bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep reinforcement learning for multiple reservoir operation planning in the Chao Phraya River Basin
Authors: Phankamolsil Yutthana , Rittima Areeya , Sawangphol Wudhichart , Kraisangka Jidapa , Tabucanon Allan Sriratana , Talaluxmana Yutthana , Vudhivanich Varawoot
Published: January 2025

This study demonstrates application of Deep Deterministic Policy Gradient (DDPG)-based algorithm to provide comprehensive and flexible plans for reservoir operation planning of the multiple reservoir system in the Chao Phraya River Basin (CPYRB), Thailand aiming to mitigate flood and drought risks in the region. The multi-agent-based Deep Reinforcement Learning (DRL) model is accordingly constructed considering 7-D predicted inflow, reservoir water released from adjacent reservoir, downstream flow condition, and changes in reservoir water storage, as state variables. The desired goal is to increase water storage levels in all reservoirs by 10–15% to ensure higher potential in supplying water for crop cultivation over the dry seasons and preventing flood occurrences during wet season. Simulation results from 2009 to 2022 indicate that DRL–DDPG-based algorithm can perform well in solving sequential decision problems for optimal operation of multiple reservoir system to achieve the desired water storage goal. It can offer realistic simulation results of seasonal and annual release schemes and reservoir release ratios among reservoirs in the system compared to actual operation and Fmincon and ANFIS optimizations. Importantly, DRL model demonstrates a significant advantage in view of increasing the long-term water storage levels in all reservoirs as targeted in the modelling process while maintaining the similar and consistent release schemes in the reservoir system. For the multipurpose multiple reservoir system operation, adjusting the dynamic desired goals within multi-agent-based RL model is advisable to attain the specific desired outcomes and address various water scenarios.
What colors are the bricks? Unboxing the DeFi model- A literature survey, empirical study, and taxonomy of decentralized finance
Authors: Schueffel Patrick
Published: January 2025

Decentralized finance (DeFi) is gaining momentum in the world of banking, finance, and beyond. Yet, there remains a notable lack of scholarly research addressing the foundational principles and concepts underlying DeFi. In response to this gap, this study undertakes an extensive investigation into DeFi, drawing upon existing academic literature and insights from industry experts to develop a taxonomy of DeFi's attributes, operational models, and associated risks. This classification sharpens the definition of DeFi and yields critical insights for scholars and industry professionals keen on advancing DeFi's technological applications. By pinpointing essential characteristics of DeFi, mapping out its diverse business models, and highlighting the risks for DeFi users, this research contributes to the academic dialogue. It lays down a comprehensive framework for understanding DeFi, paving the way for subsequent studies and practical implementations in this dynamic area.
The translation initiation factor eIF2 is phosphorylated to inhibit protein translation through reactive oxygen species under nutrient deficiencies in Arabidopsis
Authors: Cui Xiaona , Cao Yuanyuan , Lv Mengyang , Zhou Shuhao , Chen Meijun , Li Chengwei , Zhang Hairong
Published: January 2025

Nitrogen (N), phosphorus (P) or potassium (K) deficiency in plants can lead to a decrease in amino acid and protein synthesis. However, it is unknown how protein translation gets repressed during macronutrient deficiencies. Previous research has shown that general control non-depressible 1 (GCN1) cooperate with GCN2 to phosphorylate the alpha subunit of eukaryotic translation initiation factor (eIF2α). In this study, we observed phosphorylation of eIF2α under N, P, and K deficiencies, which was found to be lost in gcn1. Mutant gcn1 displayed higher sensitivity to macronutrient deficiencies compared to the wild-type (WT). The evidence of in situ reactive oxygen species (ROS) accumulation in leaves indicated that macronutrient starvation triggers ROS production. Treatment with Dimethylthiourea (DMTU), a ROS scavenger, eliminated ROS and reversed eIF2α phosphorylation induced by nutrient deficiency. Moreover, it was discovered that protein translation was reduced under N or K deficiency in the WT but not in gcn1, whereas under P deprivation, protein translation was reduced in both the WT and gcn1. We additionally found that DMTU can partially recover translation inhibition under N or K deprivation. Taken together, it is concluded that GCN1-GCN2-eIF2α pathway is regulated by ROS and is essential for plant survival under macronutrient starvation conditions.
The effect of commodity index trading in agricultural futures markets: a Factor-Augmented Vector Autoregressive (FAVAR) approach
Authors: Braeuel Felix , Thomassin Paul J.
Published: January 2025

Commodity index trading in futures markets is a relatively new investment strategy whose consequences are not fully understood. This paper tests the hypothesis that long-only, passive index trading in agricultural futures markets influences futures prices. Vector Autoregressive (VAR) models are a common empirical research approach for analyzing index trading. Factor-Augmented Vector Autoregression (FAVAR) models are a new approach to analyzing index trading. FAVAR models can incorporate a large data set into the traditional VAR framework. Using a FAVAR model improves the analysis by including additional market factors relevant to futures price formation. Models were estimated for 13 agricultural commodities (corn, soybean, soybean oil, soybean meal, soft red winter wheat, hard red winter wheat, cotton, cocoa, sugar, coffee, live cattle, feeder cattle, and lean hog) from January 2006 to December 2022. The results demonstrate the added value of FAVAR models in explaining the dynamics between prices and index trading. The conclusions are similar to other findings that prices lead index positions; however, adding demand-related data through a FAVAR model allows for a better understanding of market dynamics.
Why the marketplace of ideas needs more markets
Authors: Chomanski Bartlomiej
Published: January 2025

It is frequently argued that false and misleading claims, spread primarily on social media, are a serious problem in need of urgent response. Current strategies to address the problem – relying on fact-checks, source labeling, limits on the visibility of certain claims, and, ultimately, content removals – face two serious shortcomings: they are ineffective and biased. Consequently, it is reasonable to want to seek alternatives. This paper provides one: to address the problems with misinformation, social media platforms should abandon third-party fact-checks and rely instead on user-driven prediction markets. This solution is likely less biased and more effective than currently implemented alternatives and, therefore, constitutes a superior way of tackling misinformation.
Una cocina para el procesamiento de Chenopodium quinoa Willd. en el poblado alto del pukara El Carmen 1, Tucumán, Argentina (ca. 1200-1450 dC)
Authors: Longo Agustina , López María Laura
Published: January 2025

El objetivo del presente trabajo es analizar el registro de Chenopodium recuperado en el poblado pukara El Carmen 1, sector centro-occidental del valle de Santa María, Tucumán (ca. 1200-1450 dC). Para ello se trabajó con una muestra de 310 macrorrestos provenientes de las excavaciones realizadas en el poblado alto (recinto 13, sector VI). El predominio y alta densidad de granos de Chenopodium quinoa Willd. y Chenopodium cf. quinoa Willd. con evidencias de procesamiento en la estructura de combustión, podría corresponder a prácticas de tostado y/o hidratación en el marco de preparaciones culinarias. La ubicación del recinto 13 en el espacio de mayor jerarquía dentro del sitio y su posición centralizada dentro del sector, sugieren la importancia de la quinoa para los habitantes del poblado y llevan a pensar en su rol en el marco de encuentros, ceremonias o eventos rituales en los que el procesamiento y la elaboración de comidas y/o bebidas adquieren importancia.
Time perception in bipolar disorder: a systematic review
Authors: Escelsior Andrea , Amadeo Maria Bianca , Inuggi Alberto , Guzzetti Margherita , Massalha Yara , Trabucco Alice , Marenco Giacomo , Pereira da Silva Beatriz , Gori Monica , Northoff Georg , Amore Mario , Serafini Gianluca
Published: January 2025

Objective:

Time distortions characterise severe mental disorders, exhibiting different clinical and neurobiological manifestations. This systematic review aims to explore the existing literature encompassing experimental studies on time perception in patients with bipolar disorder (BD), considering psychopathological and cognitive correlates.

Methods:

Studies using an experimental paradigm to objectively measure the capacity to judge time have been searched for. Selected studies have been described based on whether i) explicit or implicit time perception was investigated, ii) the temporal intervals involved were sub-second or supra-second, and iii) a perceptual or motor timing paradigm was used.

Results:

Only 11 met the criteria for inclusion in the review. The available literature shows that the performance of BD patients mostly aligns with controls within sub-second timeframes (six articles), while a different pattern emerges within supra-second intervals based on the clinical phase of the disease (seven articles). Specifically, for longer temporal spans, BD patients tend to overestimate the duration during manic states and underestimate it during depressive states. Notably, no studies have directly investigated the neurobiological mechanisms associated with time perception.

Conclusion:

This review indicates that BD patients exhibit time perception similar to controls within sub-second intervals, but tend to overestimate time and underestimate it based on the clinical phase within supra-second intervals. Expanding the understanding of time perception in BD, particularly in relation to clinical phases and cognitive function, is of great importance. Such insights could deepen our understanding of the disorder, refine diagnostic processes, and guide the development of innovative therapeutic interventions.
Measuring legislators’ ideological position in large chambers using pairwise-comparisons
Authors: Breunig Christian , Guinaudeau Benjamin
Published: January 2025

Our understanding of politics often relies on the ideological placement of political actors—ranging from scaling legislative roll-call voting in the United States to text-based classifications of political parties in Europe. A particularly thorny problem remains estimating individual positions in legislatures with strong partisan discipline. We improve upon recently developed measurement strategies and propose a novel approach for estimating legislators’ ideological positions: an expert survey in which respondents compare pairs of representatives on a left-right dimension. The innovation of our approach lies in the combination of four particular features. First, we rely on political youth leaders who are insightful and easy to recruit. Second, the rating task does not involve numeric scaling and consists of simple pairwise comparisons. Third, we efficiently and automatically detect informative comparisons to reduce the cost and length of the survey without compromising our estimates. Fourth, we use a Bayesian Davidson model with random effects to generate an ideological position for each legislator. As an empirical illustration, we estimate the placement of the 709 members of the 19th German Bundestag. Several validity tests show that our model captures variation within and across political parties. Our estimates offer a thorough benchmark to validate alternative measurement strategies. The presented measurement strategy is flexible and easily extendable to diverse political settings because it can capture comparisons among political actors across time and space.
Breakbulk Pasts and Containerized Futures: Submergent Histories on a Saltwater Frontier
Authors: Kahn Jeffrey S.
Published: January 2025

This article examines the history of Haitian-owned freighters that have been trading between Haiti and the Miami River since the 1970s, how this shipping economy became racialized in ways that marked it and the river with a “threatening” Haitian Blackness, and how local government agencies, real estate developers, and law enforcement officials worked to remake the aesthetics of the river as something other than Haitian and Black. Projects to re-racialize the riverway played with the spurious surface-and-subsurface spatial logic of racial discourses more generally—that is, the mistaken but widely-held belief that visible, physical markers of race reveal hidden capacities and propensities. Policing that pushed Haitian commerce into an economy of containerization—a race- and class-marked shipping technology on the river—allowed the Haiti trade to “pass” as non-Haitian on a gentrifying waterway. Law enforcement programs that seized and sank Haitian freighters to create artificial reefs off the Florida coast bluewashed the river’s surface and its ethnoracially coded, “polluting” vessels by transforming them into subsurface, “White” recreational ecologies. These processes reveal how politically fraught contests over racialization recruit layered material environments as part of larger projects of policing, re-racialization, and urban renewal. In exploring this history, the article pushes against arguments from some quarters for a “post-critical” turn by demonstrating that reflexive critique, with its focus on the hidden and the submerged, remains necessary for grasping the ways racialization processes operate through structures of material and discursive layering.
The kinetic ion-temperature-gradient-driven instability and its localisation
Authors: Rodríguez E. , Zocco A.
Published: January 2025

We construct a description of ion-temperature-gradient (ITG)-driven localised linear modes which retains both wave–particle and magnetic drift resonant effects while capturing the field-line dependence of the electrostatic potential. We exploit the smallness of the magnetic drift and the strong localisation of the mode to resolve the problem with a polynomial–Gaussian expansion in the field-following coordinate. A simple semianalytical formula for the spectrum of the mode is shown to capture long wavelength Landau damping, ion-scale Larmor radius stabilisation, weakening of Larmor radius effects at short wavelengths and magnetic-drift resonant stabilisation. These elements lead to linear spectra with multiple maxima as observed in gyrokinetic simulations in stellarators. Connections to the transition to extended eigenfunctions and those localised by less unfavourable curvature regions (hopping solutions) are also made. The model provides a clear qualitative framework with which to interpret numerically simulated ITG modes’ linear spectra with realistic geometries, despite its limitations for exact quantitative predictions.
Exploring the language of Swedish social media: A contrastive corpus analysis
Authors: Coussé Evie , Adesam Yvonne
Published: January 2025

This article explores the language of social media by analyzing a selection of linguistic features in four corpora of Swedish social media available at Språkbanken Text: Blog mix, Familjeliv, Flashback, and Twitter. Previous research describes the language of these corpora as informal, spoken-like, unedited, non-standard, and innovative. Our corpus analysis confirms the informal and spoken-like nature of social media, while also showing that these traits are unevenly distributed across the various social media corpora and that they are also present in other traditional written corpora, such as novels. Our findings also reveal that the social media corpora show traits of involved and interactional language.
The role of dialect in comedy performances: focus on enregisterment and humor
Authors: GERWIN JOHANNA
Published: January 2025

Many of the most popular comedy performances are rich in non-standard linguistic features of English. This article addresses how dialect contributes to the humor in comedy performances, and how humorous dialect performance leads to the enregisterment of a dialect. It applies enregisterment theory to online clips of three live comedy performances by Stephen Buchanan (‘How to survive Glasgow’), Ali G (‘Harvard Commencement Speech 2004’) and Riaad Moosa (‘I have a weird accent’), and one clip from the British sitcom PhoneShop (2009–13). All four dialectal performances showcase the metalinguistic activity central to enregisterment processes. However, in each performance, the dialect also fulfils a dedicated function in the construction of humor, ranging from building audience rapport to the subversion of a (linguistic) status quo. It is argued that just as dialect can help performers to be funnier, humor can help a dialect to become more enregistered.
Exploring socio-economic inequalities in mental healthcare utilization in adults with self-reported psychological distress: a survey-registry linked cohort design
Authors: Muwonge J. J. , Dalman C. , Burström B. , Jablonska B. , Hollander A-C.
Published: January 2025

Aims

Although individuals with lower socio-economic position (SEP) have a higher prevalence of mental health problems than others, there is no conclusive evidence on whether mental healthcare (MHC) is provided equitably. We investigated inequalities in MHC use among adults in Stockholm County (Sweden), and whether inequalities were moderated by self-reported psychological distress.

Methods

MHC use was examined in 31,433 individuals aged 18–64 years over a 6-month follow-up period, after responding to the General Health Questionnaire-12 (GHQ-12) in 2014 or the Kessler Six (K6) in 2021. Information on their MHC use and SEP indicators, education, and household income, were sourced from administrative registries. Logistic and negative binomial regression analyses were used to estimate inequalities in gained MHC access and frequency of outpatient visits, with psychological distress as a moderating variable.

Results

Individuals with lower education or income levels were more likely to gain access to MHC than those with high SEP, irrespective of distress levels. Education-related differences in gained MHC access diminished with increasing distress, from a 74% higher likelihood when reporting no distress (odds ratio, OR = 1.74 [95% confidence interval, 95% CI: 1.43–2.12]) to 30% when reporting severe distress (OR = 1.30 [0.98–1.72]). Comparable results were found for secondary care but not primary care i.e., lower education predicted reduced access to primary care in moderate-to-severe distress groups (e.g., OR = 0.63 [0.45–0.90]), and for physical but not digital services. Income-related differences in gained MHC access remained stable or increased with distress, especially for secondary care and physical services.

Among MHC users, we found marginal socio-economic differences in the frequency of outpatient visits, and these differences decreased with increasing distress. Yet, having only primary education with severe distress was associated with fewer outpatient visits compared with having post-secondary education (rate ratio, RR = 0.82; 95% CI: 0.67–1.00). These inequities were especially evident among women and for visits to psychologists, counsellors, or psychotherapists.

Although lower-income groups used services more than others, they still had higher odds of not using services when reporting distress (i.e., those not in contact with services despite scoring ≥3 on the GHQ-12 or ≥8 on the K6; OR = 1.27; 95% CI: 1.15–1.40).

Conclusions

Overall, individuals with lower education and income used MHC services more than their counterparts with higher socio-economic status; however, low-educated individuals faced inequities in primary care and underutilized non-physician services such as visits to psychologists.
First Observation of Dominant Quasi‐Two‐Day Wave With Westward Zonal Wavenumber 3 at the December Solstice During Austral Summer: Links to Persistent Winter Stratopause Warming
Authors: Qin Yusong , Gu Sheng‐Yang , Dou Xiankang , Wei Yafei , Liu Yuxuan , Chen Hao
Published: January 2025

During the 2023/2024 austral summer, the quasi‐two‐day (QTDW) with westward zonal wavenumber 3 (W3) abnormally reached its maximum amplitude at the December solstice (22 December 2023) for the first time in 20 years of Aura Microwave Limb Sounder observations, while the strongest event during austral summer usually occurs ∼2–6 weeks after the December solstice (on average January 21). Diagnostic analysis reveals that the westward winds in the Southern (summer) Hemisphere were anomalously strong (maximum of ∼90 m/s) during December 2023, which significantly shortened the e‐folding time of QTDW‐W3, and additionally generated the QTDW‐W3 critical layers at the tropical summer stratopause from December 7. These two factors contributed to the earliest amplification of QTDW‐W3. In essence, the cold equatorial stratosphere triggered the exceptionally strong westward winds in the Southern Hemisphere via thermal wind balance, which was related to the enhanced upward middle‐atmosphere Hadley circulation during a prolonged Arctic stratopause warming event.
Regulatory non-coding somatic mutations as drivers of neuroblastoma
Authors: Montella Annalaura , Tirelli Matilde , Lasorsa Vito Alessandro , Aievola Vincenzo , Cerbone Vincenza , Manganiello Rosa , Iolascon Achille , Capasso Mario
Published: January 2025

Background

Emerging evidence suggests that non-coding somatic single nucleotide variants (SNVs) in cis-regulatory elements (CREs) contribute to cancer by disrupting gene expression networks. However, the role of non-coding SNVs in cancer, particularly neuroblastoma, remains largely unclear.

Methods

SNVs effect on CREs activity was evaluated by luciferase assays. Motif analysis and ChIP-qPCR experiments were employed to reveal the transcription factors (TFs) involved in these processes. We exploited CRISPR-Cas9 experiments to elucidate the role of these SNVs on the CREs target genes expression. Cell proliferation and invasion assays were performed to assess their role in neuroblastoma tumorigenesis.

Results

Our findings demonstrate that non-coding SNVs modify the transcriptional activity of two CREs altering the binding of STAT3 and SIN3A. Therefore, these SNVs reduce the expression of CTTNBP2 and MCF2L. We demonstrate that these two genes act as tumor suppressor in neuroblastoma. These pathogenetic SNVs may serve as oncogenic drivers by impairing the transcriptional programs essential for neuronal development and differentiation in which both the investigated TFs and target genes are involved.

Conclusion

Overall, the understanding of the functional role of non-coding variants elucidates their impact on tumorigenesis and can uncover new potential targets of cancer therapeutic strategies.
Investigating the association between human brainstem microstructural integrity and hypertension using magnetic resonance relaxometry
Authors: Laporte John P. , Akhonda Mohammad A. B. S. , Cortina Luis E. , Faulkner Mary E. , Gong Zhaoyuan , Guo Alex , Bae Jonghyun , Fox Noam Y. , Zhang Nathan , Bergeron Christopher M. , Ferrucci Luigi , Egan Josephine M. , Bouhrara Mustapha
Published: January 2025

The brainstem plays a vital role in regulating blood pressure, and disruptions to its neural pathways have been linked to hypertension. However, it remains unclear whether subtle microstructural changes in the brainstem are associated with an individual’s blood pressure status. This exploratory, cross-sectional study investigated the relationship between brainstem microstructure, myelination, and hypertensive status in 116 cognitively unimpaired adults (aged 22–94 years). Advanced MRI techniques, including relaxometry (R1, R2) and myelin water fraction (MWF) analysis, were employed to assess microstructural integrity and myelin content in ten brainstem subregions. Our results revealed significant associations between higher microstructural damage or lower myelin content (indicated by lower R1, R2, or MWF values) and hypertensive status, particularly in the midbrain tegmentum. Notably, combining these MRI metrics yielded high classification accuracy (AUC > 0.85). Our findings suggest a potential link between disrupted brainstem tissue integrity, myelin content, and elevated blood pressure, warranting further longitudinal investigations to explore this relationship.
Cell-free expression and SMA copolymer encapsulation of a functional receptor tyrosine kinase disease variant, FGFR3-TACC3
Authors: Snow Alexander J. D. , Wijesiriwardena Tharushi , Lane Benjamin J. , Farrell Brendan , Dowdle Polly C. , Katan Matilda , Muench Stephen P. , Breeze Alexander L.
Published: January 2025

Despite their high clinical relevance, obtaining structural and biophysical data on transmembrane proteins has been hindered by challenges involved in their expression and extraction in a homogeneous, functionally-active form. The inherent enzymatic activity of receptor tyrosine kinases (RTKs) presents additional challenges. Oncogenic fusions of RTKs with heterologous partners represent a particularly difficult-to-express protein subtype due to their high flexibility, aggregation propensity and the lack of a known method for extraction within the native lipid environment. One such protein is the fibroblast growth factor receptor 3 fused with transforming acidic coiled-coil-containing protein 3 (FGFR3-TACC3), which has failed to express to sufficient quality or functionality in traditional expression systems. Cell-free protein expression (CFPE) is a burgeoning arm of synthetic biology, enabling the rapid and efficient generation of recombinant proteins. This platform is characterised by utilising an optimised solution of cellular machinery to facilitate protein synthesis in vitro. In doing so, CFPE can act as a surrogate system for a range of proteins that are otherwise difficult to express through traditional host cell-based approaches. Here, functional FGFR3-TACC3 was expressed through a novel cell-free expression system in under 48 h. The resultant protein was reconstituted using SMA copolymers with a specific yield of 300 µg/mL of lysate. Functionally, the protein demonstrated significant kinase domain phosphorylation (t < 0.0001). Currently, there is no published, high-resolution structure of any full-length RTK. These findings form a promising foundation for future research on oncogenic RTKs and the application of cell-free systems for synthesising functional membrane proteins.
Calcium hydroxide nanoparticles induce cell death, genomic instability, oxidative stress and apoptotic gene dysregulation on human HepG2 cells
Authors: Mohamed Hanan R. H. , Ibrahim Esraa H. , Shaheen Shahd E. E. , Hussein Nesma O. E. , Diab Ayman , Safwat Gehan
Published: January 2025

Calcium hydroxide nanoparticles (Ca(OH)2NPs) possess potent antimicrobial activities and unique physical and chemical properties, making them valuable across various fields. However, limited information exists regarding their effects on genomic DNA integrity and their potential to induce apoptosis in normal and cancerous human cell lines. This study thus aimed to evaluate the impact of Ca(OH)2NPs on cell viability, genomic DNA integrity, and oxidative stress induction in human normal skin fibroblasts (HSF) and cancerous hepatic (HepG2) cells. Cell viability and genomic DNA stability were assessed using the Sulforhodamine B (SRB) assay and alkaline comet assay, respectively. Reactive oxygen species (ROS) levels were measured using 2,7-dichlorofluorescein diacetate, while the expression level of apoptosis-related genes (p53, Bax, and Bcl-2) were quantified using real-time PCR (qRT-PCR). The SRB cytotoxicity assay revealed that a 48-hour exposure to Ca(OH)2NPs caused concentration-dependent cell death and proliferation inhibition in both HSF and HepG2 cells, with IC50 values of 271.93 µg/mL for HSF and 291.8 µg/mL for HepG2 cells. Treatment with the IC50 concentration of Ca(OH)2NPs selectively induced significant DNA damage, excessive ROS generation, and marked dysregulation of apoptotic (p53 and Bax) and anti-apoptotic (Bcl-2) gene expression in HepG2 cells, triggering apoptosis. In contrast, exposure of HSF cells to the IC50 concentration of Ca(OH)2NPs caused no significant changes in genomic DNA integrity, ROS generation, or apoptotic gene expression. These findings indicate that Ca(OH)2NPs exhibit concentration-dependent cytotoxicity in both normal HSF and cancerous HepG2 cells. However, exposure to the IC50 concentration was non-genotoxic to normal HSF cells while selectively inducing genotoxicity and apoptosis in HepG2 cancer cells through DNA breaks and ROS-mediated mechanisms. Further studies are required to explore the biological and toxicological properties and therapeutic potential of Ca(OH)2NPs in hepatic cancer treatment.
Identification of candidate genes involved in Zika virus-induced reversible paralysis of mice
Authors: Morrey John D. , Siddharthan Venkatraman , Wang Hong , Oliveira Alexandre L. R. , Susuki Keiichiro , Kaundal Rakesh , Freeman Sara M. , Thomas Aaron J. , Duhan Naveen , Corry Nathan G.
Published: January 2025

Zika virus (ZIKV) causes a variety of peripheral and central nervous system complications leading to neurological symptoms such as limb weakness. We used a mouse model to identify candidate genes potentially involved in causation or recovery from ZIKV-induced acute flaccid paralysis. Using Zikv and Chat chromogenic and fluorescence in situ RNA hybridization, electron microscopy, immunohistochemistry, and ZIKV RT-qPCR, we determined that some paralyzed mice had infected motor neurons, but motor neurons are not reduced in number and the infection was not present in all paralyzed mice; hence infection of motor neurons were not strongly correlated with paralysis. Consequently, paralysis was probably caused by by-stander effects. To address this, we performed bioinformatics analysis on spinal cord RNA to identify 2058 differentially expressed genes (DEGs) that were altered during paralysis and then normalized after paralysis. Of these “biphasic” DEGs, 951 were up-regulated and 1107 were down-regulated during paralysis, followed by recovery. To refine the search for candidate DEGs we used gene ontology analysis and RT-qPCR to select 3 DEGs that could be involved with the node of Ranvier function and 5 DEGs that could be involved with synaptic function. Among these, SparcL1:Sparc DEG ratios were identified to be inversely correlated with ZIKV-induced paralysis, which is consistent with the known function of SPARC protein to antagonize the synaptogenesis of SPARCL1. Ank3, Sptbn1, and Epb41l3 affecting the structures at and near the nodes of Ranvier were significantly downregulated during ZIKV-induced paralysis. The primary contribution is the identification of 8 candidate genes that may be involved in the causation or recovery of ZIKV-induced paralysis.
Exploration of transfer learning techniques for the prediction of PM10
Authors: Poelzl Michael , Kern Roman , Kecorius Simonas , Lovrić Mario
Published: January 2025

Modelling of pollutants provides valuable insights into air quality dynamics, aiding exposure assessment where direct measurements are not viable. Machine learning (ML) models can be employed to explore such dynamics, including the prediction of air pollution concentrations, yet demanding extensive training data. To address this, techniques like transfer learning (TL) leverage knowledge from a model trained on a rich dataset to enhance one trained on a sparse dataset, provided there are similarities in data distribution. In our experimental setup, we utilize meteorological and pollutant data from multiple governmental air quality measurement stations in Graz, Austria, supplemented by data from one station in Zagreb, Croatia to simulate data scarcity. Common ML models such as Random Forests, Multilayer Perceptrons, Long-Short-Term Memory, and Convolutional Neural Networks are explored to predict particulate matter in both cities. Our detailed analysis of PM10 suggests that similarities between the cities and the meteorological features exist and can be further exploited. Hence, TL appears to offer a viable approach to enhance PM10 predictions for the Zagreb station, despite the challenges posed by data scarcity. Our results demonstrate the feasibility of different TL techniques to improve particulate matter prediction on transferring a ML model trained from all stations of Graz and transferred to Zagreb. Through our investigation, we discovered that selectively choosing time spans based on seasonal patterns not only aids in reducing the amount of data needed for successful TL but also significantly improves prediction performance. Specifically, training a Random Forest model using data from all measurement stations in Graz and transferring it with only 20% of the labelled data from Zagreb resulted in a 22% enhancement compared to directly testing the trained model on Zagreb.
Optimal network sizes for most robust Turing patterns
Authors: Shaberi Hazlam S. Ahmad , Kappassov Aibek , Matas-Gil Antonio , Endres Robert G.
Published: January 2025

Many cellular patterns exhibit a reaction-diffusion component, suggesting that Turing instability may contribute to pattern formation. However, biological gene-regulatory pathways are more complex than simple Turing activator-inhibitor models and generally do not require fine-tuning of parameters as dictated by the Turing conditions. To address these issues, we employ random matrix theory to analyze the Jacobian matrices of larger networks with robust statistical properties. Our analysis reveals that Turing patterns are more likely to occur by chance than previously thought and that the most robust Turing networks have an optimal size, consisting of only a handful of molecular species, thus significantly increasing their identifiability in biological systems. Broadly speaking, this optimal size emerges from a trade-off between the highest stability in small networks and the greatest instability with diffusion in large networks. Furthermore, we find that with multiple immobile nodes, differential diffusion ceases to be important for Turing patterns. Our findings may inform future synthetic biology approaches and provide insights into bridging the gap to complex developmental pathways.
Magmatic evolution of the Kikai caldera revealed by zircon triple dating and its chemistry
Authors: Ito Hisatoshi
Published: January 2025

Reconstructing the volcanic history of the Kikai caldera, a large active volcano that produced a ~ 160 km3 eruption at 7.3 ka off the southern coast of Kyushu Island (southwest Japan), is crucial to assess potential future volcanic hazards at both regional and global scales. However, revealing its volcanic history before the 7.3 ka eruption has been challenging due to the caldera being mostly submerged. In this study, we present evidence that the Kikai caldera erupted a geochemically distinct silicic lava at ~ 250 ka by using zircon triple (U-Pb, Th-Pb, U-Th) dating and its chemistry. The presence of 1.5–1.0 Ma zircons in the 7.3 ka eruption deposits suggests that zircon crystallization in the Kikai caldera began during this period. We further infer large eruptions occurred around 0.7–0.6 Ma, suggesting that the Kikai caldera may have experienced at least 5 major eruptions during its 1.0–1.5-million-year magmatic evolution.
Systemic IFN-I combined with topical TLR7/8 agonists promotes distant tumor suppression by c-Jun-dependent IL-12 expression in dendritic cells
Authors: Sanlorenzo Martina , Novoszel Philipp , Vujic Igor , Gastaldi Tommaso , Hammer Martina , Fari Ourania , De Sa Fernandes Cristiano , Landau Alina D. , Göcen-Oguz Bilge V. , Holcmann Martin , Monshi Babak , Rappersberger Klemens , Csiszar Agnes , Sibilia Maria
Published: January 2025

Dendritic cell (DC) activation by pattern recognition receptors like Toll-like-receptors (TLRs) is crucial for cancer immunotherapies. Here, we demonstrate the effectiveness of the TLR7/8 agonist imiquimod (IMQ) in treating both local tumors and distant metastases. Administered orally, IMQ activates plasmacytoid DCs (pDCs) to produce systemic type I interferons (IFN-I) required for TLR7/8 upregulation in DCs and macrophages, sensitizing them to topical IMQ treatment, which is essential for therapeutic efficacy. The mechanism involves c-Jun/AP-1 mediating TLR7/8 signaling in IFN-I-primed DCs, upregulating the pDC-recruiting chemokine CCL2 and the anti-angiogenic cytokine interleukin-12, which suppresses VEGF-A production leading to tumor necrosis and regression. Combining topical and systemic IMQ or IFN-I generates a CD8+ T cell-dependent response at metastatic sites, reinforced by PD-1 blockade, leading to long-lasting memory. Analysis of cohorts of patients with melanoma demonstrates DC-specific TLR7/8 upregulation by IFN-I, supporting the translational potential of combining systemic IFN-I and topical IMQ to improve immunotherapy of topically accessible tumors.
Biochemical characterization and discovery of inhibitors for PfSir2A: new tricks for an old enzyme
Authors: Donu Dickson , Boyle Emily , Curry Alyson , Cen Yana
Published: January 2025

PfSir2A controls the var virulence gene expression in malaria parasites. Inhibitors targeting PfSir2A are potential antimalarial agents. In the current study, 3-TYP and NR are identified as lead compounds for further inhibitor development.
From 20% single-junction organic photovoltaics to 26% perovskite/organic tandem solar cells: self-assembled hole transport molecules matter
Authors: Sun Xiaokang , Wang Fei , Yang Guo , Ding Xiaoman , Lv Jie , Sun Yonggui , Wang Taomiao , Gao Chuanlin , Zhang Guangye , Liu Wenzhu , Xu Xiang , Satapathi Soumitra , Ouyang Xiaoping , Ng Annie , Ye Long , Yuan Mingjian , Zhang Hongyu , Hu Hanlin
Published: January 2025

The stacking of SAM layers was regulated to form “face-on” orientation via incorporating the volatile solid additive TCB.
Study of the electrochemical performance of Zanthoxylum armatum seed-derived potassium hydroxide-assisted activated carbon as a negatrode material for supercapacitor applications
Authors: Bhattarai Deval Prasad , Aryal Sabin , Shrestha Khem Raj , Mishra Pawan Kumar , Shrestha Timila , Homagai Puspa Lal , Oli Hari Bhakta , Shrestha Ram Lal (Swagat)
Published: January 2025

Activated carbon prepared from the waste biomass of Z. armatum seed by potassium hydroxide activation.
Advancements in drug discovery: integrating CADD tools and drug repurposing for PD-1/PD-L1 axis inhibition
Authors: Sobral Patrícia S. , Carvalho Tiago , Izadi Shiva , Castilho Alexandra , Silva Zélia , Videira Paula A. , Pereira Florbela
Published: January 2025

A pioneering strategy to expedite drug discovery for PD-1/PD-L1 axis inhibition is offered by an integrated approach combining computer-aided drug design (CADD) tools, QSAR modelling, drug repurposing, and molecular docking.
Research on transition metals for the multicomponent synthesis of benzo-fused γ-lactams
Authors: Sead Fadhil Faez , Jain Vicky , Ballal Suhas , Singh Abhayveer , Devi Anita , Chandra Sharma Girish , Joshi Kamal Kant , Kazemi Mosstafa , Javahershenas Ramin
Published: January 2025

Benzo-fused γ-lactams are fundamental in medicinal chemistry, acting as essential elements for various therapeutic agents due to their structural adaptability and capability to enhance biological activity.
Ultrasonically induced liquid-phase exfoliation boosts excellent performance of Bi0.5Sb1.5Te3/PVDF thermoelectric films
Authors: Li Haotian , Ke Shaoqiu , Yu Xiaoxiao , Zhang Haojun , Zhang Xinyang , Nie Xiaolei , Zhu Wanting , Wei Ping , Zhao Wenyu , Zhang Qingjie
Published: January 2025

High thermoelectric performance and excellent cooling performance of flexible Bi2Te3 based films have been achieved via flaky Bi2Te3 powders with weak surface oxidation, prepared by ultrasonically induced liquid-phase exfoliation.
Correction: In vivo transplantation of intrahepatic cholangiocyte organoids with decellularized liver-derived hydrogels supports hepatic cellular proliferation and differentiation in chronic liver injury
Authors: Kaur Impreet , Vasudevan Ashwini , Sanchez-Romero Natalia , Sanyal Arka , Sharma Aarushi , Hemati Hamed , Juneja Pinky , Sharma Aarti , Pla Palacin Iris , Rastogi Archana , Vijayaraghavan Pooja , Ghosh Sourabh , Ramakrishna Seeram , Sarin Shiv K. , Baptista Pedro M. , Tripathi Dinesh M. , Kaur Savneet
Published: January 2025

Correction for ‘In vivo transplantation of intrahepatic cholangiocyte organoids with decellularized liver-derived hydrogels supports hepatic cellular proliferation and differentiation in chronic liver injury’ by Impreet Kaur et al., J. Mater. Chem. B, 2025, 13, 918–928, https://doi.org/10.1039/D4TB01503G.
Effect of heat stabilizer content on the gel characteristic of the modified-recycled PET for 3D printing filament application
Authors: Parneam Nismar , Na Ayutthaya Siriorn Isarankura , Sukhawipat Nathapong
Published: January 2025

This research identified the type of gel in the modified-recycled poly (ethylene terephthalate) (modified-rPET) filament, with various content of heat stabilizer, Pentaerythritol tetrakis(3-(3,5-di-tert-butyl-4-hydroxyphenyl) propionate. The content of the heat stabilizer used in this study were 0, 0.05, 0.1, 0.2, 0.3, 0.4 and 0.5 pph. Gel characteristics of the modified-rPET filament were characterized by using the hot stage microscopy technique. It was found that gels with heat stabilizer at 0-0.3 pph showed the unmeltgel formation characteristic. On the other hand, the addition of heat stabilizer at 0.4-0.5 pph showed the formation of crosslinked-gel characteristic, this gel does not melt even if the temperature reached to the melting temperature. This gel affects the process-ability of 3D printing. Therefore, it becomes clogged at the nozzle of 3D printer. Furthermore, this research also determined the crosslinked-gel contents inside the modified-rPET filaments, with various content of heat stabilizer, by a solvent extraction technique. Using trifluoroacetic acid/dichloromethane blended solution, it was found that at increase of the heat stabilizer content, the higher the content of crosslinked gel were observed significantly.
Growth and bioactivity of Phellinus linteus in the mushroom farm, at different cultivation times
Authors: Jitchum Supapitch , Tabtimmai Lueacha , Phoohinkong Weerachon , Thumthanaruk Benjawan , Zhang Xiaoshuan , Suttisintong Khomson , Rungsardthong Vilai
Published: January 2025

Phellinus linteus (PL) growth depends on environmental conditions such as light intensity, humidity, temperature, and CO2. This research investigated the growth of PL and their bioactive activities in the PL fruiting body from different locations of Top, Middle, and Bottom zones in the mushroom farm, harvested at different cultivation times, up to 18 months. Results showed that PL weights increased from 9.35 g/fruiting body to 46.89 g/fruiting body at 18 months. PL growths at each location were not significantly different during 12 months, while a bit higher growth of PL at the Bottom zone was observed at 18 months. The temperature during the cultivation was 30-35°C with high humidity (83-100%). The Bottom zone indicated the higher CO2 than the other two zones. The bioactivity in PL extracts from the cultivation during at 3-18 months showed a non-significant difference in both TPC, and antioxidant activities analyzed by DPPH. PL extract presented an anti-inflammatory effect comparable to the medicine diclofenac. The potential applications of PL extract inhibit cancer; particularly, the low survival rate of cell cancer by the PL extract present its possible use as a functional ingredient. Further studies of their toxicity on normal cells would benefit the application of PL extract.
Development of functional beverage with rice bran protein (Hom mali 105)
Authors: Saveboworn Wanticha , Rittisak Sriwiang , Schoenlechner Regine , Wangtueai Sutee , Charoen Ratchanee
Published: January 2025

In this research, rice bran protein extracted was added into food model such as fruit juices, and fruit-flavored beverages that are consumed for refreshment, quenching thirst, and nutritional value to make consumers refreshed, quench and provide nutritional value based on important substances added to functional beverages. The development of ready-to-drink fruit juice offers consumers convenience and creates new experiences from functional beverages that were available in the market. The value-added of rice bran by extract the protein and extend its application in food. The enzymetic method was used to extract protein from rice bran (Hom mali 105). Physical and functional properties of rice bran protein extracted had 0.45 g/ml of density, 7.73% of moisture content, 22.32% of protein and 7.28 mg gallic/g for phenolic content and 2,495.26 mg ASC/g sample of ABTS values. The development of functional fruit juice consisted of two concentrate fruit juice (80 red grapes : 20 apples ratio), the mixture was mixed with 60% fruit juice, 30% water, 8% syrup and 2% rice bran protein powder, which was pasteurized under 75 °C for 2 minutes 50 s. Microbial analysis showed that the values met the standard (microbial count less than 250 colonies/ml, Coliform bacteria and Escherichia coli less than <1.1 MPN/100 g). Sensory evaluation of color, flavor, sourness, sweetness, and overall acceptance (n=30) was conducted. The assessment scores for the various attributes were moderately favorable. 91% of consumers accepted of the product. The extracted protein with functional beverage was offers a new alternative for consumers who want to increase the nutritional value in a beverage and diversify the a new alternative beverage product.
Sustainable charcoal production from rubber tree branches (Hevea brasiliensis)
Authors: Sairod Suriyan , Jiamrittiwong Prayut , Puangngernmak Nutdechatorn
Published: January 2025

Dwindling firewood supplies for charcoal production necessitate exploration of alternative sources. Agricultural residues, particularly abundant rubber tree branches, present a promising solution. To evaluate their viability, a study employed a 200-liter charcoal retort kiln with wood gas circulation to carbonize rubber tree branches. The resultant charcoal underwent analysis for moisture content, fixed carbon, volatile matter, ash content, and higher heating value. The findings revealed a 6-hour carbonization process with a peak temperature of 600°C. The produced charcoal displayed favorable properties: 4.78±0.53% moisture content, 11.46±0.99% volatile matter, 6.03±0.22 ash content, 77.73±0.42% fixed carbon, and a higher heating value of 30.97±0.50 MJ/kg. Notably, rubber tree branch charcoal surpassed bamboo, coconut shell, and commercially available options in higher heating value, signifying its potential as a sustainable alternative. Furthermore, it complies with Thai Community Product Standards for wood charcoal used for cooking. These results underscore the promising potential of rubber branches as a sustainable charcoal feedstock, addressing the critical issue of firewood scarcity through waste repurposing.