bluuebunny/crossref_metadata_2025_split huggingface dataset:
Farrerol directly activates the deubiqutinase UCHL3 to promote DNA repair and reprogramming when mediated by somatic cell nuclear transfer
Authors: Zhang Weina , Wang Mingzhu , Song Zhiwei , Fu Qianzheng , Chen Jiayu , Zhang Weitao , Gao Shuai , Sun Xiaoxiang , Yang Guang , Zhang Qiang , Yang Jiaqing , Tang Huanyin , Wang Haiyan , Kou Xiaochen , Wang Hong , Mao Zhiyong , Xu Xiaojun , Gao Shaorong , Jiang Ying 
Published: April 2023

AbstractFarrerol, a natural flavanone, promotes homologous recombination (HR) repair to improve genome-editing efficiency, but the specific protein that farrerol directly targets to regulate HR repair and the underlying molecular mechanisms have not been determined. Here, we find that the deubiquitinase UCHL3 is the direct target of farrerol. Mechanistically, farrerol enhanced the deubiquitinase activity of UCHL3 to promote RAD51 deubiquitination, thereby improving HR repair. Importantly, we find that embryos of somatic cell nuclear transfer (SCNT) exhibited defective HR repair, increased genomic instability and aneuploidy, and that the farrerol treatment post nuclear transfer enhances HR repair, restores transcriptional and epigenetic network, and promotes SCNT embryo development. Ablating UCHL3 significantly attenuates farrerol-mediated stimulation in HR and SCNT embryo development. In summary, we identify farrerol as an activator of the deubiquitinase UCHL3, highlighted the importance of HR and epigenetic changes in SCNT reprogramming and provide a feasible method to promote SCNT efficiency.
Direct synthesis of extra-heavy olefins from carbon monoxide and water
Authors: Wang Chuanhao , Du Junjie , Zeng Lin , Li Zhongling , Dai Yizhou , Li Xu , Peng Zijun , Wu Wenlong , Li Hongliang , Zeng Jie 
Published: April 2023

AbstractExtra-heavy olefins (C12+=), feedstocks to synthesize a wide range of value-added products, are conventionally generated from fossil resources via energy-intensive wax cracking or multi-step processes. Fischer-Tropsch synthesis with sustainably obtained syngas as feed-in provides a potential way to produce C12+=, though there is a trade-off between enhancing C-C coupling and suppressing further hydrogenation of olefins. Herein, we achieve selective production of C12+=via the overall conversion of CO and water, denoted as Kölbel-Engelhardt synthesis (KES), in polyethylene glycol (PEG) over a mixture of Pt/Mo2N and Ru particles. KES provides a continuously high CO/H2 ratio, thermodynamically favoring chain propagation and olefin formation. PEG serves as a selective extraction agent to hinder hydrogenation of olefins. Under an optimal condition, the yield ratio of CO2 to hydrocarbons reaches the theoretical minimum, and the C12+= yield reaches its maximum of 1.79 mmol with a selectivity (among hydrocarbons) of as high as 40.4%.
An integrase toolbox to record gene-expression during plant development
Authors: Guiziou Sarah , Maranas Cassandra J. , Chu Jonah C. , Nemhauser Jennifer L. 
Published: April 2023

AbstractThere are many open questions about the mechanisms that coordinate the dynamic, multicellular behaviors required for organogenesis. Synthetic circuits that can record in vivo signaling networks have been critical in elucidating animal development. Here, we report on the transfer of this technology to plants using orthogonal serine integrases to mediate site-specific and irreversible DNA recombination visualized by switching between fluorescent reporters. When combined with promoters expressed during lateral root initiation, integrases amplify reporter signal and permanently mark all descendants. In addition, we present a suite of methods to tune the threshold for integrase switching, including: RNA/protein degradation tags, a nuclear localization signal, and a split-intein system. These tools improve the robustness of integrase-mediated switching with different promoters and the stability of switching behavior over multiple generations. Although each promoter requires tuning for optimal performance, this integrase toolbox can be used to build history-dependent circuits to decode the order of expression during organogenesis in many contexts.
Towards the ground state of molecules via diffusion Monte Carlo on neural networks
Authors: Ren Weiluo , Fu Weizhong , Wu Xiaojie , Chen Ji 
Published: April 2023

AbstractDiffusion Monte Carlo (DMC) based on fixed-node approximation has enjoyed significant developments in the past decades and become one of the go-to methods when accurate ground state energy of molecules and materials is needed. However, the inaccurate nodal structure hinders the application of DMC for more challenging electronic correlation problems. In this work, we apply the neural-network based trial wavefunction in fixed-node DMC, which allows accurate calculations of a broad range of atomic and molecular systems of different electronic characteristics. Our method is superior in both accuracy and efficiency compared to state-of-the-art neural network methods using variational Monte Carlo (VMC). We also introduce an extrapolation scheme based on the empirical linearity between VMC and DMC energies, and significantly improve our binding energy calculation. Overall, this computational framework provides a benchmark for accurate solutions of correlated electronic wavefunction and also sheds light on the chemical understanding of molecules.
Chance promoter activities illuminate the origins of eukaryotic intergenic transcriptions
Authors: Xu Haiqing , Li Chuan , Xu Chuan , Zhang Jianzhi 
Published: April 2023

AbstractIt is debated whether the pervasive intergenic transcription from eukaryotic genomes has functional significance or simply reflects the promiscuity of RNA polymerases. We approach this question by comparing chance promoter activities with the expression levels of intergenic regions in the model eukaryoteSaccharomyces cerevisiae. We build a library of over 105strains, each carrying a 120-nucleotide, chromosomally integrated, completely random sequence driving the potential transcription of a barcode. Quantifying the RNA concentration of each barcode in two environments reveals that 41–63% of random sequences have significant, albeit usually low, promoter activities. Therefore, even in eukaryotes, where the presence of chromatin is thought to repress transcription, chance transcription is prevalent. We find that only 1–5% of yeast intergenic transcriptions are unattributable to chance promoter activities or neighboring gene expressions, and these transcriptions exhibit higher-than-expected environment-specificity. These findings suggest that only a minute fraction of intergenic transcription is functional in yeast.
Amyloid-polysaccharide interfacial coacervates as therapeutic materials
Authors: Peydayesh Mohammad , Kistler Sabrina , Zhou Jiangtao , Lutz-Bueno Viviane , Victorelli Francesca Damiani , Meneguin Andréia Bagliotti , Spósito Larissa , Bauab Tais Maria , Chorilli Marlus , Mezzenga Raffaele 
Published: April 2023

AbstractCoacervation via liquid-liquid phase separation provides an excellent opportunity to address the challenges of designing nanostructured biomaterials with multiple functionalities. Protein-polysaccharide coacervates, in particular, offer an appealing strategy to target biomaterial scaffolds, but these systems suffer from the low mechanical and chemical stabilities of protein-based condensates. Here we overcome these limitations by transforming native proteins into amyloid fibrils and demonstrate that the coacervation of cationic protein amyloids and anionic linear polysaccharides results in the interfacial self-assembly of biomaterials with precise control of their structure and properties. The coacervates present a highly ordered asymmetric architecture with amyloid fibrils on one side and the polysaccharide on the other. We demonstrate the excellent performance of these coacervates for gastric ulcer protection by validating via an in vivo assay their therapeutic effect as engineered microparticles. These results point at amyloid-polysaccharides coacervates as an original and effective biomaterial for multiple uses in internal medicine.
Shorter leukocyte telomere length protects against NAFLD progression in children
Authors: Wojcicki Janet M. , Gill Ryan M. , Wilson Laura , Lin Jue , Rosenthal Philip 
Published: April 2023

AbstractLeukocyte telomere length (LTL) gets shorter with each cell division and is also sensitive to reactive oxygen species damage and inflammatory processes. Studies in adults with non-alcoholic fatty liver disease (NAFLD) have found that increased fibrosis but not ALT levels are associated with shorter LTL. Few pediatric studies have been conducted; as such, we sought to evaluate potential associations between LTL and liver disease and liver disease progression in pediatric patients. Using data from the Treatment of NAFLD in Children (TONIC) randomized controlled trial, we assessed the potential predictive relationship between LTL and liver disease progression based on two successive liver biopsies over 96 weeks. We assessed the potential relationship between LTL and child age, sex, and race/ethnicity and features of liver disease including components of histology. We subsequently evaluated predictors for improvement in non-alcoholic steatohepatitis (NASH) at 96 weeks including LTL. We also assessed predictors of lobular inflammation improvement at 96 weeks using multivariable models. Mean LTL at baseline was 1.33 ± 0.23 T/S. Increasing lobular and portal inflammation were associated with longer LTL. In multivariable models, greater lobular inflammation at baseline was associated with longer LTL (Coeff 0.03, 95% CI 0.006–0.13; p = 0.03). Longer LTL at baseline was associated with worsening lobular inflammation at 96 weeks (Coeff 2.41, 95% CI 0.78–4.04; p < 0.01). There was no association between liver fibrosis and LTL. The association between LTL and pediatric NASH does not parallel adults with no association between fibrosis stage and NASH. Conversely, longer LTL was associated with more lobular inflammation at baseline and increased lobular inflammation over the 96-week period. Longer LTL in children may indicate greater risk for future complications from NASH.
Dynamics of inflammatory cytokine expression in bovine endometrial cells exposed to cow blood plasma small extracellular vesicles (sEV) may reflect high fertility
Authors: Abeysinghe Pevindu , Turner Natalie , Mosaad Eman , Logan Jayden , Mitchell Murray D. 
Published: April 2023

AbstractAberrant inflammation in the endometrium impairs reproduction and leads to poor fertility. Small extracellular vesicles (sEV) are nanoparticles 30–200 nm in-size and contain transferable bioactive molecules that reflect the parent cell. Holstein–Friesian dairy cows with divergent genetic merit, high- (n = 10) and low-fertile (n = 10), were identified based on fertility breeding value (FBV), cow ovulation synchronization and postpartum anovulatory intervals (PPAI). In this study, we evaluated the effects of sEVs enriched from plasma of high-fertile (HF-EXO) and low-fertile (LF-EXO) dairy cows on inflammatory mediator expression by bovine endometrial epithelial (bEEL) and stromal (bCSC) cells. Exposure to HF-EXO in bCSC and bEEL cells yielded lower expression of PTGS1 and PTGS2 compared to the control. In bCSC cells exposed to HF-EXO, pro-inflammatory cytokine IL1-α was downregulated compared to the untreated control, IL-12α and IL-8 were downregulated compared to the LF-EXO treatment. Our findings demonstrate that sEVs interact with both endometrial epithelial and stromal cells to initiate differential gene expression, specifically genes relate to inflammation. Therefore, even subtle changes on the inflammatory gene cascade in the endometrium via sEV may affect reproductive performance and/or outcomes. Further, sEV from high-fertile animals acts in a unique direction to deactivate prostaglandin synthases in both bCSC and bEEL cells and deactivate pro-inflammatory cytokines in the endometrial stroma. The results suggest that circulating sEV may serve as a potential biomarker of fertility.
A smart privacy preserving framework for industrial IoT using hybrid meta-heuristic algorithm
Authors: Kumar Mohit , Mukherjee Priya , Verma Sahil , Kavita  , Shafi Jana , Wozniak Marcin , Ijaz Muhammad Fazal 
Published: April 2023

AbstractIndustrial Internet of Things (IIoT) seeks more attention in attaining enormous opportunities in the field of Industry 4.0. But there exist severe challenges related to data privacy and security when processing the automatic and practical data collection and monitoring over industrial applications in IIoT. Traditional user authentication strategies in IIoT are affected by single factor authentication, which leads to poor adaptability along with the increasing users count and different user categories. For addressing such issue, this paper aims to implement the privacy preservation model in IIoT using the advancements of artificial intelligent techniques. The two major stages of the designed system are the sanitization and restoration of IIoT data. Data sanitization hides the sensitive information in IIoT for preventing it from leakage of information. Moreover, the designed sanitization procedure performs the optimal key generation by a new Grasshopper–Black Hole Optimization (G–BHO) algorithm. A multi-objective function involving the parameters like degree of modification, hiding rate, correlation coefficient between the actual data and restored data, and information preservation rate was derived and utilized for generating optimal key. The simulation result establishes the dominance of the proposed model over other state-of the-art models in terms of various performance metrics. In respect of privacy preservation, the proposed G–BHO algorithm has achieved 1%, 15.2%, 12.6%, and 1% enhanced result than JA, GWO, GOA, and BHO, respectively.
Effects of continuous positive airway pressure therapy on left ventricular performance in patients with severe obstructive sleep apnea
Authors: Kim Se-Eun , Seo Jiwon , Kwon Younghoon , Cho Iksung , Shim Chi Young , Ha Jong-Won , Hong Geu-Ru 
Published: April 2023

AbstractWe investigated myocardial performance concerning obstructive sleep apnea (OSA) severity and the benefits of continuous positive airway pressure (CPAP) therapy. In this randomized sham-controlled trial, 52 patients (mean age, 49 years; 92%, males; mean AHI, 59) with severe OSA were randomly assigned to receive either CPAP or sham treatment for 3 months. The severity of OSA was determined using the apnea/hypopnea index (AHI), oxygen desaturation index (ODI), percentage of sleep time below 90% oxygen saturation (T90), and average O2 saturation during sleep (mean SpO2). We compared the changes in myocardial work after 3 months of CPAP (n = 26) versus the sham group (n = 26) at rest and during an exercise stress test. Unlike AHI or ODI, indices of hypoxemia including T90 and mean SpO2 were significantly correlated with global constructive work, as defined by work of left ventricle (LV) that contributes to LV ejection during systole (T90, β = 0.393, p = 0.012; mean SpO2, β = 0.331, p = 0.048), and global wasted work (GWW), as defined by work of LV that does not contribute to LV ejection (T90, β = 0.363, p = 0.015; mean SpO2, β =  − 0.370, p = 0.019). After 3 months, GWW decreased (80.0 ± 49.2 to 60.8 ± 26.3, p = 0.009) and global work efficiency increased (94.0 ± 4.5 to 95.7 ± 2.0, p = 0.008) in the CPAP group compared to those in the sham group. At the 3-month follow-up exercise stress echocardiography, worsening of GWW during exercise was significantly decreased in the CPAP group compared to that in the sham group (p = 0.045 at 50 W). Hypoxemia indices were closely associated with myocardial performance in patients with severe OSA. CPAP treatment for 3 months improved left ventricular myocardial performance by decreasing wasted work and increasing work efficacy compared to the sham treatment.
Guilt-inducing interaction with others modulates subsequent attentional orienting via their gaze
Authors: Zhao Wen , Yang Jiajia , Hu Zhonghua 
Published: April 2023

AbstractGaze direction can trigger social attentional orientation, characterised by a speeded reaction time in detecting targets appearing in a gazed-at location compared with those appearing in other locations. This is called the ‘gaze-cueing effect’ (GCE). Here, we investigated whether a feeling of guilt established through prior interaction with a cueing face could modulate the gaze-cueing effect. Participants first completed a guilt-induction task using a modified dot-estimation paradigm to associate the feeling of guilt with a specific face, after which the face that had established the binding relationship was used as the stimulus in a gaze-cueing task. The results showed that guilt-directed faces and control faces induce equal magnitudes of gaze-cueing effect in 200 ms of stimulus onset asynchrony (SOA), while guilt-directed faces induce a smaller gaze-cueing effect than control faces in 700 ms SOA. These findings provide preliminary evidence that guilt may modulate social attention triggered by eye gaze at a later stage of processing but not in the earlier stages.
Suppressive effects of increasing mungbean density on growth and reproduction of junglerice and feather fingergrass
Authors: Matloob Amar , Mobli Ahmadreza , Chauhan Bhagirath Singh 
Published: April 2023

AbstractIncreased planting density can provide crops a competitive advantage over weeds. This study appraised the growth and seed production of two noxious grassy weeds, i.e. feather fingergrass (Chloris virgata SW.) and junglerice [Echinochloa colona (L.) Link] in response to different mungbean [Vigna radiata (L.) R. Wilczek] densities (0, 82, 164, 242, and 328 plants m−2). A target-neighbourhood study was conducted using a completely randomized design with five replications, and there were two experimental runs in 2016–2017. The leaf, stem, and total aboveground biomass of C. virgata was 86, 59, and 76% greater than E. colona. For seed production, E. colona outnumbered C. virgata by producing 74% more seeds. Mungbean density-mediated suppression of height was more pronounced for E. colona compared with C. virgata during the first 42 days. The presence of 164–328 mungbean plants m−2 reduced the number of leaves of E. colona and C. virgata by 53–72% and 52–57%, respectively. The reduction in the inflorescence number caused by the highest mungbean density was higher for C. virgata than E. colona. C. virgata and E. colona growing with mungbean produced 81 and 79% fewer seeds per plant. An increase in mungbean density from 82 to 328 plants m−2 reduced the total aboveground biomass of C. virgata and E. colona by 45–63% and 44–67%, respectively. Increased mungbean plant density can suppress weed growth and seed production. Although increased crop density contributes to better weed management, supplemental weed control will be needed.
Adsorption of methylene blue from textile industrial wastewater using activated carbon developed from Rumex abyssinicus plant
Authors: Fito Jemal , Abewaa Mikiyas , Mengistu Ashagrie , Angassa Kenatu , Ambaye Abera Demeke , Moyo Welldone , Nkambule Thabo 
Published: April 2023

AbstractMethylene blue (MB) is abundantly found in textile industrial effluent which can cause severe health problems for public and environmental ecology. Therefore, this study aimed to remove MB from textile wastewater using the activated carbon developed from Rumexabyssinicus. The adsorbent was activated using chemical and thermal methods, and then it was characterized by SEM, FTIR, BET, XRD, and pH zero-point charge (pHpzc). The adsorption isotherm and kinetics were also investigated. The experimental design was composed of four factors at three levels (pH (3, 6, and 9), initial MB concentration (100, 150, and 200 mg/L), adsorbent dosage (20, 40, and 60 mg/100 mL), and contact time (20, 40, and 60 min)). The adsorption interaction was evaluated using response surface methodology. The characterization of a Rumexabyssinicus activated carbon was found to have multiple functional groups (FTIR), an amorphous structure (XRD), crack with ups and down morphology (SEM), pHpzc of 5.03 and a high BET-specific surface area of 2522 m2/g. The optimization of MB dye removal was carried out using the Response Surface methodology coupled with the Box Behnken approach. The maximum removal efficiency of 99.9% was recorded at optimum conditions of pH 9, MB concentration of 100 mg/L, the adsorbent dosage of 60 mg/100 mL, and contact time of 60 min. Among the three adsorption isotherm models, the Freundlich isotherm model was the best fit with an experimental value at R2 0.99 showing the adsorption process was heterogeneous and multilayer whereas the kinetics study revealed that pseudo-second-order at R2 0.88. Finally, this adsorption process is quite promising to be used at an industrial level.
Modelling impacts of climate change and anthropogenic activities on inflows and sediment loads of wetlands: case study of the Anzali wetland
Authors: Mahdian Mehran , Hosseinzadeh Majid , Siadatmousavi Seyed Mostafa , Chalipa Zohreh , Delavar Majid , Guo Ming , Abolfathi Soroush , Noori Roohollah 
Published: April 2023

AbstractUnderstanding the effects of climate change and anthropogenic activities on the hydrogeomorpholgical parameters in wetlands ecosystems is vital for designing effective environmental protection and control protocols for these natural capitals. This study develops methodological approach to model the streamflow and sediment inputs to wetlands under the combined effects of climate and land use / land cover (LULC) changes using the Soil and Water Assessment Tool (SWAT). The precipitation and temperature data from General Circulation Models (GCMs) for different Shared Socio-economic Pathway (SSP) scenarios (i.e., SSP1-2.6, SSP2-4.5, and SSP5-8.5) are downscaled and bias-corrected with Euclidean distance method and quantile delta mapping (QDM) for the case of the Anzali wetland watershed (AWW) in Iran. The Land Change Modeler (LCM) is adopted to project the future LULC at the AWW. The results indicate that the precipitation and air temperature across the AWW will decrease and increase, respectively, under the SSP1-2.6, SSP2-4.5, and SSP5-8.5 scenarios. Streamflow and sediment loads will reduce under the sole influence of SSP2-4.5 and SSP5-8.5 climate scenarios. An increase in sediment load and inflow was observed under the combined effects of climate and LULC changes, this is mainly due to the projected increased deforestation and urbanization across the AWW. The findings suggest that the densely vegetated regions, mainly located in the zones with steep slope, significantly prevents large sediment load and high streamflow input to the AWW. Under the combined effects of the climate and LULC changes, by 2100, the projected total sediment input to the wetland will reach 22.66, 20.83, and 19.93 million tons under SSP1-2.6, SSP2-4.5, and SSP5-8.5 scenarios, respectively. The results highlight that without any robust environmental interventions, the large sediment inputs will significantly degrade the Anzali wetland ecosystem and partly-fill the wetland basin, resulting in resigning the wetland from the Montreux record list and the Ramsar Convention on Wetlands of International Importance.