bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atmospheric Advection and Precipitation Control Fog's Occurrence Over the Southern Ocean in Summer
Authors: Jiang Keyue , Liu Changwei , Yang Qinghua , Vihma Timo , Chen Dake , Han Bo 
Published: February 2025

AbstractSea fog strongly affects human activities in the Southern Ocean (SO), but little is known about the factors controlling its occurrence and properties. Using multi‐year ship‐based observations and state‐of‐the‐art atmospheric reanalysis data, we summarize two methods to identify sea fog episodes on a climatologic scale and estimate the sea fog occurrence in SO from 1979 to 2019. The first method considers the sea‐air temperature difference and atmospheric humidity, while the second explores the similarity between fog and low‐level clouds. Both methods revealed three centers of sea fog occurrence in the SO. Further analysis shows that the downward surface sensible heat flux due to the southward heat advection in the lower troposphere determines the monthly climatology and linear trends of sea fog occurrence. Precipitation suppresses summer sea fog over the entire SO and partly determines the latter's response to the Southern Annular Mode on an interannual scale.
Numerical Investigation Into Mechanical Behavior of Metastable Olivine During Phase Transformation: Implications for Deep‐Focus Earthquakes
Authors: Sindhusuta S. , Chi Sheng‐Wei , Foster Craig , Officer Timothy , Wang Yanbin 
Published: February 2025

AbstractOne hypothesized mechanism that triggers deep‐focus earthquakes in oceanic subducting slabs below ∼300 km depth is transformational faulting due to the olivine‐to‐spinel phase transition. This study uses finite element modeling to investigate phase transformation‐induced stress redistribution and material weakening in olivine. A thermodynamically consistent constitutive model is developed to capture the evolution of phase transformation in olivine under different pressure and temperature conditions. The overall numerical model enables considering multiscale material features, including the polycrystalline structure, mesoscale heterogeneity, and various phases or variants of phases at the microscopic level, and accounts for viscoplastic behaviors with thermo‐mechanical coupling effects. The model is validated with several benchmarks, including a phase diagram of phase transformation from olivine to spinel. The validated model is used to study the interactive behaviors between defects (heterogeneity) and phase transformation. The simulation results reveal that spinel formation under pressure initiates near inclusions and along the grain boundaries, consistent with experimental observations. At lower temperatures, the transformation leads to the formation of thin conjugate bands of spinel diagonal to the compression loading direction. Local stress analysis along these bands also suggests the initiation of faulting. In contrast, the numerical results at higher transformation rates show that significant spinel formation occurs over a larger area at elevated temperatures, leading to ductile behavior, which agrees with experimental findings. Numerical simulation of multiple inclusions under confined pressure also shows the formation of a network of spinel bands resembling phase‐transformation patterns observed in the laboratory experiments. Additionally, stress softening patterns due to phase transformation are similar to experimental observations.
Leaf Spectroscopy Reveals Drought Response Variation in Fagus sylvatica Saplings From Across the Species' Range
Authors: Kurath Dave , van Moorsel Sofia J. , Klaver Jolanda , Voortman Tis , Siegfried Barbara , Brügger Yves‐Alain , Moradi Aboubakr , Czyż Ewa A. , de La Harpe Marylaure , Wiesenberg Guido L. , Schaepman Michael E. , Schuman Meredith C. 
Published: February 2025

AbstractThe common European beech (Fagus sylvatica), sensitive to prolonged drought, is expected to shift its distribution with climate change. To persist in novel environments, young trees rely on the capacity to express diverse response phenotypes. Several methods exist to study drought effects on trees and their diverse adaptive mechanisms, but these are usually destructive and challenging for the large sample numbers needed to investigate biological variation. We conducted a common garden experiment outdoors, but under controlled watering conditions, with 180 potted 2‐year‐old saplings from 16 beech provenances across the species' range, representing three distinct genetic clusters. Drought stress was simulated by interrupting irrigation and stomatal conductance and soil moisture were used to assess drought severity. We measured leaf reflectance of visible to short‐wave infrared electromagnetic radiation to determine drought‐induced changes in biochemical and structural traits derived from spectral indices and a model of leaf optical properties. We quantified changes in pigmentation, water balance, nitrogen, lignin, epicuticular wax, and leaf mass per area in drought‐treated saplings, revealing differences in likely adaptive responses to drought. F. sylvatica saplings from the Iberian Peninsula showed signatures of greater drought resistance, that is, the least drought‐induced change in spectrally derived traits related to leaf pigments and leaf water content. We demonstrate that high‐resolution leaf spectroscopy is an effective and non‐destructive tool to assess individual drought responses that can characterize functional intraspecific variation among young beech trees. Next, this approach should be scaled up to canopy‐level or airborne spectroscopy to support drought response assessments of forests.
Opportunities in the translational pipeline for pediatric brain cancer therapies
Authors: Rumberger Rivera Lindsay , Springer Nora L. , Bailey Katherine , Patel Jenny , Brett Christopher , Barker Elizabeth 
Published: February 2025

Abstract
Primary malignant central nervous system (CNS) tumors are the leading cause of cancer-related mortality in the pediatric population. Moreover, survivors often experience significant long-term treatment-related morbidity. Challenges unique to drug delivery to the central nervous system have hampered therapeutic progress. In the past decade, significant advancements in our understanding of molecular biology, genetic alterations, and the tumor microenvironment have allowed us to improve our in vitro and laboratory animal models to better replicate diseases seen in the pediatric population. Recently, a comparative approach using naturally-occurring CNS malignancies in dogs with similar disease progression, histologic presentation, and treatment response has been proposed as an enticing model system. Given these improvements in the translational pipeline, there is an opportunity to identify and implement effective therapies more efficiently to pediatric CNS malignancy populations.

Impact

Relevant and translational pre-clinical studies are needed to find chemotherapeutics and targeted agents that can reach therapeutic doses within tumors in children without causing systemic adverse effects.

A discussion of comparative oncology is provided with the intent to foster veterinary/human oncology collaboration.

While the traditional pipeline for translating medications from bench to bedside has been evolving and improving over the last decade, the advances and remaining roadblocks of this pipeline are reviewed and discussed in this article.
Long noncoding RNA GDIL acts as a scaffold for CHAC1 and XRN2 to promote platinum resistance of colorectal cancer through inhibition of glutathione degradation
Authors: Deng Xuan , Chang Lu , Tang Lingyu , Jiang Haoqin , Xu Xiao , Zhang Xinju , Chen Jian , Dong Liu , Xu Qianqian , Cao Ruoshui , Xiang Jianbin , Guan Ming 
Published: February 2025

Abstract
Acquired resistance poses a significant obstacle to the effectiveness of platinum-based treatment for cancers. As the most abundant antioxidant, glutathione (GSH) enables cancer cell survival and chemoresistance, by scavenging excessive reactive oxygen species (ROS) induced by platinum. Therapeutic strategy targeting GSH synthesis has been developed, however, failed to produce desirable effects in preventing cancer progression. Thus, uncovering mechanisms of rewired GSH metabolism may aid in the development of additional therapeutic strategies to overcome or delay resistance. Here, we identify upregulation of long noncoding RNA (lncRNA) GDIL (GSH Degradation Inhibiting LncRNA) in platinum resistant colorectal cancer (CRC) and ovarian cancer cells compared with parental ones. High expression of GDIL in resistant CRC is associated with poor survival and hyposensitivity to chemotherapy. We demonstrate that GDIL boosted GSH levels and enhances clearance of ROS induced by platinum. Metabolomic and metabolic flux analysis further reveals that GDIL promotes GSH accumulation by inhibiting GSH degradation. This is attributed by downregulation of CHAC1, an enzyme that specifically degrades intracellular GSH. Mechanistically, GDIL binds and re-localizes the nuclear protein XRN2 to the cytoplasm, where GDIL further serve as a scaffold for XRN2 to identify and degrade CHAC1 mRNA. Suppression of GDIL with selective antisense oligonucleotide, restored drug sensitivity in platinum resistant cell lines and delayed drug resistance in cell line- and patient-derived xenografts. Thus, lncRNA GDIL is a novel target to promote GSH degradation and augment platinum therapy.
GTPase GPN3 facilitates cell proliferation and migration in non-small cell lung cancer by impeding clathrin-mediated endocytosis of EGFR
Authors: Xu Linlin , Guo Jiankun , Xie Xinsheng , Wang Hailong , Jiang Alan , Huang Changhua , Yang Hua , Luo Shiwen , Chen Limin 
Published: February 2025

Abstract
Small GTPases play a critical role as regulatory molecules in signaling transduction and various cellular processes, contributing to the development of human diseases, including cancers. GPN3, an evolutionarily conserved member of the GPN-loop GTPase subfamily classified in 2007 according to its structure, has limited knowledge regarding its cellular functions and molecular mechanisms. In this study, we demonstrate that GPN3 interacts with clathrin light chain A (CLTA), a vesicle coat protein, as well as clathrin-mediated endocytosis associated modulators AP2B1 and AP2S1. Upregulation of GPN3 leads to the inhibition of clathrin-coated pit invagination. Furthermore, we discovered that GPN3 interacts with the epidermal growth factor receptor (EGFR) and regulates the co-localization of EGFR and CLTA, as well as the localization of EGFR in early endosomes upon EGF stimulation. As a result, this leads to a decrease in endocytic levels of EGFR and an increase in the accumulation of EGFR on the cell membrane surface, thereby prolonging activation of EGFR signaling. The functional effects exerted by GPN3 are dependent on cellular levels of GTP abundance. Furthermore, our findings indicate that aberrant overexpression of GPN3 is observed in non-small cell lung cancer (NSCLC) tissues compared to adjacent normal tissues, and high expression levels of GPN3 are associated with poor prognosis for NSCLC patients. Collectively, these findings reveal that GPN3 acts as an oncogene promoting cell proliferation and migration in NSCLC through regulation of clathrin-dependent EGFR endocytosis. These results suggest that targeting GPN3 could serve as a novel prognostic biomarker and therapeutic strategy for NSCLC treatment.
Visual and patient-reported outcomes of an enhanced versus monofocal intraocular lenses in cataract surgery: a systematic review and meta-analysis
Authors: Fernández Joaquín , Ribeiro Filomena , Burguera Noemí , Rodríguez-Calvo-de-Mora Marina , Rodríguez-Vallejo Manuel 
Published: February 2025

Abstract
Understanding the functional outcomes achieved with new enhanced monofocal intraocular lenses (IOLs) is crucial for adequately managing patient expectations. This study evaluated visual and patient-reported outcomes of an enhanced range of field IOL versus other monofocal IOLs in cataract patients. A systematic review and meta-analysis, pre-registered on PROSPERO (CRD42024561611), included studies from Medline (PubMed), Embase (Ovid), and trial registries (2019-2024) focused on binocular cataract surgeries with various IOL models. Primary outcomes assessed were monocular distance-corrected visual acuities (CDVA, DCIVA, DCNVA), defocus curves, and contrast sensitivity; secondary measures included binocular visual acuities and patient-reported outcomes such as spectacle independence and photic phenomena. Out of 31 studies (8 randomized clinical trials, 23 case series), high-certainty evidence indicated no significant difference in CDVA between enhanced and conventional IOLs. However, enhanced IOLs demonstrated better intermediate (DCIVA: −0.11 logMAR, CI 95%: −0.13 to −0.10) and near (DCNVA: −0.12 logMAR, CI 95%: −0.17 to −0.07) visual acuities, supported by defocus curves, though with lower-certainty evidence. No significant differences were observed in contrast sensitivity or photic phenomena, and evidence for positive dysphotopsia was moderate to low. Enhanced IOLs significantly favored intermediate-distance spectacle independence, with an odds ratio of 7.85 (CI 95%: 4.08–15.09), though no differences were observed for distance spectacle independence. Near-distance spectacle independence also favored enhanced IOLs, though with low-certainty evidence. In summary, enhanced IOLs provide improved intermediate and near visual acuities compared to conventional monofocal IOLs, though further studies are needed to confirm outcomes in contrast sensitivity and patient-reported outcomes across various enhanced monofocal IOLs.
Adherence to american urological association (AUA) vasectomy guidelines: a systematic review of current practice among healthcare providers
Authors: Mahdi Mohammed , Hammad Muhammed A. M. , Abou Chawareb Elia , Almuhaideb Mana , Yafi Faysal A. 
Published: February 2025

Abstract
Vasectomy, a common male sterilization procedure, has seen a surge in popularity following the 2022 reversal of Roe v. Wade. The American Urological Association (AUA) vasectomy guidelines provide essential guidance for providers, outlining best practices for the procedure. We reviewed studies that examined adherence to the AUA vasectomy guidelines with regard to pre-procedure counseling, surgical technique, and post vasectomy semen analysis (PVSA) practice, as well as studies evaluating the impact of these guidelines on urology and non-urology practices. A total of five studies were identified that assessed adherence to the guidelines. Only one of these studies evaluated adherence to all three aspects of the guidelines. The remaining four studies focused solely on the practice of PVSA. Overall, urologists exhibited greater adherence to the guidelines compared to other healthcare providers. However, the adherence rates were still suboptimal. Five additional studies were included that evaluated the use of home-based PVSA, which is not part of the AUA guidelines. Conflicting results were found regarding the test compliance. While the studies evaluating home-based PVSA may raise the question of including this approach in the guidelines panel discussion, it is important to consider the potential benefits and drawbacks before incorporating it as an option in future guidelines.
Rapid learning with phase-change memory-based in-memory computing through learning-to-learn
Authors: Ortner Thomas , Petschenig Horst , Vasilopoulos Athanasios , Renner Roland , Brglez Špela , Limbacher Thomas , Piñero Enrique , Linares-Barranco Alejandro , Pantazi Angeliki , Legenstein Robert 
Published: February 2025

Abstract
There is a growing demand for low-power, autonomously learning artificial intelligence (AI) systems that can be applied at the edge and rapidly adapt to the specific situation at deployment site. However, current AI models struggle in such scenarios, often requiring extensive fine-tuning, computational resources, and data. In contrast, humans can effortlessly adjust to new tasks by transferring knowledge from related ones. The concept of learning-to-learn (L2L) mimics this process and enables AI models to rapidly adapt with only little computational effort and data. In-memory computing neuromorphic hardware (NMHW) is inspired by the brain’s operating principles and mimics its physical co-location of memory and compute. In this work, we pair L2L with in-memory computing NMHW based on phase-change memory devices to build efficient AI models that can rapidly adapt to new tasks. We demonstrate the versatility of our approach in two scenarios: a convolutional neural network performing image classification and a biologically-inspired spiking neural network generating motor commands for a real robotic arm. Both models rapidly learn with few parameter updates. Deployed on the NMHW, they perform on-par with their software equivalents. Moreover, meta-training of these models can be performed in software with high-precision, alleviating the need for accurate hardware models.
Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding
Authors: Huynh Duyen , Hoffmeister Philipp , Friedrich Tobias , Zhang Kefan , Bartkuhn Marek , Ferrante Francesca , Giaimo Benedetto Daniele , Kovall Rhett A. , Borggrefe Tilman , Oswald Franz , Gebhardt J. Christof M. 
Published: February 2025

Abstract
Transcription factors (TFs) such as RBPJ in Notch signaling bind to specific DNA sequences to regulate transcription. How TF-DNA binding kinetics and cofactor interactions modulate gene regulation is mostly unknown. We determine the binding kinetics, transcriptional activity, and genome-wide chromatin occupation of RBPJ and mutant variants by live-cell single-molecule tracking, reporter assays, and ChIP-Seq. Importantly, the search time of RBPJ exceeds its residence time, indicating kinetic rather than thermodynamic binding stability. Impaired RBPJ-DNA binding as in Adams-Oliver-Syndrome affect both target site association and dissociation, while impaired cofactor binding mainly alters association and unspecific binding. Moreover, our data point to the possibility that cofactor binding contributes to target site specificity. Findings for other TFs comparable to RBPJ indicate that kinetic rather than thermodynamic DNA binding stability might prevail in vivo. We propose an effective in vivo binding energy landscape of TF-DNA interactions as instructive visualization of binding kinetics and mutation-induced changes.
Transcriptome size matters for single-cell RNA-seq normalization and bulk deconvolution
Authors: Lu Songjian , Yang Jiyuan , Yan Lei , Liu Jingjing , Wang Judy Jiaru , Jain Rhea , Yu Jiyang 
Published: February 2025

Abstract
The variation of transcriptome size across cell types significantly impacts single-cell RNA sequencing (scRNA-seq) data normalization and bulk RNA-seq cellular deconvolution, yet this intrinsic feature is often overlooked. Here we introduce ReDeconv, a computational algorithm that incorporates transcriptome size into scRNA-seq normalization and bulk deconvolution. ReDeconv introduces a scRNA-seq normalization approach, Count based on Linearized Transcriptome Size (CLTS), which corrects differential expressed genes typically misidentified by standard count per 10 K normalization, as confirmed by orthogonal validations. By maintaining transcriptome size variation, CLTS-normalized scRNA-seq enhances the accuracy of bulk deconvolution. Additionally, ReDeconv mitigates gene length effects and models expression variances, thereby improving deconvolution outcomes, particularly for rare cell types. Evaluated with both synthetic and real datasets, ReDeconv surpasses existing methods in precision. ReDeconv alters the practice and provides a new standard for scRNA-seq analyses and bulk deconvolution. The software packages and a user-friendly web portal are available.
Cyclic di AMP phosphodiesterase nanovaccine elicits protective immunity against Burkholderia cenocepacia infection in mice
Authors: Gawad Wesam E. , Nagy Yosra I. , Samir Tamer M. , Mansour Ahmed Mohamed Ibrahim , Helmy Omneya M. 
Published: February 2025

Abstract

Burkholderia cenocepacia causes life-threatening infections in immunocompromised patients. Treatment is challenging due to intrinsic antibiotic multiresistance, so vaccination provides an alternative approach. We aimed to identify vaccine candidates using reverse vaccinology and evaluate their efficacy as protein-loaded chitosan: pectin nanoparticles (C:P NPs) in a vaccine model. Applying strict subtractive channels, three proteins were shortlisted: WP_006481710.1 (LY), WP_012493605.1 (KT), and WP_006492970.1 (BD). Proteins were cloned, purified as His-tagged proteins, and loaded onto C:P NPs. Vaccinated mice had significantly higher systemic IgG and mucosal IgA antibody responses and induced IL-6 and IL-17A. 6x-His-LY-CS:P NPs and 6x-His-KT-CS:P NPs vaccines induced TNF-α. Vaccines conferred significant protection against B. cenocepacia intranasal infections. In conclusion, cyclic-di-AMP phosphodiesterase (WP_012493605.1) is a promising vaccine candidate that elicited IgG and IgA antibodies, Th1, Th2, and Th17 cellular immunity in BALB/c mice and protected against B. cenocepacia infection. This provides hope for saving lives of people at high risk of infection.
Federated and reusable processing of Earth observation data
Authors: Mohr Matthias , Pebesma Edzer , Dries Jeroen , Lippens Stefaan , Janssen Bram , Thiex Daniel , Milcinski Grega , Schumacher Benjamin , Briese Christian , Claus Michele , Jacob Alexander , Sacramento Paulo , Griffiths Patrick 
Published: February 2025

Abstract
The unprecedented and continuously growing volume of Earth Observation (EO) and geospatial data has necessitated a paradigm change where compute is collocated with the data archives in public clouds. However, as no single cloud platform can host all of this data, federated processing solutions that work across multiple cloud platforms are becoming increasingly relevant. A community-based approach to federated processing has started using openEO, a common Application Programming Interface (API) and set of well-defined processes that simplifies reuse and provides a valuable level of abstraction when handling large EO data volumes. We present key concepts for federated processing and related interoperability aspects based on openEO Platform, a federated public cloud platform.
The expanded genome of Hexamita inflata, a free-living diplomonad
Authors: Akdeniz Zeynep , Havelka Michal , Stoklasa Michal , Jiménez-González Alejandro , Žárský Vojtěch , Xu Feifei , Stairs Courtney W. , Jerlström-Hultqvist Jon , Kolísko Martin , Provazník Jan , Svärd Staffan , Andersson Jan O. , Tachezy Jan 
Published: February 2025

Abstract
Diplomonads are anaerobic, flagellated protists, being part of the Metamonada group of Eukaryotes. Diplomonads either live as endobionts (parasites and commensals) of animals or free-living in low-oxygen environments. Genomic information is available for parasitic diplomonads like Giardia intestinalis and Spironucleus salmonicida, while little is known about the genomic arrangements of free-living diplomonads. We have generated the first reference genome of a free-living diplomonad, Hexamita inflata. The final version of the genome assembly is fragmented (1241 contigs) but substantially larger (142 Mbp) than the parasitic diplomonad genomes (9.8–14.7 Mbp). It encodes 79,341 proteins; 29,874 have functional annotations and 49,467 are hypothetical proteins. Interspersed repeats comprise 34% of the genome (9617 Retroelements, 2676 DNA transposons). The large expansion of protein-encoding capacity and the interspersed repeats are the major reasons for the large genome size. This genome from a free-living diplomonad will be the basis for further studies of the Diplomonadida lineage and the evolution of parasitism-free living style transitions.