycle progression and glycolysis. In a cell line-derived xenograft (CDX) mouse model, TMEM45A knockdown significantly restores sensitivity to palbociclib and suppresses tumor growth. Additionally, the use of engineered exosomes loaded with siRNA targeting TMEM45A presents a promising strategy for enhancing CDK4/6 inhibitor sensitivity without observable toxic side effects in a patient-derived xenograft (PDX) model. Collectively, our findings suggest that TMEM45A may be a therapeutic target for overcoming palbociclib resistance, and exosomal siRNA delivery could be a viable strategy for precision medicine in HR+ breast cancer.
A genetic perspective on the recent demographic history of Ireland and Britain
Authors: Shanmugam Ashwini , Merrigan Michael , O’Reilly Seamus , Molloy Anne M. , Brody Lawrence , Hardiman Orla , Bodmer Walter , McLaughlin Russell L. , Cavalleri Gianpiero L. , Byrne Ross P. , Gilbert Edmund H. 
Published: February 2025

Abstract
While subtle yet discrete clusters of genetic identity across Ireland and Britain have been identified, their recent demographic history is unclear. Using genotype data from 6574 individuals with associated regional Irish or British ancestry, we identified genetic communities by applying Leiden community detection. Using haplotype segments segregated by length as proxy for time, we inferred regional Irish and British demographic histories. Using a subset of Irish participants, we provide genealogical context by estimating the enrichment/depletion of surnames within the Irish genetic communities. Through patterns of haplotype sharing, we find evidence of recent population bottlenecks in Orcadian, Manx and Welsh genetic communities. We observed temporal changes in genetic affinities within and between genetic communities in Ireland and Britain. Structure in Ireland is subtler compared to neighbouring British communities, with the Irish groups sharing relatively more short haplotype segments. In addition, we detected varying degrees of genetic isolation in peripheral Irish and British genetic communities across different time periods. Further, we observe a stable migration corridor between north-east Ireland and south-west Scotland while there is a recent migration barrier between south-east and west Ireland. Genealogical analysis of surnames in Ireland reflects history—Anglo-Norman surnames are enriched in the Wexford community while Scottish and Gallowglass surnames were enriched in the Ulster community. Using these new insights into the regional demographic history of Ireland and Britain across different time periods, we hope to understand the driving forces of rare allele frequencies and disease risk association within these populations.
Coalescence of carbon nanotubes while preserving the chiral angles
Authors: Takakura Akira , Nishihara Taishi , Harano Koji , Cretu Ovidiu , Tanaka Takeshi , Kataura Hiromichi , Miyauchi Yuhei 
Published: February 2025

Abstract
Atomically precise coalescence of graphitic nanocarbon molecules is one of the most challenging reactions in sp
2 carbon chemistry. Here, we demonstrate that two carbon nanotubes with the same chiral indices (n, m) are efficiently coalesced into a single (2n, 2 m) nanotube with preserved chiral angles via heat treatment at less than 1000 °C. The (2n, 2 m) nanotubes constitute up to ≈ 20%–40% of the final sample in the most efficient case. Additional optical absorption peaks of the (2n, 2 m) nanotubes emerge, indicating that the reaction occurs over the entire sample. The reaction efficiency strongly depends on the chiral angle, implying that C–C bond cleavage and recombination occurs sequentially. Furthermore, the reaction occurs efficiently even at 600 °C in an atmosphere containing trace amounts of oxygen. These findings offer routes for the structure-selective synthesis of large-diameter nanotubes and modification of the properties of nanotube assemblies via postprocessing.
Leveraging public AI tools to explore systems biology resources in mathematical modeling
Authors: Kannan Meera , Bridgewater Gabrielle , Zhang Ming , Blinov Michael L. 
Published: February 2025

Abstract
Predictive mathematical modeling is an essential part of systems biology and is interconnected with information management. Systems biology information is often stored in specialized formats to facilitate data storage and analysis. These formats are not designed for easy human readability and thus require specialized software to visualize and interpret results. Therefore, comprehending modeling and underlying networks and pathways is contingent on mastering systems biology tools, which is particularly challenging for users with no or little background in data science or system biology. To address this challenge, we investigated the usage of public Artificial Intelligence (AI) tools in exploring systems biology resources in mathematical modeling. We tested public AI’s understanding of mathematics in models, related systems biology data, and the complexity of model structures. Our approach can enhance the accessibility of systems biology for non-system biologists and help them understand systems biology without a deep learning curve.
Transforming US agriculture for carbon removal with enhanced weathering
Authors: Beerling David J. , Kantzas Euripides P. , Lomas Mark R. , Taylor Lyla L. , Zhang Shuang , Kanzaki Yoshiki , Eufrasio Rafael M. , Renforth Phil , Mecure Jean-Francois , Pollitt Hector , Holden Philip B. , Edwards Neil R. , Koh Lenny , Epihov Dimitar Z. , Wolf Adam , Hansen James E. , Banwart Steven A. , Pidgeon Nick F. , Reinhard Christopher T. , Planavsky Noah J. , Val Martin Maria 
Published: February 2025

Abstract
Enhanced weathering (EW) with agriculture uses crushed silicate rocks to drive carbon dioxide removal (CDR)1,2. If widely adopted on farmlands, it could help achieve net-zero emissions by 20502–4. Here we show, with a detailed US state-specific carbon cycle analysis constrained by resource provision, that EW deployed on agricultural land could sequester 0.16–0.30 GtCO2 yr−1 by 2050, rising to 0.25–0.49 GtCO2 yr−1 by 2070. Geochemical assessment of rivers and oceans suggests effective transport of dissolved products from EW from soils, offering CDR on intergenerational timescales. Our analysis further indicates that EW may temporarily help lower ground-level ozone and concentrations of secondary aerosols in agricultural regions. Geospatially mapped CDR costs show heterogeneity across the USA, reflecting a combination of cropland distance from basalt source regions, timing of EW deployment and evolving CDR rates. CDR costs are highest in the first two decades before declining to about US$100–150 tCO2
−1 by 2050, including for states that contribute most to total national CDR. Although EW cannot be a substitute for emission reductions, our assessment strengthens the case for EW as an overlooked practical innovation for helping the USA meet net-zero 2050 goals5,6. Public awareness of EW and equity impacts of EW deployment across the USA require further exploration7,8 and we note that mobilizing an EW industry at the necessary scale could take decades.
Antibody prophylaxis may mask subclinical SIV infections in macaques
Authors: Gonelli Christopher A. , King Hannah A. D. , Ko SungYoul , Fennessey Christine M. , Iwamoto Nami , Mason Rosemarie D. , Heimann Ashley , Flebbe Dillon R. , Todd John-Paul , Foulds Kathryn E. , Keele Brandon F. , Lifson Jeffrey D. , Koup Richard A. , Roederer Mario 
Published: February 2025

Abstract
Broadly neutralizing antibodies (bNAbs) show potential to prevent human immunodeficiency virus (HIV-1) infection in humans1. However, there are limited data on the antibody concentrations required to prevent infection. Clinical trials of bNAb prophylaxis have demonstrated partial efficacy2, but the sampling frequency typically does not allow precise timing of infection events and concurrent antibody levels. Here, using simian immunodeficiency virus (SIV) infection of rhesus macaques, we show that although potent bNAbs can delay the onset of acute viremia, subclinical infections occur while bNAb levels remain high. Serial SIV challenge of monkeys given partially and fully neutralizing bNAbs revealed that ‘viral blips’—low and transient plasma viremia—often occur while serum bNAb concentrations are well above currently accepted protective levels. To understand the precise timing of the infections resulting in such blips, we performed plasma viral sequencing on monkeys that were serially challenged with genetically barcoded SIV after bNAb administration. These analyses showed that subclinical infections occurred in most animals that were given potent bNAb prophylaxis. These subclinical infections occurred while antibody concentrations were 2- to 400-fold higher than the levels required to prevent fully viremic breakthrough infection. This study demonstrates that immunoprophylaxis can mask subclinical infections, which may affect the interpretation of prophylactic HIV-1 bNAb clinical trials.
Rapid and sensitive protein complex alignment with Foldseek-Multimer
Authors: Kim Woosub , Mirdita Milot , Levy Karin Eli , Gilchrist Cameron L. M. , Schweke Hugo , Söding Johannes , Levy Emmanuel D. , Steinegger Martin 
Published: February 2025

Abstract
Advances in computational structure prediction will vastly augment the hundreds of thousands of currently available protein complex structures. Translating these into discoveries requires aligning them, which is computationally prohibitive. Foldseek-Multimer computes complex alignments from compatible chain-to-chain alignments, identified by efficiently clustering their superposition vectors. Foldseek-Multimer is 3–4 orders of magnitudes faster than the gold standard, while producing comparable alignments; this allows it to compare billions of complex pairs in 11 h. Foldseek-Multimer is open-source software available at GitHub via https://github.com/steineggerlab/foldseek/, https://search.foldseek.com/search/ and the BFMD database.
Pause before action: Waiting short time as a simple and resource-rational boost
Authors: Shirasuna Masaru , Kagawa Rina , Honda Hidehito 
Published: February 2025

Abstract
Many workers today engage in straightforward judgment tasks, increasing the need for interventions to improve accuracy. We propose a resource-rational and psychohygienic intervention, “wait short time”, which introduces a brief pause before displaying alternatives. This pause works as a harmonious triad: it clears the mind of prior judgment bias, restores present attention, and prepares the mind for future judgments; and all this without additional instructions. Based on a resource rationality framework, cognitive costs (e.g., irritation, cognitive conflict) are associated with prolonged thinking because of humans limited cognitive resources. Therefore, there should be an appropriately short thinking time to achieve higher accuracy with minimal workload. We investigated the effectiveness of the proposed intervention both theoretically and empirically. The computer simulations demonstrated that, under assumptions of limited cognitive resources, there was an optimal time at the early stages for maximizing total benefits. The results of behavioral experiment was consistent with the theoretical findings: Providing a waiting time (1 s or 2.5 s) improved judgment accuracy, but cognitive conflicts increased over time and an unnecessarily long time (2.5 s) induced more subjective irritation. Consequently, an appropriate time (1 s) could enhance judgment accuracy with less workload. We discuss the implications and limitations of the proposed intervention.