bluuebunny/crossref_metadata_2025 huggingface dataset:
Autophagy regulates the maturation of hematopoietic precursors in the embryo
Authors: Liu Yumin , Shi Linjuan , Chen Yifan , Luo Sifan , Chen Yuehang , Chen Hongtian , Lan Wenlang , Lu Xun , Cao Zhan , Ye Zehua , Li Jinping , Yu Bo , Dzierzak Elaine , Li Zhuan
Published: March 2024

An understanding of the mechanisms regulating embryonic hematopoietic stem cell (HSC) development would facilitate their regeneration. The aorta-gonad-mesonephros region is the site for HSC production from hemogenic endothelial cells (HEC). While several distinct regulators are involved in this process, it is not yet known whether macroautophagy (autophagy) plays a role in hematopoiesis in the pre-liver stage. Here, we show that different states of autophagy exist in hematopoietic precursors and correlate with hematopoietic potential based on the LC3-RFP-EGFP mouse model. Deficiency of autophagy-related gene 5 (Atg5) specifically in endothelial cells disrupts endothelial to hematopoietic transition (EHT), by blocking the autophagic process. Using combined approaches, including single-cell RNA-sequencing (scRNA-seq), we have confirmed that Atg5 deletion interrupts developmental temporal order of EHT to further affect the pre-HSC I maturation, and that autophagy influences hemogenic potential of HEC and the formation of pre-HSC I likely via the nucleolin pathway. These findings demonstrate a role for autophagy in the formation/maturation of hematopoietic precursors.
Triboelectric micro-flexure-sensitive fiber electronics
Authors: Lin Shaomei , Yang Weifeng , Zhu Xubin , Lan Yubin , Li Kerui , Zhang Qinghong , Li Yaogang , Hou Chengyi , Wang Hongzhi
Published: March 2024

Developing fiber electronics presents a practical approach for establishing multi-node distributed networks within the human body, particularly concerning triboelectric fibers. However, realizing fiber electronics for monitoring micro-physiological activities remains challenging due to the intrinsic variability and subtle amplitude of physiological signals, which differ among individuals and scenarios. Here, we propose a technical approach based on a dynamic stability model of sheath-core fibers, integrating a micro-flexure-sensitive fiber enabled by nanofiber buckling and an ion conduction mechanism. This scheme enhances the accuracy of the signal transmission process, resulting in improved sensitivity (detectable signal at ultra-low curvature of 0.1 mm−1; flexure factor >21.8% within a bending range of 10°.) and robustness of fiber under micro flexure. In addition, we also developed a scalable manufacturing process and ensured compatibility with modern weaving techniques. By combining precise micro-curvature detection, micro-flexure-sensitive fibers unlock their full potential for various subtle physiological diagnoses, particularly in monitoring fiber upper limb muscle strength for rehabilitation and training.
Biosynthesis of the highly oxygenated tetracyclic core skeleton of Taxol
Authors: Yang Chengshuai , Wang Yan , Su Zhen , Xiong Lunyi , Wang Pingping , Lei Wen , Yan Xing , Ma Dawei , Zhao Guoping , Zhou Zhihua
Published: March 2024

Taxol is a widely-applied anticancer drug that inhibits microtubule dynamics in actively replicating cells. Although a minimum 19-step biosynthetic pathway has been proposed and 16 enzymes likely involved have been characterized, stepwise biosynthetic reactions from the well-characterized di-oxygenated taxoids to Taxol tetracyclic core skeleton are yet to be elucidated. Here, we uncover the biosynthetic pathways for a few tri-oxygenated taxoids via confirming the critical reaction order of the second and third hydroxylation steps, unearth a taxoid 9α-hydroxylase catalyzing the fourth hydroxylation, and identify CYP725A55 catalyzing the oxetane ester formation via a cascade oxidation-concerted acyl rearrangement mechanism. After identifying a acetyltransferase catalyzing the formation of C7-OAc, the pathway producing the highly-oxygenated 1β-dehydroxybaccatin VI with the Taxol tetracyclic core skeleton is elucidated and its complete biosynthesis from taxa-4(20),11(12)-diene-5α-ol is achieved in an engineered yeast. These systematic studies lay the foundation for the complete elucidation of the biosynthetic pathway of Taxol.
Local prediction-learning in high-dimensional spaces enables neural networks to plan
Authors: Stöckl Christoph , Yang Yukun , Maass Wolfgang
Published: March 2024

Planning and problem solving are cornerstones of higher brain function. But we do not know how the brain does that. We show that learning of a suitable cognitive map of the problem space suffices. Furthermore, this can be reduced to learning to predict the next observation through local synaptic plasticity. Importantly, the resulting cognitive map encodes relations between actions and observations, and its emergent high-dimensional geometry provides a sense of direction for reaching distant goals. This quasi-Euclidean sense of direction provides a simple heuristic for online planning that works almost as well as the best offline planning algorithms from AI. If the problem space is a physical space, this method automatically extracts structural regularities from the sequence of observations that it receives so that it can generalize to unseen parts. This speeds up learning of navigation in 2D mazes and the locomotion with complex actuator systems, such as legged bodies. The cognitive map learner that we propose does not require a teacher, similar to self-attention networks (Transformers). But in contrast to Transformers, it does not require backpropagation of errors or very large datasets for learning. Hence it provides a blue-print for future energy-efficient neuromorphic hardware that acquires advanced cognitive capabilities through autonomous on-chip learning.
Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis
Authors: Ghashghaei Maryam , Liu Yilin , Ettles James , Bombaci Giuseppe , Ramkumar Niveditha , Liu Zongmin , Escano Leo , Miko Sandra Spencer , Kim Yerin , Waldron Joseph A. , Do Kim , MacPherson Kyle , Yuen Katie A. , Taibi Thilelli , Yue Marty , Arsalan Aaremish , Jin Zhen , Edin Glenn , Karsan Aly , Morin Gregg B. , Kuchenbauer Florian , Perna Fabiana , Bushell Martin , Vu Ly P.
Published: March 2024

Protein synthesis is frequently deregulated during tumorigenesis. However, the precise contexts of selective translational control and the regulators of such mechanisms in cancer is poorly understood. Here, we uncovered CNOT3, a subunit of the CCR4-NOT complex, as an essential modulator of translation in myeloid leukemia. Elevated CNOT3 expression correlates with unfavorable outcomes in patients with acute myeloid leukemia (AML). CNOT3 depletion induces differentiation and apoptosis and delayed leukemogenesis. Transcriptomic and proteomic profiling uncovers c-MYC as a critical downstream target which is translationally regulated by CNOT3. Global analysis of mRNA features demonstrates that CNOT3 selectively influences expression of target genes in a codon usage dependent manner. Furthermore, CNOT3 associates with the protein network largely consisting of ribosomal proteins and translation elongation factors in leukemia cells. Overall, our work elicits the direct requirement for translation efficiency in tumorigenesis and propose targeting the post-transcriptional circuitry via CNOT3 as a therapeutic vulnerability in AML.
Mechanistic insight into the competition between interfacial and bulk reactions in microdroplets through N2O5 ammonolysis and hydrolysis
Authors: Fang Ye-Guang , Tang Bo , Yuan Chang , Wan Zhengyi , Zhao Lei , Zhu Shuang , Francisco Joseph S. , Zhu Chongqin , Fang Wei-Hai
Published: March 2024

Reactive uptake of dinitrogen pentaoxide (N2O5) into aqueous aerosols is a major loss channel for NOx in the troposphere; however, a quantitative understanding of the uptake mechanism is lacking. Herein, a computational chemistry strategy is developed employing high-level quantum chemical methods; the method offers detailed molecular insight into the hydrolysis and ammonolysis mechanisms of N2O5 in microdroplets. Specifically, our calculations estimate the bulk and interfacial hydrolysis rates to be (2.3 ± 1.6) × 10−3 and (6.3 ± 4.2) × 10−7 ns−1, respectively, and ammonolysis competes with hydrolysis at NH3 concentrations above 1.9 × 10−4 mol L−1. The slow interfacial hydrolysis rate suggests that interfacial processes have negligible effect on the hydrolysis of N2O5 in liquid water. In contrast, N2O5 ammonolysis in liquid water is dominated by interfacial processes due to the high interfacial ammonolysis rate. Our findings and strategy are applicable to high-chemical complexity microdroplets.
Quantum symmetrization transition in superconducting sulfur hydride from quantum Monte Carlo and path integral molecular dynamics
Authors: Taureau Romain , Cherubini Marco , Morresi Tommaso , Casula Michele
Published: March 2024

We study the structural phase transition, originally associated with the highest superconducting critical temperature Tc measured in high-pressure sulfur hydride. A quantitative description of its pressure dependence has been elusive for any ab initio theory attempted so far, raising questions on the actual mechanism leading to the maximum of Tc. Here, we estimate the critical pressure of the hydrogen bond symmetrization in the Im$$\bar{3}$$

3

¯

m structure, by combining density functional theory and quantum Monte Carlo simulations for electrons with path integral molecular dynamics for quantum nuclei. We find that the Tc maximum corresponds to pressures where local dipole moments dynamically form on the hydrogen sites, as precursors of the ferroelectric Im$$\bar{3}$$

3

¯

m-R3m transition, happening at lower pressures. For comparison, we also apply the self-consistent harmonic approximation, whose ferroelectric critical pressure lies in between the ferroelectric transition estimated by path integral molecular dynamics and the local dipole formation. Nuclear quantum effects play a major role in a significant reduction (≈50 GPa) of the classical ferroelectric transition pressure at 200 K and in a large isotope shift (≈25 GPa) upon hydrogen-to-deuterium substitution of the local dipole formation pressure, in agreement with the corresponding change in the Tc maximum location.
Smoking affects symptom improvement in schizophrenia: a prospective longitudinal study of male patients with first-episode schizophrenia
Authors: Mu Xishu , Wu Wenjing , Wang Sisi , Su Xiuru , Guan Hengyong , Guan Xiaoni , Lu Xiaobing , Li Zezhi
Published: March 2024

Patients with schizophrenia (SCZ) smoke up to three times more than general people. However, there are conflicting results regarding the relationship between tobacco smoke and clinical symptom severity in SCZ. The aim of this study was to assess the impact of smoking on clinical symptoms after antipsychotic treatment in a 12-week cohort study after controlling for confounding factors. One hundred and forty-five male patients with drug-naïve first-episode (DNFE) SCZ received antipsychotic monotherapy for 12 weeks. Symptom severity was assessed at baseline and at week 12 by the Positive and Negative Syndrome Scale (PANSS). We found no differences in clinical symptoms among male smokers with SCZ compared with male nonsmokers. However, male smokers showed greater improvement in negative symptoms after 12 weeks of treatment, controlling for age, years of education, onset age, and baseline body mass index (BMI). Our study showed that after 12 weeks of treatment with antipsychotics, male smokers showed greater improvement in negative symptoms than male nonsmokers.
Math items about real-world content lower test-scores of students from families with low socioeconomic status
Authors: Muskens Marjolein , Frankenhuis Willem E. , Borghans Lex
Published: March 2024

In many countries, standardized math tests are important for achieving academic success. Here, we examine whether content of items, the story that explains a mathematical question, biases performance of low-SES students. In a large-scale cohort study of Trends in International Mathematics and Science Studies (TIMSS)—including data from 58 countries from students in grades 4 and 8 (N = 5501,165)—we examine whether item content that is more likely related to challenges for low-SES students (money, food, social relationships) improves their performance, compared with their average math performance. Results show that low-SES students scored lower on items with this specific content than expected based on an individual’s average performance. The effect sizes are substantial: on average, the chance to answer correctly is 18% lower. From a hidden talents approach, these results are unexpected. However, they align with other theoretical frameworks such as scarcity mindset, providing new insights for fair testing.
High quality assemblies of four indigenous chicken genomes and related functional data resources
Authors: Wu Siwen , Wang Kun , Dou Tengfei , Yuan Sisi , Yan Shixiong , Xu Zhiqiang , Liu Yong , Jian Zonghui , Zhao Jingying , Zhao Rouhan , Zi Xiannian , Gu Dahai , Liu Lixian , Li Qihua , Wu Dong-Dong , Jia Junjing , Su Zhengchang , Ge Changrong
Published: March 2024

Many lines of evidence indicate that red jungle fowl (RJF) is the primary ancestor of domestic chickens. Although multiple versions of RJF (galgal2-galgal5 and GRCg6a) and commercial chickens (GRCg7b/w and Huxu) genomes have been assembled since 2004, no high-quality indigenous chicken genomes have been assembled, hampering the understanding of chicken domestication and evolution. To fill the gap, we sequenced the genomes of four indigenous chickens with distinct morphological traits in southwest China, using a combination of short, long and Hi-C reads. We assembled each genome (~1.0 Gb) into 42 chromosomes with chromosome N50 90.5–90.9 Mb, amongst the highest quality of chicken genome assemblies. To provide resources for gene annotation and functional analysis, we also sequenced transcriptomes of 10 tissues for each of the four chickens. Moreover, we corrected many mis-assemblies and assembled missing micro-chromosomes 29 and 34–39 for GRCg6a. Our assemblies, sequencing data and the correction of GRCg6a can be valuable resources for studying chicken domestication and evolution.
Computational identification of natural senotherapeutic compounds that mimic dasatinib based on gene expression data
Authors: Meiners Franziska , Hinz Burkhard , Boeckmann Lars , Secci Riccardo , Sueto Salem , Kuepfer Lars , Fuellen Georg , Barrantes Israel
Published: March 2024

The major risk factor for chronic disease is chronological age, and age-related chronic diseases account for the majority of deaths worldwide. Targeting senescent cells that accumulate in disease-related tissues presents a strategy to reduce disease burden and to increase healthspan. The senolytic combination of the tyrosine-kinase inhibitor dasatinib and the flavonol quercetin is frequently used in clinical trials aiming to eliminate senescent cells. Here, our goal was to computationally identify natural senotherapeutic repurposing candidates that may substitute dasatinib based on their similarity in gene expression effects. The natural senolytic piperlongumine (a compound found in long pepper), and the natural senomorphics parthenolide, phloretin and curcumin (found in various edible plants) were identified as potential substitutes of dasatinib. The gene expression changes underlying the repositioning highlight apoptosis-related genes and pathways. The four compounds, and in particular the top-runner piperlongumine, may be combined with quercetin to obtain natural formulas emulating the dasatinib + quercetin formula.
Bionanofactory for green synthesis of collagen nanoparticles, characterization, optimization, in-vitro and in-vivo anticancer activities
Authors: El-Sawah Asmaa A. , El-Naggar Noura El-Ahmady , Eldegla Heba E. , Soliman Hoda M.
Published: March 2024

Collagen nanoparticles (collagen-NPs) are promising biological polymer nanoparticles due to their exceptional biodegradability and biocompatibility. Collagen-NPs were bio-fabricated from pure marine collagen using the cell-free supernatant of a newly isolated strain, Streptomyces sp. strain NEAA-3. Streptomyces sp. strain NEAA-3 was identified as Streptomyces plicatus strain NEAA-3 based on its cultural, morphological, physiological properties and 16S rRNA sequence analysis. The sequence data has been deposited under accession number OR501412.1 in the GenBank database. The face-centered central composite design (FCCD) was used to improve collagen-NPs biosynthesis. The maximum yield of collagen-NPs was 9.33 mg/mL with a collagen concentration of 10 mg/mL, an initial pH of 7, an incubation time of 72 h, and a temperature of 35 °C. Using the desirability function approach, the collagen-NPs biosynthesis obtained after FCCD optimization (9.53 mg/mL) was 3.92 times more than the collagen-NPs biosynthesis obtained before optimization process (2.43 mg/mL). The TEM analysis of collagen-NPs revealed hollow sphere nanoscale particles with an average diameter of 33.15 ± 10.02 nm. FTIR spectra confirmed the functional groups of the collagen, collagen-NPs and the cell-free supernatant that are essential for the efficient capping of collagen-NPs. The biosynthesized collagen-NPs exhibited antioxidant activity and anticancer activity against HeP-G2, MCF-7 and HCT116 cell lines. Collagen-NPs assessed as an effective drug loading carrier with methotrexate (MTX), a chemotherapeutic agent. The TEM analysis revealed that the average size of MTX-loaded collagen-NPs was 35.4 ± 8.9 nm. The percentages of drug loading (DL%) and encapsulation efficiency (EE%) were respectively 22.67 and 45.81%.
Potential of Pinus eldarica Medw. tree bark for biomonitoring polycyclic aromatic hydrocarbons in ambient air
Authors: Hasheminejad Sohrab , Moradi Hossein , Soleimani Mohsen
Published: March 2024

Urban trees' biomonitoring of pollutants such as polycyclic aromatic hydrocarbons (PAHs) yields pertinent and useful data for air pollution management. The aim of this study was to biomonitor PAHs in pine (Pinus eldarica Medw.) trees in the city of Isfahan and identify their sources. In total, 34 samples of outer bark of the trees were collected and their contents of 16 EPA PAHs were analyzed. With a median value of 136.3 ng/g, the total PAH contents in tree barks varied from 53.4 to 705.2 ng/g. The average values of the diagnostic ratios for Ant/(Ant + Phe), Flu/(Flu + Py), BaA/(BaA + Chr) and IP/(IP + BP) were 0.19, 0.49, 0.45 and 0.49, respectively, revealing the PAHs majority source of pyrogenic. Meanwhile, principal component analysis showed two major types of PAHs sources including pyrogenic (fossil fuel combustion and industrial activities) and petrogenic (uncombusted) sources. The average ratio An/(An + Phe) and Flu/(Flu + Py) in bark samples was close to their relevant ratios in ambient air which demonstrated the potential use of this approach for biomonitoring of PAHs.
Plant–plant communication in Camellia japonica and C. rusticana via volatiles
Authors: Sakurai Yusuke , Ishizaki Satomi
Published: March 2024

Plants emit volatile compounds when they are subjected to herbivorous, pathogenic, or artificial damages. Both the damaged plant and the neighboring intact plants induce resistance when they receive these volatiles, a phenomenon known as plant–plant communication. However, field observations of this phenomenon are limited. To understand the nature of plant–plant communication, we collected information about intra- and inter-plant signaling via volatiles in Camellia japonica and C. rusticana under natural conditions. We exposed intact branches of damaged plant (intra-plant) or neighboring plant (inter-plant) to artificially damaged plant volatiles (ADPVs). Leaf damage reduced in ADPVs-exposed branches in the neighboring plants compared to branches that were exposed to volatiles from intact leaves, thus, indicating that inter-plant signaling occur by the emission of volatiles from damaged leaves. We also conducted an air-transfer experiment wherein the headspace air of the damaged branch was transferred to the headspace of intact branches. Leaf damage reduced on the ADPVs-transferred branch compared to the control branch. The effect of volatiles on damage reduction lasted for three months. Our results indicate that ADPVs in Camellia species contain cues that induce resistance in neighboring plants. Our findings improve understanding of plant defense strategies that may be used in horticulture and agriculture.
Multitemporal analysis of land subsidence induced by open-pit mining activity using improved combined scatterer interferometry with deep learning algorithm optimization
Authors: Fadhillah Muhammad Fulki , Hakim Wahyu Luqmanul , Lee Seul-ki , Lee Kwang-Jae , Lee Seung-Jae , Chae Sung-Ho , Lee Hoonyol , Lee Chang-Wook
Published: March 2024

Mine operational safety is an important aspect of maintaining the operational continuity of a mining area. In this study, we used the InSAR time series to analyze land surface changes using the ICOPS (improved combined scatterers with optimized point scatters) method. This ICOPS method combines persistent scatterers (PS) with distributed scatterers (DS) to increase surface deformation analysis’s spatial coverage and quality. One of the improvements of this study is the use of machine learning in postprocessing, based on convolutional neural networks, to increase the reliability of results. This study used data from the Sentinel-1 SAR C-band satellite during the 2016–2022 observation period at the Musan mine, North Korea. In the InSAR surface deformation time analysis, the maximum average rate of land subsidence was approximately > 15.00 cm per year, with total surface deformation of 170 cm and 70 cm for the eastern dumping area and the western dumping area, respectively. Analyzing the mechanism of land surface changes also involved evaluating the geological conditions in the Musan mining area. Our research findings show that combining machine learning and statistical methods has great potential to enhance the understanding of mine surface deformation.
Assessment of voltage harmonics’ impact on the maximum load capacity of the power supply transformer for the LHCD system
Authors: Chen Hui , Wang Junjia , Hu Hejun , Huang Yiyun
Published: March 2024

To study the influence of the voltage total harmonic distortion (THDV) and its spectrum on the harmonic loss factor (FHL) and the maximum allowable load capacity ratio (Imax(pu)) for the transformer of the LHCD system, we use MATLAB software to model the LHCD system and study the winding loss and maximum allowed load capacity of the LHCD system transformer when the supply voltage source is sinusoidal and non-sinusoidal, respectively. The calculation is carried out by the method of IEEE standard C57.110 and the method of considering the skin effect. The calculation results of both methods clearly show that the THDV value of the supply voltage has a significant effect on the harmonic dissipation factor (FHL) and the maximum allowable load capacity ratio (Imax(pu)) of the transformer. And the calculation method considering the skin effect increases the maximum allowable load capacity ratio of the LHCD system transformer by about 2%. The research results have important reference value for the future retrofit design of LHCD system transformers.
Laser-induced changes in the gene expression, growth and development of Gladiolus grandiflorus cv. “White Prosperity”
Authors: Hassan Manar , Shaaban Shimaa A. , El Ziat Rasha A. , Khaled Khaled A.
Published: March 2024

Corms of Gladiolus grandiflorus cv. “White Prosperity” was irradiated via red laser at wavelength 635 nm. Various morphological, flowering, elemental and chemical characterizations were studied. Irradiation with different power (5, 20, and 50 mW) and various irradiation time (0.0, 0.5, 1, 3, 5 and 10 min) was studied. Several characters), totaletermined include vegetative growth parameter (spouting days, plant height (cm), leaves number, leaves fresh and dry weights (g/plant), diameter of plant middle part (mm) and leaf area (cm2), floral parameters (flowering days, vase life (day), fresh and dry weights of inflorescence (g/plant), number of flowers per inflorescence, inflorescence length(cm), flowers diameter(cm), number of corms per plant, corms fresh weight(g/plant), circumference/ corms), pigments [total chlorophylls in leaves (SPAD), anthocyanin content (mg/100 g F.W.) in petals], NPK (%) in new corms and chemical composition in corms; total carbohydrates (%),total phenol (μg CE/g (%),total flavonoid (μg CE/g) (%), antioxidant (DPPH IC50 (μg /ml (%), and proline content (μ moles/g). The results showed that the medium level (20 mW) of He–Ne laser at 5 min caused favorable changes in the leaf anatomical structures and other studied characters followed by the low level (5 mW) of He–Ne laser at 5min. 112 bands emerged from 22 SSR primers, ranging between 130 and 540 bp, with 32 bands having polymorphism ranging from 17–100%. Out of the 22 SSR primers, 3 primers exhibited a high polymorphism percentage, i.e., SSR6, SSR16 and SSR22 which exhibited 7 positive markers. These findings revealed the efficiency of SSR primers for differentiating gladiolus plants and revealed that some alleles were affected by laser in their corms and the expression resulted in color or abnormalities in leaves and/or flowers. Mutation in some alleles could result in abnormalities like mutation in the allele with 410 bp revealed by SSR16.
Risk control of heavy metal in waste incinerator ash by available solidification scenarios in cement production based on waste flow analysis
Authors: Valizadeh Behzad , Abdoli Mohammad Ali , Dobaradaran Sina , Mahmoudkhani Rouhalla , Asl Yousef Abdossalami
Published: March 2024

Incineration is a common method in municipal solid waste management, which has several advantages such as reducing the volume of waste, but with concerns about exhaust gas and ash management. In this study, heavy metals in bottom ash, secondary furnace ash and fly ash of two waste incinerators in Tehran and Nowshahr were analyzed and its control in cement production was investigated. For this purpose, twelve monthly samples of three types of incinerator ash were analyzed. By combining the studied ashes in the raw materials, the quantity of metals in the cement was analyzed. Finally, by investigating four scenarios based on quantitative variations in the routes of municipal solid waste, ash quantity and the related risk caused by its heavy metals were studied. The results showed that the concentration of heavy metals in the three ash samples of the studied incinerators was 19,513–23,972 µg/g and the composition of the metals included Hg (less than 0.01%), Pb (2.93%), Cd (0.59%), Cu (21.51%), Zn (58.7%), As (less than 0.01%), Cr (15.88%), and Ni (0.91%). The best quality of produced cement included 20% ash and 10% zeolite, which was the basis of the next calculations. It was estimated that the reduction of the release of metals into the environment includes 37 gr/day in best scenario equal to 10.6 tons/year. Ash solidification can be considered as a complementary solution in waste incinerator management.
Absolute and non-invasive determination of the electron bunch length in a free electron laser using a bunch compressor monitor
Authors: Orlandi Gian Luca
Published: March 2024

In a linac driven Free Electron Laser (FEL), the shot-to-shot and non-invasive monitoring of the electron bunch length is normally ensured by Bunch Compressor Monitors (BCMs). The bunch-length dependent signal of a BCM results from the detection and integration—over a given frequency band—of the temporal coherent enhancement of the radiation spectral energy emitted by the electron beam while experiencing a longitudinal compression. In this work, we present a method that permits to express the relative variation of the bunch length as a function of the relative statistical fluctuations of the BCM and charge signals. Furthermore, in the case of a BCM equipped with two detectors simultaneously operating in two distinct wavelength bands, the method permits an absolute determination of the electron bunch length. The proposed method is beneficial to a FEL. Thanks to it, the machine compression feedback can be tuned against the absolute measurement of the bunch length rather than a bunch-length dependent signal. In a CW-superconducting-linac driven FEL, it can offer the precious opportunity to implement a fully non-invasive and absolute diagnostics of the bunch length.
Gamma power and beta envelope correlation are potential neural predictors of deep hypnosis
Authors: Farahzadi Yeganeh , Alldredge Cameron , Kekecs Zoltán
Published: March 2024

Hypnosis is a psychological intervention that is commonly used to enhance the effectiveness of therapeutic suggestions. Despite extensive fascination and study, the neural mechanisms behind hypnosis remain elusive. In the current study, we undertook a systematic exploration of these neural correlates. We first extracted well-studied neurophysiological features from EEG sensors and source-localized data using spectral analysis and two measures of functional connectivity: weighted phase lag index (wPLI) and power envelope correlation (PEC). Next, we developed classification models that predicted self-rated hypnotic experience based on the extracted feature sets. Our findings reveal that gamma power computed on sensor-level data and beta PEC computed between source-localized brain networks are the top predictors of hypnosis depth. Further, a SHapley Additive exPlanations (SHAP) analysis suggested reduced gamma power in the midline frontal area and increased beta PEC between interhemispheric Dorsal Attention Networks (DAN) contribute to the hypnotic experience. These results broaden our understanding of the neural correlates of deep hypnosis, highlighting potential targets for future research. Moreover, this study demonstrates the potential of using predictive models in understanding the neural underpinnings of self-reported hypnotic depth, offering a template for future investigations.
Contribution of intramacrophage stages to Pseudomonas aeruginosa infection outcome in zebrafish embryos: insights from mgtC and oprF mutants
Authors: Hajjar Hélène , Berry Laurence , Wu Yongzheng , Touqui Lhousseine , Vergunst Annette C. , Blanc-Potard Anne-Béatrice
Published: March 2024

Pseudomonas aeruginosa often colonizes immunocompromised patients, causing acute and chronic infections. This bacterium can reside transiently inside cultured macrophages, but the contribution of the intramacrophic stage during infection remains unclear. MgtC and OprF have been identified as important bacterial factors when P. aeruginosa resides inside cultured macrophages. In this study, we showed that P. aeruginosa mgtC and oprF mutants, particular the latter one, had attenuated virulence in both mouse and zebrafish animal models of acute infection. To further investigate P. aeruginosa pathogenesis in zebrafish at a stage different from acute infection, we monitored bacterial load and visualized fluorescent bacteria in live larvae up to 4 days after infection. Whereas the attenuated phenotype of the oprF mutant was associated with a rapid elimination of bacteria, the mgtC mutant was able to persist at low level, a feature also observed with the wild-type strain in surviving larvae. Interestingly, these persistent bacteria can be visualized in macrophages of zebrafish. In a short-time infection model using a macrophage cell line, electron microscopy revealed that internalized P. aeruginosa wild-type bacteria were either released after macrophage lysis or remained intracellularly, where they were localized in vacuoles or in the cytoplasm. The mgtC mutant could also be detected inside macrophages, but without causing cell damage, whereas the oprF mutant was almost completely eliminated after phagocytosis, or localized in phagolysosomes. Taken together, our results show that the main role of OprF for intramacrophage survival impacts both acute and persistent infection by this bacterium. On the other hand, MgtC plays a clear role in acute infection but is not essential for bacterial persistence, in relation with the finding that the mgtC mutant is not completely eliminated by macrophages.
Development of extended pharmacokinetic models for propofol based on measured blood and brain concentrations
Authors: Kawata Masayoshi , Yonezawa Atsushi , Mineharu Yohei , Itohara Kotaro , Mizota Toshiyuki , Matsui Yoshihiro , Kikuchi Takayuki , Yamao Yukihiro , Hattori Etsuko Yamamoto , Hamada Miho , Hira Daiki , Furukawa Keiko , Miyamoto Susumu , Terada Tomohiro , Matsubara Kazuo , Arakawa Yoshiki
Published: March 2024

Propofol’s pharmacokinetics have been extensively studied using human blood samples and applied to target-controlled infusion systems; however, information on its concentration in the brain remains scarce. Therefore, this study aimed to simultaneously measure propofol plasma and brain concentrations in patients who underwent awake craniotomy and establish new pharmacokinetic model. Fifty-seven patients with brain tumors or brain lesions who underwent awake craniotomy were sequentially assigned to model-building and validating groups. Plasma and brain (lobectomy or uncapping margins) samples were collected at five time-points. The concentration of propofol was measured using high-performance liquid chromatography. Population pharmacokinetic analysis was conducted through a nonlinear mixed-effects modeling program using a first-order conditional estimation method with interactions. Propofol’s brain concentrations were higher than its plasma concentrations. The measured brain concentrations were higher than the effect site concentrations using the previous models. Extended models were constructed based on measured concentrations by incorporating the brain/plasma partition coefficient (Kp value). Extended models showed good predictive accuracy for brain concentrations in the validating group. The Kp value functioned as a factor explaining retention in the brain. Our new pharmacokinetic models and Kp value can predict propofol’s brain and plasma concentrations, contributing to safer and more stable anesthesia.
Metagenomic insights into the wastewater resistome before and after purification at large‑scale wastewater treatment plants in the Moscow city
Authors: Begmatov Shahjahon , Beletsky Alexey V. , Dorofeev Alexander G. , Pimenov Nikolai V. , Mardanov Andrey V. , Ravin Nikolai V.
Published: March 2024

Wastewater treatment plants (WWTPs) are considered to be hotspots for the spread of antibiotic resistance genes (ARGs). We performed a metagenomic analysis of the raw wastewater, activated sludge and treated wastewater from two large WWTPs responsible for the treatment of urban wastewater in Moscow, Russia. In untreated wastewater, several hundred ARGs that could confer resistance to most commonly used classes of antibiotics were found. WWTPs employed a nitrification/denitrification or an anaerobic/anoxic/oxic process and enabled efficient removal of organic matter, nitrogen and phosphorus, as well as fecal microbiota. The resistome constituted about 0.05% of the whole metagenome, and after water treatment its share decreased by 3–4 times. The resistomes were dominated by ARGs encoding resistance to beta-lactams, macrolides, aminoglycosides, tetracyclines, quaternary ammonium compounds, and sulfonamides. ARGs for macrolides and tetracyclines were removed more efficiently than beta-lactamases, especially ampC, the most abundant ARG in the treated effluent. The removal efficiency of particular ARGs was impacted by the treatment technology. Metagenome-assembled genomes of multidrug-resistant strains were assembled both for the influent and the treated effluent. Ccomparison of resistomes from WWTPs in Moscow and around the world suggested that the abundance and content of ARGs depend on social, economic, medical, and environmental factors.
Identification of ALYREF in pan cancer as a novel cancer prognostic biomarker and potential regulatory mechanism in gastric cancer
Authors: Yuan Yujie , Fan Yiyang , Tang Wenqing , Sun Hui , Sun Jinghan , Su Hongmeng , Fan Hong
Published: March 2024

ALYREF is considered as a specific mRNA m5C-binding protein which recognizes m5C sites in RNA and facilitates the export of RNA from the nucleus to the cytoplasm. Expressed in various tissues and highly involved in the transcriptional regulation, ALYREF has the potential to become a novel diagnostic marker and therapeutic target for cancer patients. However, few studies focused on its function during carcinogenesis and progress. In order to explore the role of ALYREF on tumorigenesis, TCGA and GTEx databases were used to investigate the relationship of ALYREF to pan-cancer. We found that ALYREF was highly expressed in majority of cancer types and that elevated expression level was positively associated with poor prognosis in many cancers. GO and KEGG analysis showed that ALYREF to be essential in regulating the cell cycle and gene mismatch repair in tumor progression. The correlation analysis of tumor heterogeneity indicated that ALYREF could be specially correlated to the tumor stemness in stomach adenocarcinoma (STAD). Furthermore, we investigate the potential function of ALYREF on gastric carcinogenesis. Prognostic analysis of different molecular subtypes of gastric cancer (GC) unfolded that high ALYREF expression leads to poor prognosis in certain subtypes of GC. Finally, enrichment analysis revealed that ALYREF-related genes possess the function of regulating cell cycle and apoptosis that cause further influences in GC tumor progression. For further verification, we knocked down the expression of ALYREF by siRNA in GC cell line AGS. Knockdown of ALYREF distinctly contributed to inhibition of GC cell proliferation. Moreover, it is observed that knocked-down of ALYREF induced AGS cells arrested in G1 phase and increased cell apoptosis. Our findings highlighted the essential function of ALYREF in tumorigenesis and revealed the specific contribution of ALYREF to gastric carcinogenesis through pan-cancer analysis and biological experiments.
Efficacy and safety of durable versus biodegradable polymer drug-eluting stents in patients with acute myocardial infarction complicated by cardiogenic shock
Authors: Jang Woo Jin , Park Ik Hyun , Oh Ju Hyeon , Choi Ki Hong , Song Young Bin , Hahn Joo-Yong , Choi Seung-Hyuk , Gwon Hyeon-Cheol , Ahn Chul-Min , Yu Cheol Woong , Kim Hyun-Joong , Bae Jang-Whan , Kwon Sung Uk , Lee Hyun Jong , Lee Wang Soo , Jeong Jin-Ok , Park Sang-Don , Yang Jeong Hoon
Published: March 2024

The clinical impact of different polymer technologies in newer-generation drug-eluting stents (DESs) for patients with acute myocardial infarction (AMI) complicated by cardiogenic shock (CS) remains poorly understood. We investigated the efficacy and safety of durable polymer DESs (DP-DESs) compared with biodegradable polymer DESs (BP-DESs). A total of 620 patients who underwent percutaneous coronary intervention with newer-generation DESs for AMI complicated by CS was divided into two groups based on polymer technology: the DP-DES group (n = 374) and the BP-DES group (n = 246). The primary outcome was target vessel failure (TVF) during a 12-month follow-up, defined as a composite of cardiac death, myocardial infarction, or target vessel revascularization. Both the DP-DES and BP-DES groups exhibited low stent thrombosis rates (1.3% vs. 1.6%, p = 0.660). The risk of TVF did not significantly differ between the two groups (34.2% vs. 28.5%, hazard ratio [HR] 0.94, 95% confidence interval [CI] 0.69–1.29, p = 0.721). This finding remained consistent after adjustment with inverse probability of treatment weighting (28.1% vs. 25.1%, HR 0.98, 95% CI 0.77–1.27, p = 0.899). In AMI patients complicated by CS, the risk of a composite of cardiac death, myocardial infarction, or target vessel revascularization was not significantly different between those treated with DP-DESs and those treated with BP-DESs.

Trial registration: RESCUE registry, https://clinicaltrials.gov/ct2/show/NCT02985008, NCT02985008.
Role of gut-derived bacterial lipopolysaccharide and peripheral TLR4 in immobilization stress-induced itch aggravation in a mouse model of atopic dermatitis
Authors: Cho Da-Eun , Hong Joon-Pyo , Kim Yoongeun , Sim Ju Yeon , Kim Heenam Stanley , Kim Song-rae , Lee Bombi , Cho Hyo-Sung , Cho Ik-Hyun , Shin Sooan , Yeom Mijung , Kwon Soon-Kyeong , Lee In-Seon , Park Hijoon , Kim Kyuseok , Hahm Dae-Hyun
Published: March 2024

Psychological stress and intestinal leakage are key factors in atopic dermatitis (AD) recurrence and exacerbation. Here, we demonstrate the mechanism underlying bacterial translocation across intestinal epithelial barrier damaged due to stress and further aggravation of trimellitic anhydride (TMA)–induced itch, which remain unclear, in AD mice. Immobilization (IMO) stress exacerbated scratching bouts and colon histological damage, and increased serum corticosterone and lipopolysaccharide (LPS). Orally administered fluorescein isothiocyanate (FITC)-dextran and surgically injected (into the colon) Cy5.5-conjugated LPS were detected in the serum and skin after IMO stress, respectively. The relative abundance of aerobic or facultative anaerobic bacteria was increased in the colon mucus layer, and Lactobacillus murinus, E. coli, Staphylococcus nepalensis, and several strains of Bacillus sp. were isolated from the spleens and mesenteric lymph nodes. Oral antibiotics or intestinal permeability blockers, such as lubiprostone (Lu), 2,4,6-triaminopyrimidine (TAP) and ML-7, inhibited IMO stress-associated itch; however, it was reinduced through intradermal or i.p. injection of LPS without IMO stress. I.p. injection of TAK-242 (resatorvid), a TLR4 inhibitor, abrogated IMO stress-associated itch, which was also confirmed in TLR4-KO mice. IMO stress alone did not cause itch in naïve mice. IMO stress-induced itch aggravation in TMA-treated AD mice might be attributed to the translocation of gut-derived bacterial cells and LPS, which activates peripheral TLR4 signaling.
Empowering coffee farming using counterfactual recommendation based RNN driven IoT integrated soil quality command system
Authors: Selvanarayanan Raveena , Rajendran Surendran , Algburi Sameer , Ibrahim Khalaf Osamah , Hamam Habib
Published: March 2024

Soil health is essential for whirling stale soil into rich coffee-growing land. By keeping healthy soil, coffee producers may improve plant growth, leaf health, buds, cherry and bean quality, and yield. Traditional soil monitoring is tedious, time-consuming, and error-prone. Enhancing the monitoring system using AI-based IoT technologies for quick and precise changes. Integrated soil fertility control system to optimize soil health, maximize efficiency, promote sustainability, and prevent crop threads using real-time data analysis to turn infertile land into fertile land. The RNN-IoT approach uses IoT sensors in the coffee plantation to collect real-time data on soil temperature, moisture, pH, nutrient levels, weather, CO2 levels, EC, TDS, and historical data. Data transmission using a wireless cloud platform. Testing and training using recurrent neural networks (RNNs) and gated recurrent units gathered data for predicting soil conditions and crop hazards. Researchers are carrying out detailed qualitative testing to evaluate the proposed RNN-IoT approach. Utilize counterfactual recommendations for developing alternative strategies for irrigation, fertilization, fertilizer regulation, and crop management, taking into account the existing soil conditions, forecasts, and historical data. The accuracy is evaluated by comparing it to other deep learning algorithms. The utilization of the RNN-IoT methodology for soil health monitoring enhances both efficiency and accuracy in comparison to conventional soil monitoring methods. Minimized the ecological impact by minimizing water and fertilizer utilization. Enhanced farmer decision-making and data accessibility with a mobile application that provides real-time data, AI-generated suggestions, and the ability to detect possible crop hazards for swift action.
Symbiotic efficiency of Rhizobium leguminosarum sv. trifolii strains originating from the subpolar and temperate climate regions
Authors: Janczarek Monika , Kozieł Marta , Adamczyk Paulina , Buczek Katarzyna , Kalita Michał , Gromada Anna , Mordzińska-Rak Aleksandra , Polakowski Cezary , Bieganowski Andrzej
Published: March 2024

Red clover (Trifolium pratense L.) is a forage legume cultivated worldwide. This plant is capable of establishing a nitrogen-fixing symbiosis with Rhizobium leguminosarum symbiovar trifolii strains. To date, no comparative analysis of the symbiotic properties and heterogeneity of T. pratense microsymbionts derived from two distinct geographic regions has been performed. In this study, the symbiotic properties of strains originating from the subpolar and temperate climate zones in a wide range of temperatures (10–25 °C) have been characterized. Our results indicate that all the studied T. pratense microsymbionts from two geographic regions were highly efficient in host plant nodulation and nitrogen fixation in a wide range of temperatures. However, some differences between the populations and between the strains within the individual population examined were observed. Based on the nodC and nifH sequences, the symbiotic diversity of the strains was estimated. In general, 13 alleles for nodC and for nifH were identified. Moreover, 21 and 61 polymorphic sites in the nodC and nifH sequences were found, respectively, indicating that the latter gene shows higher heterogeneity than the former one. Among the nodC and nifH alleles, three genotypes (I–III) were the most frequent, whereas the other alleles (IV–XIII) proved to be unique for the individual strains. Based on the nodC and nifH allele types, 20 nodC-nifH genotypes were identified. Among them, the most frequent were three genotypes marked as A (6 strains), B (5 strains), and C (3 strains). Type A was exclusively found in the temperate strains, whereas types B and C were identified in the subpolar strains. The remaining 17 genotypes were found in single strains. In conclusion, our data indicate that R. leguminosarum sv. trifolii strains derived from two climatic zones show a high diversity with respect to the symbiotic efficiency and heterogeneity. However, some of the R. leguminosarum sv. trifolii strains exhibit very good symbiotic potential in the wide range of the temperatures tested; hence, they may be used in the future for improvement of legume crop production.