bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase Saturation Control on Vorticity Enhances Mixing in Porous Media
Authors: Velásquez‐Parra Andrés , Marone Federica , Kaufmann Rolf , Griffa Michele , Jiménez‐Martínez Joaquín 
Published: April 2024

AbstractMixing controls the fate of any solute entering porous media. Hence, an understanding of the involved processes is essential for assessing subsurface contamination and planning for its protection. However, the three‐dimensional mechanisms dominating solute mixing in the presence of several fluid phases in the pore space, and their dependency on phase saturation degree (fraction of the pore volume occupied by a phase) are unknown. Here, we analyze solute mixing in unsaturated porous media at the pore scale using X‐ray micro‐tomography performed with synchrotron radiation at unprecedented temporal and spatial resolutions for such an investigation. Transport experiments through a synthetic, sand‐like porous medium, followed in 4D using a contrast solution, are performed at different liquid phase saturation degrees. The results reveal larger solute's front deformation at lower saturation, which translates into an enhanced mixing with time. Using different topological indexes, defined based on a description of the liquid phase geometry and of the resulting hydrodynamics, we show an increase in the spatial convergence of flow streamlines at lower saturation, which, in turn, leads to a strengthened helical flow inside the liquid phase. Consequently, this increases the number of shear‐ and vorticity‐dominated deformation regions, as characterized by larger negative and positive Q‐criterion values, respectively. These findings represent a major step toward understanding the control of both saturation and the system's heterogeneity on solute mixing, essential, among others, to assess reactivity in porous media.
An Analytical Framework to Investigate Groundwater‐Atmosphere Interactions Influenced by Soil Properties
Authors: Vogelbacher Anastasia , Aminzadeh Milad , Madani Kaveh , Shokri Nima 
Published: April 2024

AbstractThe interaction between climate and groundwater forms a complex, coupled system that affects land‐atmosphere feedback processes and thus local climatic parameters. We propose an analytical framework that integrates local groundwater information and soil hydrophysical characteristics to identify regions with bidirectional (two‐way) coupling where groundwater is influenced by climatic factors (e.g., precipitation) and may affect local climate (e.g., through surface fluxes). The framework capitalizes on the concept of the evaporation characteristic length to quantify the hydraulic connection of groundwater to the soil surface. To evaluate the framework, we calculate the maximum depth of hydraulic connection (Dmax) between groundwater and the soil surface in Hamburg, Germany. For regions with Dmax exceeding the groundwater depth (d), a bidirectional mode of coupling is defined, while Dmax < d implies a unidirectional coupling mode. Our results indicate that climate driven evaporation changes potentially alter the coupling between groundwater and climate depending on soil texture. Moreover, soil hydraulic properties and shallow groundwater tables could play a crucial role in shifting land‐atmosphere feedback processes by influencing the coupling mode. This research provides insights into the groundwater‐climate interactions under various climatic conditions and soil textures which could contribute to sustainable land‐use management practices, particularly in regions characterized by bidirectional coupling.
Skeletal interoception in osteoarthritis
Authors: Yang Dinglong , Xu Jiawen , Xu Ke , Xu Peng 
Published: April 2024

AbstractThe interoception maintains proper physiological conditions and metabolic homeostasis by releasing regulatory signals after perceving changes in the internal state of the organism. Among its various forms, skeletal interoception specifically regulates the metabolic homeostasis of bones. Osteoarthritis (OA) is a complex joint disorder involving cartilage, subchondral bone, and synovium. The subchondral bone undergoes continuous remodeling to adapt to dynamic joint loads. Recent findings highlight that skeletal interoception mediated by aberrant mechanical loads contributes to pathological remodeling of the subchondral bone, resulting in subchondral bone sclerosis in OA. The skeletal interoception is also a potential mechanism for chronic synovial inflammation in OA. In this review, we offer a general overview of interoception, specifically skeletal interoception, subchondral bone microenviroment and the aberrant subchondral remedeling. We also discuss the role of skeletal interoception in abnormal subchondral bone remodeling and synovial inflammation in OA, as well as the potential prospects and challenges in exploring novel OA therapies that target skeletal interoception.
NCAPD3 exerts tumor-promoting effects in prostatic cancer via dual impact on miR-30a-5p by STAT3-MALAT1 and MYC
Authors: Zhang Yi , Shao Yingying , Ren Jia , Fang Yuanyuan , Yang Bolin , Lu Shan , Liu Ping 
Published: April 2024

AbstractNon-SMC condensin II complex subunit D3 (NCAPD3) is a subunit of the non-structural maintenance of chromosomes condensin II complex, which involves chromosome condensation and segregation during mitosis. NCAPD3 has recently been demonstrated as a crucial oncogenic factor. However, the underlying mechanism of NCAPD3 in prostate cancer (PCa) remains not completely clear. In this study, we confirmed that lncRNA MALAT1 was induced by NCAPD3-STAT3, and the expression of miR-30a-5p was controlled by NCAPD3 in PCa cells by miRNA-seq. Through quantitative real-time PCR, fluorescence in situ hybridization, western blotting, and immunohistochemistry assay, we demonstrated that miR-30a-5p was lowly expressed in PCa cells and tissues compared to the controls, which was contrary to NCAPD3 expression and markedly downregulated by NCAPD3. Then, MALAT1 was analyzed for the complementary sequence in the potential interaction with miR-30a-5p by using the predicted target module of public databases. Dual-luciferase reporter assay and RNA immunoprecipitation were carried out to verify that MALAT1 functioned as a sponge for miR-30a-5p to reduce miR-30a-5p expression. Meanwhile, MYC acted as a transcriptional repressor to directly bind the promoter of the miR-30a-5p located gene and repress the miR-30a-5p expression. Furthermore, the upregulation of NCAPD3 on cell viability and migration was significantly attenuated in PC-3 cells when miR-30a-5p was overexpressed. NCAPD3 overexpression also accelerated tumor growth in the xenograft mouse model and repressed miR-30-5p. In summary, this work elucidates NCAPD3 inhibits miR-30a-5p through two pathways: increasing STAT3-MALAT1 to sponge miR-30a-5p and increasing MYC to directly inhibit miR-30a-5p transcription, which could serve as potential therapeutic targets for prostate cancer.
Transcriptional signature of durable effector T cells elicited by a replication defective HCMV vaccine
Authors: Ye Xiaohua , Shih David J. H. , Ku Zhiqiang , Hong Junping , Barrett Diane F. , Rupp Richard E. , Zhang Ningyan , Fu Tong-Ming , Zheng W. Jim , An Zhiqiang 
Published: April 2024

AbstractHuman cytomegalovirus (HCMV) is a leading infectious cause of birth defects and the most common opportunistic infection that causes life-threatening diseases post-transplantation; however, an effective vaccine remains elusive. V160 is a live-attenuated replication defective HCMV vaccine that showed a 42.4% efficacy against primary HCMV infection among seronegative women in a phase 2b clinical trial. Here, we integrated the multicolor flow cytometry, longitudinal T cell receptor (TCR) sequencing, and single-cell RNA/TCR sequencing approaches to characterize the magnitude, phenotype, and functional quality of human T cell responses to V160. We demonstrated that V160 de novo induces IE-1 and pp65 specific durable polyfunctional effector CD8 T cells that are comparable to those induced by natural HCMV infection. We identified a variety of V160-responsive T cell clones which exhibit distinctive “transient” and “durable” expansion kinetics, and revealed a transcriptional signature that marks durable CD8 T cells post-vaccination. Our study enhances the understanding of human T-cell immune responses to V160 vaccination.
A serine-conjugated butyrate prodrug with high oral bioavailability suppresses autoimmune arthritis and neuroinflammation in mice
Authors: Cao Shijie , Budina Erica , Raczy Michal M. , Solanki Ani , Nguyen Mindy , Beckman Taryn N. , Reda Joseph W. , Hultgren Kevin , Ang Phillip S. , Slezak Anna J. , Hesser Lauren A. , Alpar Aaron T. , Refvik Kirsten C. , Shores Lucas S. , Pillai Ishita , Wallace Rachel P. , Dhar Arjun , Watkins Elyse A. , Hubbell Jeffrey A. 
Published: April 2024

AbstractButyrate—a metabolite produced by commensal bacteria—has been extensively studied for its immunomodulatory effects on immune cells, including regulatory T cells, macrophages and dendritic cells. However, the development of butyrate as a drug has been hindered by butyrate’s poor oral bioavailability, owing to its rapid metabolism in the gut, its low potency (hence, necessitating high dosing), and its foul smell and taste. Here we report that the oral bioavailability of butyrate can be increased by esterifying it to serine, an amino acid transporter that aids the escape of the resulting odourless and tasteless prodrug (O-butyryl-l-serine, which we named SerBut) from the gut, enhancing its systemic uptake. In mice with collagen-antibody-induced arthritis (a model of rheumatoid arthritis) and with experimental autoimmune encephalomyelitis (a model of multiple sclerosis), we show that SerBut substantially ameliorated disease severity, modulated key immune cell populations systemically and in disease-associated tissues, and reduced inflammatory responses without compromising the global immune response to vaccination. SerBut may become a promising therapeutic for autoimmune and inflammatory diseases.
Identification of responsive genes to multiple abiotic stresses in rice (Oryza sativa): a meta-analysis of transcriptomics data
Authors: Azad Mahnaz , Tohidfar Masoud , Ghanbari Moheb Seraj Rahele , Mehralian Mohammad , Esmaeilzadeh-Salestani Keyvan 
Published: April 2024

AbstractAbiotic stresses limit the quantity and quality of rice grain production, which is considered a strategic crop in many countries. In this study, a meta-analysis of different microarray data at seedling stage was performed to investigate the effects of multiple abiotic stresses (drought, salinity, cold situation, high temperature, alkali condition, iron, aluminum, and heavy metal toxicity, nitrogen, phosphorus, and potassium deficiency) on rice. Comparative analysis between multiple abiotic stress groups and their control groups indicated 561 differentially expressed genes (DEGs), among which 422 and 139 genes were up-regulated and down-regulated, respectively. Gene Ontology analysis showed that the process of responding to stresses and stimuli was significantly enriched. In addition, pathways such as metabolic process and biosynthesis of secondary metabolites were identified by KEGG pathway analysis. Weighted correlation network analysis (WGCNA) uncovered 17 distinct co-expression modules. Six modules were significantly associated with genes involved in response to abiotic stresses. Finally, to validate the results of the meta-analysis, five genes, including TIFY9 (JAZ5), RAB16B, ADF3, Os01g0124650, and Os05g0142900 selected for qRT-PCR analysis. Expression patterns of selected genes confirmed the results of the meta-analysis. The outcome of this study could help introduce candidate genes that may be beneficial for use in genetic engineering programs to produce more tolerant crops or as markers for selection.
Development and validation of prognostic nomographs for patients with cervical cancer: SEER-based Asian population study
Authors: Zeng Siyuan , Yang Ping , Xiao Simin , Liu Lifeng 
Published: April 2024

AbstractTo develop and validate a nomograph to predict the long-term survival probability of cervical cancer (CC) patients in Asia, Surveillance, Epidemiology, and End Results (SEER) were used to collect information about CC patients in Asia. The patient data were randomly sampled and divided into a training group and a validation group by 7:3. Least absolute shrinkage and selection operator (LASSO) regression was used to screen key indicators, and multivariate Cox regression model was used to establish a prognostic risk prediction model for CC patients. The receiver operating characteristic (ROC) curve and decision curve analysis (DCA) were adopted to comprehensively evaluate the nomogram model. LASSO regression and multivariate Cox proportional hazards model analysis showed that age, American Joint Committee on Cancer (AJCC) Stage, AJCC T, tumor size, and surgery were independent risk factors for prognosis. The ROC curve results proved that the area under curve (AUC) values of the training group in 3 and 5 years were 0.837 and 0.818, The AUC values of the validation group in 3 and 5 years were 0.796 and 0.783. DCA showed that the 3- and 5-year overall survival (OS) nomograms had good clinical potential value. The nomogram model developed in this study can effectively predict the prognosis of Asian patients with CC, and the risk stratification system based on this nomogram prediction model has some clinical value for discriminating high-risk patients.
Simultaneous removal of caesium and strontium using different removal mechanisms of probiotic bacteria
Authors: Endo Rin , Karasawa Satoshi , Aoyagi Hideki 
Published: April 2024

AbstractWhen radioactive materials are released into the environment due to nuclear power plant accidents, they may enter into the body, and exposing it to internal radiation for long periods of time. Although several agents have been developed that help excrete radioactive elements from the digestive tract, only one type of radioactive element can be removed using a single agent. Therefore, we considered the simultaneous removal of caesium (Cs) and strontium (Sr) by utilising the multiple metal removal mechanisms of probiotic bacteria. In this study, the Cs and Sr removal capacities of lactobacilli and bifidobacteria were investigated. Observation using an electron probe micro analyser suggested that Cs was accumulated within the bacterial cells. Since Sr was removed non metabolically, it is likely that it was removed by a mechanism different from that of Cs. The amount of Cs and Sr that the cells could simultaneously retain decreased when compared to that for each element alone, but some strains showed only a slight reduction in removal. For example, Bifidobacterium adolescentis JCM1275 could simultaneously retain 55.7 mg-Cs/g-dry cell and 8.1 mg-Sr/g-dry cell. These results demonstrated the potentials of utilizing complex biological system in simultaneous removal of multiple metal species.
Hybrid genetic algorithm-simulated annealing based electric vehicle charging station placement for optimizing distribution network resilience
Authors: Kumar Boya Anil , Jyothi B. , Singh Arvind R. , Bajaj Mohit , Rathore Rajkumar Singh , Tuka Milkias Berhanu 
Published: April 2024

AbstractRapid placement of electric vehicle charging stations (EVCSs) is essential for the transportation industry in response to the growing electric vehicle (EV) fleet. The widespread usage of EVs is an essential strategy for reducing greenhouse gas emissions from traditional vehicles. The focus of this study is the challenge of smoothly integrating Plug-in EV Charging Stations (PEVCS) into distribution networks, especially when distributed photovoltaic (PV) systems are involved. A hybrid Genetic Algorithm and Simulated Annealing method (GA-SAA) are used in the research to strategically find the optimal locations for PEVCS in order to overcome this integration difficulty. This paper investigates PV system situations, presenting the problem as a multicriteria task with two primary objectives: reducing power losses and maintaining acceptable voltage levels. By optimizing the placement of EVCS and balancing their integration with distributed generation, this approach enhances the sustainability and reliability of distribution networks.
Inhibition of co-occurring weeds and young sugarcane seedling growth by perennial sugarcane root extract
Authors: Wang Xiaoming , Wang Shilong , Zhu Jinghuan , Li Lei , Ma Junjun , Zuo Linzhi , Sun Xiaobo , Chen Bi , Yang Zuli 
Published: April 2024

AbstractAllelopathy is a process whereby a plant directly or indirectly promotes or inhibits growth of surrounding plants. Perennial sugarcane root extracts from various years significantly inhibited Bidens pilosa, Digitaria sanguinalis, sugarcane stem seedlings, and sugarcane tissue-cultured seedlings (P < 0.05), with maximum respective allelopathies of − 0.60, − 0.62, − 0.20, and − 0.29. Allelopathy increased with increasing concentrations for the same-year root extract, and inhibitory effects of the neutral, acidic, and alkaline components of perennial sugarcane root extract from different years were significantly stronger than those of the control for sugarcane stem seedlings (P < 0.05). The results suggest that allelopathic effects of perennial sugarcane root extract vary yearly, acids, esters and phenols could be a main reason for the allelopathic autotoxicity of sugarcane ratoons and depend on the type and content of allelochemicals present, and that allelopathy is influenced by other environmental factors within the rhizosphere such as the presence of old perennial sugarcane roots. This may be a crucial factor contributing to the decline of perennial sugarcane root health.
TCAD simulation study of heavy ion radiation effects on hetero junctionless tunnel field effect transistor
Authors: Aishwarya K. , Lakshmi B. 
Published: April 2024

AbstractSemiconductor devices used in radiation environment are more prone to degradation in device performance. Junctionless Tunnel Field Effect Transistor (JLTFET) is one of the most potential candidates which overcomes the short channel effects and fabrication difficulties. In this work, 20 nm JLTFET is proposed with Silicon in the drain/channel region whereas source uses different materials, Silicon Germanium (SiGe), Gallium Nitride (GaN), Gallium Arsenide (GaAs), Indium Arsenide (InAs). The device performance is examined by subjecting it to heavy ion radiation at a lower and higher dose of linear energy transfer (LET) values. It can be seen that the most sensitive location is the source/channel (S/C) interface for SiGe, GaN and GaAs whereas the drain/channel (D/C) interface for InAs. Further analysis is carried out at these vulnerable regions by matching IONof all materials. The parameters, transient peak current (Ipeak), collected charge (QC), threshold voltage shift (ΔVth) and bipolar gain (β) are extracted using transient simulations. It is observed that for a lower dose of LET, Ipeakof SiGe is 27% lesser than InAs and for higher dose of LET, SiGe shows 56% lesser Ipeakthan InAs. SiGe is less sensitive at lower and higher dose of LET due to reduced ΔVth, tunneling and electron density.
The epidemic forest reveals the spatial pattern of the spread of acute respiratory infections in Jakarta, Indonesia
Authors: Nasution Yuki Novia , Sitorus Marli Yehezkiel , Sukandar Kamal , Nuraini Nuning , Apri Mochamad , Salama Ngabila 
Published: April 2024

AbstractAcute respiratory infection (ARI) is a communicable disease of the respiratory tract that implies impaired breathing. The infection can expand from one to the neighboring areas at a region-scale level through a human mobility network. Specific to this study, we leverage a record of ARI incidences in four periods of outbreaks for 42 regions in Jakarta to study its spatio-temporal spread using the concept of the epidemic forest. This framework generates a forest-like graph representing an explicit spread of disease that takes the onset time, spatio-temporal distance, and case prevalence into account. To support this framework, we use logistic curves to infer the onset time of the outbreak for each region. The result shows that regions with earlier onset dates tend to have a higher burden of cases, leading to the idea that the culprits of the disease spread are those with a high load of cases. To justify this, we generate the epidemic forest for the four periods of ARI outbreaks and identify the implied dominant trees (that with the most children cases). We find that the primary infected city of the dominant tree has a relatively higher burden of cases than other trees. In addition, we can investigate the timely ($$R_t$$

R
t

) and spatial reproduction number ($$R_c$$

R
c

) by directly evaluating them from the inferred graphs. We find that $$R_t$$

R
t

for dominant trees are significantly higher than non-dominant trees across all periods, with regions in western Jakarta tend to have higher values of $$R_c$$

R
c

. Lastly, we provide simulated-implied graphs by suppressing 50% load of cases of the primary infected city in the dominant tree that results in a reduced $$R_c$$

R
c

, suggesting a potential target of intervention to depress the overall ARI spread.
Emission and performance analysis of diesel engine running with CeO2 nanoparticle additive blended into castor oil biodiesel as a substitute fuel
Authors: Tamrat Samuel , Ancha Venkata Ramayya , Gopal Rajendiran , Nallamothu Ramesh Babu , Seifu Yared 
Published: April 2024

AbstractThe implications of adding cerium oxide (CeO2) nanoparticles as a fuel additive to a castor oil biodiesel–diesel fuel blend on engine performance and emissions in a single-cylinder four-stroke diesel engine under various speed were examined in the current study. The test fuels used were fossil diesel fuels, B5 blend biodiesel (as 5% biodiesel and 95% diesel), B10 blend biodiesel (as 10% biodiesel and 90% diesel), B15 blend biodiesel (as 15% biodiesel and 85% diesel), B20 blend biodiesel (as 20% biodiesel and 80% diesel), and B25 blend biodiesel (as 25% biodiesel and 75% diesel), with cerium oxide (CeO2) nanoparticle additive (75 ppm). The result of the physio-chemical properties of the oil samples was within the limit of the ASTM standard. The addition of CeO2 nano additive to the biodiesel–diesel blends has demonstrated a significant reduction in emission and increased in engine performance for all biodiesel–diesel blends for the engine operating speed range. From the result B25 have the maximum reduction rate in BSFC and B10 have the minimum reduction rate in BSFC. The average maximum increment of thermal efficiency was 22.2% for B10 with CeO2 inclusion. CO emission increased as engine speed increased. HC emission was reduced for all blend, with and without CeO2 nano additions as speed increased. Maximum NOx emission was seen at the rated speed of 2700 rpm without nano additive and at 2900 rpm with nano additive. CeO2 nano additive reduced the soot opacity by 11.56% for all biodiesel–diesel blends for the engine operating speed range. As the objective of this study the results indicates CeO2 nano additive reduced emissions and improved the performance. So, using sustainable biodiesel–diesel blends made from castor oil with CeO2 nano additive advisable in ideal operating conditions for diesel engines.