bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant interactions can lead to emergent relationships between plant community diversity, productivity and vulnerability to invasion
Authors: Trevenen Elizabeth J. , Veneklaas Erik J. , Teste François P. , Dobrowolski Mark P. , Mucina Ladislav , Renton Michael 
Published: June 2024

AbstractUnderstanding what makes a community vulnerable to invasion is integral to the successful management of invasive species. Our understanding of how characteristics of resident plant interactions, such as the network architecture of interactions, can affect the invasibility of plant communities is limited. Using a simulation model, we tested how successfully a new plant invader established in communities with different network architectures of species interactions. We also investigated whether species interaction networks lead to relationships between invasibility and other community properties also affected by species interaction networks, such as diversity, species dominance, compositional stability and the productivity of the resident community. We found that higher invasibility strongly related with a lower productivity of the resident community. Plant interaction networks influenced diversity and invasibility in ways that led to complex but clear relationships between the two. Heterospecific interactions that increased diversity tended to decrease invasibility. Negative conspecific interactions always increased diversity and invasibility, but increased invasibility more when they increased diversity less. This study provides new theoretical insights into the effects of plant interaction networks on community invasibility and relationships between diversity and invasibility. Combined with increasing empirical evidence, these insights could have useful implications for the management of invasive plant species.
Geographic origin, ancestry, and death circumstances at the Cornaux/Les Sauges Iron Age bridge, Switzerland
Authors: Laffranchi Zita , Zingale Stefania , Indra Lara , Coia Valentina , Salazar García Domingo C. , Paladin Alice , Kaeser Marc-Antoine , Delley Géraldine , Szidat Sönke , Lösch Sandra , Zink Albert , Milella Marco 
Published: June 2024

AbstractCornaux/Les Sauges (Switzerland, Late Iron Age) revealed remnants of a wooden bridge, artifacts, and human and animal skeletal remains. The relationship between the collapsed structure and the skeletal material, whether it indicates a potential accident or cultural practices, remains elusive. We evaluate the most plausible scenario for Cornaux based on osteological, taphonomic, isotopic, and paleogenomic analysis of the recovered individuals. The latter amount to at least 20 individuals, mostly adult males. Perimortem lesions include only blunt force traumas. Radiocarbon data fall between the 3rd and 1st c. BCE, although in some cases predating available dendrochronological estimates from the bridge. Isotopic data highlight five to eight nonlocals. No close genetic relatedness links the analyzed skeletons. Paleogenomic results, the first for Iron Age Switzerland, point to a genetic affinity with other Central and Western European Iron Age groups. The type of skeletal lesions supports an accidental event as the more plausible explanation. Radiocarbon data and the demographic structure of the sample may suggest a sequence of different events possibly including executions and/or sacrifices. Isotopic and paleogenomic data, while not favoring one scenario over the other, do support earlier interpretations of the last centuries BCE in Europe as a dynamic period from a biocultural perspective.
Exploring affinity between organic probes and Prussian Blue Analogues via inverse gas chromatography
Authors: Paulusma Stijn , Singh Kaustub , Smeding Tom , Gamaethiralalage Jayaruwan G. , Claassen Frank W. , Beijleveld Hans , Janssen Hans-Gerd , de Smet Louis C. P. M. 
Published: June 2024

AbstractPrussian Blue Analogues (PBAs), which are characterized by their open structure, high stability, and non-toxic properties, have recently been the subject of research for various applications, including their use as electrode precursors for capacitive deionization, gas storage, and environmental purification. These materials can be readily tailored to enhance their affinity towards gases for integration with sensing devices. An improved understanding of PBA-gas interactions is expected to enhance material development and existing sensor deposition schemes greatly. The use of inverse gas chromatography (IGC) is a robust approach for examining the relationship between porous materials and gases. In this study, the adsorption properties of (functionalized) hydrocarbons, i.e., probe molecules, on the copper hexacyanoferrate (CuHCF) lattice were studied via IGC, demonstrating that alkylbenzenes have a higher affinity for this material than n-alkanes. This difference was rationalized by steric hindrance, π–π interactions, and vapour pressure effects. Along the same line, the five isomers of hexane showed decreasing selectivity upon increased steric hindrance. Enthalpy values for n-pentane, n-hexane and n-heptane were lower than that of toluene. The introduction of increased probe masses resulted in a surface coverage of 46% for toluene. For all n-alkane probe molecules this percentage was lower. However, the isotherms of these probes did not show saturation points and the observed linear regime proves beneficial for gas sensing. Our work demonstrates the versatility of CuHCF for gas sensing purposes and the potential of IGC to characterize the adsorption characteristics of such a porous nanomaterial.
Implementation of theoretical non-photochemical quenching (NPQ(T)) to investigate NPQ of chickpea under drought stress with High-throughput Phenotyping
Authors: Lauterberg Madita , Tschiersch Henning , Zhao Yusheng , Kuhlmann Markus , Mücke Ingo , Papa Roberto , Bitocchi Elena , Neumann Kerstin 
Published: June 2024

AbstractNon-photochemical quenching (NPQ) is a protective mechanism for dissipating excess energy generated during photosynthesis in the form of heat. The accelerated relaxation of the NPQ in fluctuating light can lead to an increase in the yield and dry matter productivity of crops. Since the measurement of NPQ is time-consuming and requires specific light conditions, theoretical NPQ (NPQ(T)) was introduced for rapid estimation, which could be suitable for High-throughput Phenotyping. We investigated the potential of NPQ(T) to be used for testing plant genetic resources of chickpea under drought stress with non-invasive High-throughput Phenotyping complemented with yield traits. Besides a high correlation between the hundred-seed-weight and the Estimated Biovolume, significant differences were observed between the two types of chickpea desi and kabuli for Estimated Biovolume and NPQ(T). Desi was able to maintain the Estimated Biovolume significantly better under drought stress. One reason could be the effective dissipation of excess excitation energy in photosystem II, which can be efficiently measured as NPQ(T). Screening of plant genetic resources for photosynthetic performance could take pre-breeding to a higher level and can be implemented in a variety of studies, such as here with drought stress or under fluctuating light in a High-throughput Phenotyping manner using NPQ(T).
The matricellular protein CCN5 prevents anti-VEGF drug-induced epithelial-mesenchymal transition of retinal pigment epithelium
Authors: Im Sora , Song Min Ho , Elangovan Muthukumar , Woo Kee Min , Park Woo Jin 
Published: June 2024

AbstractAge-related macular degeneration (AMD) is one of the major causes of blindness in the elderly worldwide. Anti-vascular endothelial growth factor (VEGF) drugs have been widely used to treat the neovascular type of AMD (nAMD). However, VEGF acts not only as a pro-angiogenic factor but also as an anti-apoptotic factor in the eyes. In this study, we found that anti-VEGF drugs, including bevacizumab (Bev), ranibizumab (Ran), and aflibercept (Afl), induced epithelial-mesenchymal transition (EMT) in ARPE-19 cells in vitro, accompanied by the induction of CCN2, a potent pro-fibrotic factor. Similarly, intravitreal injection of Afl into mouse eyes resulted in EMT in the retinal pigmented epithelium (RPE). Co-treatment with CCN5, an anti-fibrotic factor that down-regulates CCN2 expression, significantly attenuated the adverse effects of the anti-VEGF drugs both in vitro and in vivo. Inhibition of the VEGF signaling pathway with antagonists of VEGF receptors, SU5416 and ZM323881, induced EMT and up-regulated CCN2 in ARPE-19 cells. Additionally, knock-down of CCN2 with siRNA abolished the adverse effects of the anti-VEGF drugs in ARPE-19 cells. Collectively, these results suggest that anti-VEGF drugs induce EMT in RPE through the induction of CCN2 and that co-treatment with CCN5 attenuates the adverse effects of anti-VEGF drugs in mouse eyes.
A dilute sodium hydroxide technique for radiolarian extraction from cherts
Authors: Onoue Tetsuji , Hori Sakiko , Tomimatsu Yuki , Rigo Manuel 
Published: June 2024

AbstractRadiolarians have been used to determine geological ages and have contributed markedly to our understanding of Earth’s history. Hydrofluoric acid (HF) has traditionally been used to extract radiolarian fossils from siliceous deposits (i.e., radiolarian cherts), but this acid is strictly regulated because of environmental and human health concerns. Here we report on the successful extraction of radiolarians from cherts using a low-concentration NaOH solution (1 mol/L NaOH) as an alternative to HF. The degree of chert dissolution in NaOH is strongly temperature-dependent and is limited at < 80 °C. However, even a 1 mol/L NaOH solution is sufficient to dissolve chert at 100 °C. Our new NaOH method yields better-preserved radiolarian fossils compared with the conventional HF method. The 1 mol/L NaOH solution is less hazardous, easier to handle, and has fewer effects on the environment and human health than HF. Therefore, this method can be widely used for research and teaching purposes in studies of radiolarian fossils, even in institutions where HF cannot be used owing to chemical restrictions.
In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells
Authors: Jado Juan Carlos , Dow Michelle , Carolino Krypton , Klie Adam , Fonseca Gregory J. , Ideker Trey , Carter Hannah , Winzeler Elizabeth A. 
Published: June 2024

AbstractIn vitro evolution and whole genome analysis has proven to be a powerful method for studying the mechanism of action of small molecules in many haploid microbes but has generally not been applied to human cell lines in part because their diploid state complicates the identification of variants that confer drug resistance. To determine if haploid human cells could be used in MOA studies, we evolved resistance to five different anticancer drugs (doxorubicin, gemcitabine, etoposide, topotecan, and paclitaxel) using a near-haploid cell line (HAP1) and then analyzed the genomes of the drug resistant clones, developing a bioinformatic pipeline that involved filtering for high frequency alleles predicted to change protein sequence, or alleles which appeared in the same gene for multiple independent selections with the same compound. Applying the filter to sequences from 28 drug resistant clones identified a set of 21 genes which was strongly enriched for known resistance genes or known drug targets (TOP1, TOP2A, DCK, WDR33, SLCO3A1). In addition, some lines carried structural variants that encompassed additional known resistance genes (ABCB1, WWOX and RRM1). Gene expression knockdown and knockout experiments of 10 validation targets showed a high degree of specificity and accuracy in our calls and demonstrates that the same drug resistance mechanisms found in diverse clinical samples can be evolved, discovered and studied in an isogenic background.
CACSNet for automatic robust classification and segmentation of carotid artery calcification on panoramic radiographs using a cascaded deep learning network
Authors: Yoo Suh-Woo , Yang Su , Kim Jo-Eun , Huh Kyung-Hoe , Lee Sam-Sun , Heo Min-Suk , Yi Won-Jin 
Published: June 2024

AbstractStroke is one of the major causes of death worldwide, and is closely associated with atherosclerosis of the carotid artery. Panoramic radiographs (PRs) are routinely used in dental practice, and can be used to visualize carotid artery calcification (CAC). The purpose of this study was to automatically and robustly classify and segment CACs with large variations in size, shape, and location, and those overlapping with anatomical structures based on deep learning analysis of PRs. We developed a cascaded deep learning network (CACSNet) consisting of classification and segmentation networks for CACs on PRs. This network was trained on ground truth data accurately determined with reference to CT images using the Tversky loss function with optimized weights by balancing between precision and recall. CACSNet with EfficientNet-B4 achieved an AUC of 0.996, accuracy of 0.985, sensitivity of 0.980, and specificity of 0.988 in classification for normal or abnormal PRs. Segmentation performances for CAC lesions were 0.595 for the Jaccard index, 0.722 for the Dice similarity coefficient, 0.749 for precision, and 0.756 for recall. Our network demonstrated superior classification performance to previous methods based on PRs, and had comparable segmentation performance to studies based on other imaging modalities. Therefore, CACSNet can be used for robust classification and segmentation of CAC lesions that are morphologically variable and overlap with surrounding structures over the entire posterior inferior region of the mandibular angle on PRs.
Centaurea behen leaf extract mediated green synthesized silver nanoparticles as antibacterial and removing agent of environmental pollutants with blood compatible and hemostatic effects
Authors: Abdoli Mohadese , Khaledian Salar , Mavaei Maryamosadat , Hajmomeni Pouria , Ghowsi Mahnaz , Qalekhani Farshad , Nemati Houshang , Fattahi Ali , Sadrjavadi Komail 
Published: June 2024

AbstractThe present study focused on evaluating the antibacterial properties, radical scavenging, and photocatalytic activities of Centaurea behen-mediated silver nanoparticles (Cb-AgNPs). The formation of Cb-AgNPs was approved by UV–Vis spectrometry, Fourier-transform infrared spectroscopy, transmission electron microscopy, scanning electron microscopy (SEM), energy dispersive X-ray and X-ray diffraction. The results showed that the obtained AgNPs have a maximum absorbance peak at 450 nm with spherical morphology and an average size of 13.03 ± 5.8 nm. The catalytic activity of the Cb-AgNPs was investigated using Safranin O (SO) solution as a cationic dye model. The Cb-AgNPs performed well in the removal of SO. The coupled physical adsorption/photocatalysis reaction calculated about 68% and 98% degradation of SO dye under solar irradiation. The Cb-AgNPs inhibited the growth of gram-negative or positive bacteria strains and had excellent DPPH radicals scavenging ability (100% in a concentration of 200 µg/ml) as well as a good effect on reducing coagulation time (at concentrations of 200 and 500 µg/mL reduced clotting time up to 3 min). Considering the fact that green synthesized Cb-AgNPs have antioxidant and antibacterial properties and have a good ability to reduce coagulation time, they can be used in wound dressings. As well as these NPs with good photocatalytic activity can be a suitable option for degrading organic pollutants.
Elucidating the function of STING in systemic lupus erythematosus through the STING Goldenticket mouse mutant
Authors: Vejvisithsakul Pichpisith Pierre , Thumarat Chisanu , Leelahavanichkul Asada , Hirankan Nattiya , Pisitkun Trairak , Paludan Soren Riis , Pisitkun Prapaporn 
Published: June 2024

AbstractThe complexity of systemic lupus erythematosus (SLE) arises from intricate genetic and environmental interactions, with STING playing a pivotal role. This study aims to comprehend the function of STING using the pristane-induced lupus (PIL) model in Sting missense mutant mice (Goldenticket or StingGt), which contrasts with previous research using Sting knockout mice. Investigating two-month-old StingGt mice over six months post-PIL induction, we observed a profound reduction in autoimmune markers, including antinuclear and anti-dsDNA antibodies, germinal center B cells, and plasma cells, compared to their wild-type counterparts. A pivotal finding was the marked decrease in IL-17-producing T cells. Notably, the severity of lupus nephritis and pulmonary hemorrhages was significantly diminished in StingGt mice. These findings demonstrate that different genetic approaches to interfere with STING signaling can lead to contrasting outcomes in SLE pathogenesis, which highlights the need for a nuanced understanding of the role of STING in drug development for SLE. In summary, the loss of Sting function in Goldenticket mutant mice rescued autoimmune phenotypes in PIL. This study reveals the critical nature of STING in SLE, suggesting that the method of STING modulation significantly influences disease phenotypes and should be a key consideration in developing targeted therapies.
N-butyl-β-carboline-3-carboxylate (β-CCB) systemic administration promotes remyelination in the cuprizone demyelinating model in mice
Authors: Vélez-Uriza Fidel , Ordaz Rainald Pablo , Garay Edith , Cisneros-Mejorado Abraham J. , Arellano Rogelio O. 
Published: June 2024

AbstractDemyelination is generated in several nervous system illnesses. Developing strategies for effective clinical treatments requires the discovery of promyelinating drugs. Increased GABAergic signaling through γ-aminobutyric acid type A receptor (GABAAR) activation in oligodendrocytes has been proposed as a promyelinating condition. GABAAR expressed in oligodendroglia is strongly potentiated by n-butyl-β-carboline-3-carboxylate (β-CCB) compared to that in neurons. Here, mice were subjected to 0.3% cuprizone (CPZ) added in the food to induce central nervous system demyelination, a well-known model for multiple sclerosis. Then β-CCB (1 mg/Kg) was systemically administered to analyze the remyelination status in white and gray matter areas. Myelin content was evaluated using Black-Gold II (BGII) staining, immunofluorescence (IF), and magnetic resonance imaging (MRI). Evidence indicates that β-CCB treatment of CPZ-demyelinated animals promoted remyelination in several white matter structures, such as the fimbria, corpus callosum, internal capsule, and cerebellar peduncles. Moreover, using IF, it was observed that CPZ intake induced an increase in NG2+ and a decrease in CC1+ cell populations, alterations that were importantly retrieved by β-CCB treatment. Thus, the promyelinating character of β-CCB was confirmed in a generalized demyelination model, strengthening the idea that it has clinical potential as a therapeutic drug.
Calibration of contact parameters of sandy soil for planting tiger nut based on non-linear tools
Authors: Qi Jiangtao , Chen Sirui , Yang Luoyi , An Shiguan , Meng Hewei , Kan Za 
Published: June 2024

AbstractA methodology combining physical experiments with simulation was employed to acquire contact parameters of sandy soil precisely for planting tiger nuts in the desert area of Xinjiang. The stacking angle under different parameter combinations was applied as a response value. Through the Plackett–Burman test, several factors that have a significant influence were determined. The steepest ascent test was conducted to establish the finest scope of values for these parameters. The stacking angle was considered the response variable, and non-linear tools were used to optimize these parameters for simulation. The findings showed that applying response surface methodology (RSM) resulted in a relative error of 1.24%. In the case of BP-GA, the relative error compared to the physical test value was 0.34%, while for BP, it was 2.18%. After optimization using Wavelet Neural Network (WNN), the relative error was reduced to only 0.15%. Results suggest that WNN outperforms the RSM model, and the sandy soil model and parameters generated using WNN can be effectively utilized for discrete element simulation research.
RUNX1 regulates MCM2/CDC20 to promote COAD progression modified by deubiquitination of USP31
Authors: Tian Wei , Zhao Jingyuan , Zhang Xinyu , Li Pengfei , Li Xuening , Hong Yuan , Li Shuai 
Published: June 2024

AbstractColon adenocarcinoma (COAD) is the second leading cause of cancer death, and there is still a lack of diagnostic biomarkers and therapeutic targets. In this study, bioinformatics analysis of the TCGA database was used to obtain RUNX1, a gene with prognostic value in COAD. RUNX1 plays an important role in many malignancies, and its molecular regulatory mechanisms in COAD remain to be fully understood. To explore the physiological role of RUNX1, we performed functional analyses, such as CCK-8, colony formation and migration assays. In addition, we investigated the underlying mechanisms using transcriptome sequencing and chromatin immunoprecipitation assays. RUNX1 is highly expressed in COAD patients and significantly correlates with survival. Silencing of RUNX1 significantly slowed down the proliferation and migratory capacity of COAD cells. Furthermore, we demonstrate that CDC20 and MCM2 may be target genes of RUNX1, and that RUNX1 may be physically linked to the deubiquitinating enzyme USP31, which mediates the upregulation of RUNX1 protein to promote transcriptional function. Our results may provide new insights into the mechanism of action of RUNX1 in COAD and reveal potential therapeutic targets for this disease.
Regulatory network analysis based on integrated miRNA-TF reveals key genes in heart failure
Authors: Zhang Ziyue , Zou Ziying , Zhang Hui , Zhang Dai-Min 
Published: June 2024

AbstractThe etiology and pathophysiology of heart failure are still unknown. Increasing evidence suggests that abnormal microRNAs (miRNAs) and transcription factors (TFs) expression may be associated with the development of heart failure. Therefore, this study aims to explore key miRNAs, TFs, and related genes in heart failure to gain a greater understanding of the pathogenesis of heart failure. To search and download the dataset of mRNA chips related to heart failure from the GEO database (GSE59867, GSE9128, and GSE134766), we analyzed differential genes and screened the common differentially expressed genes on two chips using R language software. The binary interactions and circuits among miRNAs, TFs, and corresponding genes were determined by Pearson correlation coefficient. A regulatory network of miRNAs, TFs, and target genes was constructed based on bioinformatics. By comparing the sequences of patients with and without heart failure, five downregulated genes with hypermethylated mRNA and three upregulated genes with hypomethylated mRNA were identified. The miRNA-TF gene regulatory network consisted of 26 miRNAs, 22 TFs and six genes. GO and KEGG analysis results revealed that BP terms like cellular response to organic substance, cellular response to cytokine stimulus, and KEGG pathways like osteoclast differentiation, MAPK signaling pathway, and legionellosis were enriched of the DEGs. TMEM87A, PPP2R2A, DUSP1, and miR-92a have great potential as biomarkers for heart failure. The integrated analysis of the mRNA expression spectrum and microRNA-transcription factor-gene revealed the regulatory network of heart failure, which may provide clues to its alternative treatment.