bluuebunny/crossref_metadata_2025_split huggingface dataset:
System biology mediated assessment of molecular mechanism for sinapic acid against breast cancer: via network pharmacology and molecular dynamic simulation
Authors: Dwivedi Prarambh S. R. , Shastry C. S. 
Published: December 2023

AbstractSinapic acid is a hydroxycinnamic acid widespread in the plant kingdom, known to be a potent anti-oxidant used for the treatment of cancer, infections, oxidative stress, and inflammation. However, the mode of action for its chemotherapeutic properties has yet not been unleashed. Hence, we aimed to identify potential targets to propose a possible molecular mechanism for sinapic acid against breast cancer. We utilized multiple system biology tools and databases like DisGeNET, DIGEP-Pred, Cytoscape, STRING, AutoDock 4.2, AutoDock vina, Schrodinger, and gromacs to predict a probable molecular mechanism for sinapic acid against breast cancer. Targets for the disease breast cancer, were identified via DisGeNET database which were further matched with proteins predicted to be modulated by sinapic acid. In addition, KEGG pathway analysis was used to identify pathways; a protein-pathway network was constructed via Cytoscape. Molecular docking was performed using three different algorithms followed by molecular dynamic simulations and MMPBSA analysis. Moreover, cluster analysis and gene ontology (GO) analysis were performed. A total of 6776 targets were identified for breast cancer; 95.38% of genes predicted to be modulated by sinapic acid were common with genes of breast cancer. The ‘Pathways in cancer’ was predicted to be modulated by most umber of proteins. Further,PRKCA,CASP8, andCTNNB1were predicted to be the top 3 hub genes. In addition, molecular docking studies revealedCYP3A4,CYP1A1, andSIRT1to be the lead proteins identified from AutoDock 4.2, AutoDock Vina, and Schrodinger suite Glide respectively. Molecular dynamic simulation and MMPBSA were performed for the complex of sinapic acid with above mentioned proteins which revealed a stable complex throughout simulation. The predictions revealed that the mechanism of sinapic acid in breast cancer may be due to regulation of multiple proteins likeCTNNB1,PRKCA,CASP8,SIRT1, and cytochrome enzymes (CYP1A1&CYP3A4); the majorly regulated pathway was predicted to be ‘Pathways in cancer’. This indicates the rationale for sinapic acid to be used in the treatment of breast cancer. However, these are predictions and need to be validated and looked upon in-depth to confirm the exact mechanism of sinapic acid in the treatment of breast cancer; this is future scope as well as a drawback of the current study.
Giant enhancement of nonreciprocity in gyrotropic heterostructures
Authors: Katsantonis Ioannis , Tasolamprou Anna C. , Koschny Thomas , Economou Eleftherios N. , Kafesaki Maria , Valagiannopoulos Constantinos 
Published: December 2023

AbstractNonreciprocity is a highly desirable feature in photonic media since it allows for control over the traveling electromagnetic waves, in a way that goes far beyond ordinary filtering. One of the most conventional ways to achieve nonreciprocity is via employing gyrotropic materials; however, their time-reversal-symmetry-breaking effects are very weak and, hence, large, bulky setups combined with very strong magnetic biases are required for technologically useful devices. In this work, artificial heterostructures are introduced to enhance the effective nonreciprocal behavior by reducing the contribution of the diagonal susceptibilities in the collective response; in this way, the off-diagonal ones, that are responsible for nonreciprocity, seem bigger. In particular, alternating gyrotropic and metallic or plasmonic films make an epsilon-near-zero (ENZ) effective-medium by averaging the diagonal permittivities of opposite sign, representing the consecutive layers. The homogenization process leaves unaltered the nonzero off-diagonal permittivities of the original gyrotropic substance, which become dominant and ignite strong nonreciprocal response. Realistic material examples that could be implemented experimentally in the mid-infrared spectrum are provided while the robustness of the enhanced nonreciprocity in the presence of actual media losses is discussed and bandwidth limitations due to the unavoidable frequency dispersion are elaborated. The proposed concept can be extensively utilized in designing optical devices that serve a wide range of applications from signal isolation and wave circulation to unidirectional propagation and asymmetric power amplification.
Pilot-scale genome-wide association mapping in diverse sorghum germplasms identified novel genetic loci linked to major agronomic, root and stomatal traits
Authors: Ramalingam Ajay Prasanth , Mohanavel Williams , Kambale Rohit , Rajagopalan Veera Ranjani , Marla Sandeep R. , Prasad P. V. Vara , Muthurajan Raveendran , Perumal Ramasamy 
Published: December 2023

AbstractThis genome-wide association studies (GWAS) used a subset of 96 diverse sorghum accessions, constructed from a large collection of 219 accessions for mining novel genetic loci linked to major agronomic, root morphological and physiological traits. The subset yielded 43,452 high quality single nucleotide polymorphic (SNP) markers exhibiting high allelic diversity. Population stratification showed distinct separation between caudatum and durra races. Linkage disequilibrium (LD) decay was rapidly declining with increasing physical distance across all chromosomes. The initial 50% LD decay was ~ 5 Kb and background level was within ~ 80 Kb. This study detected 42 significant quantitative trait nucleotide (QTNs) for different traits evaluated using FarmCPU, SUPER and 3VmrMLM which were in proximity with candidate genes related and were co-localized in already reported quantitative trait loci (QTL) and phenotypic variance (R2) of these QTNs ranged from 3 to 20%. Haplotype validation of the candidate genes from this study resulted nine genes showing significant phenotypic difference between different haplotypes. Three novel candidate genes associated with agronomic traits were validated including Sobic.001G499000, a potassium channel tetramerization domain protein for plant height, Sobic.010G186600, a nucleoporin-related gene for dry biomass, and Sobic.002G022600 encoding AP2-like ethylene-responsive transcription factor for plant yield. Several other candidate genes were validated and associated with different root and physiological traits including Sobic.005G104100, peroxidase 13-related gene with root length, Sobic.010G043300, homologous to Traes_5BL_8D494D60C, encoding inhibitor of apoptosis with iWUE, and Sobic.010G125500, encoding zinc finger, C3HC4 type domain with Abaxial stomatal density. In this study, 3VmrMLM was more powerful than FarmCPU and SUPER for detecting QTNs and having more breeding value indicating its reliable output for validation. This study justified that the constructed subset of diverse sorghums can be used as a panel for mapping other key traits to accelerate molecular breeding in sorghum.
Earthworms do not increase greenhouse gas emissions (CO2 and N2O) in an ecotron experiment simulating a three-crop rotation system
Authors: Forey Oswaldo , Sauze Joana , Piel Clément , Gritti Emmanuel S. , Devidal Sébastien , Faez Abdelaziz , Ravel Olivier , Nahmani Johanne , Rouch Laly , Blouin Manuel , Pérès Guénola , Capowiez Yvan , Roy Jacques , Milcu Alexandru 
Published: December 2023

AbstractEarthworms are known to stimulate soil greenhouse gas (GHG) emissions, but the majority of previous studies have used simplified model systems or lacked continuous high-frequency measurements. To address this, we conducted a 2-year study using large lysimeters (5 m2 area and 1.5 m soil depth) in an ecotron facility, continuously measuring ecosystem-level CO2, N2O, and H2O fluxes. We investigated the impact of endogeic and anecic earthworms on GHG emissions and ecosystem water use efficiency (WUE) in a simulated agricultural setting. Although we observed transient stimulations of carbon fluxes in the presence of earthworms, cumulative fluxes over the study indicated no significant increase in CO2 emissions. Endogeic earthworms reduced N2O emissions during the wheat culture (− 44.6%), but this effect was not sustained throughout the experiment. No consistent effects on ecosystem evapotranspiration or WUE were found. Our study suggests that earthworms do not significantly contribute to GHG emissions over a two-year period in experimental conditions that mimic an agricultural setting. These findings highlight the need for realistic experiments and continuous GHG measurements.
Protein and lipid expansion microscopy with trypsin and tyramide signal amplification for 3D imaging
Authors: Wang Ueh-Ting Tim , Tian Xuejiao , Liou Yae-Huei , Lee Sue-Ping , Hu Hsiao-Tang , Lu Chieh-Han , Lin Po-Ting , Cheng Ya-Jen , Chen Peilin , Chen Bi-Chang 
Published: December 2023

AbstractExpansion microscopy, whereby the relative positions of biomolecules are physically increased via hydrogel expansion, can be used to reveal ultrafine structures of cells under a conventional microscope. Despite its utility for achieving super-resolution imaging, expansion microscopy suffers a major drawback, namely reduced fluorescence signals caused by excessive proteolysis and swelling effects. This caveat results in a lower photon budget and disfavors fluorescence imaging over a large field of view that can cover an entire expanded cell, especially in 3D. In addition, the complex procedures and specialized reagents of expansion microscopy hinder its popularization. Here, we modify expansion microscopy by deploying trypsin digestion to reduce protein loss and tyramide signal amplification to enhance fluorescence signal for point-scanning-based imaging. We name our new methodology TT-ExM to indicate dual trypsin and tyramide treatments. TT-ExM may be applied for both antibody and lipid staining. TT-ExM displayed enhanced protein retention for endoplasmic reticulum and mitochondrial markers in COS-7 cell cultures. Importantly, TT-ExM-based lipid staining clearly revealed the complex 3D membrane structures in entire expanded cells. Through combined lipid and DNA staining, our TT-ExM methodology highlighted mitochondria by revealing their DNA and membrane structures in cytoplasm, as well as the lipid-rich structures formed via phase separation in nuclei at interphase. We also observed lipid-rich chromosome matrices in the mitotic cells. These high-quality 3D images demonstrate the practicality of TT-ExM. Thus, readily available reagents can be deployed in TT-ExM to significantly enhance fluorescence signals and generate high-quality and ultrafine-resolution images under confocal microscopy.
Correlates of minimum dietary diversity among pregnant women on antenatal care follow up at public health facility in Puntland, Somalia
Authors: Mohammed Feiruza , Abdirizak Najma , Jibril Abdulfetah , Oumer Abdu 
Published: December 2023

AbstractIn Somalia, where a poorly diversified diet is leading to adverse pregnancy and neonatal outcomes, there is a significant dearth of evidence that needs to be studied. Hence, this study was to identify factors associated with minimum dietary diversity among pregnant women in Somalia. A facility-based survey was conducted among 361 pregnant women attending antenatal care (ANC) using a structured questionnaire. Dietary diversity was measured using consumption of 10-food groups. Bivariable and multivariable binary logistic regression analyses were used, along with odds ratios and 95% confidence intervals. About 48.2% (42.9–53.5) of women had an inadequately diversified diet. The risk of having an inadequately diversified diet was higher among rural residents (AOR = 1.20; 0.30–4.75), multigravida (AOR = 2.85; 1.43–5.68), young women (AOR = 2.15; 0.82–5.61), extended families (AOR = 1.19; 0.68–2.10), with infrequent ANC visits (AOR = 4.12; 2.06–8.27), fewer frequent meals (AOR = 1.84; 1.09–3.10) and from food-insecure households (AOR = 3.84; 2.28–6.49) as compared to their counterparts. Consumption of poorly diversified diet was prevalent and associated with dietary diversity was prevalent among women which could be strongly predicted by parity, ante-natal care and food security, which needs to be targeted for interventions.
Potential bioremediation of lead and phenol by sunflower seed husk and rice straw-based biochar hybridized with bacterial consortium: a kinetic study
Authors: El-Gamal Eman H. , Rashad Mohamed , Saleh Maher E. , Zaki Sahar , Eltarahony Marwa 
Published: December 2023

AbstractEnvironmental pollution is a global phenomenon and troublesome fact that poses a grave risk to all living entities. Via coupling carbonaceous feedstocks with outstanding microbial activity, kinetic experiments were established using the consortium of Proteus mirabilis and Raoultella planticola, biochar-derived sunflower seed husk (SHB) and rice straw (RSB), and their composites, which investigated at 30 °C (150 rpm) to eliminate 700 mg L−1 lead (120 h) and phenol (168 h) from synthetic wastewater. The derived biochars physicochemical properties of were studied. According to adsorption capacity (qe), consortium-SHB composites and consortium-RSB composites removed lead completely (70 mg g−1) within 48 h and 66 h, respectively. Besides, phenol was remediated entirely after 42 h and 48 h by both composite systems (69.90 mg g−1), respectively, comparing with bacterial consortium only or parent SHB and RSB. Moreover, four kinetic models were studied to describe the bioremediation process. Fractional power and Elovich models could be recommended for describing the adsorption kinetics for lead and phenol removal by the studied biomaterials with high correlation coefficient (R2 ≥ 0.91 for Pb2+ and ≥ 0.93 for phenol) and lower residual root mean square error (RMSE) and chi-square (X2). Overall, bacterial consortium-biochar composites exhibited greater remediation of lead and phenol than the sum of each single bacterial consortium and biochar systems; reflecting synergistic interaction of adsorptive capability of biochar and metabolic performance of bacterial consortium, as denoted by scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX). The current study addressed the successful design of employing functional remediating consortium immobilized on waste biomass-derived biochar as a conducive alternative eco-sorbent and economic platform to detoxify organic and inorganic pollutants.
Mir324 knockout regulates the structure of dendritic spines and impairs hippocampal long-term potentiation
Authors: Parkins Emma V. , Brager Darrin H. , Rymer Jeffrey K. , Burwinkel John M. , Rojas Diego , Tiwari Durgesh , Hu Yueh-Chiang , Gross Christina 
Published: December 2023

AbstractMicroRNAs are an emerging class of synaptic regulators. These small noncoding RNAs post-transcriptionally regulate gene expression, thereby altering neuronal pathways and shaping cell-to-cell communication. Their ability to rapidly alter gene expression and target multiple pathways makes them interesting candidates in the study of synaptic plasticity. Here, we demonstrate that the proconvulsive microRNA miR-324-5p regulates excitatory synapse structure and function in the hippocampus of mice. Both Mir324 knockout (KO) and miR-324-5p antagomir treatment significantly reduce dendritic spine density in the hippocampal CA1 subregion, and Mir324 KO, but not miR-324-5p antagomir treatment, shift dendritic spine morphology, reducing the proportion of thin, “unstable” spines. Western blot and quantitative Real-Time PCR revealed changes in protein and mRNA levels for potassium channels, cytoskeletal components, and synaptic markers, including MAP2 and Kv4.2, which are important for long-term potentiation (LTP). In line with these findings, slice electrophysiology revealed that LTP is severely impaired in Mir324 KO mice, while neurotransmitter release probability remains unchanged. Overall, this study demonstrates that miR-324-5p regulates dendritic spine density, morphology, and plasticity in the hippocampus, potentially via multiple cytoskeletal and synaptic modulators.
Seismic behavior of precast columns with unbonded prestressed tendons and energy-dissipating bars: physical and numerical investigations
Authors: Ma Chao , Zheng Xiaobo , Zhu Zhao , Zhou Mi 
Published: December 2023

AbstractThe study of the strength and failure modes of construction components has become increasingly important with the advent of industrialized construction. Recently, because of the need to promote the survivability of both structures and persons, it has encompassed failure modes associated with seismic threats. This study reports the seismic behavior of precast segmented columns designed with both unbonded prestressed tendons (UPTs) and energy-dissipating (ED) bars. A physical specimen was subjected to a quasi-static cyclic test; this permitted the evaluation of the damage mode and behavior of the energy dissipation mechanism, and permitted the establishment and verification of a fiber beam element simulation model. The model was then used to evaluate the effects of the variation of the design parameters on the behavior of precast assembled columns. The test specimen exhibited stable energy dissipation and a pinching effect during cyclic loading. An analysis using the fiber beam element model with varying design parameters revealed that high-strength concrete could mitigate the concrete damage and residual deformation after an earthquake, and that the concrete strength and steel bar strength should be matched when enhancing the seismic resilience of precast columns with high-strength steel bars. It was determined that increasing the prestress mechanism, namely the ratio of the UPTs, could greatly improve the residual deformation, while the ratio of ED bars is the key factor in enhancing the energy dissipation capacity of the precast columns. Suitable ratios of UPTs and ED bars are the keys to ensuring stable energy dissipation and low residual drifts. Moreover, an increased axial load ratio and prestress level are able to restrain the joint opening and improve the bearing capacity of the precast columns; however, an excessive axial load or prestressing force would result in the rapid degeneration of the carrying capacity and larger residual displacements.
Robot locomotion by fluid–fluid interaction
Authors: Kitamori Hiroto , Kudoh Shunsuke , Shintake Jun 
Published: December 2023

AbstractThis paper describes a locomotion strategy for robots based on the interaction between two fluids, through the development of an untethered mobile robot. The fundamental principle of robot locomotion is to exploit the active deformations of ferrofluid caused by internal magnetic fields, which generate reaction forces to the surrounding fluid (in this study, water). The developed robot is equipped with two permanent magnets (PMs), two electromagnets (EMs), two clusters of ferrofluid, and a control unit with batteries. It has a length, width, and mass of 107 mm, 94 mm, and 127 g, respectively. In the robot, PMs are used to hold clusters of ferrofluid. The activation of EMs by the controller achieves forward and rotational movements of the robot. Experimental results show the forward speed and rotational speed in water to be 2.7 mm/s (at a driving frequency of 9 Hz) and 1.2°/s (at a driving frequency of 7 Hz), respectively. The measured thrust force of the robot is 2 mN, further supporting the concept of robot locomotion by fluid–fluid interaction.
In vivo mapping of hemodynamic responses mediated by tubuloglomerular feedback in hypertensive kidneys
Authors: Lee Blaire , Postnov Dmitry D. , Sørensen Charlotte M. , Sosnovtseva Olga 
Published: December 2023

AbstractThe kidney has a sophisticated vascular structure that performs the unique function of filtering blood and managing blood pressure. Tubuloglomerular feedback is an intra-nephron negative feedback mechanism stabilizing single-nephron blood flow, glomerular filtration rate, and tubular flow rate, which is exhibited as self-sustained oscillations in single-nephron blood flow. We report the application of multi-scale laser speckle imaging to monitor global blood flow changes across the kidney surface (low zoom) and local changes in individual microvessels (high zoom) in normotensive and spontaneously hypertensive rats in vivo. We reveal significant differences in the parameters of TGF-mediated hemodynamics and patterns of synchronization. Furthermore, systemic infusion of a glucagon-like-peptide-1 receptor agonist, a potential renoprotective agent, induces vasodilation in both groups but only alters the magnitude of the TGF in Sprague Dawleys, although the underlying mechanisms remain unclear.
Combination strategy for prognostication in patients undergoing post-resuscitation care after cardiac arrest
Authors: Park Jung Soo , Kim Eun Young , You Yeonho , Min Jin Hong , Jeong Wonjoon , Ahn Hong Joon , In Yong Nam , Lee In Ho , Kim Jae Moon , Kang Changshin 
Published: December 2023

AbstractThis study investigated the prognostic performance of combination strategies using a multimodal approach in patients treated after cardiac arrest. Prospectively collected registry data were used for this retrospective analysis. Poor outcome was defined as a cerebral performance category of 3–5 at 6 months. Predictors of poor outcome were absence of ocular reflexes (PR/CR) without confounding factors, a highly malignant pattern on the most recent electroencephalography, defined as suppressed background with or without periodic discharges and burst-suppression, high neuron-specific enolase (NSE) after 48 h, and diffuse injury on imaging studies (computed tomography or diffusion-weighted imaging [DWI]) at 72–96 h. The prognostic performances for poor outcomes were analyzed for sensitivity and specificity. A total of 130 patients were included in the analysis. Of these, 68 (52.3%) patients had poor outcomes. The best prognostic performance was observed with the combination of absent PR/CR, high NSE, and diffuse injury on DWI [91.2%, 95% confidence interval (CI) 80.7–97.1], whereas the combination strategy of all available predictors did not improve prognostic performance (87.8%, 95% CI 73.8–95.9). Combining three of the predictors may improve prognostic performance and be more efficient than adding all tests indiscriminately, given limited medical resources.