Browse Articles

Integrative metabolomics and transcriptomics profiling reveals differential expression of flavonoid synthesis in Ophiopogon japonicus (L. f.) Ker-Gawl. in adaptation to drought

Drought is one of the consequences of climate change that severely affects plant growth and development. Ophiopogon japonicus (L. f.) Ker-Gawl. (Chinese name: Chuanmaidong, abbreviated as CMD) is a commonly used herbaceous plant whose growth and development are strongly affected by drought. Here, we comprehensively analyzed the transcriptomic and metabolic responses of two CMD varieties (EP and CP) to drought stress. CP utilized a small number of differentially expressed genes to regulate a greater number of differential metabolites compared to EP, suggesting that it may be more drought tolerant. In addition, integrated transcriptome and metabolome analyses revealed that transcription factors such as WRKY, TIFY, and C2H2 regulate flavonoid synthesis in CMD. These findings provide ideas for in-depth analysis of the mechanism of CMD against drought stress, and provide a theoretical basis for breeding high-quality drought-tolerant varieties.

Comparative analysis of improved m6A sequencing based on antibody optimization for low-input samples

Structural insight into sodium ion pathway in the bacterial flagellar stator from marine <i>Vibrio</i>

Many bacteria swim in liquid or swarm on surface using the flagellum rotated by a motor driven by specific ion flow. The motor consists of the rotor and stator, and the stator converts the energy of ion flow to mechanical rotation. However, the ion pathway and the mechanism of stator rotation coupled with specific ion flow are still obscure. Here, we determined the structures of the sodium-driven stator of Vibrio , namely PomAB, in the presence and absence of sodium ions and the structure with its specific inhibitor, phenamil, by cryo-electron microscopy. The structures and following functional analysis revealed the sodium ion pathway, the mechanism of ion selectivity, and the inhibition mechanism by phenamil. We propose a model of sodium ion flow coupled with the stator rotation based on the structures. This work provides insights into the molecular mechanisms of ion specificity and conversion of the electrochemical potential into mechanical functions.

Innovameter: Agent-based modeling of innovation determinants in American and European countries

This article discusses the dynamics of innovation in America and Europe, focusing on variables such as access to technology, education, and life expectancy. To do this, the article proposes an agent-based model called the Innovameter. The dependent variable is the Global Innovation Index. The paper focuses on data analysis through correlation analysis and multiple hierarchical regressions to determine the contribution of specific variables related to the pillars of the Global Innovation Index and indicators of the Human Development Index. After analyzing the data, an agent-based model was built to parameterize these main variables by defining two levels of abstraction: at the global level, there is the country, where birth rates, life expectancy, ICT use, and research and development are defined. At the local level, we define the individuals who have an age, years of schooling, and income. A series of experiments were conducted by selecting data from 30 countries. From the results of the experiments, a nonparametric correlation analysis was performed, and correlation indices were obtained indicating a relationship between the predicted outcomes and the outcomes in the global index. The proposed model aims to provide suggestions on how the different variables can become the norm in most of the countries studied.

Hybrid spin coating and evaporation techniques for fabricating double-layer stacked dual-color perovskite LEDs

Palmitoylation-dependent association with Annexin II directs hepatitis E virus ORF3 sorting into vesicles and quasi-enveloped virions

Historically considered to be nonenveloped, hepatitis E virus (HEV), an important zoonotic pathogen, has recently been discovered to egress from infected cells as quasi-enveloped virions. These quasi-enveloped virions circulating in the blood are resistant to neutralizing antibodies, thereby facilitating the stealthy spread of infection. Despite abundant evidence of the essential role of the HEV-encoded ORF3 protein in quasi-enveloped virus formation, the underlying mechanism remains unclear. Here, we demonstrate that the HEV ORF3 protein possesses an inherent capacity for self-secretion and that palmitoylation at two cysteine residues within the ORF3 N-terminal region is essential for its secretion and quasi-enveloped virus formation. We further found that only palmitoylated ORF3 proteins hijacked Annexin II for transport to the cytoskeleton and are then directed into multivesicular bodies through the nSMase-endosomal sorting complexes required for transport-III pathway for secretion. Finally, we show that infection of gerbils with HEV mutants harboring mutations at palmitoylation sites within ORF3 showed no fecal viral shedding but competent replication in the liver. Our study fills a gap in the understanding of the assembly and release of quasi-enveloped virions mediated by ORF3 and offers the potential for designing therapeutic strategies to control HEV infection.

Experimental research on the structural optimization of grouting holes in circular and rectangular pipe sections for trenchless pipe jacking

Profile of Stefan W. Hell

Ln-MOF in production of durable antimicrobial and UV-Protective fluorescent cotton fabric for potential application in military textiles

AbstractIndustrialization of military textiles faces many challenges and some requirements such as durability, protection and suitability for hostile environment must be provided. Herein, fluorescent protective cotton with ultraviolet radiation (UVR)-protection and antimicrobial property was currently prepared via the immobilization of lanthanide-metal organic framework (Ln-MOF). Cotton fabrics were primarily activated via cationization process with 3-Chloro-2-hydroxypropyltrimethyl ammonium chloride to obtain the cationized cotton (Q-cotton). Subsequently, Ln-MOFs based on Europium (Eu) and Terbium (Tb) were separately immobilized within cotton and Q-cotton fabrics. The obtained Ln-MOF@fabrics showed good fluorescent character, while three and four emission bands were estimated for Eu-MOF@fabric and Tb-MOF@fabric, respectively, related to the electron transition from 5D0 to 7F0-4 in Eu3+ and from 5D4 to 7F3-6 in Tb3+. After Ln-MOF incorporation, UVR-protection factor (UPF) was significantly enlarged from 1.9 (insufficient UPF) to 22.1–25.6 (good UPF) without cationization and to 32.4–37.8 (very good UPF) for Q-cotton. Against three different pathogens (Escherichia coli, staphylococcus Aureus and Candida albicans), Ln-MOF@fabrics exhibited good microbial reduction of 68–79% and 81–91% in case of cotton and Q-cotton, respectively. The cationization improved the functionality and durability of fabrics, while the acquired functions were still existed even after 10 repetitive washings.

A single-center, single-arm, prospective, open-label, and comparative trial to evaluate the safety and tolerability profile of a 90-day oral L-arginine hydrochloride intervention for patients with amyotrophic lateral sclerosis

Modular DNA origami–based electrochemical detection of DNA and proteins

The diversity and heterogeneity of biomarkers has made the development of general methods for single-step quantification of analytes difficult. For individual biomarkers, electrochemical methods that detect a conformational change in an affinity binder upon analyte binding have shown promise. However, because the conformational change must operate within a nanometer-scale working distance, an entirely new sensor, with a unique conformational change, must be developed for each analyte. Here, we demonstrate a modular electrochemical biosensor, built from DNA origami, which is easily adapted to diverse molecules by merely replacing its analyte binding domains. Instead of relying on a unique nanometer-scale movement of a single redox reporter, all sensor variants rely on the same 100-nm scale conformational change, which brings dozens of reporters close enough to a gold electrode surface that a signal can be measured via square-wave voltammetry, a standard electrochemical technique. To validate our sensor’s mechanism, we used single-stranded DNA as an analyte, and optimized the number of redox reporters and various linker lengths. Adaptation of the sensor to streptavidin and Platelet-Derived Growth Factor-BB (PDGF-BB) analytes was achieved by simply adding biotin or anti-PDGF aptamers to appropriate DNA linkers. Geometrically optimized streptavidin sensors exhibited signal gain and limit of detection markedly better than comparable reagentless electrochemical sensors. After use, the same sensors could be regenerated under mild conditions: Performance was largely maintained over four cycles of DNA strand displacement and rehybridization. By leveraging the modularity of DNA nanostructures, our work provides a straightforward route to the single-step quantification of arbitrary nucleic acids and proteins.

Wavefront-aberration-tolerant diffractive deep neural networks using volume holographic optical elements

AbstractAs the demand for computational performance in artificial intelligence (AI) continues to increase, diffractive deep neural networks (D2NNs), which can perform AI computing at the speed of light by repeated optical modulation with diffractive optical elements (DOEs), are attracting attention. DOEs are varied in terms of fabrication methods and materials, and among them, volume holographic optical elements (vHOEs) have unique features such as high selectivity and multiplex recordability for wavelength and angle. However, when those are used for D2NNs, they suffer from unknown wavefront aberrations compounded by multiple fabrication errors. Here, we propose a training method to adapt the model to be unknown wavefront aberrations and demonstrate a D2NN using vHOEs. As a result, the proposed method improved the classification accuracy by approximately 58 percentage points in the optical experiment, with the model trained to classify handwritten digits. The achievement of this study can be extended to the D2NN that enables the independent modulation of multiple wavelengths owing to their wavelength selectivity and wavelength division multiplex recordability. Therefore, it might be promising for various applications that require multiple wavelengths in parallel optical computing, bioimaging, and optical communication.

Geometrically modulated contact forces enable hula hoop levitation

Mechanical systems with moving points of contact—including rolling, sliding, and impacts—are common in engineering applications and everyday experiences. The challenges in analyzing such systems are compounded when an object dynamically explores the complex surface shape of a moving structure, as arises in familiar but poorly understood contexts such as hula hooping. We study this activity as a unique form of mechanical levitation against gravity and identify the conditions required for the stable suspension of an object rolling around a gyrating body. We combine robotic experiments involving hoops twirling on surfaces of various geometries and a model that links the motions and shape to the contact forces generated. The in-plane motions of the hoop involve synchronization to the body gyration that is shown to require damping and sufficiently high launching speed. Further, vertical equilibrium is achieved only for bodies with “hips” or a critical slope of the surface, while stability requires an hourglass shape with a “waist” and whose curvature exceeds a critical value. Analysis of the model reveals dimensionless factors that successfully organize and unify observations across a wide range of geometries and kinematics. By revealing and explaining the mechanics of hula hoop levitation, these results motivate strategies for motion control via geometry-dependent contact forces and for accurately predicting the resulting equilibria and their stability.

Evaluating quality of life improvements in endometriosis patients following laparoscopic surgery using EHP-30 scale

Across the firewall: Foreign media’s role in shaping Chinese social media narratives on the Russo-Ukrainian War

There is a widespread perception that China’s digital censorship distances its people from the global internet, and the Chinese Communist Party, through state-controlled media, is the main gatekeeper of information about foreign affairs. Our analysis of narratives about the Russo-Ukrainian War circulating on the Chinese social media platform Weibo challenges this view. Comparing narratives on Weibo with 8.26 million unique news articles from 2,500 of some of the most trafficked websites in China, Russia, Ukraine, and the United States (totaling 10,000 sites), we find that Russian news websites published more articles matching narratives found on Weibo than news websites from China, Ukraine, or the United States. Similarly, a plurality of Weibo narratives were most associated with narratives found on Russian news websites while less than ten percent were most associated with narratives from Chinese news sites. Narratives later appearing on Weibo were more likely to first appear on Russian rather than Chinese, Ukrainian, or US news websites, and Russian websites were highly influential for narratives appearing on Weibo. Altogether, these results show that Chinese state media was not the main gatekeeper of information about Russia’s invasion of Ukraine for Weibo users.

Age estimation using dental and hand-wrist radiography among a sample of Egyptian children

Abstract The current study aimed to evaluate the accuracy of Willems, Cameriere’s and Greulich and Pyle method in age estimation among a sample of Egyptian children aged 8–16 years based on analysis of 140 panoramic dental X-ray and hand-wrist radiographs (70 girls and 70 boys). Using Willems method, the mean dental age underestimated chronological age by (0.20 ± 0.91 years) for boys and by (0.24 ± 1.33 year) for girls; these differences were not statistically significant. Also, Cameriere’s method underestimated chronological age in both sexes by mean difference of (1.10 ± 1.22 year) in boys and (1.13 ± 1.31 year) in girls; these differences were statistically significant. Regarding Greulich and Pyle atlas, the mean of skeletal age was overestimated when compared to the real age in boys with a mean difference (0.04 ± 0.86 year). In girls; the age was underestimated by a mean difference of (0.15 ± 1.32 years) when compared to chronological age; these differences were not statistically significant. Comparing the two dental methods, the mean absolute error using Willems method was less than one year (0.94 and 0.96 years) in boys and girls respectively, while in Cameriere’s method, it was more than one year in both groups. Moreover; the mean absolute error using Greulich and Pyle atlas was less than two years (1.02 and 1.38 years) in boys and girls respectively. Since Willems and the atlas methods were more accurate, the combination of both of them could be used for age estimation in the Egyptian population.

Enhancing in search of Milankovitch cycles from stratigraphic record using convex optimization algorithm

AbstractAccurately identifying Milankovitch cycles has been a significant challenge in cyclostratigraphic studies, as it is essential for improving geochronology. This manuscript focuses on developing a method that distinguishes Milankovitch cycles from sedimentary noise to enhance stratigraphic precision. Despite their often-conspicuous magnitude, these periodicities frequently intertwine with noise, posing a challenge for conventional spectral analysis. Therefore, to address this issue, we have developed an algorithm that enhances the resolution of the Milankovitch signal by employing convex optimization in spectral analysis. To evaluate the effectiveness of this new algorithm, we applied it to four distinct types of local stratigraphy where the Milankovitch signal has been confirmed. These include the stratigraphic sections in the middle Miocene molluscan beds of Java and the Mahakam Delta, Pleistocene sediments of Hominin Flores, and the Towuti Lake in Sulawesi Island, Indonesia. Our findings demonstrate the preservation of all targeted signals, with a confidence level surpassing 99%. By setting the significance level to 1%, we can reject the null hypothesis, which assumes noise or the absence of a Milankovitch signal in the stratigraphic data being tested. The absence of deviations from the identified periodicities further strengthens the Milankovitch signal, underscoring the robustness of our algorithm. However, we acknowledge that achieving optimal results still hinges on the accurate selection of the initial parameters z and λ.

Oppositional and competitive instigation of hippocampal synaptic plasticity by the VTA and locus coeruleus

The novelty, saliency, and valency of ongoing experiences potently influence the firing rate of the ventral tegmental area (VTA) and the locus coeruleus (LC). Associative experience, in turn, is recorded into memory by means of hippocampal synaptic plasticity that is regulated by noradrenaline sourced from the LC, and dopamine, sourced from both the VTA and LC. Two persistent forms of synaptic plasticity, long-term potentiation (LTP), and long-term depression (LTD) support the encoding of different kinds of spatial experience. To what extent the VTA and the LC influence the direction of change of synaptic plasticity and therefore the content of stored experience is not clear. Here, we report that test-pulse activation of Schaffer-collateral–CA1 synapses of freely behaving male rats, in conjunction with VTA stimulation, results in LTP (&gt;24 h), whereas concomitant hippocampal afferent and LC stimulation results in LTD (&gt;24 h). Effects are frequency-dependent (1 to 50 Hz) and competitive: high-frequency (25 Hz), but not low-frequency (5 Hz) optogenetic activation of tyrosine hydroxylase-positive (TH+) neurons in the VTA, results in D1/D5R-dependent LTP, whereas 5 Hz (but not 1, or 25 Hz) activation of TH+ neurons in the LC results in hippocampal LTD that is both D1/D5 and β-AR-dependent. These results suggest that the VTA and LC do not work in synergy, but rather function in a competing fashion to drive different forms of information encoding through synaptic plasticity. Our findings indicate that information transmitted by the VTA and LC is likely to play a decisive role in the shaping of hippocampal information storage and the nature of learned experience.

Association of Body Mass Index trajectory with thyroid nodules during young adulthood in China

Electron transfer in polysaccharide monooxygenase catalysis

Polysaccharide monooxygenase (PMO) catalysis involves the chemically difficult hydroxylation of unactivated C–H bonds in carbohydrates. The reaction requires reducing equivalents and will utilize either oxygen or hydrogen peroxide as a cosubstrate. Two key mechanistic questions are addressed here: 1) How does the enzyme regulate the timely and tightly controlled electron delivery to the mononuclear copper active site, especially when bound substrate occludes the active site? and 2) How does this electron delivery differ when utilizing oxygen or hydrogen peroxide as a cosubstrate? Using a computational approach, potential paths of electron transfer (ET) to the active site copper ion were identified in a representative AA9 family PMO from Myceliophthora thermophila ( Mt PMO9E). When Y62, a buried residue 12 Å from the active site, is mutated to F, lower activity is observed with O 2 . However, a WT-level activity is observed with H 2 O 2 as a cosubstrate indicating an important role in ET for O 2 activation. To better understand the structural effects of mutations to Y62 and axial copper ligand Y168, crystal structures were solved of the wild type Mt PMO9E and the variants Y62W, Y62F, and Y168F. A bioinformatic analysis revealed that position 62 is conserved as either Y or W in the AA9 family. The Mt PMO9E Y62W variant has restored activity with O 2 . Overall, the use of redox-active residues to supply electrons for the reaction with O 2 appears to be widespread in the AA9 family. Furthermore, the results provide a molecular framework to understand catalysis with O 2 versus H 2 O 2 .