bluuebunny/crossref_metadata_2025_split huggingface dataset:
The interplay of age, gender and amyloid on brain and cognition in mid-life and older adults
Authors: Borne Léonie , Thienel Renate , Lupton Michelle K. , Guo Christine , Mosley Philip , Behler Anna , Giorgio Joseph , Adam Robert , Ceslis Amelia , Bourgeat Pierrick , Fazlollahi Amir , Maruff Paul , Rowe Christopher C. , Masters Colin L. , Fripp Jurgen , Robinson Gail A. , Breakspear Michael 
Published: November 2024

AbstractDeficits in memory are seen as a canonical sign of aging and a prodrome to dementia in older adults. However, our understanding of age-related cognition and brain morphology occurring throughout a broader spectrum of adulthood remains limited. We quantified the relationship between cognitive function and brain morphology (sulcal width, SW) using three cross-sectional observational datasets (PISA, AIBL, ADNI) from mid-life to older adulthood, assessing the influence of age, sex, amyloid (Aβ) and genetic risk for dementia. The data comprised cognitive, genetic and neuroimaging measures of a total of 1570 non-clinical mid-life and older adults (mean age 72, range 49–90 years, 1330 males) and 1365 age- and sex-matched adults with mild cognitive impairment (MCI) or Alzheimer’s disease (AD). Among non-clinical adults, we found robust modes of co-variation between regional SW and multidomain cognitive function that differed between the mid-life and older age range. These cortical and cognitive profiles derived from healthy cohorts predicted out-of-sample AD and MCI. Furthermore, Aβ-deposition and educational attainment levels were associated with cognition but not SW. These findings underscoring the complex interplay between factors influencing cognition and brain structure from mid-life onwards, providing valuable insights for future research into neurodegeneration and the development of future screening algorithms.
Socioeconomic disparities in Plasmodium falciparum infection risk in Southern Malawi: mediation analyses
Authors: Wafula Solomon T. , Maiga-Ascofare Oumou , Struck Nicole S. , Mathanga Don P. , Cohee Lauren M. , May Jürgen , Puradiredja Dewi I. , Lorenz Eva 
Published: November 2024

AbstractThis study investigated the mediators of the association between socioeconomic position (SEP) and Plasmodium falciparum (Pf) infection in Southern region of Malawi. We utilized data from the 2014 International Center of Excellence for Malaria Research (ICEMR) surveys from Malawi in which blood samples of all individuals from selected households in Blantyre, Thyolo and Chikhwawa were tested for Pf parasitemia. We assessed household SEP and potential mediators – housing quality, food security, education status of household heads, and use of long-lasting Insecticide-treated nets (LLINs) and nutritional status. We conducted causal mediation analyses to assess the proportion of SEP effect that is attributed to each mediator and combination of mediators. The mediation analysis shows that during the rainy season, improved housing and educational attainment explained 39.4% and 17.0% of the SEP effect on Pf infection, respectively, and collectively 66.4%. In the dry season, housing, educational attainment, and LLIN usage collectively mediated 33.4% of SEP’s effect with individual contributions of 15.6%, 11.2%, and 3.8%, respectively. Nutrition also played a role, particularly for children, mediating 9.2% of SEP’s effect in the rainy season and 3.7% in the dry season. The study concluded that multifaceted interventions targeting housing, education, LLIN usage, and nutrition are vital to reducing socioeconomic disparities in Pf infection risk in the Southern region of Malawi.
Impact of thermal seed treatment on spermosphere microbiome, metabolome and viability of winter wheat
Authors: Karlsson Maria E. , Forsberg Gustaf , Rosberg Anna Karin , Thaning Christian , Alsanius Beatrix 
Published: November 2024

AbstractThermal seed treatment can be used as an alternative method to prevent infection by seed-borne diseases, but exposure duration and temperature during thermal treatment are important to maintain high seed viability and emergence whilst decreasing infection rate. A method for predicting suitable treatment parameters to maintain viability and eliminate seed-borne pathogens is therefore needed. Seeds of winter wheat were subjected to thermal treatment at four levels of intensity and pre-treatments with or without imbibition. Treatment impact was measured by metabolome analysis using LC-MS and GC-MS, analysis of spermosphere bacterial and fungal metagenomes using Illumina MiSeq, and detection of presence of Fusarium spp. and Microdochium spp. using ddPCR. The results showed that moderate treatment intensity reduced signs of infection and increased seedling emergence. In imbibed samples, myo-inositol concentration and myo-inositol: glucose ratio were positively correlated with treatment intensity, whereas concentrations of glucose and citric acid were negatively correlated. No correlations were found for non-imbibed samples. Imbibition had a large significant impact on microbial community composition of the wheat spermosphere. Imbibition of wheat seeds prior to thermal treatment altered wheat spermosphere microbiota. The concentration of myo-inositol, potentially in combination with glucose, could be a candidate predictor for suitable thermal treatment intensity of wheat seeds.
Effect of electrode size and distance to tissue on unipolar and bipolar voltage electrograms and their implications for a near-field cutoff
Authors: Schlageter Vincent , Luca Adrian , Badertscher Patrick , Krisai Philipp , Kueffer Thomas , Spreen David , Katic Josip , Osswald Stefan , Schaer Beat , Sticherling Christian , Kühne Michael , Knecht Sven 
Published: November 2024

AbstractCharacteristics of electrograms depend on the electrode design and distance to the electric source. Our aim was to assess the impact of electrode design and distance from the myocardial electric source on the unipolar and bipolar electrograms to deduce a far-field cut-off. We retrospectively analyzed left atrial electroanatomical maps of 25 patients acquired using an ablation catheter with a 4.5 mm tip-, mini- and 2 mm ring electrodes. The unipolar and bipolar electrograms were characterized based on peak-to-peak amplitude, signal duration, maximal slope, and relative power of the high frequency spectrum above 50 Hz (HF_rel). The unipolar electrograms of ring electrodes showed an increased amplitude (140%), slope (150%) and HF_rel (16% vs. 11%) compared to the tip- and mini-electrodes. The median amplitude, slope, and HF_rel for the ring electrodes followed a power-law decay with distance with a steep decline up to 4 mm. This near-field cut-off can be identified based on a HF_rel above 10% in unipolar electrograms. In conclusion, we observed a higher unipolar amplitude for small ring-electrodes compared to larger tip-electrodes. The rapid decay of the amplitude, slope, and HF_rel up to a distance of 4 mm is suggestive for near-field cut-off identified based on HF_rel above 50 Hz.Clinical Trial Registration: NCT04095559.
A simple and cost-effective real-time PCR method using diluted and heat-treated whole blood lysate
Authors: Güllü Amuran Gökçe , Polat Büşra , Kahraman Abdülkadir , Akkiprik Mustafa 
Published: November 2024

AbstractAlthough DNA extraction is a crucial step before polymerase chain reaction (PCR), attempts to perform PCR without DNA isolation have been ongoing since the 1990s. While partial success has been achieved with direct conventional PCR, the DNA isolation step has remained indispensable for real-time PCR. Here, we developed a method that does not require complete DNA isolation by lysing EDTA-treated whole blood samples through the application of osmotic pressure and heat, followed by centrifugation to get a clear lysate. Blood samples were mixed with distilled water, incubated at 95 °C for 20 min before centrifugation at 14,000 rpm for 5 min. The resulting lysates were used as templates for real-time PCR. Real-time PCRs were performed under identical conditions with lysates and DNA samples using 9 different primer sets. Target genes were successfully amplified using 1:10 and 1:5 diluted blood lysates both at 60 °C and 61 °C. The PCR efficiency for ACTB and PIK3CA differed by 20% and 14%, respectively, between the DNA samples and blood lysates. We successfully amplified all selected genes using “GG-RT PCR”, greater temperature, greater speed method, without the need for additional enzymes or buffers. GG-RT PCR presents a cost effective option for applications such as SNP analysis and deletion detection if appropriate primer designs are made.
ZBTB18 regulates cytokine expression and affects microglia/macrophage recruitment and commitment in glioblastoma
Authors: Ferrarese Roberto , Joseph Kevin , Andrieux Geoffroy , Haase Ira Verena , Zanon Francesca , Kling Eva , Izzo Annalisa , Corrales Eyleen , Schwabenland Marius , Prinz Marco , Ravi Vidhya Madapusi , Boerries Melanie , Heiland Dieter Henrik , Carro Maria Stella 
Published: November 2024

AbstractGlioma associated macrophages/microglia (GAMs) play an important role in glioblastoma (GBM) progression, due to their massive recruitment to the tumor site and polarization to a tumor promoting phenotype. GAMs secrete a variety of cytokines, which facilitate tumor cell growth and invasion, and prevent other immune cells from mounting an immune response against the tumor. Here, we demonstrate that zinc finger and BTB containing domain 18 (ZBTB18), a transcriptional repressor with tumor suppressive function in glioblastoma, impairs the production of key cytokines, which function as chemoattractant for GAMs. Consistently, we observe a reduced migration of GAMs when ZBTB18 is expressed by glioblastoma cells, both in cell culture and in vivo experiments. Moreover, RNA sequencing analysis shows that the presence of ZBTB18 in glioblastoma cells alters the commitment of conditioned microglia, suggesting the loss of the immune-suppressive phenotype and the acquisition of pro-inflammatory features. Thus, therapeutic approaches to increase ZBTB18 expression in GBM cells could represent an effective adjuvant to immune therapy in GBM.
Endosome rupture enables enteroviruses from the family Picornaviridae to infect cells
Authors: Ishemgulova Aygul , Mukhamedova Liya , Trebichalská Zuzana , Rájecká Veronika , Payne Pavel , Šmerdová Lenka , Moravcová Jana , Hrebík Dominik , Buchta David , Škubník Karel , Füzik Tibor , Vaňáčová Štěpánka , Nováček Jiří , Plevka Pavel 
Published: November 2024

AbstractMembrane penetration by non-enveloped viruses is diverse and generally not well understood. Enteroviruses, one of the largest groups of non-enveloped viruses, cause diseases ranging from the common cold to life-threatening encephalitis. Enteroviruses enter cells by receptor-mediated endocytosis. However, how enterovirus particles or RNA genomes cross the endosome membrane into the cytoplasm remains unknown. Here we used cryo-electron tomography of infected cells to show that endosomes containing enteroviruses deform, rupture, and release the virus particles into the cytoplasm. Blocking endosome acidification with bafilomycin A1 reduced the number of particles that released their genomes, but did not prevent them from reaching the cytoplasm. Inhibiting post-endocytic membrane remodeling with wiskostatin promoted abortive enterovirus genome release in endosomes. The rupture of endosomes also occurs in control cells and after the endocytosis of very low-density lipoprotein. In summary, our results show that cellular membrane remodeling disrupts enterovirus-containing endosomes and thus releases the virus particles into the cytoplasm to initiate infection. Since the studied enteroviruses employ different receptors for cell entry but are delivered into the cytoplasm by cell-mediated endosome disruption, it is likely that most if not all enteroviruses, and probably numerous other viruses from the family Picornaviridae, can utilize endosome rupture to infect cells.
scGraphformer: unveiling cellular heterogeneity and interactions in scRNA-seq data using a scalable graph transformer network
Authors: Fan Xingyu , Liu Jiacheng , Yang Yaodong , Gu Chunbin , Han Yuqiang , Wu Bian , Jiang Yirong , Chen Guangyong , Heng Pheng-Ann 
Published: November 2024

AbstractThe precise classification of cell types from single-cell RNA sequencing (scRNA-seq) data is pivotal for dissecting cellular heterogeneity in biological research. Traditional graph neural network (GNN) models are constrained by reliance on predefined graphs, limiting the exploration of complex cell-to-cell relationships. We introduce scGraphformer, a transformer-based GNN that transcends these limitations by learning an all-encompassing cell-cell relational network directly from scRNA-seq data. Through an iterative refinement process, scGraphformer constructs a dense graph structure that captures the full spectrum of cellular interactions. This comprehensive approach enables the identification of subtle and previously obscured cellular patterns and relationships. Evaluated on multiple datasets, scGraphformer demonstrates superior performance in cell type identification compared to existing methods and showcases its scalability with large-scale datasets. Our method not only provides enhanced cell type classification ability but also reveals the underlying cell interactions, offering deeper insights into functional cellular relationships. The scGraphformer thus holds the potential to significantly advance the field of single-cell analysis and contribute to a more nuanced understanding of cellular behavior.
Spatial transcriptomics reveals strong association between SFRP4 and extracellular matrix remodeling in prostate cancer
Authors: Andersen Maria K. , Krossa Sebastian , Midtbust Elise , Pedersen Christine A. , Wess Maximilian , Høiem Therese S. , Viset Trond , Størkersen Øystein , Nervik Ingunn , Sandsmark Elise , Bertilsson Helena , Giskeødegård Guro F. , Rye Morten B. , Tessem May-Britt 
Published: November 2024

AbstractProstate tumor heterogeneity is a major obstacle when studying the biological mechanisms of molecular markers. Increased gene expression levels of secreted frizzled-related protein 4 (SFRP4) is a biomarker in aggressive prostate cancer. To understand how SFRP4 relates to prostate cancer we performed comprehensive spatial and multiomics analysis of the same prostate cancer tissue samples. The experimental workflow included spatial transcriptomics, bulk transcriptomics, proteomics, DNA methylomics and tissue staining. SFRP4 mRNA was predominantly located in cancer stroma, produced by fibroblasts and smooth muscle cells, and co-expressed with extracellular matrix components. We also confirmed that higher SFRP4 gene expression is associated with cancer aggressiveness. Gene expression of SFRP4 was affected by gene promotor methylation. Surprisingly, the high mRNA levels did not reflect SFRP4 protein levels, which was much lower. This study contributes previously unknown insights of SFRP4 mRNA in the prostate tumor environment that potentially can improve diagnosis and treatment.
Thermodynamic evidence for polaron stabilization inside the antiferromagnetic order of Eu5In2Sb6
Authors: Dawczak-Dębicki Hubert , Ale Crivillero M. Victoria , Cook Matthew S. , Thomas Sean M. , Rosa Priscila F. S. , Müller Jens , Rößler Ulrich K. , Schlottmann Pedro , Wirth Steffen 
Published: November 2024

AbstractMaterials exhibiting electronic inhomogeneities at the nanometer scale have enormous potential for applications. Magnetic polarons are one such type of inhomogeneity which link the electronic, magnetic and lattice degrees of freedom in correlated matter and often give rise to colossal magnetoresistance. Here, we investigate single crystals of Eu5In2Sb6 by thermal expansion and magnetostriction along different crystallographic directions. These data provide compelling evidence for the formation of magnetic polarons in Eu5In2Sb6 well above the magnetic ordering temperature. More specifically, our results are consistent with anisotropic polarons with varying extent along the different crystallographic directions. A crossover revealed within the magnetically ordered phase can be associated with a surprising stabilization of ferromagnetic polarons within the global antiferromagnetic order upon decreasing temperature. These findings make Eu5In2Sb6 a rare example of such coexisting and competing magnetic orders and, importantly, shed new light on colossal magnetoresistive behavior beyond manganites.
The unique biogeochemical role of carbonate-associated organic matter in a subtropical seagrass meadow
Authors: Zeller Mary A. , Van Dam Bryce R. , Lopes Christian , McKenna Amy M. , Osburn Christopher L. , Fourqurean James W. , Kominoski John S. , Böttcher Michael Ernst 
Published: November 2024

AbstractThe particulate organic matter buried in carbonate-rich seagrass ecosystems is an important blue carbon reservoir. While carbonate sediments are affected by alkalinity produced or consumed in seagrass-mediated biogeochemical processes, little is known about the corresponding impact on organic matter. A portion of particulate organic matter is carbonate-associated organic matter. Here, we explore its biogeochemistry in a carbonate seagrass meadow in central Florida Bay, USA. We couple inorganic stable isotope analyses (δ34S, δ18O) with a molecular characterization of dissolved and carbonate associated organic matter (21 tesla Fourier-transform ion cyclotron resonance mass spectrometry). We find that carbonate-associated molecular formulas are highly sulfurized compared to surface water dissolved organic matter, with multiple sulfurization pathways at play. Furthermore, 97% of the formula abundance of surface water dissolved organic matter is shared with carbonate-associated organic matter, indicating connectivity between these two pools. We estimate that 9.2% of the particulate organic matter is carbonate-associated, and readily exchangeable with the broader aquatic system as the sediment dissolves and reprecipitates.
Towards a unified approach to prioritization of regenerative agricultural practices across cropping systems
Authors: Sela Shai , Dobermann Achim , Cerri Carlos Eduardo , Svoray Tal , van-Es Harold , Amsili Joseph , Biradar Sanjay , Luzon Uria , Katz Sagi 
Published: November 2024

AbstractPrioritizing field practices according to their contribution to regenerative efforts, in a structured and standardized manner, can enable efficient resource allocation and higher adoption rates. However, it is remarkably hampered by the diversity of production environments and their respective best management practices. This paper proposes prioritizing regenerative practices using a multicriteria assessment method informed by expert knowledge. To develop it, we mined and synthesized knowledge from eleven experts for three diverse cropping systems, showing that the prioritization of practices varies greatly across production environments. By integrating the multicriteria approach with a multi-indicator sustainability framework, we demonstrate how practice weights can be used to monitor sustainability efforts and outcomes of thirty vineyard farms in Maharashtra, India. The suggested prioritization approach can be used to standardize the assessment of the importance of regenerative practices in different cropping systems and be adopted in sustainable sourcing schemes of the agro-food industry.
Expeditious synthesis of CF3-phenanthridones through a base-mediated cross-conjugated vinylogous benzannulation (VBA)
Authors: Desagoni Madhu , Nagababu Chavakula , Punna Nagender 
Published: November 2024

An efficient strategy is disclosed for synthesizing CF3-phenanthridones via a cross-conjugated vinylogous [4 + 2] benzannulation of easily accessible 4-methyl-3-trifluoroacetylquinolones and nitro-olefins.
Solvent-free confinement of ordered microparticle monolayers: effect of host substrate and pattern symmetry
Authors: Jimidar Ignaas S. M. , de Waard Mitch T. J. , Roozendaal Gijs , Sotthewes Kai 
Published: November 2024

We report a solvent-free assembly method where microspheres align on fluorocarbon patterns without rigid boundaries, creating tunable crystal patterns. Our findings highlight the impact of tribocharging and substrate elasticity on particle ordering.
Resilient and robust control strategy against deception attacks in the platoon of vehicles
Authors: Mokari Hassan , Firouzmand Elnaz , Sharifi Iman , Doustmohammadi Ali 
Published: November 2024

AbstractA platoon must ensure the security of conducting missions due to the susceptibility of the vehicles to cyber‐attacks. The deception attack is a common type of cyber‐attack that might be introduced during data exchange through communication channels. Therefore, it can divert each vehicle by injecting uncertainty into the communication link between the agents in the cyber domain. This paper employs a leader–follower consensus system as a reference model to control the platoon vehicles. Accordingly, each agent in the reference model sends its information as a reference trajectory to its corresponding vehicle within the platoon. The vehicles are equipped with a robust local controller, enabling them to follow their desired trajectory in the presence of external disturbances. Furthermore, each vehicle employs an unknown input observer to detect a deception attack while decoupling it from external disturbances. Moreover, by introducing a switching strategy based on mode‐dependent average dwell time to the leader–follower consensus system, a novel resilient control strategy against the deception attack is implemented in the cyber domain. The resultant resilient leader–follower consensus system in the platoon retrieves and restores the attacked vehicle in the platoon to its associated states. The applicability of the proposed method is shown via simulation.
Global feature fusion generative adversarial network for underwater image enhancement
Authors: Liu Chunyou , Qi Ping , Tang Zhibin 
Published: November 2024

AbstractMost CNN‐based networks treat features in different channels and pixels similarly. However, the dispersion of light underwater results in uneven haze distribution throughout the images. To alleviate these problems, the global feature fusion generative adversarial network is proposed, to separate and enhance the global feature by channels and pixels simultaneously. The key novelty of our method is utilizing the attention mechanism to emphasize features in different channels and pixels in fusion block, which allocates higher weights to more important features. The network's reliability is further optimized through the incorporation of condition information to restrict the training of the network. Both qualitative and quantitative evaluations verify that the proposed method is capable of greater visual quality compared with other classic and state‐of‐the‐art methods.