bluuebunny/crossref_metadata_2025_split huggingface dataset:
The WAVE complex in developmental and adulthood brain disorders
Authors: Kim Hyung-Goo , Berdasco Clara , Nairn Angus C. , Kim Yong 
Published: January 2025

Abstract
Actin polymerization and depolymerization are fundamental cellular processes required not only for the embryonic and postnatal development of the brain but also for the maintenance of neuronal plasticity and survival in the adult and aging brain. The orchestrated organization of actin filaments is controlled by various actin regulatory proteins. Wiskott‒Aldrich syndrome protein-family verprolin-homologous protein (WAVE) members are key activators of ARP2/3 complex-mediated actin polymerization. WAVE proteins exist as heteropentameric complexes together with regulatory proteins, including CYFIP, NCKAP, ABI and BRK1. The activity of the WAVE complex is tightly regulated by extracellular cues and intracellular signaling to execute its roles in specific intracellular events in brain cells. Notably, dysregulation of the WAVE complex and WAVE complex-mediated cellular processes confers vulnerability to a variety of brain disorders. De novo mutations in WAVE genes and other components of the WAVE complex have been identified in patients with developmental disorders such as intellectual disability, epileptic seizures, schizophrenia, and/or autism spectrum disorder. In addition, alterations in the WAVE complex are implicated in the pathophysiology of Alzheimer’s disease and Parkinson’s disease, as well as in behavioral adaptations to psychostimulants or maladaptive feeding.
Integrated proteogenomic characterization of ampullary adenocarcinoma
Authors: Zhang Qiao , Xu Xiaomeng , Jiang Dongxian , Wang Yunzhi , Wang Haixing , Zhu Jiajun , Tang Shaoshuai , Wang Ronghua , Zhao Shuang , Li Kai , Feng Jinwen , Xiang Hang , Yao Zhenmei , Xu Ning , Fang Rundong , Guo Wenjia , Liu Yu , Hou Yingyong , Ding Chen 
Published: January 2025

AbstractAmpullary adenocarcinoma (AMPAC) is a rare and heterogeneous malignancy. Here we performed a comprehensive proteogenomic analysis of 198 samples from Chinese AMPAC patients and duodenum patients. Genomic data illustrate that 4q loss causes fatty acid accumulation and cell proliferation. Proteomic analysis has revealed three distinct clusters (C-FAM, C-AD, C-CC), among which the most aggressive cluster, C-AD, is associated with the poorest prognosis and is characterized by focal adhesion. Immune clustering identifies three immune clusters and reveals that immune cluster M1 (macrophage infiltration cluster) and M3 (DC cell infiltration cluster), which exhibit a higher immune score compared to cluster M2 (CD4+ T-cell infiltration cluster), are associated with a poor prognosis due to the potential secretion of IL-6 by tumor cells and its consequential influence. This study provides a comprehensive proteogenomic analysis for seeking for better understanding and potential treatment of AMPAC.
DNA methylation modulates nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos
Authors: Fanourgakis Grigorios , Gaspa-Toneu Laura , Komarov Pavel A. , Papasaikas Panagiotis , Ozonov Evgeniy A. , Smallwood Sebastien A. , Peters Antoine H. F. M. 
Published: January 2025

AbstractIn the germ line and during early embryogenesis, DNA methylation (DNAme) undergoes global erasure and re-establishment to support germ cell and embryonic development. While DNAme acquisition during male germ cell development is essential for setting genomic DNA methylation imprints, other intergenerational roles for paternal DNAme in defining embryonic chromatin are unknown. Through conditional gene deletion of the de novo DNA methyltransferases Dnmt3a and/or Dnmt3b, we observe that DNMT3A primarily safeguards against DNA hypomethylation in undifferentiated spermatogonia, while DNMT3B catalyzes de novo DNAme during spermatogonial differentiation. Failing de novo DNAme in Dnmt3a/Dnmt3b double deficient spermatogonia is associated with increased nucleosome occupancy in mature sperm, preferentially at sites with higher CpG content, supporting the model that DNAme modulates nucleosome retention in sperm. To assess the impact of altered sperm chromatin in formatting embryonic chromatin, we measure H3K4me3 occupancy at paternal and maternal alleles in 2-cell embryos using a transposon-based tagging approach. Our data show that reduced DNAme in sperm renders paternal alleles permissive for H3K4me3 establishment in early embryos, independently of possible paternal inheritance of sperm born H3K4me3. Together, this study provides evidence that paternally inherited DNAme directs chromatin formation during early embryonic development.
Endothelial-secreted Endocan activates PDGFRA and regulates vascularity and spatial phenotype in glioblastoma
Authors: Bastola Soniya , Pavlyukov Marat S. , Sharma Neel , Ghochani Yasmin , Nakano Mayu A. , Muthukrishnan Sree Deepthi , Yu Sang Yul , Kim Min Soo , Sohrabi Alireza , Biscola Natalia P. , Yamashita Daisuke , Anufrieva Ksenia S. , Kovalenko Tatyana F. , Jung Grace , Ganz Tomas , O’Brien Beatrice , Kawaguchi Riki , Qin Yue , Seidlits Stephanie K. , Burlingame Alma L. , Oses-Prieto Juan A. , Havton Leif A. , Goldman Steven A. , Hjelmeland Anita B. , Nakano Ichiro , Kornblum Harley I. 
Published: January 2025

AbstractExtensive neovascularization is a hallmark of glioblastoma (GBM). In addition to supplying oxygen and nutrients, vascular endothelial cells provide trophic support to GBM cells via paracrine signaling. Here we report that Endocan (ESM1), an endothelial-secreted proteoglycan, confers enhanced proliferative, migratory, and angiogenic properties to GBM cells and regulates their spatial identity. Mechanistically, Endocan exerts at least part of its functions via direct binding and activation of the PDGFRA receptor. Subsequent downstream signaling enhances chromatin accessibility of the Myc promoter and upregulates Myc expression inducing stable phenotypic changes in GBM cells. Furthermore, Endocan confers radioprotection on GBM cells in vitro and in vivo. Inhibition of Endocan-PDGFRA signaling with ponatinib increases survival in the Esm1 wild-type but not in the Esm1 knock-out mouse GBM model. Our findings identify Endocan and its downstream signaling axis as a potential target to subdue GBM recurrence and highlight the importance of vascular-tumor interactions for GBM development.
DNA targeting by compact Cas9d and its resurrected ancestor
Authors: Ocampo Rodrigo Fregoso , Bravo Jack P. K. , Dangerfield Tyler L. , Nocedal Isabel , Jirde Samatar A. , Alexander Lisa M. , Thomas Nicole C. , Das Anjali , Nielson Sarah , Johnson Kenneth A. , Brown Christopher T. , Butterfield Cristina N. , Goltsman Daniela S. A. , Taylor David W. 
Published: January 2025

AbstractType II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases.
Activity of the mammalian DNA transposon piggyBat from Myotis lucifugus is restricted by its own transposon ends
Authors: Hickman Alison B. , Lannes Laurie , Furman Christopher M. , Hong Christina , Franklin Lidiya , Ghirlando Rodolfo , Ghosh Arpita , Luo Wentian , Konstantinidou Parthena , Lorenzi Hernán A. , Grove Anne , Haase Astrid D. , Wilson Matthew H. , Dyda Fred 
Published: January 2025

AbstractMembers of the piggyBac superfamily of DNA transposons are widely distributed in host genomes ranging from insects to mammals. The human genome has retained five piggyBac-derived genes as domesticated elements although they are no longer mobile. Here, we have investigated the transposition properties of piggyBat from Myotis lucifugus, the only known active mammalian DNA transposon, and show that its low activity in human cells is due to subterminal inhibitory DNA sequences. Activity can be dramatically improved by their removal, suggesting the existence of a mechanism for the suppression of transposon activity. The cryo-electron microscopy structure of the piggyBat transposase pre-synaptic complex showed an unexpected mode of DNA binding and recognition using C-terminal domains that are topologically different from those of the piggyBac transposase. Here we show that structure-based rational re-engineering of the transposase through the removal of putative phosphorylation sites and a changed domain organization - in combination with truncated transposon ends - results in a transposition system that is at least 100-fold more active than wild-type piggyBat.
Novel GSIP: GAN-based sperm-inspired pixel imputation for robust energy image reconstruction
Authors: Mahmoud Gamal M. , Said Wael , Fadel Magdy M. , Elbaz Mostafa 
Published: January 2025

AbstractMissing pixel imputation is a critical task in image processing, where the presence of high percentages of missing pixels can significantly degrade the performance of downstream tasks such as image segmentation and object detection. This paper introduces a novel approach for missing pixel imputation based on Generative Adversarial Networks (GANs). We propose a new GAN architecture incorporating an identity module and a sperm motility-inspired heuristic during filtration to optimize the selection of pixels used in reconstructing missing data. The intelligent sperm motility heuristic navigates the image’s pixel space, identifying the most influential neighboring pixels for accurate imputation. Our approach includes three essential modifications: (1) integration of an identity module within the GAN architecture to mitigate the vanishing gradient problem; (2) introduction of a metaheuristic algorithm based on sperm motility to select the top 10 pixels that most effectively contribute to the generation of the missing pixel; and (3) the implementation of an adaptive interval mechanism between the discriminator’s actual value and the weighted average of the selected pixels, enhancing the generator’s efficiency and ensuring the coherence of the imputed pixels with the surrounding image context. We evaluate the proposed method on three distinct datasets (Energy Images, NREL Solar Images, and NREL Wind Turbine Dataset), demonstrating its superior performance in maintaining pixel integrity during the imputation process. Our experiments also confirm the approach’s effectiveness in addressing everyday challenges in GANs, such as mode collapse and vanishing gradients, across various GAN architectures.
Water and seawater splitting with MgB2 plasmonic metal-based photocatalyst
Authors: Kravets Vasyl G. , Grigorenko Alexander N. 
Published: January 2025

Abstract
Plasmonic nanostructures can help to drive chemical photocatalytic reactions powered by sunlight. These reactions involve excitation of plasmon resonances and subsequent charge transfer to molecular orbitals under study. Here we engineered photoactive plasmonic nanostructures with enhanced photocatalytic performance using non-noble metallic MgB2 high-temperature superconductor which represents a new family of photocatalysts. Ellipsometric study of fabricated MgB2 nanostructures demonstrates that this covalent binary metal with layered graphite-like structure could effectively absorb visible and infrared light by excitation of multi-wavelengths surface plasmon resonances. We show that a MgB2 plasmonic metal-based photocatalyst exhibit fundamentally different behaviour compared to that of a semiconductor photocatalyst and provides several advantages in photovoltaics applications. Excitation of localised surface plasmon resonances in MgB2 nanostructures allows one to overcome the limiting factors of photocatalytic efficiency observed in semiconductors with a wide energy bandgap due to the usage of a broader spectrum range of solar radiation for water splitting catalytic reactions conditioned by enhanced local electromagnetic fields of localised plasmons. Excitation of localised surface plasmon resonances induced by absorption of light in MgB2 nanosheets could help to achieve near full-solar spectrum harvesting in this photocatalytic system. We demonstrate a conversion efficiency of ~ 5% at bias voltage of V

bias
= 0.3 V for magnesium diboride working as a catalyst for the case of plasmon-photoinduced seawater splitting. Our work could result in inexpensive and stable photocatalysts that can be produced in large quantities using a mechanical rolling mill procedure.
Genome-wide identification, characterization, and functional analysis of the CHX, SOS, and RLK genes in Solanum lycopersicum under salt stress
Authors: Maghraby Amaal , Alzalaty Mohamed 
Published: January 2025

AbstractThe cation/proton exchanger (CHX), salt overly sensitive (SOS), and receptor-like kinase (RLK) genes play significant roles in the response to salt stress in plants. This study is the first to identify the SOS gene in Solanum lycopersicum (tomato) through genome-wide analysis under salt stress conditions. Quantitative reverse transcription PCR (qRT-PCR) results indicated that the expression levels of CHX, SOS, and RLK genes were upregulated, with fold changes of 1.83, 1.49, and 1.55, respectively, after 12 h of exposure to salt stress. Genome-wide analysis revealed 21 CHX, 5 SOS, and 86 RLK genes in S. lycopersicum. CHX genes were found on chromosomes 2, 3, 4, 5, 6, 7, 8, 9, 11, and 12 of S. lycopersicum. SOS genes were found on chromosomes 1, 4, 6, and 10. RLK genes were found on all chromosomes of S. lycopersicum. The Ka/Ks ratios indicate that the CHX, SOS, and RLK genes have been primarily influenced by purifying selection. This suggests that these genes have faced strong environmental pressures throughout their evolution. Purifying selection typically results in a decrease in genetic diversity. The estimated duplication time for CHX paralogous gene pairs ranged from approximately 26.965 to 245.413 million years ago (Mya), while the duplication time for SOS paralogous gene pairs ranged from around 116.682 to 275.631 Mya. For RLK paralogous gene pairs, the duplication time varied from approximately 27.689 to 239.376 Mya. Synteny analysis of the CHX, SOS, and RLK genes demonstrated collinear relationships with orthologous genes in Arabidopsis thaliana, but no collinearity orthologous relationships in Oryza sativa (rice). Furthermore, the analysis revealed that there were 6 orthologous SlCHX genes, 2 orthologous SlSOS genes, and 44 orthologous SlRLK genes paired with those in A. thaliana. The results of the present study may help to elucidate the role of the CHX, SOS, and RLK genes in salt stress in S. lycopersicum.
Patchiness of plankton ecosystem structure due to nutrient mixing along the shelf edge in the North Sea
Authors: Cordier Axelle , Bendtsen Jørgen , Daugbjerg Niels , From Nikolaj , Jónasdóttir Sigrún Huld , Mousing Erik Askov , Christensen Jens Tang , Silva Teresa , Richardson Katherine 
Published: January 2025

AbstractMid-water column turbulence has been shown to cause elevated vertical nutrient flux at the shelf edge in the northeastern North Sea. Here, we demonstrate that phytoplankton communities in this region tend to be dominated by larger cells (estimated from percentage of chlorophyll captured on a 10 μm filter) than beyond the shelf edge. Fv/Fm (PSII electron transport capacity) corrected for photoinhibition in the surface layer correlated in this study with the percentage of chlorophyll captured on a 10 µm filter (assumed to be large cells), suggesting that the phytoplankton community was responding to increased nutrients in the euphotic zone by increasing photosynthetic efficiency and altering community composition. The greatest abundances of larger copepods and the highest rates of Centropages typicus egg production were also generally found at the shelf edge. These results suggested that impact from increased nutrient fluxes cascaded up the planktonic food web. As these regions of nutrient flux were very localised, this led to sub-mesoscale heterogeneity in plankton ecosystem structure. Reports of higher abundances of fish and mammals at the shelf edge are common and we hypothesise that their distributions are a response to the impact of mid-water column nutrient upwelling on the plankton food web in the region.
Optimising detector readout settings for the detection of spatial correlations between SPDC photon-pairs
Authors: Roberts K. , Gregory T. , Wolley O. , Padgett M. J. 
Published: January 2025

AbstractSPDC photon-pairs exhibit spatial correlations which can be measured using detector arrays sensitive to single photons. However, these detector arrays have multiple readout modes and in order to optimise detection it is important to select the optimum mode to detect the correlations against a background of optical and electronic noise. These quantum correlations enable applications in imaging, sensing, communication, and optical processing. Here we compare the measurement of spatial correlations for a broad range of readout modes of an EMCCD camera and attempt to characterise the optimal readout mode for our purposes. This assessment is important for the use of detector arrays of different types for use in quantum, low-light, enhanced resolution, imaging systems.
Qualitative comparison of decalcifiers for mouse bone cryosections for subsequent biophotonic analysis
Authors: Mandal Shibarjun , Motganhalli Ravikumar Ramya , Tannert Astrid , Urbanek Annett , Guliev Rustam R. , Naumann Max , Coldewey Sina M. , Dahmen Uta , Carvalho Lina , Bastião Silva Luís , Neugebauer Ute 
Published: January 2025

AbstractBone tissue, with its complex structure, often necessitates decalcification of the hard tissue for ex vivo morphological studies. The choice of a suitable decalcification method plays a crucial role in preserving desired features and ensuring compatibility with diverse imaging techniques. The search for a universal decalcification method that is suitable for a range of biophotonic analyses remains an ongoing challenge. In this study, we systematically assessed five standard bone decalcification protocols, encompassing strong mineralic acids (3% and 5% nitric acid), a commercially available formulation of hydrochloric and formic acid), as well as weak organic acids (5% trichloroacetic acid and 8% formic acid), and a chelating agent (25% ethylenediamine-tetraacetic acid) with varying decalcification durations, using mouse long bones as our experimental model. Our imaging analysis panel included classical histological staining (Hematoxylin and Eosin, H&E), immunofluorescence staining, and label-free Raman microspectroscopic imaging. We used cryosections instead of paraffin sections since paraffin interferes with tissue Raman signals. This approach is not as commonly used as it is more prone to handling artifacts, but is the preferred method for subsequent Raman analysis. Decalcification efficacy was evaluated based on various qualitative and some quantitative imaging parameters by 2–3 independent observers. Our systematic approach revealed that the chelating agent, when used for 24 h, optimally preserved bone features and, thus, would be the ideal decalcifying agent for comprehensive subsequent analysis. However, the choice of decalcifier and the ideal decalcification duration may vary depending on the type and thickness of bone, necessitating tailored adjustments to meet specific experimental requirements.
Impact of early initiation of renal replacement therapy in patients on venoarterial ECMO using target trial emulation with Japanese nationwide data
Authors: Kubo Toshihiro , Takeuchi Tomonori , Inoue Norihiko , Cama-Olivares Augusto , Chandramohan Deepak , Tolwani Ashita J. , Wille Keith M. , Fushimi Kiyohide , Neyra Javier A. , Wakabayashi Kenji 
Published: January 2025

AbstractWhile renal replacement therapy (RRT) allows for precise fluid management as well as addressing electrolyte imbalances and the removal of other necessary compounds, its early initiation has not shown benefit in the general critically ill population. Moreover, the effects of early RRT initiation specifically in patients on venoarterial extracorporeal membrane oxygenation (VA-ECMO) also remain unclear. This retrospective study investigated adult patients who underwent VA-ECMO between April 2018 and March 2022 and used the clone-censor-weight method to emulate a hypothetical target trial and compare two groups: patients who initiated RRT within 2 days of VA-ECMO initiation (Early) and those who did not (Late). The primary outcomes were 28-day and 90-day hospital mortality analyzed by Cox proportional hazards models and the secondary outcome was 90-day RRT dependence by pooled logistic regression models. Inverse probability censoring weights were applied to adjust the models. A total of 2,513 VA-ECMO patients were cloned into both groups. The 28-day and 90-day mortalities were lower in the Early group (HR 0.59 [95% CI 0.53–0.68] and 0.67 [0.61–0.75]). However, the early group experienced greater RRT dependence at 90 days than the late group (OR 2.58 [1.94–3.46]). In conclusion, early initiation of RRT (within 2 days of VA-ECMO) was associated with lower hospital mortality but with a higher likelihood of 90-day RRT dependence in adult patients on VA-ECMO.
Repeated 5-aminolevulinic acid mediated sonodynamic therapy using magnetic resonance guided focused ultrasound in rat brain tumour models
Authors: Wu Sheng-Kai , Tsai Chia-Lin , Mir Aisha , Marcus Stuart L. , Hynynen Kullervo 
Published: January 2025

AbstractSonodynamic therapy is an emerging therapeutic approach against brain tumours. However, the treatment scheme and ultrasound parameters have yet to be explored for clinical translation. Our study aimed to optimize ultrasound parameters for sonodynamic therapy (SDT) with 5-ALA as a sonosensitizing agent and to evaluate its therapeutic outcome on the rodent 9L gliosarcoma and the human U87 glioblastoma models. We stereotactically implanted brain tumour cells in rats and monitored tumour volume via MRI. SDT was conducted weekly using a 60 mg/kg dose of 5-ALA, injected intravenously 6 h before sonication. We used a driving frequency of 580 kHz with 0.75 MPa and evaluated the effect of different burst lengths to optimize ultrasound parameters. We also tested SDT against advanced-stage brain tumours to verify its efficacy further. Our results showed that a longer burst length could improve therapeutic outcomes. Tumour growth inhibition was established only in the first three weeks with 10 ms and 50 ms burst length sonication, but 86 ms burst length greatly improved the survival outcome. Therefore, the therapeutic efficacy is proportionate to the burst length and, thus, the total delivered energy. Repeated SDT using multiple targets to cover the entire tumour volume with optimal ultrasound parameters can achieve significant anti-tumour effects in both 9L and U87 models. Lastly, our results on late-stage tumour treatments showed that SDT can still provide prolonged survival. These promising findings demonstrate that repeated SDT using transcranial-focused ultrasound together with 5-ALA can optimize anti-tumour effects and even lead to complete clearance of the tumours. This weekly treatment with pulsed ultrasound sonication strategy is practical for future clinical translation.