bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Subsurface Soil Moisture Estimation Using a 2‐Dimensional Data Assimilation Framework Incorporated With a Dual State‐Parameter Scheme
Authors: Liao Dehai , Niu Jun , Du Taisheng , Kang Shaozhong 
Published: August 2024

AbstractAccurate subsurface soil moisture (SM) estimation is critical for vegetation growth, drought monitoring, and climate change mitigation, yet remains a significant challenge. Previous data assimilation (DA) approaches are limited to only surface SM assimilation. In this study, we utilized the proxy subsurface SM estimated via the exponential filter method (ExpF) as another assimilation variable in our 2‐dimensional DA. Meanwhile, the dual updating DA scheme was implemented to simultaneously update model parameters and states. The two DA pathways were incorporated into the proposed framework (DA_1E_D), which enhanced the subsurface SM accuracy, with the effects of 2‐dimensional assimilation being more significant. Under 2‐dimensional DA, the information transfer between layers was more accurately characterized, leading to overall improvements with unbiased root‐mean‐square error (ubRMSE) reductions of 0.015 and 0.005 m3 · m−3, and Kling–Gupta efficiency (KGE) increases of 0.248 and 0.067 for surface and subsurface SM, respectively, across five SM networks. The soil thickness (d2) and hydraulic conductivity exponent (expt2) are the most influential parameters affecting subsurface SM dynamics through model propagation. DA_1E_D also outperformed ExpF in subsurface SM accuracy, particularly in SM networks with weak surface‐subsurface correlation, achieving an average ubRMSE reduction of 0.003 m3 · m−3 and an average KGE increase of 0.202. It was also applied to Soil Moisture Active Passive data at regional scale, demonstrating significant improvements. The model surface‐subsurface SM coupling was adjusted toward the actual coupling after subsurface assimilation and dual updating. This study may provide new insights into the diagnosis and refinements of the model representation of surface‐subsurface processes.
The Foxo1-YAP-Notch1 axis reprograms STING-mediated innate immunity in NASH progression
Authors: Xu Dongwei , Qu Xiaoye , Yang Tao , Sheng Mingwei , Bian Xiyun , Zhan Yongqiang , Tian Yizhu , Lin Yuanbang , Jin Yuting , Wang Xiao , Ke Michael , Jiang Longfeng , Li Changyong , Xia Qiang , Farmer Douglas G. , Ke Bibo 
Published: August 2024

AbstractInnate immune activation is critical for initiating hepatic inflammation during nonalcoholic steatohepatitis (NASH) progression. However, the mechanisms by which immunoregulatory molecules recognize lipogenic, fibrotic, and inflammatory signals remain unclear. Here, we show that high-fat diet (HFD)-induced oxidative stress activates Foxo1, YAP, and Notch1 signaling in hepatic macrophages. Macrophage Foxo1 deficiency (Foxo1M-KO) ameliorated hepatic inflammation, steatosis, and fibrosis, with reduced STING, TBK1, and NF-κB activation in HFD-challenged livers. However, Foxo1 and YAP double knockout (Foxo1/YAPM-DKO) or Foxo1 and Notch1 double knockout (Foxo1/Notch1M-DKO) promoted STING function and exacerbated HFD-induced liver injury. Interestingly, Foxo1M-KO strongly reduced TGF-β1 release from palmitic acid (PA)- and oleic acid (OA)-stimulated Kupffer cells and decreased Col1α1, CCL2, and Timp1 expression but increased MMP1 expression in primary hepatic stellate cells (HSCs) after coculture with Kupffer cells. Notably, PA and OA challenge in Kupffer cells augmented LIMD1 and LATS1 colocalization and interaction, which induced YAP nuclear translocation. Foxo1M-KO activated PGC-1α and increased nuclear YAP activity, modulating mitochondrial biogenesis. Using chromatin immunoprecipitation (ChIP) coupled with massively parallel sequencing (ChIP-Seq) and in situ RNA hybridization, we found that NICD colocalizes with YAP and targets Mb21d1 (cGAS), while YAP functions as a novel coactivator of the NICD, which is crucial for reprogramming STING function in NASH progression. These findings highlight the importance of the macrophage Foxo1–YAP–Notch1 axis as a key molecular regulator that controls lipid metabolism, inflammation, and innate immunity in NASH.
Clinical relevance of brain MRI changes in primary central nervous system lymphoma after high-dose-chemotherapy and autologous stem cell transplantation
Authors: Beer Sina A. , Möhle Robert , Tabatabai Ghazaleh , Merle David A. , Ernemann Ulrike , Richter Vivien , Lengerke Claudia 
Published: August 2024

AbstractPrimary central nervous system lymphoma (PCNSL) is a potentially curable disease, but affected patients often struggle in everyday life due to disease- and therapy-associated sequelae. High-dose chemotherapy followed by autologous stem cell transplantation (HDC/ASCT) is the standard consolidation therapy, replacing whole brain radiation therapy (WBRT) amongst others due to less long-term cognitive decline. Nevertheless, white matter lesions (WML) are common findings in brain MRI after HDC/ASCT, but their clinical significance remains underexplored. Here, we correlate WML and brain atrophy with neuropsychological and quality-of-life evaluations collected post-treatment. We found that a significant part of PNCSL long-term survivors develop a high WML burden after HDC/ASCT, but we fail to associate them with specific patient or therapy characteristics. Intriguingly, even a high WML burden does not seem to affect QoL, basic neurocognition testing or performance status negatively. These results contrast findings in previous neuroimaging studies on healthy and cancer patients.
Chairside learning on undergraduate clinics: general dental and human disease themes
Authors: Atkin Philip A. , Khan Anum , Simms Melanie L. 
Published: August 2024

AbstractIntroduction Chairside teaching is an important part of dental undergraduate clinical education. Bedside teaching is well-reported in relation to undergraduate medicine but few publications relate to undergraduate dentistry.Aims and objectives To investigate the experience and benefits from chairside teaching/learning in the clinical years of a five-year dental programme in a UK university. We asked about general dental topic learning as well as human disease (HD) learning.Materials and methods An online survey gathered dental students' opinions on their recognition, knowledge and experience of chairside teaching/learning. We asked about clinics and clinicians and where they gained most from chairside teaching/learning. We encouraged free-text responses.Results Altogether, 127 students took part (62% response). Response rates approximated 60% for all three years. In total, 93% felt that chairside teaching/learning helped to a moderate/great extent for general dental topics and 73% felt that chairside teaching/learning helped to a moderate/great extent for HD topics. Free-text comments revealed students valued chairside teaching/learning and from which grade/level of staff they learned most.Discussion and conclusion Chairside teaching/learning is largely unreported and unrecognised in undergraduate education. Although not formally timetabled, enthusiastic staff with enough time to engage in chairside teaching can have a positive impact on student learning.
Integrative single-cell RNA-seq and spatial transcriptomics analyses reveal diverse apoptosis-related gene expression profiles in EGFR-mutated lung cancer
Authors: Izumi Motohiro , Fujii Masanori , Kobayashi Ikei S. , Ho Vivian , Kashima Yukie , Udagawa Hibiki , Costa Daniel B. , Kobayashi Susumu S. 
Published: August 2024

AbstractIn EGFR-mutated lung cancer, the duration of response to tyrosine kinase inhibitors (TKIs) is limited by the development of acquired drug resistance. Despite the crucial role played by apoptosis-related genes in tumor cell survival, how their expression changes as resistance to EGFR-TKIs emerges remains unclear. Here, we conduct a comprehensive analysis of apoptosis-related genes, including BCL-2 and IAP family members, using single-cell RNA sequence (scRNA-seq) and spatial transcriptomics (ST). scRNA-seq of EGFR-mutated lung cancer cell lines captures changes in apoptosis-related gene expression following EGFR-TKI treatment, most notably BCL2L1 upregulation. scRNA-seq of EGFR-mutated lung cancer patient samples also reveals high BCL2L1 expression, specifically in tumor cells, while MCL1 expression is lower in tumors compared to non-tumor cells. ST analysis of specimens from transgenic mice with EGFR-driven lung cancer indicates spatial heterogeneity of tumors and corroborates scRNA-seq findings. Genetic ablation and pharmacological inhibition of BCL2L1/BCL-XL overcome or delay EGFR-TKI resistance. Overall, our findings indicate that BCL2L1/BCL-XL expression is important for tumor cell survival as EGFR-TKI resistance emerges.
Hydrogel crosslinking modulates macrophages, fibroblasts, and their communication, during wound healing
Authors: Butenko Sergei , Nagalla Raji R. , Guerrero-Juarez Christian F. , Palomba Francesco , David Li-Mor , Nguyen Ronald Q. , Gay Denise , Almet Axel A. , Digman Michelle A. , Nie Qing , Scumpia Philip O. , Plikus Maksim V. , Liu Wendy F. 
Published: August 2024

AbstractBiomaterial wound dressings, such as hydrogels, interact with host cells to regulate tissue repair. This study investigates how crosslinking of gelatin-based hydrogels influences immune and stromal cell behavior and wound healing in female mice. We observe that softer, lightly crosslinked hydrogels promote greater cellular infiltration and result in smaller scars compared to stiffer, heavily crosslinked hydrogels. Using single-cell RNA sequencing, we further show that heavily crosslinked hydrogels increase inflammation and lead to the formation of a distinct macrophage subpopulation exhibiting signs of oxidative activity and cell fusion. Conversely, lightly crosslinked hydrogels are more readily taken up by macrophages and integrated within the tissue. The physical properties differentially affect macrophage and fibroblast interactions, with heavily crosslinked hydrogels promoting pro-fibrotic fibroblast activity that drives macrophage fusion through RANKL signaling. These findings suggest that tuning the physical properties of hydrogels can guide cellular responses and improve healing, offering insights for designing better biomaterials for wound treatment.
Axion topology in photonic crystal domain walls
Authors: Devescovi Chiara , Morales-Pérez Antonio , Hwang Yoonseok , García-Díez Mikel , Robredo Iñigo , Luis Mañes Juan , Bradlyn Barry , García-Etxarri Aitzol , Vergniory Maia G. 
Published: August 2024

AbstractAxion insulators are 3D magnetic topological insulators supporting hinge states and quantized magnetoelectric effects, recently proposed for detecting dark-matter axionic particles via their axionic excitations. Beyond theoretical interest, obtaining a photonic counterpart of axion insulators offers potential for advancing magnetically-tunable photonic devices and axion haloscopes based on axion-photon conversion. This work proposes an axionic 3D phase within a photonic setup. By building inversion-symmetric domain-walls in gyrotropic photonic crystals, we bind chiral modes on inversion-related hinges, ultimately leading to the realization of an axionic channel of light. These states propagate embedded in a 3D structure, thus protected from radiation in the continuum. Employing a small external gyromagnetic bias, we transition across different axionic mode configurations, enabling effective topological switching of chiral photonic fibers. While demonstrating the possibility of realizing axion photonic crystals within state-of-the-art gyrotropic setups, we propose a general scheme for rendering axion topology at domain walls of Weyl semimetals.
Robust consistent single quantum dot strong coupling in plasmonic nanocavities
Authors: Hu Shu , Huang Junyang , Arul Rakesh , Sánchez-Iglesias Ana , Xiong Yuling , Liz-Marzán Luis M. , Baumberg Jeremy J. 
Published: August 2024

AbstractStrong coupling between a single quantum emitter and an optical cavity (at rate Ω) accesses fundamental quantum optics and provides an essential building block for photonic quantum technologies. However, the minimum mode volume of conventional dielectric cavities restricts their operation to cryogenic temperature for strong coupling. Here we harness surface self-assembly to make deterministic strong coupling at room temperature using CdSe/CdS quantum dots (QDs) in nanoparticle-on-mirror (NPoM) plasmonic nanocavities. We achieve a fabrication yield of ~70% for single QD strong coupling by optimizing their size and nano-assembly. A clear and reliable Rabi splitting is observed both in the scattering of each nanocavity and their photoluminescence, which are however not equal. Integrating these quantum elements with electrical pumping allows demonstration of strong coupling in their electroluminescence. This advance provides a straightforward way to achieve practical quantum devices at room temperature, and opens up exploration of their nonlinear, electrical, and quantum correlation properties.
Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation
Authors: Shao Zengyu , Lu Jiuwei , Khudaverdyan Nelli , Song Jikui 
Published: August 2024

AbstractFunctional crosstalk between DNA methylation, histone H3 lysine-9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1) is essential for proper heterochromatin assembly and genome stability. However, how repressive chromatin cues guide DNA methyltransferases for region-specific DNA methylation remains largely unknown. Here, we report structure-function characterizations of DNA methyltransferase Defective-In-Methylation-2 (DIM2) in Neurospora. The DNA methylation activity of DIM2 requires the presence of both H3K9me3 and HP1. Our structural study reveals a bipartite DIM2-HP1 interaction, leading to a disorder-to-order transition of the DIM2 target-recognition domain that is essential for substrate binding. Furthermore, the structure of DIM2-HP1-H3K9me3-DNA complex reveals a substrate-binding mechanism distinct from that for its mammalian orthologue DNMT1. In addition, the dual recognition of H3K9me3 peptide by the DIM2 RFTS and BAH1 domains allosterically impacts the DIM2-substrate binding, thereby controlling DIM2-mediated DNA methylation. Together, this study uncovers how multiple heterochromatin factors coordinately orchestrate an activity-switching mechanism for region-specific DNA methylation.
Introducing IsoMad, a compilation of isotopic datasets for Madagascar
Authors: Hixon Sean W. , Fernandes Ricardo , Andriamahaihavana Antonin , Baden Andrea L. , Blanco Marina B. , Caulier Guillaume , Dammhahn Melanie , Eeckhaut Igor , Eppley Timothy M. , Frédérich Bruno , Ganzhorn Jörg U. , Garbaras Andrius , Gibson Dean , Goodman Steven M. , Irwin Mitchell , Kelley Elizabeth A. , Michel Loïc N. , Lepoint Gilles , Loudon James E. , Mittelheiser Laurent , Rakotondranary Jacques , Rasamisoa Delaïd C. , Rasolofonirina Richard , Ratovonamana Yedidya , Razafindramanana Josia , Reisdorff Christoph , Sponheimer Matt , Terrana Lucas , Vasey Natalie , Crowley Brooke E. 
Published: August 2024

AbstractWe present the first open-access, island-wide isotopic database (IsoMad) for modern biologically relevant materials collected on Madagascar within the past 150 years from both terrestrial and nearshore marine environments. Isotopic research on the island has increasingly helped with biological studies of endemic organisms, including evaluating foraging niches and investigating factors that affect the spatial distribution and abundance of species. The IsoMad database should facilitate future work by making it easy for researchers to access existing data (even for those who are relatively unfamiliar with the literature) and identify both research gaps and opportunities for using various isotope systems to answer research questions. We also hope that this database will encourage full data reporting in future publications.
Phenotypic variation in 1,100 provenances of Picea abies measured over 50 years on 33 German trial sites
Authors: Liepe Katharina J. , Rieckmann Christoph A. , Mittelberg Hannah S. , Liesebach Mirko 
Published: August 2024

AbstractWe present a database of Norway spruce phenotypic traits measured over a period of 51 years in provenance trials planted across western Germany. These trials are part of the ‘Inventory Provenance Test 1964/68 with Norway spruce’ (IPTNS) that tested a total of 1,100 provenances collected across Europe, both from the species natural and artificial range. Phenotypic traits (first height, later diameter at breast height, survival) were recorded at 33 trial sites of 100 provenances, each a subsample from the entire collection area that represents an approximately comparable climate space. The dataset contains 424,781 records of the same 65,518 trees ranging from age 7 to 51. Overall, it captures the considerable genetic and phenotypic intraspecific variation present in Norway spruce and should be of interest to various fields including quantitative genetics, ecology, biogeography and the adaptive management of forests.
Performance of machine learning algorithms for lung cancer prediction: a comparative approach
Authors: Maurya Satya Prakash , Sisodia Pushpendra Singh , Mishra Rahul , singh Devesh Pratap 
Published: August 2024

AbstractDue to the excessive growth of PM 2.5 in aerosol, the cases of lung cancer are increasing rapidly and are most severe among other types as the highest mortality rate. In most of the cases, lung cancer is detected with least symptoms at its later stage. Hence, clinical records may play a vital role to diagnose this disease at the correct stage for suitable medication to cure it. To detect lung cancer an accurate prediction method is needed which is significantly reliable. In the digital clinical record era with advancement in computing algorithms including machine learning techniques opens an opportunity to ease the process. Various machine learning algorithms may be applied over realistic clinical data but the predictive power is yet to be comprehended for accurate results. This paper envisages to compare twelve potential machine learning algorithms over clinical data with eleven symptoms of lung cancer along with two major habits of patients to predict a positive case accurately. The result has been found based on classification and heat map correlation. K-Nearest Neighbor Model and Bernoulli Naive Bayes Model are found most significant methods for early lung cancer prediction.
Ventriculoatrial shunt remains a safe surgical alternative for hydrocephalus: a systematic review and meta-analysis
Authors: Bue Enrico Lo , Morello Alberto , Bellomo Jacopo , Bradaschia Leonardo , Lacatena Filippo , Colonna Stefano , Fiumefreddo Alessandro , Stieglitz Lennart , Regli Luca , Lanotte Michele Maria , Garbossa Diego , Cofano Fabio 
Published: August 2024

AbstractHydrocephalus is a commonly encountered pathology in the neurosurgical practice. Since the first permanent ventriculo-subarachnoid-subgaleal shunt described by Mikulicz in 1893, there were multiple attempts to find solutions for draining the excess production/less reabsorption of the cerebrospinal fluid (CSF) from the brain. Nowadays, the most common technique is the ventriculoperitoneal shunt (VPS), whereas the ventriculoatrial shunt (VAS) is applied only in some rare conditions. To date there are still no specific guidelines or strong evidence in literature that guide the surgeon in the choice between the two methods, and the decision usually relies on the confidence and expertise of the surgeon. Considering the lack of established recommendations, this systematic review and meta-analysis aims to evaluate the effectiveness and safety of these two shunting techniques. This systematic review was conducted following the PRISMA protocol (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). No chronological limits of study publications were included. Prospective and retrospective clinical studies, and reports of case series with at least five patients per group and reporting data on comparison between VAS and VPS techniques were eligible for inclusion. Nine studies reporting 3197 patients meeting the inclusion and exclusion criteria were identified and included in the quantitative synthesis. The risk of shunt dysfunction/obstruction was significantly lower in the VAS group [odds ratio (OR) 0.49, 95%-CI 0.34–0.70, I2 0%]. The risk of infection was not significantly different between the two groups (OR 1.02, 95%-CI 0.59–1.74, I2 0%). The risk of revision was not significantly different between the two groups; however, the heterogeneity between the studies was significant (OR 0.73, 95%-CI 0.36–1.49, I2 91%). Additionally, the risk of death was not significantly different between the two groups; however, the heterogeneity between the studies was high (OR 1.93, 95%-CI 0.81–4.62, I2 64%). VAS remains a safe surgical alternative for hydrocephalus. The results of this study highlight a lower risk of shunt dysfunction/obstruction variable in the VAS group, with no significant statistical differences regarding the occurrence of at least one infection-related complication. In consequence, the choice between these two techniques must be tailored to the specific characteristics of the patient.Protocol Registration: The review protocol was registered and published in Prospective Register of Systematic Reviews (PROSPERO) (www.crd.york.ac.uk/PROSPERO) website with registration number: CRD42023479365.
The analysis of different types of anorectal abscesses was conducted using the MRI 3D reconstruction technique
Authors: Ma Xutao , Li Yikun , Xu Siming , Wang Bo , Wang Chen 
Published: August 2024

AbstractIt has not yet been proven whether sepsis affects the tissue around the anal canal. To address this issue, we established three-dimensional models for various types of anorectal abscesses and utilize 3D reconstruction of Magnetic Resonance Imaging scans to assess the extent of muscle damage caused by anorectal abscesses. Patients diagnosed with anorectal abscess, selected from January 2019 to January 2022 underwent pre- and post-operative scanning of pelvic floor and perianal tissues. The aforementioned structures were segmented for the reconstruction of a three-dimensional visual model and measurement of volumes for the abscess as well as the internal and external sphincters and levator ani muscle. The study included a total of 42 patients. Three-dimensional visualization models were created for different types of anorectal abscesses, including perianal, intersphincteric, ischiorectal, and supralevator abscesses. No statistically significant differences were observed in the volume of the internal sphincter, external sphincter, and levator ani muscle between pre- and post-operative patients. The 3D model of anorectal abscess, reconstructed from MRI data, offers a precise and direct visualization of the anatomical structures associated with various types of anorectal abscesses. The infection did not result in any damage to the internal and external anal sphincter and levator ani muscle.
Hard X-ray inverse Compton scattering at photon energy of 87.5 keV
Authors: Sakai Yusuke , Babzien Marcus , Fedurin Mikhail , Kusche Karl , Williams Oliver , Fukasawa Atsushi , Naranjo Brian , Murokh Alex , Agustsson Ronald , Simmonds Andrew , Jacob Paul , Stenby George , Malone Robert , Polyanskiy Mikhail , Pogorelsky Igor , Palmer Mark , Rosenzweig James 
Published: August 2024

AbstractProduction of hard X-ray via inverse Compton scattering at photon energies below 100 keV range aimed at potential applications in medicine and material research is reported. Experiments have been performed at the Brookhaven National Laboratory, Accelerator Test Facility, employing the counter collision of a 70 MeV, 0.3 nC electron beam with a near infra-red Nd: YAG laser (1064 nm wavelength) pulse containing ~ 100 mJ in a single shot basis. The radiation distribution of the scattered photon beam is assessed to be sufficiently quasi monochromatic to produce clear contrast from the Au K- edge at 80.7 keV.