bluuebunny/crossref_metadata_2025 huggingface dataset:
TET2 and TET3 loss disrupts small intestine differentiation and homeostasis
Authors: Ansari Ihab , Solé-Boldo Llorenç , Ridnik Meshi , Gutekunst Julian , Gilliam Oliver , Korshko Maria , Liwinski Timur , Jickeli Birgit , Weinberg-Corem Noa , Shoshkes-Carmel Michal , Pikarsky Eli , Elinav Eran , Lyko Frank , Bergman Yehudit
Published: July 2023

TET2/3 play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood. Here we show that ablation of TET2/3 in intestinal epithelial cells results in a murine phenotype characterized by a severe homeostasis imbalance in the small intestine. Tet2/3-deleted mice show a pronounced loss of mature Paneth cells as well as fewer Tuft and more Enteroendocrine cells. Further results show major changes in DNA methylation at putative enhancers, which are associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescues the methylation and cellular defects. TET2/3 loss also alters the microbiome, predisposing the intestine to inflammation under homeostatic conditions and acute inflammation-induced death. Together, our results uncover previously unrecognized critical roles for DNA demethylation, possibly occurring subsequently to chromatin opening during intestinal development, culminating in the establishment of normal intestinal crypts.
SpatialDM for rapid identification of spatially co-expressed ligand–receptor and revealing cell–cell communication patterns
Authors: Li Zhuoxuan , Wang Tianjie , Liu Pentao , Huang Yuanhua
Published: July 2023

Cell-cell communication is a key aspect of dissecting the complex cellular microenvironment. Existing single-cell and spatial transcriptomics-based methods primarily focus on identifying cell-type pairs for a specific interaction, while less attention has been paid to the prioritisation of interaction features or the identification of interaction spots in the spatial context. Here, we introduce SpatialDM, a statistical model and toolbox leveraging a bivariant Moran’s statistic to detect spatially co-expressed ligand and receptor pairs, their local interacting spots (single-spot resolution), and communication patterns. By deriving an analytical null distribution, this method is scalable to millions of spots and shows accurate and robust performance in various simulations. On multiple datasets including melanoma, Ventricular-Subventricular Zone, and intestine, SpatialDM reveals promising communication patterns and identifies differential interactions between conditions, hence enabling the discovery of context-specific cell cooperation and signalling.
Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase
Authors: Li Zhong , Zhang Lilan , Xu Kangwei , Jiang Yuanyuan , Du Jieke , Zhang Xingwang , Meng Ling-Hong , Wu Qile , Du Lei , Li Xiaoju , Hu Yuechan , Xie Zhenzhen , Jiang Xukai , Tang Ya-Jie , Wu Ruibo , Guo Rey-Ting , Li Shengying
Published: July 2023

Diterpene synthase VenA is responsible for assembling venezuelaene A with a unique 5-5-6-7 tetracyclic skeleton from geranylgeranyl pyrophosphate. VenA also demonstrates substrate promiscuity by accepting geranyl pyrophosphate and farnesyl pyrophosphate as alternative substrates. Herein, we report the crystal structures of VenA in bothapoform andholoform in complex with a trinuclear magnesium cluster and pyrophosphate group. Functional and structural investigations on the atypical115DSFVSD120motif of VenA,versusthe canonical Asp-rich motif of DDXX(X)D/E, reveal that the absent second Asp of canonical motif is functionally replaced by Ser116 and Gln83, together with bioinformatics analysis identifying a hidden subclass of type I microbial terpene synthases. Further structural analysis, multiscale computational simulations, and structure-directed mutagenesis provide significant mechanistic insights into the substrate selectivity and catalytic promiscuity of VenA. Finally, VenA is semi-rationally engineered into a sesterterpene synthase to recognize the larger substrate geranylfarnesyl pyrophosphate.
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms
Authors: Erdem Cemal , Gross Sean M. , Heiser Laura M. , Birtwistle Marc R.
Published: July 2023

Robust identification of context-specific network features that control cellular phenotypes remains a challenge. We here introduce MOBILE (Multi-Omics Binary Integration via Lasso Ensembles) to nominate molecular features associated with cellular phenotypes and pathways. First, we use MOBILE to nominate mechanisms of interferon-γ (IFNγ) regulated PD-L1 expression. Our analyses suggest that IFNγ-controlled PD-L1 expression involvesBST2,CLIC2,FAM83D,ACSL5, andHIST2H2AA3genes, which were supported by prior literature. We also compare networks activated by related family members transforming growth factor-beta 1 (TGFβ1) and bone morphogenetic protein 2 (BMP2) and find that differences in ligand-induced changes in cell size and clustering properties are related to differences in laminin/collagen pathway activity. Finally, we demonstrate the broad applicability and adaptability of MOBILE by analyzing publicly available molecular datasets to investigate breast cancer subtype specific networks. Given the ever-growing availability of multi-omics datasets, we envision that MOBILE will be broadly useful for identification of context-specific molecular features and pathways.
Natural statistics support a rational account of confidence biases
Authors: Webb Taylor W. , Miyoshi Kiyofumi , So Tsz Yan , Rajananda Sivananda , Lau Hakwan
Published: July 2023

Previous work has sought to understand decision confidence as a prediction of the probability that a decision will be correct, leading to debate over whether these predictions are optimal, and whether they rely on the same decision variable as decisions themselves. This work has generally relied on idealized, low-dimensional models, necessitating strong assumptions about the representations over which confidence is computed. To address this, we used deep neural networks to develop a model of decision confidence that operates directly over high-dimensional, naturalistic stimuli. The model accounts for a number of puzzling dissociations between decisions and confidence, reveals a rational explanation of these dissociations in terms of optimization for the statistics of sensory inputs, and makes the surprising prediction that, despite these dissociations, decisions and confidence depend on a common decision variable.
Deep quantum neural networks on a superconducting processor
Authors: Pan Xiaoxuan , Lu Zhide , Wang Weiting , Hua Ziyue , Xu Yifang , Li Weikang , Cai Weizhou , Li Xuegang , Wang Haiyan , Song Yi-Pu , Zou Chang-Ling , Deng Dong-Ling , Sun Luyan
Published: July 2023

Deep learning and quantum computing have achieved dramatic progresses in recent years. The interplay between these two fast-growing fields gives rise to a new research frontier of quantum machine learning. In this work, we report an experimental demonstration of training deep quantum neural networks via the backpropagation algorithm with a six-qubit programmable superconducting processor. We experimentally perform the forward process of the backpropagation algorithm and classically simulate the backward process. In particular, we show that three-layer deep quantum neural networks can be trained efficiently to learn two-qubit quantum channels with a mean fidelity up to 96.0% and the ground state energy of molecular hydrogen with an accuracy up to 93.3% compared to the theoretical value. In addition, six-layer deep quantum neural networks can be trained in a similar fashion to achieve a mean fidelity up to 94.8% for learning single-qubit quantum channels. Our experimental results indicate that the number of coherent qubits required to maintain does not scale with the depth of the deep quantum neural network, thus providing a valuable guide for quantum machine learning applications with both near-term and future quantum devices.
Tumor collagens predict genetic features and patient outcomes
Authors: Guo Kevin S. , Brodsky Alexander S.
Published: July 2023

The extracellular matrix (ECM) is a critical determinant of tumor fate that reflects the output from myriad cell types in the tumor. Collagens constitute the principal components of the tumor ECM. The changing collagen composition in tumors along with their impact on patient outcomes and possible biomarkers remains largely unknown. The RNA expression of the 43 collagen genes from solid tumors in The Cancer Genome Atlas (TCGA) was clustered to classify tumors. PanCancer analysis revealed how collagens by themselves can identify the tissue of origin. Clustering by collagens in each cancer type demonstrated strong associations with survival, specific immunoenvironments, somatic gene mutations, copy number variations, and aneuploidy. We developed a machine learning classifier that predicts aneuploidy, and chromosome arm copy number alteration (CNA) status based on collagen expression alone with high accuracy in many cancer types with somatic mutations, suggesting a strong relationship between the collagen ECM context and specific molecular alterations. These findings have broad implications in defining the relationship between cancer-related genetic defects and the tumor microenvironment to improve prognosis and therapeutic targeting for patient care, opening new avenues of investigation to define tumor ecosystems.
Sensitivity of Arctic CH4 emissions to landscape wetness diminished by atmospheric feedbacks
Authors: de Vrese Philipp , Beckebanze Lutz , Galera Leonardo de Aro , Holl David , Kleinen Thomas , Kutzbach Lars , Rehder Zoé , Brovkin Victor
Published: July 2023

Simulations using land surface models suggest future increases in Arctic methane emissions to be limited by the thaw-induced drying of permafrost landscapes. Here we use the Max Planck Institute Earth System Model to show that this constraint may be weaker than previously thought owing to compensatory atmospheric feedbacks. In two sets of extreme scenario simulations, a modification of the permafrost hydrology resulted in diverging hydroclimatic trajectories that, however, led to comparable methane fluxes. While a wet Arctic showed almost twice the wetland area compared with an increasingly dry Arctic, the latter featured greater substrate availability due to higher temperatures resulting from reduced evaporation, diminished cloudiness and more surface solar radiation. Given the limitations of present-day models and the potential model dependence of the atmospheric response, our results provide merely a qualitative estimation of these effects, but they suggest that atmospheric feedbacks play an important role in shaping future Arctic methane emissions.
Groundwater springs formed during glacial retreat are a large source of methane in the high Arctic
Authors: Kleber Gabrielle E. , Hodson Andrew J. , Magerl Leonard , Mannerfelt Erik Schytt , Bradbury Harold J. , Zhu Yizhu , Trimmer Mark , Turchyn Alexandra V.
Published: July 2023

Permafrost and glaciers in the high Arctic form an impermeable ‘cryospheric cap’ that traps a large reservoir of subsurface methane, preventing it from reaching the atmosphere. Cryospheric vulnerability to climate warming is making releases of this methane possible. On Svalbard, where air temperatures are rising more than two times faster than the average for the Arctic, glaciers are retreating and leaving behind exposed forefields that enable rapid methane escape. Here we document how methane-rich groundwater springs have formed in recently revealed forefields of 78 land-terminating glaciers across central Svalbard, bringing deep-seated methane gas to the surface. Waters collected from these springs during February–May of 2021 and 2022 are supersaturated with methane up to 600,000 times greater than atmospheric equilibration. Spatial sampling reveals a geological dependency on the extent of methane supersaturation, with isotopic evidence of a thermogenic source. We estimate annual methane emissions from proglacial groundwaters to be up to 2.31 kt across the Svalbard archipelago. Further investigations into marine-terminating glaciers indicate future methane emission sources as these glaciers transition into fully land-based systems. Our findings reveal that climate-driven glacial retreat facilitates widespread release of methane, a positive feedback loop that is probably prevalent across other regions of the rapidly warming Arctic.
A panel dataset of COVID-19 vaccination policies in 185 countries
Authors: Cameron-Blake Emily , Tatlow Helen , Andretti Bernardo , Boby Thomas , Green Kaitlyn , Hale Thomas , Petherick Anna , Phillips Toby , Pott Annalena , Wade Adam , Zha Hao
Published: July 2023

We present a panel dataset of COVID-19 vaccine policies, with data from 01 January 2020 for 185 countries and a number of subnational jurisdictions, reporting on vaccination prioritization plans, eligibility and availability, cost to the individual and mandatory vaccination policies. For each of these indicators, we recorded who is targeted by a policy using 52 standardized categories. These indicators document a detailed picture of the unprecedented scale of international COVID-19 vaccination rollout and strategy, indicating which countries prioritized and vaccinated which groups, when and in what order. We highlight key descriptive findings from these data to demonstrate uses for the data and to encourage researchers and policymakers in future research and vaccination planning. Numerous patterns and trends begin to emerge. For example: ‘eliminator’ countries (those that aimed to prevent virus entry into the country and community transmission) tended to prioritize border workers and economic sectors, while ‘mitigator’ countries (those that aimed to reduce the impact of community transmission) tended to prioritize the elderly and healthcare sectors for the first COVID-19 vaccinations; high-income countries published prioritization plans and began vaccinations earlier than low- and middle-income countries. Fifty-five countries were found to have implemented at least one policy of mandatory vaccination. We also demonstrate the value of combining this data with vaccination uptake rates, vaccine supply and demand data, and with further COVID-19 epidemiological data.
A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration
Authors: Gomes Moreira Diana , Jan Asad
Published: July 2023

The discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a starting point, we introduce the readers to several open access resources, which contain gene expression profiles and proteomics datasets from patient studies in common NDDs, including proteomics analyses of cerebrospinal fluid (CSF). Then, we illustrate the method for curated gene expression analyses across select brain regions from four cohorts of Parkinson disease patients (and from one study in common NDDs), probing glutathione biogenesis, calcium signaling and autophagy. These data are complemented by findings of select markers in CSF-based studies in NDDs. Additionally, we enclose several annotated microarray studies, and summarize reports on CSF proteomics across the NDDs, which the readers can utilize for translational purposes. We anticipate that this “beginner’s guide” will benefit the research community in NDDs, and would serve as a useful educational tool.
Chromosome-level genome assembly of the Asian aspen Populus davidiana Dode
Authors: Bae Eun-Kyung , Kang Min-Jeong , Lee Seung-Jae , Park Eung-Jun , Kim Ki-Tae
Published: July 2023

The genome ofPopulus davidiana, a keystone aspen species, has been sequenced to improve our understanding of the evolutionary and functional genomics of thePopulusgenus. The Hi-C scaffolding genome assembly resulted in a 408.1 Mb genome with 19 pseudochromosomes. The BUSCO assessment revealed that 98.3% of the genome matched the embryophytes dataset. A total of 31,862 protein-coding sequences were predicted, of which 31,619 were functionally annotated. The assembled genome was composed of 44.9% transposable elements. These findings provide new knowledge about the characteristics of theP. davidianagenome and will facilitate comparative genomics and evolutionary research on the genusPopulus.
Wildfire immediately reduces nest and adult survival of greater sage-grouse
Authors: Tyrrell Emmy A. , Coates Peter S. , Prochazka Brian G. , Brussee Brianne E. , Espinosa Shawn P. , Hull Joshua M.
Published: July 2023

Wildfire events are becoming more frequent and severe on a global scale. Rising temperatures, prolonged drought, and the presence of pyrophytic invasive grasses are contributing to the degradation of native vegetation communities. Within the Great Basin region of the western U.S., increasing wildfire frequency is transforming the ecosystem toward a higher degree of homogeneity, one dominated by invasive annual grasses and declining landscape productivity. Greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) are a species of conservation concern that rely on large tracts of structurally and functionally diverse sagebrush (Artemisia spp.) communities. Using a 12-year (2008–2019) telemetry dataset, we documented immediate impacts of wildfire on demographic rates of a population of sage-grouse that were exposed to two large wildfire events (Virginia Mountains Fire Complex—2016; Long Valley Fire—2017) near the border of California and Nevada. Spatiotemporal heterogeneity in demographic rates were accounted for using a Before-After Control-Impact Paired Series (BACIPS) study design. Results revealed a 40% reduction in adult survival and a 79% reduction in nest survival within areas impacted by wildfires. Our results indicate that wildfire has strong and immediate impacts to two key life stages of a sagebrush indicator species and underscores the importance of fire suppression and immediate restoration following wildfire events.
Relationship between radioactivity and toxicity in some medicinal plants
Authors: Abdelfadeel Eman H. , El-Halim E. S. Abd , Hegazy T. M. , Ghany H. A. Abdel
Published: July 2023

Plants absorb water, nutrients and minerals from the soil through their root. Also, minerals, the radionuclides present in the growing media also are absorbed by plant parts following the same pathway. Consequently, it is important to determine the concentrations of these radionuclides in edible plants to access the associated risk to human health. In the present work, the levels of natural radioactivity and the level of some toxic elements in 17 medicinal plants, commonly used in Egypt, were measured using high-purity germanium gamma spectrometry and atomic absorption, respectively. The investigated plants were sub-grouped according to the edible parts into leave samples (n = 8), roots (n = 3), and seeds (n = 6). Also, the specific activity of both radon and thoron was measured by using alpha emitters registration which is emitted from radon and thoron gases in CR-39 nuclear track detectors. Additionally, the concentration of some toxic elements (Cu, Zn, Cd and, Pb) in six samples of medicinal plants was determined by atomic absorption spectrometry.
Boosting the thermal management performance of a PCM-based module using novel metallic pin fin geometries: Numerical study
Authors: Elshaer Abdelrahman M. , Soliman A. M. A. , Kassab M. , Hawwash A. A.
Published: July 2023

Satellite avionics and electronic components are getting compact and have high power density. Thermal management systems are essential for their optimal operational performance and survival. Thermal management systems keep the electronic components within a safe temperature range. Phase change materials (PCMs) have high thermal capacity, so they are promising for thermal control applications. This work adopted a PCM-integrated thermal control device (TCD) to manage the small satellite subsystems under zero gravity conditions thermally. The TCD's outer dimensions were selected upon a typical small satellite subsystem. The PCM adopted was the organic PCM of RT 35. Pin fins with different geometries were adopted to boost the lower thermal conductivity of the PCM. Six-pin fins geometries were used. First, the conventional geometries were square, circular, and triangular. Second, the novel geometries were cross-shaped, I-shaped, and V-shaped fins. The fins were designed at two-volume fractions of 20% and 50%. The electronic subsystem was assumed to be "ON" for 10 min releasing 20 W of heat, and "OFF" for 80 min. The findings show a remarkable decrease in the TCD's base plate temperature by 5.7 ℃ as the fins' number changed from 15 to 80 for square fins. The results also show that the novel cross-shaped, I-shaped, and V-shaped pin fins could significantly enhance thermal performance. The cross-shaped, I-shaped, and V-shaped reported a decrease in the temperature by about 1.6%, 2.6%, and 6.6%, respectively, relative to the circular fin geometry. V-shaped fins could also increase the PCM melt fraction by 32.3%.
Laboratory evaluation of anti-plaque and remineralization efficacy of sugarless probiotic jelly candy supplemented with natural nano prebiotic additive
Authors: Elgamily Hanaa M. , El-Sayed Samah M. , El-Sayed Hoda S. , Youssef Ahmed M.
Published: July 2023

We evaluated the anti-cariogenic effect of an experimental synbiotic compound containing probiotic Lacticaseibacillus rhamnosus (NRRL B-442)-based jelly candy supplemented with natural prebiotic grape seed extract (GSE) in a nanoemulsion formula on the colonization and establishment of Streptococcus mutans (ATCC 25175) and Actinomyces viscosus (ATTCC 19246) biofilms through counting colony forming units, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). We were then analysing the remineralizing effect of synbiotic jelly candy on human enamel surface lesions using Vickers microhardness testers, atomic force microscopy (AFM), SEM, energy-dispersive X-ray spectroscopy (EDAX), and confocal laser scanning microscopy (CLSM) at three stages (sound, after demineralization, and after pH cycling). We found after 21 days of treatment of the pH-cycled enamel discs with jelly candy for 10 min twice daily, a 68% decrease in S. mutans colony formation, reducing biofilm development, trapping S. mutans visualized in jelly candy under SEM examination, and significantly altering the morphological structure of these bacteria under TEM analysis. For remineralization measurements, statistically significant differences in microhardness integrated mineral loss, and lesion depth through CLSM between demineralization and treatment stages. These findings provide an effective anti-cariogenic synbiotic compound of grape seed extract and probiotic jelly candy with potential remineralizing activity.
Feasibility of using KardiaMobile-L6 for QT interval monitoring during the early phase of the COVID-19 pandemic in critical care patients
Authors: Zaballos Matilde , Fernández Ignacio , Rodríguez Lucia , Orozco Silvia , García Amparo , Juncos Mónica , Alvarez-Zaballos Sara , Piñeiro Patricia , Hortal Javier
Published: July 2023

The electrocardiogram (ECG) represents an essential tool to determine cardiac electrical abnormalities in COVID-19 patients, the effects of anti-SARS-CoV-2 drugs, and potential drug interactions. Smartphone-based heart monitors have increased the spectrum of ECG monitoring however, we are not aware of its reliability in critically ill COVID-19 patients. We aim to evaluate the feasibility and reliability of nurse-performed smartphone electrocardiography for QT interval monitoring in critically ill COVID-19 patients using KardiaMobile-6L compared with the standard 12-lead ECG. An observational comparative study was conducted comparing consecutive KardiaMobile-6L and 12-lead ECG recordings obtained from 20 patients admitted to the intensive care unit with SARS-CoV-2 infection and on invasive mechanical ventilation. The heart rate-corrected QT (QTc) intervals measured by KardiaMobile-6L and 12-lead ECG were compared. In 60 percent of the recordings, QTc intervals measured by KardiaMobile-6L matched those by 12-lead ECG. The QTc intervals measured by KardiaMobile-6 and 12-lead ECG were 428 ± 45 ms and 425 ± 35 ms (p = 0.82), respectively. The former demonstrated good agreement (bias = 2.9 ms; standard deviation of bias = 29.6 ms) with the latter, using the Bland–Altman method of measurement agreement. In all but one recording, KardiaMobile-6L demonstrated QTc prolongation. QTc interval monitoring with KardiaMobile-6L in critically ill COVID-19 patients was feasible and demonstrated reliability comparable to the standard 12-lead ECG.
Optical and radiation shielding properties of PVC/BiVO4 nanocomposite
Authors: Kassem Said M. , Abdel Maksoud M. I. A. , El Sayed Adel M. , Ebraheem S. , Helal A. I. , Ebaid Y. Y.
Published: July 2023

This study investigates the physical and optical properties as well as the radiation shielding capacity of polyvinyl chloride (PVC) loaded with x% of bismuth vanadate (BiVO4) (x = 0, 1, 3, and 6 wt%). As a non-toxic nanofiller, the designed materials are low-cost, flexible, and lightweight plastic to replace traditional lead, which is toxic and dense. XRD patterns and FTIR spectra demonstrated a successful fabrication and complexation of nanocomposite films. In addition, the particle size, morphology, and elemental composition of the BiVO4 nanofiller were demonstrated through the utilization of TEM, SEM, and EDX spectra. The MCNP5 simulation code assessed the gamma-ray shielding effectiveness of four PVC + x% BiVO4 nanocomposites. The obtained mass attenuation coefficient data of the developed nanocomposites were comparable to the theoretical calculation performed with Phy-X/PSD software. Moreover, the initial stage in the computation of various shielding parameters, such as half-value layer, tenth value layer, and mean free path, besides the simulation of linear attenuation coefficient. The transmission factor declines while radiation protection efficiency increases with an increase in the proportion of BiVO4 nanofiller. Further, the current investigation seeks to evaluate the thickness equivalent (Xeq), effective atomic number (Zeff), and effective electron density (Neff) values as a function of the concentration of BiVO4 in a PVC matrix. The results obtained from the parameters indicate that incorporating BiVO4 into PVC can be an effective strategy for developing sustainable and lead-free polymer nanocomposites, with potential uses in radiation shielding applications.
A novel investigation using thermal modeling and optimization of waste pyrolysis reactor using finite element analysis and response surface methodology
Authors: Garg Shivi , Nayyar Anand , Buradi Abdulrajak , Shadangi Krushna Prasad , Sharma Prabhakar , Bora Bhaskor Jyoti , Jain Akshay , Asif Shah Mohd
Published: July 2023

The influence of humans on the environment is growing drastically and is pervasive. If this trend continues for a longer time, it can cost humankind, social and economic challenges. Keeping this situation in mind, renewable energy has paved the way as our saviour. This shift will not only help in reducing pollution but will also provide immense opportunities for the youth to work. This work discusses about various waste management strategies and discusses the pyrolysis process in details. Simulations were done keeping pyrolysis as the base process and by varying parameters like feeds and reactor materials. Different feeds were chosen like Low-Density Polyethylene (LDPE), wheat straw, pinewood, and a mixture of Polystyrene (PS), Polyethylene (PE), and Polypropylene (PP). Different reactor materials were considered namely, stainless steel AISI 202, AISI 302, AISI 304, and AISI 405. AISI stands for American Iron and Steel Institute. AISI is used to signify some standard grades of alloy steel bars. Thermal stress and thermal strain values and temperature contours were obtained using simulation software called Fusion 360. These values were plotted against temperature using graphing software called Origin. It was observed that these values increased with increasing temperature. LDPE got the lowest values for stress and stainless steel AISI 304 came out to be the most feasible material for pyrolysis reactor having the ability to withstand high thermal stresses. RSM was effectively used to generate a robust prognostic model with high efficiency, R2 (0.9924–0.9931), and low RMSE (0.236 to 0.347). Optimization based on desirability identified the operating parameters as 354 °C temperature and LDPE feedstock. The best thermal stress and strain responses at these ideal parameters were 1719.67 MPa and 0.0095, respectively.
Effect of continuous sugarcane bagasse-derived biochar application on rainfed cotton (Gossypium hirsutum L.) growth, yield and lint quality in the humid Mississippi delta
Authors: Pinnamaneni Srinivasa R. , Lima Isabel , Boone Stephanie A. , Anapalli Saseendran S. , Reddy Krishna N.
Published: July 2023

Optimizing soil health through soil amendments is a promising strategy for enhancing rainwater efficiency for stabilizing crop production. Biochar, obtained by torrefaction of sugarcane bagasse, a byproduct from sugar mills, has a high potential for its use as a soil amendment, which can boost crop yields, but needs further field trials for its adoption in farming systems. A field study was conducted during 2019–2021 at Stoneville, Mississippi, to assess rainfed cotton (Gossypium hirsutum L.) production under four biochar levels (0, 10, 20, and 40 t ha−1) on Dundee silt loam soil. The effects of biochar on cotton growth and lint yield and quality were examined. Biochar levels had no significant impact on cotton lint and seed yield for the first two years. Still, in the third year, a significant increase in lint yield by 13 and 21.7% was recorded at 20 and 40 t ha−1 biochar levels, respectively. In the third year, lint yields were 1523, 1586, 1721, and 1854 kg ha−1 at 0, 10, 20 and 40 t ha−1 biochar levels, respectively. Similarly, cotton seed yield increased by 10.8% and 13.4% in 20 and 40 t ha−1 biochar plots. This study demonstrated that successive biochar applications at 20 or 40 t ha−1 can enhance cotton lint and seed yields under rainfed conditions. These improved yields with biochar did not produce increased net returns due to the increased production costs. Many lint quality parameters were unaffected except for micronaire, fiber strength and fiber length. However, potential long-term benefits of enhanced cotton production from biochar application beyond the length of the study merit further investigation. Additionally, biochar application is more relevant when accrued carbon credits through carbon sequestration outweigh the increased production costs due to biochar application.
CYP4F12 is a potential biomarker and inhibits cell migration of head and neck squamous cell carcinoma via EMT pathway
Authors: Jia Wenming , Chen Shuai , Wei Ran , Yang Xiaoqi , Zhang Minfa , Qian Ye , Liu Heng , Lei Dapeng
Published: July 2023

Head and neck squamous cell carcinoma (HNSC) is the most common malignant tumor of head and neck. Due to the insidious nature of HNSC and the lack of effective early diagnostic indicators, the development of novel biomarkers to improve patient prognosis is particularly urgent. In this study, we explored and validated the correlation between cytochrome P450 family 4 subfamily F member 12 (CYP4F12) expression levels and HNSC progression using data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) datasets and collected patient samples. We analyzed the association of CYP4F12 expression with clinicopathological features, immune correlation and prognosis. Finally, we analyzed the correlation between CYP4F12 and pathways, and verified by experiments. The results showed that CYP4F12 was low expressed in tumor tissues, participated in a variety of phenotypic changes of HNSC and affected immune cell infiltration. Pathway analysis indicated that CYP4F12 may play a key role in tumor cell migration and apoptosis. Experimental results showed that over-expression of CYP4F12 inhibited cell migration and enhanced the adhesion between cells and matrix by inhibiting epithelial-mesenchymal transition (EMT) pathway in HNSC cells. In conclusion, our study provided insights into the role of CYP4F12 in HNSC and revealed that CYP4F12 may be a potential therapeutic target for HNSC.
Experimental study on flow and turbulence characteristics of jet impinging on cylinder using three-dimensional Lagrangian particle tracking velocimetry
Authors: Kim Mirae , Schanz Daniel , Novara Matteo , Godbersen Philipp , Yeom Eunseop , Schröder Andreas
Published: July 2023

When a round jet impinges on a convex cylindrical surface, complex three-dimensional (3D) flow structures occur, accompanied by the Coanda effect. To characterize the flow and turbulence properties of the general system, ensemble averages of 3D Lagrangian particle tracking velocimetry measurements were taken. The radial bin-averaging method was used in post-processing the tracked particles and corresponding instantaneous velocity vectors to generate appropriate ensemble-averaged statistics. Two impinging angles were selected, and at a fixed Reynolds number, the ensemble-averaged volumetric velocity field and turbulent stress tensor components were measured. The flow and turbulence characteristics of the impinging jet on the cylinder were notably different based on the impinging angle, especially in the downstream region. Surprisingly, the attached wall jet with a half-elliptic shape was abruptly thickened in the wall-normal direction, similar to the axis switching phenomenon observed in elliptic jets in the case of oblique impingement. In the jet-impinging region, the flow spread in all directions with high mean vorticity values. With the development of a 3D curved wall jet, both the Coanda effect and centrifugal force played a significant role in the flow behavior. A notable feature of the self-preserving region was the similarity of mean velocity profiles with scaling by the maximum velocity and the jet half-width for both impinging angle cases. Local isotropy of turbulent normal stresses was observed in this region, supporting the existence of self-preservation in the 3D curved wall jet. The volumetric ensemble-averaged Reynolds stress tensor revealed strong inhomogeneous turbulence in the boundary layer region and the curvature effect on the Reynolds shear stress in the free shear layer.
On the yield criterion of porous materials by the homogenization approach and Steigmann–Ogden surface model
Authors: Zheng Chenyi , Wang Hongzhen , Jiang Yali , Li Gaohui
Published: July 2023

In this work, we investigate the yield criterion of nanoporous materials by using homogenization approach and Steigmann–Ogden surface model. The representative volume element is proposed as an infinite matrix containing a tiny nanovoid. The matrix is incompressible, rigid-perfectly plastic, von Mises materials and nanovoids are dilute and equal in size. First, the constitutive of microscopic stress and microscopic strain rate is established based on the flow criterion. Secondly, according to the Hill’s lemma, the relationship between the macroscopic equivalent modulus and the microscopic equivalent modulus is established by homogenization approach. Thirdly, the macroscopic equivalent modulus containing the Steigmann–Ogden surface model including surface parameters, porosity and nanovoid radius is derived from the trial microscopic velocity field. Finally, an implicit macroscopic yield criterion for nanoporous materials is developed. For surface modulus, nanovoids radius and porosity studies are developed through extensive numerical experiments. The research results in this paper have reference significance for the design and manufacture of nanoporous materials.
Commensal bacteria weaken the intestinal barrier by suppressing epithelial neuropilin-1 and Hedgehog signaling
Authors: Pontarollo Giulia , Kollar Bettina , Mann Amrit , Khuu My Phung , Kiouptsi Klytaimnistra , Bayer Franziska , Brandão Inês , Zinina Valeriya V. , Hahlbrock Jennifer , Malinarich Frano , Mimmler Maximilian , Bhushan Sudhanshu , Marini Federico , Ruf Wolfram , Belheouane Meriem , Baines John F. , Endres Kristina , Reba Scott M. , Raker Verena K. , Deppermann Carsten , Welsch Christoph , Bosmann Markus , Soshnikova Natalia , Chassaing Benoit , Bergentall Mattias , Sommer Felix , Bäckhed Fredrik , Reinhardt Christoph
Published: July 2023

The gut microbiota influences intestinal barrier integrity through mechanisms that are incompletely understood. Here we show that the commensal microbiota weakens the intestinal barrier by suppressing epithelial neuropilin-1 (NRP1) and Hedgehog (Hh) signaling. Microbial colonization of germ-free mice dampens signaling of the intestinal Hh pathway through epithelial Toll-like receptor (TLR)-2, resulting in decreased epithelial NRP1 protein levels. Following activation via TLR2/TLR6, epithelial NRP1, a positive-feedback regulator of Hh signaling, is lysosomally degraded. Conversely, elevated epithelial NRP1 levels in germ-free mice are associated with a strengthened gut barrier. Functionally, intestinal epithelial cell-specific Nrp1 deficiency (Nrp1ΔIEC) results in decreased Hh pathway activity and a weakened gut barrier. In addition, Nrp1ΔIEC mice have a reduced density of capillary networks in their small intestinal villus structures. Collectively, our results reveal a role for the commensal microbiota and epithelial NRP1 signaling in the regulation of intestinal barrier function through postnatal control of Hh signaling.
Generational differences in climate-related beliefs, risk perceptions and emotions in the UK
Authors: Poortinga Wouter , Demski Christina , Steentjes Katharine
Published: July 2023

It is widely believed that younger generations are more engaged with climate change than older generations. However, evidence of a gap in climate-related perceptions and concern is mixed, likely due to the inconsistent use of outcome variables. Here we systematically examine generational differences across different types of climate engagement including cognitive and affective dimensions. Using data from three nationally-representative surveys conducted in the UK in 2020, 2021 and 2022, we show there is an overall pattern of higher levels of climate-related beliefs, risks perceptions and emotions among younger generation groups. However, the gap is larger and more consistent for climate-related emotions than for climate-related beliefs. While generational differences in climate-related emotions were found across all years, the overall gap has disappeared due to narrowing climate-related beliefs and risk perceptions. The generational differences are therefore mainly in emotional engagement rather than in beliefs about anthropogenic climate change.
The diurnal variation of wet bulb temperatures and exceedance of physiological thresholds relevant to human health in South Asia
Authors: Justine Jenix , Monteiro Joy Merwin , Shah Hardik , Rao Neethi
Published: July 2023

Extreme heat is increasingly being acknowledged as a serious hazard to human health, through a combination of physiological responses to heat, expressed as dry and wet bulb temperatures, and personal factors. Here we present an analysis of the diurnal variability of dry and wet bulb temperatures using station data in South Asia during both regular and heatwave days. We find that diurnal cycles differ, with the daily maximum wet bulb temperature occurring several hours after the daily maximum dry bulb temperature. Using radiosonde profiles, we show that the timing and amplitude of the diurnal variability of wet bulb temperature can be explained by changes in boundary layer depths and water content. Physiological thresholds for uncompensable heat stress were exceeded even in the evenings, many hours after dry bulb temperature peaks. Cumulative exceedances occurred in 105 instances, corresponding to at least 300 hours of exposure to uncompensable heat stress in South Asia between 1995 and 2020. We conclude that physiologically relevant thresholds provide a more robust way to estimate health impacts, and that wet bulb temperature alone is insufficient as an indicator of hazardous heat.
Neural ADMIXTURE for rapid genomic clustering
Authors: Dominguez Mantes Albert , Mas Montserrat Daniel , Bustamante Carlos D. , Giró-i-Nieto Xavier , Ioannidis Alexander G.
Published: July 2023

Characterizing the genetic structure of large cohorts has become increasingly important as genetic studies extend to massive, increasingly diverse biobanks. Popular methods decompose individual genomes into fractional cluster assignments with each cluster representing a vector of DNA variant frequencies. However, with rapidly increasing biobank sizes, these methods have become computationally intractable. Here we present Neural ADMIXTURE, a neural network autoencoder that follows the same modeling assumptions as the current standard algorithm, ADMIXTURE, while reducing the compute time by orders of magnitude surpassing even the fastest alternatives. One month of continuous compute using ADMIXTURE can be reduced to just hours with Neural ADMIXTURE. A multi-head approach allows Neural ADMIXTURE to offer even further acceleration by computing multiple cluster numbers in a single run. Furthermore, the models can be stored, allowing cluster assignment to be performed on new data in linear time without needing to share the training samples.
Synthesis, structures and magnetic studies of hexanuclear lanthanide complexes: SMM behavior of the DyIII analogue and MCE properties of the GdIII analogue
Authors: Kumar Pawan , Kalita Pankaj , Palacios María A. , Kumar Vierandra , Acharya Joydev , Colacio Enrique , Chandrasekhar Vadapalli
Published: July 2023

The syntheses, structures, and magnetic properties of a series of hexanuclear lanthanide (Ln3 + Ln3) assemblies have been studied in detail.
Development of novel aspartic acid-based calcium bio-MOF designed for the management of severe bleeding
Authors: Jha Chandan Bhogendra , Singh Chitrangda , Varshney Raunak , Singh Sweta , Manna Kuntal , Mathur Rashi
Published: July 2023

The synthesis of amino acid-based MOF using calcium as metal ion and l-aspartic acid biocompatible ligand for management of severe bleeding.
Synthesis and anticancer evaluation of acetylated-lysine conjugated gemcitabine prodrugs
Authors: Wang Mengmeng , Qu Kunyu , Zhao Peipei , Yin Xin , Meng Yiwei , Herdewijn Piet , Liu Chao , Zhang Lixin , Xia Xuekui
Published: July 2023

We report a series of acetylated lysine conjugated gemcitabine prodrugs that exhibit highly selective tumor cell growth inhibition and enhanced metabolic stability.
Studies on the stereochemical behaviors of a winding vine-shaped molecular wire of a bithiophene dimer with molecular asymmetry
Authors: Hosokawa Kohei , Tabuchi Kohei , Nakanishi Yuki , Okano Kentaro , Horie Masaki , Mori Atsunori
Published: July 2023

Conversion of a racemic form to a meso form occurs in the solid state of a winding vine-shaped bithiophene wire.
Ultrastrong bonding, on-demand debonding, and easy re-bonding of non-sticking materials enabled by reversibly interlocked macromolecular networks-based Janus-like adhesive
Authors: Wang Zheng Yue , You Yang , Li Ming , Rong Min Zhi , Zhang Ming Qiu
Published: July 2023

A Janus-like adhesive derived from in situ self-stratification of reversibly interlocked macromolecular networks can firmly glue hydrophobic and hydrophilic materials. Moreover, the adhesive is recyclable and reusable with the aid of warm ethanol.
Redox-active ions unlock substitutional doping in halide perovskites
Authors: Molenda Zuzanna , Politi Bastien , Clerc Raphaël , Abbas Mamatimin , Chambon Sylvain , Bassani Dario M. , Hirsch Lionel
Published: July 2023

Electrical doping of metal halide perovskites (MPHs) is a key step towards the use of this efficient and cost-effective semiconductor class in modern electronics.
Recent progress in organic–metal complexes for organic photovoltaic applications
Authors: Lv Qianglong , Yu Runnan , Shi Rui , Tan Zhan’ao
Published: July 2023

Organic–metal complexes (OMCs) are endowed with new functions and properties due to the characteristics of valence changes of metal ions and the diversity of organic molecular structures.
Synthesis and photophysical properties of helical carbon nanohoops with twisted acene panels
Authors: Liu Rui , Liu Hengxin , Shi Can , Wang Yunfei , Chu Zhuping , Wu Tianlu , Liu Yaru , Wei Wen-Mei , Zheng Ren-Hui , Du Pingwu , Lu Dapeng
Published: July 2023

Helical carbon nanohoops with inserted acene linked at 1,5-position as new finite models of chiral CNTs.
Light-driven redox-relay deracemization of cyclic sulfonamides catalyzed by a chiral-at-metal iridium complex
Authors: Liu Yunfei , Yang Junfeng , Wei Linlin , Jiang Wenfeng , Shi Lei
Published: July 2023

A visible-light-driven redox-relay deracemization of cyclic sulfonamides catalyzed by a chiral-at-metal iridium complex as a single catalyst is described.
A novel numerical method coupling CFD with PSO vs. a mathematical approach in the modeling of photocatalytic degradation of NO
Authors: Zhang Guoqing , Liu Jiayou , Jia Liuhu , Wang Haiming , Tan Zhongchao , Yu Hesheng
Published: July 2023

Coupling multiphysics CFD modeling with a PSO optimizer as a tool for determining the intrinsic kinetic parameters of NO photodegradation.
Point-of-care testing of infectious diseases: recent advances
Authors: Shang Meiyun , Guo Jiuchuan , Guo Jinhong
Published: July 2023

Next-generation POCT devices for infectious diseases will improve disease management.
Hydrochar from Sargassum muticum: a sustainable approach for high-capacity removal of Rhodamine B dye
Authors: Spagnuolo D. , Iannazzo D. , Len T. , Balu A. M. , Morabito M. , Genovese G. , Espro C. , Bressi V.
Published: July 2023

An invasive macroalga biomass was valorised by hydrothermal carbonization. The resultant carbonaceous materials exhibited efficient adsorption of hazardous organic pollutants in water due to their favourable physicochemical and textural properties.
Selective radionuclide and heavy metal sorption using functionalised magnetic nanoparticles for environmental remediation
Authors: Aberdeen Stuart , Cali Eleonora , Vandeperre Luc , Ryan Mary. P.
Published: July 2023

In this paper the removal of a wide range of heavy metal ions from different chemical environments has been explored with the use of phosphate-functionalised superparamagnetic iron oxide nanoparticles (SPIONs), specifically magnetite (Fe3O4).
A strong-alkali resistant zinc–organic framework with 1,3,6,8-tetra(pyridin-4-yl)pyrene for efficient photocatalytic hydrogen evolution
Authors: Yang Guo-Li , Xie Yao , Jiao Zhuo-Hao , Zhao Jian , Hou Sheng-Li , Shi Ying , Han Jie , Zhao Bin
Published: July 2023

A 3D Zn-MOF was for the first time synthesized from TTPy, and it exhibited excellent alkali-stability and high H2production rate (315.06 μmol g−1h−1) in photocatalytic experiments.
Mid-infrared spectroscopy and machine learning for postconsumer plastics recycling
Authors: Stavinski Nicholas , Maheshkar Vaishali , Thomas Sinai , Dantu Karthik , Velarde Luis
Published: July 2023

Machine learning of the mid-infrared spectra of postconsumer plastics will help prevent, separate, and purify wastestreams contributing to global pollution.