bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of confocal laser scanning microscopy to locate Stenocarpella maydis in corn stalk (Zea mays)
Authors: Dorigan Adriano Francis , Barros Aline Vieira , Moreira Silvino Intra , Ferreira Aline Norberto , Alves Eduardo 
Published: July 2024

Abstract

Stenocarpella maydis causes high production losses in almost all countries where corn (Zea mays) is cultivated. The rot caused by S. maydis may occur on the stalks and ears of corn plants. S. maydis in corn poses a significant threat to human and animal nutrition, mainly due to mycotoxins such as diplodiatoxin. This study aimed to validate an efficient methodology for visualizing S. maydis colonization in corn using clarification protocol, fluorochromes, and Confocal Laser Scanning Microscopy (CLSM). Conidial suspensions were inoculated into the corn stalk at the V6 stage using a syringe. Corn stalk fragments of 1 cm2 were collected 21 days after inoculation (dai) for CLSM analysis. The samples were fixed in Karnovsky’s solution and clarified in KOH and chloral hydrate. The fungal structures were labeled with Alexa488-WGA at 1.0 mg mL− 1 for 30 min under vacuum (excitation at 488 and emission at 510–540 ƞm). Thereafter, the corn plant tissues were labeled with Calcofluor White at 0.1 mg mL− 1 (excitation at 405 and emission at 440–490 ƞm) for 30 min. The Laser Confocal LSM780 Zeiss Observer Z.1 microscope, LCI Plan-Neofluar 25×/0.8, and C-Apochromat 63×/1.20 objectives were used to acquire fluorescent images. At 21 dai, it was possible to observe the colonization and formation of pycnidia with bicellular conidia of the fungus S. maydis in corn stalk fragments. The fungus colonized parenchymatic tissues and vascular bundles of the corn stalk. In contrast, at 21 dai, colonization of the fungus S. maydis was not observed in the parenchymatic tissues and vascular bundles of the corn stalk from uninoculated control plants. Our study made it possible to validate a new methodology for studying the infectious process of S. maydis in corn stalk using clarification protocols, fluorochromes, and CLSM.
179 Plasma lipids and risk of intracranial aneurysms: A genetic study of association and causality
Authors: Chen Wei , Mei Zhaojun , Zhou Zhou , Cao Weibiao , Xu Zhipeng , Cao Kan , Chen Bo , Lu Xinyu , Ding Lu 
Published: July 2024

Abstract

Background Current evidence suggests that genetic factors, hemodynamic abnormalities, and chronic inflammation of the vascular wall contribute to the onset of intracranial aneurysms (IAs). The deposition of lipid plaques is frequently observed in the walls of IAs. Therefore, the objective of this research was to determine the causal link between plasma lipids and IAs.
Methods Genetic instrumental variables for 179 plasma lipids were acquired from a genome-wide association study (GWAS) of 7174 unrelated Finnish individuals. Outcome data for individuals with IAs were retrieved from a GWAS involving 23 cohorts, comprising 79,429 individuals of European ancestry. This dataset included 7,495 cases and 71,934 controls. Three databases were utilized for the implementation of Mendelian Randomization (MR) analysis. This included an aSAH group with 5,140 aSAH cases and 71,952 controls, a uIA group with 2,070 uIA cases and 71,952 controls, and an IAs group with 7,495 IAs cases and 71,934 controls. An inverse-variance weighted (IVW) method was employed as the key analysis method. To ensure the reliability of the findings, MR-Egger regression, weighted-median, and weighted-mode methods were employed. Sensitivity analyses included Cochran’s Q test, MR-Pleiotropy RESidual Sum and Outlier (MR-PRESSO), Radial MR test, MR-Egger intercept test, and Leave-one-out (LOO) analysis. The MR-Steiger test was conducted to avoid reverse causality.
Results Following rigorous screening, MR tests, and Bonferroni correction, the genetically predicted level of Phosphatidylethanolamine(18:2_0:0)(LPE(18:2))(OR:1.28,95CI:1.13-1.46, P=1.42×10−4) ,Phosphatidylcholine (PC) (16:0_20:4)(OR:0.86,95CI:0.86-0.93, P=1.38×10−4),Phosphatidylcholine (PC) (18:0_20:3)(OR:1.29,95CI:1.12-1.47, P=2.33×10−4)and Phosphatidylcholine (PC) (O-16:0_20:4)(OR:0.83,95CI:0.75-0.91, P=2.22×10−4) showed significant causal relationships with aSAH. Two plasma lipids, LPE (18:2)(OR:1.22,95CI:1.11-1.34, P=3.14×10−5) and PC (16:1_18:2)(OR:1.19,95CI:1.09-1.31, P=1.53×10−4) exhibited a positive correlation with the risk of IAs. No significant causal link was found between uIA and 179 plasma lipids.
Conclusion Genetically determined LPE (18:2) ,PC(18:0_20:3) and PC (16:1_18:2) can increase the risk of IAs rupture;while PC(16:0_20:4) and PC (O-16:0_20:4) can reduce the risk of IAs rupture.PCs with arachidonic acid (AA) chains and the metabolism of AA may be crucially involved in the occurrence and development of IAs.
Non-linear relationship between blood urea nitrogen to albumin ratio and 3-month outcomes in acute ischemic stroke: a second analysis based on a prospective cohort study
Authors: Zhou PAN , Li Xin , Peng Gang-gang , Hu Haofei , Deng Zhe 
Published: July 2024

Abstract

Objective: Patients with acute ischemic stroke (AIS) have limited evidence regarding the relationship between blood urea nitrogen and albumin (BUN/ALB). Aiming to investigate the relationship between the BUN/ALB ratio and poor outcomes in AIS patients at 3-months was the purpose of this study.
Methods: AIS participants at a Korean hospital from January 2010 to December 2016 were included in a secondary analysis of a prospective cohort study. Logistic regression and restricted cubic splines were used to examine the relationship between BUN/ALB ratio and poor outcomes after 3 months.
Results: There is a skewed distribution of BUN/ALB ratios, ranging from 0.114 to 1.250. Model II of the binary logistic regression showed that the BUN/ALB ratio was not statistically significant in predicting poor outcomes for AIS patients after three months. However, there was a notable nonlinear relationship between them, with the inflection point of the BUN/ALB ratio identified as 0.326. The BUN/ALB ratio on the left side of the inflection point was associated with a 42% reduction in 3-month poor outcomes (OR=0.58, 95% CI: 0.40 to 0.83, P = 0.0033). Conversely, the relationship was not statistically significant on the right side of the inflection point.
Conclusion: The BUN/ALB ratio and poor outcomes in AIS patients show a nonlinear correlation with a saturation effect. For AIS patients, a BUN/ALB ratio of approximately 0.326 is associated with the lowest risk of adverse outcomes at 3 months. Specifically, for non-smoking AIS patients, a BUN/ALB ratio of approximately 0.295 is associated with the lowest risk of adverse outcomes at 3 months.
Effects of stereoisomers of proline-deoxymugineic acid on iron uptake in Poaceae plants
Authors: Namba Kosuke , Ogasa Chie , Murata Yoshiko , Inoue Haruhiko , Suzuki Motofumi , Uchikawa Yoshinori , Karanjit Sangita , Mera Akane , Watanabe Takehiro , Sato Ryota 
Published: July 2024

Abstract

All stereoisomers of proline-deoxymugineic acid, a low-cost and stable analog of phytosiderophore deoxymugineic acid, were synthesized and evaluated for their iron transport activity and growth effect in rice. In addition, the stabilities of their iron complexes were analysed by Electrospray ionization mass spectrometry (ESI-MS). All stereoisomers showed the iron transport activity in Sf9 cell assay, and a yeast assay also suggested the presence of iron transport activity in all but the DDL and LDD analogs. Rice grew better in alkaline soil by applications of stereoisomers of PDMA, and the natural LLL (PDMA) and unnatural LLD analogs in particular showed significant growth-promoting effects. The diastereomeric mixure at the 3’’ position was found to be promising as a fertilizer, as was the single isomer of LLL (PDMA). Mass spectrometry suggested that the LLD analog forms a stable iron complex, and the stability of iron complexes was correlated with rice growth activity.
An aperiodic chiral tiling by topological molecular self-assembly
Authors: Voigt Jan , Baljozovic Milos , Martin Kevin , Wäckerlin Christian , Avarvari Narcis , Ernst Karl-Heinz 
Published: July 2024

Abstract

Crystallization remains an important method for separating chiral molecules into their two mirror-image isomers, yet the molecular recognition during aggregation into solids is still not fully understood. In particular, there are no definitive rules to predict whether a pair of chiral partners will crystallize together into racemic crystals or as separate counterparts. A more manageable version of this phenomenon is crystallization in two dimensions, such as the formation of surface structures by adsorbed molecules. The relatively simple spatial arrangement of these systems, coupled with the submolecular resolution provided by modern scanning probe technologies, makes it easier to study the effects of specific chiral interactions. Here, we report spiral topological patterns in the two-dimensional aggregation of chiral molecules on a silver crystal surface. The molecules tessellate the plane in chiral nodes and supramolecular triangles. Spiral annihilation is achieved only through the chiral triangular tiling of triads, with N±1 molecules at the edges and a specific strategy of chiral offsetting of triangles. Due to a high degree of molecular flexibility, entropy is maximized by switching molecular handedness in conjunction with the number of nodes controlled by triangle size. Our results demonstrate that two-dimensional self-assembly can be governed by topological constraints and that an aperiodic tiling of the plane can be realized solely by natural forces without human intervention.
An Efficient and Non-Invasive Approach to Identify and Classify COVID-19 from CT Scan Images using Machine Learning in Combination with Hybrid Texture Features
Authors: kumar upendra 
Published: July 2024

Abstract

Rapid and accurate identification of COVID-19 and also other associated diseases is now crucial to limiting the disease's transmission, relaxing lockdown laws, and reducing the burden on public health infrastructures. Recently, several approaches and techniques have been proposed to identify the SARS-CoV-2 virus (COVID-19) using different clinical data and medical pictures. There are some limitations and shortcomings with the COVID-19 detection technologies that are currently available on the market. Because of this, it becomes essential to develop and study new diagnostic tools that have higher diagnostic accuracy while avoiding the shortcomings of existing tools. This study used the SARS-CoV-2 CT scan dataset to test non-linear SVM and Twin-SVM (TWSVM) classifiers in addition to textural characteristics such as GLCM, GLRLM, and ILMFD separately. There are a total of 2482 CT scan images in this database; 1252 of the scans show positive signs of SARS-CoV-2 infection (COVID-19), and 1230 show negative signs. Eight different models were developed in this work for the purpose of classifying and predicting COVID-19. We found that the GLCM + NLSVM model using RBF kernal, GLCM + TWSVM using linear kernal, GLRLM + NLSVM using RBF kernal, GLRLM + TWSVM using sigmoid, ILMFD + NLSVM using RBF kernal, ILMFD + TWSVM using polynomial kernal, Hybrid feature + NLSVM, and Hybrid feature + TWSVM all performed better in terms of evaluation done by performance metrics used in this work. For the given dataset, the Hybrid feature + NLSVM model with Linear Kernal yielded significantly better results out of eight models tested, including 100% accuracy, 100% recall, 100% precision, 100% F1-score, R-Squared = 1, and RMSE = 0. As a result, the high accuracy of this type of computer-aided screening method would significantly boost the speed and accuracy of COVID-19 diagnosis also encourage the study of other associated diseases with CT-scan images.
Diversity analysis in novel Turkey berry accessions (Solanum torvum Swartz) using microsatellites markers
Authors: Jena Nitish Kumar , Mishra Abinash , Nithyanandam Arumugam , Vethamoni P. Irene , Saraswathi T. , Senthil N. , Uma D. , Jena Ranjan Kumar , Arunachalam Arun 
Published: July 2024

Abstract

Turkey berry (Solanum torvum) contains anti-inflammatory properties. Traditional medical benefits of fundamental oils have been explored. A thorough biochemical and elemental characterisation was carried out in light of these facts. SSR markers were used in the current study to identify variety-specific markers, analyze genetic diversity, and perform DNA fingerprinting. The St 002, St 010, St 011, St 014 and St 019 accessions exhibited superior performance with respect to important characteristics including higher antioxidant and tannin content. The accessions of turkey berries were then used to perform genetic fingerprinting using SSR markers. Fourteen SSRs were used for genotyping. With a PIC of 0.558, the marker EM145 expressed the highest, whereas EMB01L13 expressed the lowest (0.263). The average PIC estimate was found to be modest (0.362). The twenty accessions of Turkey berries were divided into four major clusters by the dendrogram analysis. Based on their biochemical and elemental characterisation, the majority of the turkey berry accessions that are now being studied have special beneficial chemicals that may be used in industry.The limited genetic bases of the germplasms are shown by the moderate levels of both PIC and H average estimates. To create better hybrids, a hybridization program can employ the types belonging to several clusters. The combinations of varietals St018 / St006, St018 / St002, St014 / St008, St019 / St003, and St0015 / St008 show promise as potential parents.
Direct long-read RNA sequencing uncovers functional variation affecting transcript production and RNA modifications
Authors: Réal Aline , Brown Andrew , Yung Gisella Puga , Borel Christelle , Lykoskoufis Nikolaos , Seebach Jörg , Dermitzakis Emmanouil , Ramisch Anna , Viñuela Ana 
Published: July 2024

Abstract

The production of multiple transcripts per gene is a process regulated by inherited genetic variants and epitranscriptomic modifications, and plays a prominent role in modulating complex traits and diseases. To simultaneously characterize the effect of genetic variants on transcript abundance and N6-methyladenosine (m6A) modifications, we produced long-read native poly(A) RNA-seq data for 60 genetically different lymphoblastoid cell lines (LCLs) from the 1000 Genomes/Geuvadis project. We identified a high diversity of both annotated (31%) and unannotated (61%) transcripts, with only a small proportion expressed across individuals (35% and 7%, respectively). In a genome-wide genetic analysis on transcripts, we identified 105 trQTLs, of which 76 were not detected as eQTLs using a larger published short-read RNAseq dataset (317 samples). A population wide characterization of m6A methylation DRACH motifs identified an average of 40.1 m6A modifications on 6,222 genes. Genetic association analysis of highly variable modifications from 1,155 genes identified m6A modification quantitative trait loci (m6A-QTLs) for 16 transcripts. Colocalization analysis of trQTL and m6A-QTLs, identified 33 candidate transcripts mediating GWAS traits, with 46.4% of the colocalized trQTLs implicating novel risk transcripts. Overall, the simultaneous characterization of transcripts and post-transcriptional modifications identified genetic effects on transcription often missed when using other sequencing technologies.
Likelihood and unlikelihood of megaquake recurrence implied by frequency-magnitude distribution of Japanese seismicity
Authors: Nanjo Kazuyoshi , Hori Takane 
Published: July 2024

Abstract

Constraints on the recurrence of subduction-zone earthquakes are important for seismic hazard assessment. Previous studies proposed a high-likelihood of imminent recurrence for the 2011 magnitude-9 Tohoku megaquake and the 17th-century Hokkaido megaquake of comparative magnitude off the Japanese Pacific coast, although the implication of future seismicity remains uncertain. Here, the occurrence of small earthquakes was compared to larger ones, using b-values, to show that persistently high b-values occurred in the source area of the Tohoku earthquake, indicative of no imminent recurrence. In contrast, low b-values occurred in the source area of the 17th-century earthquake, indicative of a sign seen before the Tohoku event. Around the zone of low b-value, we observed phenomena providing insight into subsequent large earthquakes, which were often reported for past large earthquakes: seismic quiescence, a seismic gap, strong plate coupling, and the absence of slow earthquake activity. Monitoring b-values, together with geophysical observations, plays a role in hazard assessment off the coast of Japan.
Pharmacological neuromodulation by intracerebroventricular administration of anaerobic dopamine in the treatment of advanced Parkinson's disease
Authors: Devos David , Moreau Caroline , Odou Pascal , Labreuche Julien , Demailly Alexandre , Touzet Gustavo , Reyns Nicolas , Gouges Bastien , Duhamel Alain , Barthelemy Christine , Lannoy Damien , Carta Natacha , Palas Benjamin , Vasseur Michèle , Marchand Felix , Ollivier Thomas , Leclercq Celine , Potey Camille , Ouk Thavarak , Baigne Simon , Dujardin Kathy , Carton Louise , Rolland Anne-Sophie , Devedjian Jean Christophe , Foutel Véronique , Deplanque Dominique , Fisichella Matthieu 
Published: July 2024

Abstract

Continuous compensation of cerebral dopamine deficiency represents an ideal treatment for Parkinson's disease. However, dopamine does not cross the digestive and blood-brain barriers, and is rapidly oxidised. The new concept is continuous intra-cerebroventricular administration of anaerobic dopamine (A-dopamine) using a telemetry-controlled subcutaneous abdominal pump connected to a subcutaneous catheter implanted in the third ventricle, near the striatum. A phase I study was conducted showing no serious A-dopamine-induced adverse events in 12 patients, followed by a randomised, controlled, open-label, cross-over, phase II study of 1 month of A-dopamine vs. 1 month of optimised oral antiparkinsonian therapy. The primary endpoint, a blinded assessment of the percentage over the total target (i.e. time with dyskinesia or bradykinesia), recorded by actimetry at home using a wristwatch, was significantly reduced. All expected secondary clinical outcomes were significantly improved, providing the first promising data on the feasibility, safety and efficacy of this new device aided therapy for advanced stage patients.
ClinicalTrials.gov identifier:NCT04332276
Investigation of the potential connections between NAFLD-associated Alzheimer's disease: bioinformatics analysis of shared genes
Authors: Bhattacharya Indrajit , Bhattacharya Teeshyo , Sahu Amrita , Das Pamelika , Sarkar Sulogna , Prasanna Vani Sai , Sreed Remya , Velayutham Ravichandiran , Arumugam Somasundaram 
Published: July 2024

Abstract

NAFLD has some potential risk factors for developing Alzheimer's disease. This study attempted to establish the potential connections between NAFLD-associated Alzheimer's disease (AD) by analyzing shared genes and pathways using bioinformatics tools. Initially, prepared gene lists related to AD and NAFLD were collected from the GeneCard database, and genes with GeneCard relevance score ≥ 20 were extracted to make a new gene list. The Venn diagram identified common genes (417) between the two diseases from the new gene list. The common genes were used for further analysis of the PPI network, which was constructed using the STRING database with a minimum required interaction score ≥ 0.9 to obtain network relationships. The networks had shown 397 nodes, 1210 edges, an average node degree of 54.7, and an expected number of edges at 397. The top 25 hub genes were calculated by Cytoscape (vs3.10.2) using the bottleneck, degree, and closeness method using CytoHubba. The merged network of the top 25 hub genes from the previously mentioned three methods was contracted to identify the connection between NAFLD and AD. Our study revealed that important pathways were PI3K-Akt and AGE-RAGE in diabetic complications, NAFLD-related systemic inflammation to neuroinflammation, and LRP-1-induced amyloid and tau hyperphosphorylation. This suggests an interrelation between the two major diseases, ushering in the need for new possibilities utilizing this crosstalk.
Lichen communities across a subarctic region of Northern Quebec (Canada): conservation status, α- and β-diversity, and functional traits
Authors: Cerrejón Carlos , Valeria Osvaldo , Haughland Diane L. , Fenton Nicole J. 
Published: July 2024

Abstract

Conservation of lichens is impeded by knowledge gaps on their distribution and habitat requirements. This is a significant issue in vast, isolated and harsh environment regions such as subarctic regions, where lichen communities remain under documented. Lichen biodiversity assessments provide useful insights to better understand the functions supported by these ecologically important and sensitive species. This study aims i) to describe the conservation status of lichen communities and their α- and β-diversity components across a subarctic region in Northern Quebec (190 km2), ii) to describe their functional traits across the habitat types found in this region, and iii) to identify habitat types constituting lichen biodiversity hotspots. Lichens were sampled in 45 plots in habitats ranging from coniferous and deciduous forests to bogs, fens and rocky outcrops. A total of 115 species of largely macrolichens, calicioid lichens and allied fungi were identified, of which 18% currently have ranks of conservation concern at the provincial level, and 38% are newly reported for the region (~124,000 km2 around our study area). Richness across plots averaged 36 ± 9 species and plots richer in microhabitats often harbored more species (R2 = 0.22). Differences in species composition were identified among plots and habitat types through NMDS and perMANOVA analyses (R2 = 0.35; p < 0.001), both being supported by differences in microhabitat composition (Mantel r = 0.22 and perMANOVA R2 = 0.29, respectively; p < 0.001). Thirty-five species showed significant preferences for a habitat based on the Pearson’s phi coefficient of association. Our analysis on functional traits revealed significant patterns of association with habitat types, including i) saxicolous species with rocky outcrops, ii) epiphytic/epixylic species and vegetative reproduction traits (soredia, isidia) with coniferous stands, and iii) species belonging to the Parmeliaceae family with fens. Rocky outcrops represented the main lichen biodiversity hotspots in the region, while other habitat types were also important for maintaining total and complementary biodiversity. We are confident that our methodological approach including systematic sampling, full habitat variability representation, and the evaluation of complementary biodiversity components, can be effectively applied to fill gaps on lichen biodiversity in other underexplored regions across the globe.