bluuebunny/crossref_metadata_2025 huggingface dataset:
THE APPLICATION OF THE ARTIFICIAL NEURAL NETWORK (ANN) METHOD FOR FORECASTING THE SOUTHERN OSCILATION INDEX (SOI)
Authors: Fathia Syahla Az Zahra  , Bagus Sumargo  , Siregar Dania , Auria Yusrin Fathya
Published: January 2025

Indonesia's seasons are influenced by global phenomena such as ENSO. This phenomenon affects rainfall intensity in Indonesia through its two main phases: El Nino and La Nina. One method to detect these events is by analyzing the Southern Oscillation Index (SOI). A highly accurate SOI forecasting model is critical for both short-term and long-term development planning, particularly in anticipating future extreme seasons. One of the methods used for forecasting is the Artificial Neural Network (ANN). This study aims to develop an ANN model capable of predicting the SOI index. Based on forecasting using training data, the optimal model architecture identified is 12-7-1, which achieved the smallest MSE value of 0.0095 and a MAPE of 17.6851. With an error rate below 20%, the 12-7-1 architecture demonstrates strong forecasting capabilities. The study forecasts the SOI index for the next 12 months, indicating a trend from negative values at the beginning of the year to more positive values toward the year's end.
ANALYSIS OF BICLUSTERING ITERATIVE SIGNATURE ALGORITHM ON POVERTY DATA IN SULAWESI ISLAND IN 2022
Authors: Yekti Widyaningsih  , Safitri Nabila
Published: January 2025

Poverty in Indonesia is still a problem that must be addressed every year. According to the March 2022 Susenas report, Sulawesi Island ranks third among the six major islands in Indonesia in terms of the percentage of the population living in poverty. This shows that there are still many people living in poverty in Sulawesi. Therefore, the government needs to make the right policies to address this problem. One potential approach is to cluster districts or cities in Sulawesi based on poverty-related variables. The objective of this research is to group the data in two directions: first, by districts or cities and, second, by its variables simultaneously. The formation of these groupings will facilitate the development of the right government policies to address poverty. The appropriate method for these groupings is the biclustering method, which can group observations and characteristics simultaneously so that biclusters formed can be characterized differently. One of the biclustering algorithms is the Iterative Signature Algorithm (ISA), which requires an upper threshold value and a lower threshold value. The threshold value is the value used to determine whether a district or city and variables can be included in a bicluster. The best result is selected based on the average Mean Square Residue (MSR) per volume. Biclustering analysis of poverty data in Sulawesi in 2022 using ISA produced 2 biclusters. Based on these results, the government is expected to make the right policy to overcome poverty problems in Bicluster 1 and Bicluster 2.
Experimental Investigation of Buoyant Flow in Realistic Bedforms With Heterogeneous Wettability
Authors: Ubillus Jose Eduardo , Ni Hailun , DiCarlo David , Meckel Tip
Published: January 2025

Submeter-scale geologic heterogeneity greatly affects CO2 plume migration and retention. In this work, we present meter-scale laboratory experiments that can capture the impact of realistic submeter-scale geologic heterogeneity on multiphase flow and trapping. We produce realistic sedimentary formations consisting of ripple deposits with varying grain size contrast and wettability in a meter-scale slab chamber. Then, we conduct multiphase flow experiments with analog fluids through these structures and measure the saturation patterns, capillary heterogeneity trapping (CHT), and overall trapping performance. When we alter the ripple bedform architecture, variations in trapped saturation and CHT (10–20%) increment are exhibited. Similar growth in trapping performance is also observed when grain size contrast increases. Finally, wettability changes (water- to oil-wet) can increase nonwetting saturation and CHT up to 5% and 10–20%, respectively. These results emphasize the importance of correctly characterizing the impact of small-scale heterogeneities and wettability changes. We believe this is the first time that multiphase flow experiments were conducted in meter-scale domains with realistic ripple bedforms and heterogeneous wettability to investigate plume migration and trapping.
Influencing preference formation through imperceptible target-oriented head movements of the avatar
Authors: Yue Zixiang , Nakata Yoshihiro , Ogawa Kohei , Yoshikawa Yuichiro , Ishiguro Hiroshi
Published: January 2025

This study examined the influence of external interventions involving imperceptible target-oriented head movements of avatars on preference formation of the operators. We focused on subtly manipulating the head direction of the avatar to influence the choices of the operators, akin to natural orienting behaviors such as gaze direction. Our methodology included two preliminary experiments to identify the thresholds at which head movements of an avatar, particularly target-oriented ones, remain undetected by operators. Based on these findings, we developed a system that can discreetly influence the focus of operators toward specific targets. The primary experiment demonstrated that this system effectively affected operator preferences, thereby increasing the appeal of targeted images. This research underscores the potential of using subtle, imperceptible avatar manipulations to affect human preferences. It also highlights the need for safeguards in avatar-based systems against inconspicuous influences and emphasizes ethical and security considerations in such technologies.
Motion-driven Adaptive Frame Selection Strategy for Video Action Recognition
Authors: Ding Hao , Guo Chen , Sun Jing , Jiang Xiaoping , Shi Hongling , Li Jianjin
Published: January 2025

Frame selection is a fundamental issue in video action recognition. It aims to minimize temporal redundancy and reduce computational cost. Current frame sampling strategies either rely on uniform sampling based on motion, lacking emphasis on discriminative frames, or employ complex learning models or additional modal information, compromising generalizability. To address these challenges, this paper presents an adaptive frame selection strategy. It filters redundant frames through motion information and models relationships between each frame and others, thereby predicting the significance of each frame. This strategy combines the advantages of motion prior information and supervised learning. During training, frame importance-related constraints are integrated, guiding frames selection with strong discriminative features as inputs for the action recognition network. This frame selection method is integrated with backbone network structures such as TDN, GCTDN, AIM, and tested on three action datasets, Diving-48, UCF101 and HMDB51.The improvement on action recognition achieved is 4.4% on the Diving-48 dataset, 1.9% on the UCF101 dataset and 2.3% on HMDB51 dataset. Experimental results demonstrate that our selection strategy can be integrated with state-of-the-art action recognition models, leading to improved recognition performance.
Evolution of infrastructure burden for US cities by 2100
Authors: Sutradhar Uttara , Spearing Lauryn , Zou Bo , Chester Mikhail , Derrible Sybil
Published: January 2025

In 2020, 40% of U.S. cities were losing population. As people emigrate, maintaining the infrastructure once built for a growing population can burden the remaining residents. Using population projections, we forecast future infrastructure (following current population growth) up to 2100 and examine infrastructure burden trends across the U.S. in 2050 and 2100. By analyzing per capita residential built-up volume (RBUV) and roadway length (RL), we find that 53% of U.S. cities (out of 30,498) will face an increasing burden by 2100. The extent of this burden varies, with low-density cities being more affected than high-density cities. Around 14% of these cities may initially experience a decreasing burden, only to face an increasing burden before the end of this century. Regardless of their own population trends, cities need to rethink their planning policies to minimize existing or future infrastructure burden. While depopulation is often viewed negatively, it is inevitable. The narrative around depopulation and existing policies that focus solely on growth must change as it presents an opportunity to rethink how infrastructure is planned and managed.
From net-zero to zero-fossil in transforming the EU energy system
Authors: Schreyer Felix , Ueckerdt Falko , Pietzcker Robert , Odenweller Adrian , Merfort Anne , Rodrigues Renato , Strefler Jessica , Lécuyer Fabrice , Luderer Gunnar
Published: January 2025

The EU climate neutrality goal requires a strong reduction in
fossil fuel use by 2050. However, whether a complete phase-out is
feasible and desirable remains unclear. Here, using an integrated
assessment model, we quantify the additional effort needed to
achieve a virtually complete phase-out of fossil fuels in the EU by
2050 compared to a least-cost net-zero scenario. In this least-cost
net-zero scenario, fossil fuel use already decreases by 87% from
2020 to 2050, driven by renewable power, direct electrification and
some biofuels. However, hard-to-abate oil-based hydrocarbons and
natural gas persist and are used primarily for chemicals, aviation
and shipping. Phasing-out these remaining 13% of fossil fuels
requires the large-scale deployment of costly carbon-neutral
e-fuels, which about doubles marginal abatement costs from
300€/tCO2 to 650 €/tCO2 (500-1000 €/tCO2) by 2050. Although a
fossil phase-out target could strengthen EU climate policy
commitment, it also poses additional transformation challenges.
Building Machine Learning Predictive Models for Adolescent Internet Addiction: Key Findings on Self-Esteem and Resilience Interaction
Authors: Liu Rongmei , Wang Saiyi , Tarimo Clifford Silver , Li Quanman , Feng Yifei , Zhao Lipei , Liu Shuaibin , Chen Xinghan , Wu Jian , Zhao Qiuping
Published: January 2025

Objective: Internet addiction (IA) is a significant mental health concern among adolescents. This study aimed to develop machine learning (ML)-based predictive models to identify and explain key risk factors for IA.
Method: A total of 8176 junior high school students from Henan Province were surveyed from April to May 2023. The dataset was randomly divided into training and test sets in an 8:2 ratio. Four ML algorithms were used to predict IA, and feature importance was determined using SHapley Additive exPlanations (SHAP). The XGBoost model, which achieved the highest area under the curve (AUC), was selected for detailed analysis and individualized prediction explanations.
Results: The five most important predictors of IA were negative life events, self-esteem, school connectedness, parent-adolescent cohesion, and psychological resilience. Importantly, an interaction effect was found between self-esteem and psychological resilience: as self-esteem increased, the influence of low resilience transitioned from being a risk factor to a protective factor against IA.
Conclusion: This study demonstrates the power of ML models combined with SHAP for predicting IA and identifying its psychosocial determinants. The findings highlight the critical interplay of self-esteem and psychological resilience, offering valuable insights for clinicians and educators in addressing IA among adolescents.
Bridging Electron and Nuclear Motions in Chemical Reactions through Electrostatic Forces from Reactive Orbitals
Authors: Tsuneda Takao , Taketsugu Tetsuya
Published: January 2025

This study presents a physics-based framework for understanding chemical reactions, highlighting the critical role of the occupied reactive orbital (ORO), the most stabilized occupied orbital during a reaction, in guiding atomic nuclei via electrostatic forces. These forces, termed reactive-orbital-based electrostatic forces (ROEFs), arise from the negative gradient of orbital energy, creating a direct connection between orbital energy variations and nuclear motion. Through the analysis of 48 representative reactions, we identify two predominant types of ROEF behavior: reactions that sustain reaction-direction ROEFs either from the early stages or just before the transition state. These forces carve grooves along the intrinsic reaction coordinates on the potential energy surface (PES), shaping the reaction pathway. This clarifies which types of electron transfer contribute to lowering the reaction barrier. Remarkably, variations in OROs align closely with the curly arrow diagrams
widely used in organic chemistry, bridging the intuitive representation of electron transfer with the rigorous PES-based theoretical framework. This integration facilitates a unified discussion of electron transfer and the electrostatic forces driving nuclear motion. By unifying electronic and nuclear motion theories, this study provides a cohesive framework for understanding the driving forces behind chemical transformations, offering profound insights into the electronic basis of reaction mechanisms.
Microbial Bioheater Driven by the Alternative Oxidase Metabolic Pathway
Authors: Chávez Jorge , Williams Veronica , Beabout Kathryn , Harbaugh Svetlana
Published: January 2025

Smart materials capable of on-demand thermogenesis could be used to prevent cold-related injuries and to maintain biological functions in frigid conditions. To generate such materials, we were inspired by thermogenic plants that use an alternative oxidase respiratory pathway as a main driver of heat production. To transfer this mechanism to an engineerable organism with a small footprint, we overexpressed the alternative oxidase in Pichia pastoris and showed that our modified yeast could generate over eight times as much heat per cell as the parent strain. We have also shown that growing P. pastoris in the presence of antimycin A, which induces endogenous expression of alternative oxidase, changes the growth and heat flow dynamics of the yeast. In the future, we envision our heat-producing microbe could be used to generate smart thermogenic materials that would help maintain people, devices, pharmaceuticals, supplies, and equipment at ideal temperatures in extremely cold environments.
Covalent Docking and Molecular Dynamic Simulation of Potential α-ketothiazole Arginine Derivatives Inhibitors of Coagulation Factor XIa (FXIa). In silico study
Authors: Mercado-Camargo Jairo , Vivas-Reyes Ricardo , Gómez–Estrada Harold
Published: January 2025

While currently clinically administered anticoagulant drugs have demonstrated efficacy, they have also precipitated significant risks such as severe complications including, but not limited to, gastrointestinal bleeding, intracranial hemorrhage, and other potentially essential situations. Coagulation factor XIa (FXIa) is emerging as an important target of current anticoagulant therapies. The present work explores the search for and development of new anticoagulants and their perspectives on treating this condition. A study of molecular covalent docking, molecular dynamics, and calculation of free energy by the MM-GBSA method, followed by the determination of pharmacokinetic parameters of absorption, distribution, excretion, and prediction of the computational model of toxicity (ADME-TOX), was carried out. Four of the 59 ligands studied showed affinity energies of -10.6, -10.4, -9.4, and − 8.8 kcal/mol for molecules M1, M10, M31, and M20, respectively. The molecular dynamics performed on these four ligands showed good stability in the protein-ligand complex, as shown by the RMSD, RMSF determined at a simulation time of 100 ns. As for the free energy, MM-GBSA ligands M1, M10, M20, and M31 were − 49.87, -68.90, -63.95, and − 59.83 kcal/mol, respectively. In the ADME-TOX parameters, all ligands showed promising results in bioavailability, exceptional solubility, no side effects, and extremely low toxicity.
Assessing the potential sensitivity of Typhoon Nesat to climate change under SSP5-8.5 scenario
Authors: Chai Yujie , Nistor Ioan , Mohammadian Abdolmajid , Nakamura Ryota
Published: January 2025

In the context of climate change, understanding how future conditions influence typhoons has become a topic of interest for researchers. However, there is no consensus on how typhoons are projected to change, and the knowledge of how climate variables will affect them is still limited. This study aims to enhance the understanding of drivers of typhoons modifications under climate change through applying pseudo global warming (PGW) technique based on Weather Research and Forecasting (WRF) model under SSP5-8.5 scenario by 2100, taking Typhoon Nesat as a case study. At first, a mini-ensemble of WRF models with optimal performance in representing historical Typhoon Nesat were selected. Subsequently, PGW experiments based on this mini-ensemble were then carried out. To recognize the impacts of different climate factors, four (4) conditions were set in PGW fields: (1) only sea surface temperature (SST); (2) SST and air temperature (AT); (3) SST, AT, relative humidity (RH), and geopotential height (GPH); (4) SST, AT, RH, GPH, and wind velocity. The projections suggest that events similar to Typhoon Nesat will become more intense under future global warming conditions. Specifically, warmer SST plays the dominant role on its intensification, while increases in AT will mitigate some of this effect. These results indicate that in the context of climate change, the intensity of typhoons is likely to increase in the future. This study provides novel information which can help the development of local disaster countermeasures and with the purpose of enhancing the resiliency of local communities.
Enhancing Crop Classification through Remote Sensing: Landsat 8-9 Fusion and Feature Selection
Authors: Ramzan Zeeshan , Ahmed Nisar , Akram Qurat-ul-Ain , Asif Shahzad , Shahbaz Muhammad
Published: January 2025

Remote sensing offers a highly effective method for obtaining accurate information on total cropped area and crop types. The study focuses on crop cover identification for irrigated regions of Central Punjab. Data collection was executed in two stages: the first involved identifying and geocoding six target crops through field surveys conducted in January and February 2023. The second stage involved acquiring Landsat 8-9 imagery for each geocoded field to construct a labeled dataset. The satellite imagery underwent extensive pre-processing, including radiometric calibration for reflectance values, atmospheric correction, and georeferencing verification to ensure consistency within a common coordinate system. Subsequently, image fusion techniques were applied to combine spectral bands from both Landsat 8 and 9, creating a composite image with enhanced spectral information, followed by contrast enhancement. During data acquisition , farmers were interviewed, and fields were meticulously mapped using GPS instruments, resulting in a comprehensive dataset of 50,835 data points. This dataset facilitated the extraction of vegetation indices such as NDVI, SAVO, RECI, and NDRE. These indices, along with raw reflectance values, were utilized for classification modeling using conventional classifiers, ensemble learning, and artificial neural networks. Additionally, a feature selection approach was incorporated to identify the optimal feature set for classification learning. This study demonstrates the effectiveness of combining remote sensing data and 1 advanced modeling techniques to improve crop classification accuracy in irrigated agricultural regions.
Urinary tract infections among pregnant women in rural West Amhara, Ethiopia: Prevalence, bacterial etiology, risk factors, and antimicrobial resistance patterns
Authors: Derebe Mulatu Melese , Paladhi Unmesha Roy , Workneh Firehiwot , Munshea Abaineh , Yismaw Gizachew , Yibeltal Kalkidan , Fasil Nebiyou , Worku Alemayehu , Gebreyesus Tsehaynesh , Tafere Wudu , Tsega Alem , Christian Parul , Molina Rose L. , Wylie Blair J. , Berhane Yemane , Lee Anne CC
Published: January 2025

Urinary Tract Infections (UTIs) in pregnant women can lead to pyelonephritis and preterm birth. We assessed UTI prevalence, etiology, antimicrobial resistance, and associated risk factors among pregnant women receiving antenatal care in rural Amhara, Ethiopia. 604 pregnant women were screened for UTI at ≤ 24 weeks gestational age from August 2020 to June 2022. Urine culture, dipstick, and antibiotic sensitivity testing were completed. We conducted descriptive statistics for prevalence and logistic regression to examine UTI risk factors. UTI prevalence was 3.5% (21/604, 95%CI = 2.0%-4.9%), among which 43% were symptomatic and 57% were asymptomatic. Common uropathogens were Escherichia coli (57.1%), Klebsiella pneumoniae (14.3%), and Enterococcus faecalis (14.3%). Among all isolates, resistance was high for ampicillin (66.7%) and amoxicillin-clavulanate (40.0%). The majority of isolates (76.2%) were susceptible to nitrofurantoin, cotrimoxazole, and cefpodoxime. Maternal age > 20 years was a protective factor against UTI (OR = 0.27, 95% CI = 0.10–0.77; ref < 20 years). Urine dipstick (nitrite or leukocyte esterase) had low sensitivity (37.5%) but higher specificity (93.9%) to identify positive culture. This study emphasizes the high resistance to first-line antibiotics used in pregnancy and the need for accurate, low-cost UTI screening methods in LMICs.
FGM-Copula based Analysis of Physical Layer Security in Wireless Wiretap Channels with UAV Transmitter and Two-Sided Side Information
Authors: Asghari Hana , Hodtani Ghosheh Abed
Published: January 2025

Physical layer security, as an important practical concept, in unmanned aerial vehicle (UAV) assisted channels has been studied in the literature, where, impacts of side information and or correlation of wireless channel coefficients have not been considered. In this paper, having briefly reviewed (the discrete memoryless side information channel, physical secure rate and copula function theory), a continuous alphabet wiretap channel with UAV transmitter and two-sided side information is considered. For this channel, we obtain closed form expressions for secrecy capacities in two cases: (i) Gaussian channel with constant channel coefficients; (ii) Gaussian wireless channel with correlated coefficients by using FGM copula function to describe the correlations. Through obtained secrecy rates, we analyse the impacts of (a) UAV situation for transmitter (b) two-sided non-causal side information and (c) correlation between channel coefficients on the achievable rates. Then, analytical results are numerically assessed across various correlation structures, both with and without side information. The findings demonstrate that correlated fading adversely impacts security performance in different scenarios, while the presence of side information enhances security performance.
Sensor Infused Quantum CNN for Diabetes Disease Prediction and Diet Recommendation
Authors: Kotwal Jameer , Futane Pravin , Chavan Gurunath , Chaudhari Archana , Jose Jithina , Khan Vajid
Published: January 2025

Diabetes management requires evidence-based recommendations that enable people to manage their health. A rising diabetes rate can lead to significant health risks and financial hardships. An early diagnosis and efficient treatment are essential to reduce the effects of diabetes. With dietary recommendations and other essential components of diabetes care, complications from diabetes may be reduced, and health can be enhanced. In this paper, a novel Sensor infused QUantum CNN for diabetes Identification and Diet recommendation (SQUID) technique has been proposed, which identifies diabetes using an IoT system and provides diet recommendations for reducing diabetes. The proposed SQUID system collects data from remote patients using IoT sensors and uses the Namib Beetle Optimization (NBO) technique to select the features. The prediction phase uses the Quantum CNN technique for classifying the input into diabetes and non-diabetes. After prediction, the suggestion phase will provide the diet recommendation using the fuzzy rule for the person affected with diabetes through the mobile application. The efficacy of the proposed SQUID framework has been assessed using specific parameters such as Accuracy (AC), Precision (PN), F1 score (F1_S), Recall (RL) and Diagnostic Odds Ratio (DOR). The SQUID framework achieves a higher AC of 98.69%, whereas HCBDA, IWBSOA and e-diagnosis achieve the AC of 92%, 94%, and 96.5%. The proposed SQUID achieved an 89.90% diagnostic odds ratio where the existing HCBDA reached 69.58%, Health-Edge reached 53.86% and IWBSOA obtained a 72.93% diagnostic odds ratio respectively.
A ratiometric electrochemical sensor based on Cu@Ni/MWCNTs for detection of chloramphenicol
Authors: Liu Xiaoxue , Wang Dongyang , Xu Rongxuan , Gao Xing , Han Mingyang , Guo Yurong , Yu Lei
Published: January 2025

Signal label features robust stability and sensitivity is crucial for achieving precise electrochemical analysis. In this work, a novel signal tag was successfully designed by means of two-step reduction approach, in which CuNi nanoparticles (CuNi NPs) uniformly distributed on the surface of multiwall carbon nanotubes (MWCNTs). This composites not only inherits excellent conductivity and surface area of MWCNTs, but also endows the material with superior electrocatalytic performance due to the introduction of CuNi NPs. Then, a ratiometric sensing platform coupled with built-in correction ability for convenient direct determination of chloramphenicol (CAP) was exploited, wherein Cu@Ni/MWCNTs were used as signal label and ferrocene (Fc) as internal reference. It is noteworthy that ratiometric measurement was performed by directly incorportating Fc into the electrolyte solution. The profound investigation into the sensing performance of the implemented sensor revealed that Cu@Ni/MWCNTs nanocomposites exhibit satisfactory electrocatalytic activity and stability. Additionally, the integration of the ratiometric strategy markedly enhanced the reliability and repeatability and exhibited decent performance in CAP determination varying from 0.01 µM to 10 µM. Overall, the corporation of Cu@Ni/MWCNTs with excellent electrocatalytic ability as well as elaborated ratiometric method makes it a valuable tool for future assaying an extensive range of substances.
Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms
Authors: Xia Feifei , Verbiest Max , Lundström Oxana , Sonay Tugce Bilgin , Baudis Michael , Anisimova Maria
Published: January 2025

Background Short tandem repeats (STRs) have been reported to influence gene expression across various human tissues. While STR variations are enriched in colorectal (CRC), stomach (STAD) and endometrial (UCEC) cancers, particularly in microsatellite instable (MSI) tumors, their functional effects and regulatory mechanisms on gene expression remain poorly understood across these cancer types.
Results Here, we leverage whole-exome sequencing and gene expression data to identify STRs for which repeat lengths are associated with the expression of nearby genes (eSTRs) in CRC, STAD and UCEC tumors. Our analyses reveal that tumor STR profiles effectively capture both MSI phenotype and population structure. While most eSTRs are cancer-specific, shared eSTRs across multiple cancers exhibit consistent effects on gene expression. Notably, coding-region eSTRs identified in all three cancer types show positive correlations with nearby gene expression. We further validate the functional effects of eSTRs by demonstrating associations between somatic eSTR mutations and gene expression changes during the transition from normal to tumor tissues, suggesting their potential roles in tumorigenesis. Combined with DNA methylation data, we perform the first quantitative analysis of the interplay between STR variations and 1 DNA methylation in tumors. We identify eSTRs where repeat lengths are associated with methylation levels of nearby CpG sites (meSTRs) and show that over 70% of eSTRs are significantly linked to local DNA methylation. Importantly, the effects of meSTRs on DNA methylation remain consistent across cancer types.
Conclusions Overall, our findings enhance the understanding of how functional STR variations influence gene expression and DNA methylation. Our study highlights shared regulatory mechanisms of STRs across multiple cancers, offering a foundation for future research into their broader implications in tumor biology.
High quality de novo long read genome assembly and annotation of resistance protein families for saw toothed grain beetle
Authors: Almansouri Hatim
Published: January 2025

Saw-toothed grain beetle (Oryzaephilus surinamensis) negatively impacts food products, which are considered as common insect pests in several countries. This study reports 159 Mb high quality long reads de novo genome assembly of O. surinamensis using PacBio-Sequel sequencing technology. The genome was assembled into 3043 contigs with the largest contigs 2.35 Mb and N50 length of 0.177 Mb, L50 171 contigs, 255.8X coverage, GC content of 29.69%, 54,156 microsatellite sequences and BUSCO evaluation revealed 98.6%. Genome annotation identified 11,227 genes and predicted 34,082 protein-coding genes (93.6% Busco score), of which 32,173 (94.39%) were annotated by Pfam database. The annotation of protein families identified important genes for pesticide and Enironmental resistance. Furthermore, Wolbachia endosymbiotic identified with 1.93 Mb genome size and 2060 predicted genes while Candidatus Shikimatogenerans Silvanidophilus endosymbiotic identified with 1.92 Mb genome size and 1223 predicted genes. This study provides a new reference genome and comprehensive resource for O. surinamensis and highlights important genes and pathways that influence agriculture.
The recipe similarity network: a new powerful algorithm to extract relevant information from cookbooks
Authors: Bellingeri Michele , Badia Axel Bidon-Chanal , Rigat Marta Vila , Alfieri Roberto , Turchetto Massimiliano , Cassi Davide
Published: January 2025

This study integrates network science and intersection graph theory to analyze the structural properties of recipe networks in Catalan cuisine. Using three distinct cookbooks, two traditional and one haute cuisine, we construct the recipe similarity networks by linking recipes based on shared ingredients, with link weights reflecting ingredient similarity. We explore how different methodological approaches, such as the substitution of recipes/ingredients with their composing ingredients and link weight normalization, influence network structure, and node centrality. Our analysis reveals that recipe similarity networks are highly interconnected but exhibit structural differences across cuisines, particularly in haute cuisine, which features more specialized recipes. Node centrality metrics identify key recipes that define culinary traditions, such as "Allioli" in traditional Catalan cuisine and "Becada con brioche de su salmis" in haute cuisine. We also develop a community detection algorithm based on link removal and clique identification, which uncovers tightly-knit recipe groups. This study enhances the field of computational gastronomy and provides a methodological foundation that can be integrated with artificial intelligence techniques to enhance recipe personalization, food recommendations, and gastronomic innovation.
INFORMATIVENESS AND SPECIFICITY OF SERUM OSTEASE LEVEL IN THE DIAGNOSIS OF OSTEOPENIC SYNDROME IN CHILDREN WITH JUVENILE IDIOPATHIC ARTHRITIS
Authors: Ilchenko Svitlana , Makoviichuk Oleksii , Fialkovska Anastasiia
Published: January 2025

Introduction. Low bone mineral density (BMD) is a common phenomenon in the clinical practice of a pediatric rheumatologist. Children with juvenile idiopathic arthritis (JIA) are at risk of developing osteopenic syndrome (OS) due to both primary and secondary mechanisms. Routine laboratory diagnostic methods for bone disorders, including the determination of calcium, phosphorus, and total alkaline phosphatase (ALP) concentrations in blood serum, have low specificity in children with JIA and often remain within normal ranges for extended periods. The activity of the bone isoenzyme ALP (ostease) and its association with disease progression require further study to improve the diagnosis and prognosis of OS in pediatric patients.
The aim of the study was to establish the diagnostic significance of the level of serum ostease in the diagnosis of OS in children with JIA.
Materials and methods. A total of 50 children with JIA, aged 5 to 18 years, were examined. Laboratory research methods included determination of the concentration of 25-hydroxyvitamin D (25(OH)D), total ALP, bone isoenzyme of ALP – osteoase (BAP), marker of bone resorption – β-Cross Laps, osteocalcin in blood serum. BMD screening was conducted using the Sunlight Omnisense 9000 ultrasonic densitometer. Statistical analysis of the results was performed using the Statistica v.6.1 software package
Results and their discussion. OS was diagnosed in children with JIA in 42.0 % of cases. It was established that children with OS had significantly lower concentrations of osteoase in blood serum. The level of osteoase in children with OS was related to the level of 25(OH)D, osteocalcin, marker of bone resorption – β-Cross Laps, Z-score according to ultrasound densitometry, disease activity and the dose of methotrexate in basic therapy. At the same time, the activity of total ALP in the blood serum of children with JIA did not differ significantly between subgroups. No correlation was found between the level of total ALP and its bone isoenzyme – osteoase, as well as the level of 25(OH)D, disease activity, and Z-score. Based on ROC analysis, an optimal threshold for BAP in diagnosing OS in children with JIA was determined as >83.4 μg/L (sensitivity – 85.7 %, specificity – 93.1 %, diagnostic accuracy – 90.0 %, area under the curve (AUC) – 0.864 (95% CI 0.737–0.944)).
Conclusions. Elevated BAP levels in blood serum in children with JIA should be considered an informative and highly specific biomarker for the early diagnosis and prognosis of OS. Total ALP in children with JIA is a non-specific marker, as normal serum activity does not rule out abnormalities in the bone isoenzyme pattern.
BACTERIAL HUNGER GAMES: SMALL ALARMONE SYNTHETASES IN MRSA VS. MSSA
Authors: Mussa Ali Abdulridha , Al-Mathkhury Harith Jabbar Fahad
Published: January 2025

Introduction. Staphylococcus aureus is a significant global human pathogen associated with opportunistic infections. The stringent response in bacteria triggers the synthesis of alarmones (p(ppGpp)) upon encountering stress conditions like starvation, impacting the bacterial transcriptome. S. aureus synthesizes these alarmones using either the Rel enzyme (RelA/SpoT homolog) or the small alarmone synthetases RelP and RelQ.
Aim. This investigation aimed to (1) highlight the impact of starvation on biofilm intensity, cell count, and matrix composition (protein, polysaccharide, and DNA) in both MRSA and MSSA isolates and (2) analyze the expression levels of relP and relQ genes under normal and starved conditions in both MRSA and MSSA isolates.
Methods: S. aureus isolates were obtained from patients attending hospitals in Baghdad. Methicillin resistance was determined using the cefoxitin disc diffusion method. PCR confirmed the presence of relP and relQ genes in all isolates. Additionally, 16SrRNA gene segments from 10 isolates were amplified for sequencing. Biofilm intensity, matrix composition, and cell count were measured for 10 isolates (5 MRSA and 5 MSSA) under normal and starvation conditions. Finally, relP and relQ gene expression was compared under both conditions.
Results: Methicillin resistance was detected in 94% of S. aureus isolates. relP and relQ genes were present in 100% and 98.7% of isolates, respectively.
Biofilm thickness and cell count significantly decreased (P = 0.0020) after starvation and with treatment involving proteinase K, DNase, and sodium periodate (P < 0.0001). relP and relQ genes displayed upregulation after starvation.
Conclusion: Starvation significantly reduced biofilm formation and altered its composition, suggesting the potential involvement of the stringent response in biofilm regulation; both relP and relQ were upregulated in both MRSA and MSSA.
ALPHA-ADDUCIN 1 (ADD1) GENE, CLINICAL-DEMOGRAPHIC AND METABOLIC PREDICTORS OF ARTERIAL HYPERTENSION AND CHRONIC KIDNEY DISEASE IN WESTERN UKRAINE POPULATION
Authors: Sydorchuk Larysa , Lytvyn Bogdan
Published: January 2025

Introduction. Chronic kidney disease (CKD) is a global public health problem affecting about 10% of the population worldwide. Nowadays, the genetic predisposition to CKD development in patients with arterial hypertension (AH) is studied insufficiently. Therefore, the search for early CKD predictors due to hypertension is on the cutting edge of contemporary medicine. Objectives: to evaluate the risk of essential AH (EAH) and CKD in the population of Western Ukraine (North Bukovina) based on some demographic, clinical, and anthropometric data, gender, and alfa adducin 1 gene (ADD1; rs4961).
Materials and methods. 100 patients with EAH and 60 practically healthy (control group) participated in the study. All participants underwent clinical and laboratory examinations. Among the risk factors, a burdened anamnesis of cardiovascular disease (CVD), type 2 diabetes mellitus (DM2), waist circumference (WC), hip circumference (HC), waist-to-hip ratio (WHR), body mass index (BMI) in men (M) and women (W) were studied. CKD was defined by glomerular filtration rate (GFR) according to the CKD-EPI equation, taking into account creatinine (cr) and cystatin-C (cys) blood levels (KDIGO, 2024). ADD1 (rs4961) gene polymorphism genotyping was performed by real-time PCR.
The results. The risk of EAH is 4 times higher with CVD burdened (95% CI: 1.15-13.88; p=0.027), 8.5 times higher – in the smokers who are carriers of the GG-genotype of the ADD1 gene (rs4961) (OR=8.67; 95% CI: 1.04–72.32; p=0.02), almost 2.5 times higher – with hypercystatinemia-С (≥1.1 mg/l) in T-allele carriers (rs4961), but the difference is significant only in women – by 4.67 times (95% CI: 1.19–18.33; p=0.033). The GG-genotype of the ADD1 gene (rs4961) increases the CKD risk in EAH men by 2.67 times (95% CI: 1.0–7.34; p=0.047). The EAH risk increases regardless of ADD1 gene polymorphic variants (somewhat stronger in patients with mutated T‑allele) in subjects with obesity – by 3.37 and 12 times (95% CI: 1.23–9.24; p=0.014 and 95% CI: 2.24–64.29; p=0.001), in subjects with increased WC (W >88 cm, M >102 cm) – by 4.14 and 45 times (95% CI: 1.49–11.48; p=0.006 and 95% CI: 7.34–275.8; p<0.001), in subjects with increased BMI (≥25.0 kg/m2) and WHR (>0.85 U) – but only in women – by 5.78–9.90 and 30.33–60.67 times (95% CI: 1.12–56.96; p≤0.029–0.008 and 95% CI: 5.58–659.3; p<0.001), respectively.
Conclusions. The risk of EAH in the Western Ukraine population increases with burdened CVD heredity, smoking, hypercystatinemia-С in T-allele carriers of the ADD1 gene (rs4961), BMI, WC, and WHR elevation. The GG-genotype of the ADD1 gene increases the CKD risk in hypertensive men.
ANTIBACTERIAL AND ANTIBIOFILM ACTIVITY OF CU/CU2O NPS AGAINST MULTIDRUG-RESISTANT BACTERIA
Authors: Duzhyi Igor , Myronov Petro , Ivakhniuk Tetiana , Pshenychnyi Roman , Bidakov Oleksandr , Holubnycha Viktoriia
Published: January 2025

Introduction. Multidrug-resistant (MDR) bacteria are very dangerous and represent a major problem in all areas of healthcare: they often cause diseases that cannot be treated with antibiotics, which leads to long-term ineffective treatment, complications, and high treatment costs. Searching for new antimicrobials is one of the key components of a successful fight against infections caused by MDR. This study was designed to elucidate the antimicrobial and antibiofilm activities of copper/copper oxide nanoparticles (Cu/Cu2O NPs) against MDR bacteria.
Methods. Cubic Cu/Cu2O NPs were synthesized by the polyol method. The physicochemical characteristics of the nanoparticles were investigated using transmission electron microscope, X-ray diffraction investigation, energy dispersive spectroscopy and Fourier-transform infrared spectroscopy. Laboratory reference bacterial strains (S. aureus ATCC 25923. E. coli ATCC 25922, P. aeruginosa ATCC 27853) and MDR clinical strains isolated from patients with a purulent process (S. aureus, E. coli, P. aeruginosa) were used to examine the antibacterial effect of nanoparticles.
Results. Cubic Cu/Cu2O NPs showed antimicrobial activity against both Gram-negative and Gram-positive bacteria, but the antibiofilm activity of Cu/Cu2O NPs was more promising for targeting Gram-negative bacteria. Cu/Cu2O NPs were less effective against MDR strains of planktonic bacteria in comparison to laboratory reference strains. No significant differences were found between the action of the Cu/Cu2O NPs on biofilms formed with reference laboratory strains or MDR clinical strains.
Discussion. The findings of this research may be useful to develop new drugs and approaches for treating infection caused by MDR microorganisms. Further research is warranted to elucidate the underlying mechanisms of Cu/Cu2O NPs action, optimize their formulation, and evaluate their safety and efficacy in preclinical and clinical settings
CHARACTERIZATION OF THE EFFECT OF ACELLULAR CRYOPRESERVED BIOLOGICAL AGENTS ON THE LEVELS OF ANTI-INFLAMMATORY AND REGULATORY CYTOKINES IN EXPERIMENTAL AUTOIMMUNE ARTHRITIS
Authors: Hladkykh Fedir , Liadova Tetyana
Published: January 2025

Background. The pathogenesis of rheumatoid arthritis (RA) involves a complex cascade of cytokines that trigger the proliferation of synovial cells and cause damage to both cartilage and bone. In recent years, particular attention has been drawn to research focused on exploring the potential use of acellular cryopreserved biological agents (CBAs) for optimizing RA therapy.
Objective. The paper aims to characterize the effect of CBAs – placental cryoextract (PCE), spleen cryoextract (SCE), and conditioned medium from mesenchymal stem cells (MSC-CM) on cytokine levels in an adjuvant arthritis (AA) model.
Methods. Experimental studies were conducted on 42 male rats weighing 200–220 g. AA was modeled by administering complete Freund’s adjuvant. On day 28 of the experiment, mixed blood samples were collected. The levels of interleukins (IL-2, IL-4, IL-6, and IL-10) were determined by enzyme-linked immunosorbent assay (ELISA).
Results. It was found that on day 28 of the experiment, during AA development, there was a statistically significant (p<0.001) increase in the levels of anti-inflammatory cytokines – IL-4 by 94.9% and IL-10 by 150.7%, as well as an increase in the levels of regulatory cytokines – IL-2 by 233.3% (p<0.001) and IL-6 by 167.7% (p<0.001) compared to the intact rats. The administration of the studied cryoextracts had a pronounced effect on the levels of anti-inflammatory cytokines in AA rats. Specifically, following PCE administration, IL-4 levels decreased (p=0.004) by 31.3%, and after SCE administration, IL-10 levels decreased (p=0.02) by 20.5% compared to untreated AA rats. The most pronounced effect on the levels of regulatory cytokines was observed with the use of MSC-CM in AA rats. IL-2 levels decreased (p=0.003) by 21.5% compared to untreated AA animals.
Conclusions. It was established that the administration of CBAs influences the levels of anti-inflammatory and regulatory cytokines in AA rats, indicating their potential in the therapy of autoimmune diseases. The results showed a decrease in the levels of anti-inflammatory cytokines, particularly IL-4 and IL-10, as well as a reduction in the levels of the regulatory cytokine IL-2 after the administration of CBAs, suggesting their modulatory effect on the immune response.
DETERMINATION OF PREDICTORS OF COLORECTAL CANCER RECURRENCE IN RADICALLY OPERATED PATIENTS
Authors: Kostiuchenko Vitaliia
Published: January 2025

Introduction. The high risk of recurrence of colorectal cancer (CRC) in radically operated patients has become the reason for discussions about the issue of intensification of the observation period and the search for reliable predictors of the course of the disease. Inflammatory markers (IM) have shown promise in this aspect. The main goal of this study was to evaluate IM as predictors of CRC recurrence in radically operated patients. Of secondary importance was to determine which of the patient's and tumor's basic characteristics influence the recurrence-free survival (RFS) and overall survival (OS) in the same cohort of patients.
Materials and Methods. The data of 138 patients from the Municipal Non-Profit Enterprise of Sumy Regional Council "Sumy Regional Clinical Oncology Center" was used for the research. Patients with CRC who underwent radical surgery for stage I–III colon or rectal tumors between December 2019 and December 2020 were included. Gender, age, body mass index (BMI), tumor location, stage, T, N, neoadjuvant and adjuvant therapy, degree of tumor differentiation, and IM were evaluated as potential predictors of disease recurrence. IM were calculated based on data from clinical and biochemical blood tests performed no more than a week before the surgery. The studied IM were: neutrophil-lymphocyte ratio (NLR), lymphocyte-monocyte ratio (LMR), prognostic nutritional index (PNI), advanced lung cancer inflammation index (ALI) and level of lymphocytes x albumin (LA). ROC analysis (AUC≥0.7), Kaplan-Meier method, Log-rank test (p < 0.05) and multivariate Cox regression analysis with the Breslow method (confidence interval (CI) – 95%, p < 0.05) were used for the statistical data processing.
Results. According to the results of the ROC analysis, LA was the only statistically significant IM (AUC=0.7592). LA demonstrated a significant effect on RFS (Log-rank p=0.0000) and OS (Log-rank p=0.0023). Patients with LA<37.5 had a higher risk of relapse and death. According to the result of the multivariate Cox regression analysis with the Breslow method, age (p=0.032), BMI (p=0.048) and LA (p=0.031) were independent factors influencing the RFS and LA (р=0.008) was the only factor influencing the OS.
Conclusions. According to the results of this study, LA was determined as an independent predictor of the course of CRC after radical surgery. Patients with a low LA level had worse RFS and OS. In addition, age and BMI have been identified as basic characteristics of the patient that reliably influence RFS. Patients older than 65 years and overweight patients had a higher risk of disease recurrence.
Excitonic Bloch equations from first principles
Authors: Stefanucci Gianluca , Perfetto Enrico
Published: January 2025

The ultrafast conversion of coherent excitons into incoherent excitons, as well as the subsequent exciton diffusion and thermalization, are central topics in current scientific research due to their relevance in optoelectronics, photovoltaics and photocatalysis. Current approaches to the exciton dynamics rely on model Hamiltonians that depend on already screened electron-electron and electron-phonon couplings. In this work, we subject the state-of-the-art methods to scrutiny using the ab initio Hamiltonian for electrons and phonons. We offer a rigorous and intuitive proof demonstrating that the exciton dynamics governed by model Hamiltonians is affected by an overscreening of the electron-phonon interaction. The introduction of an auxiliary exciton species, termed the irreducible exciton, enables us to formulate a theory free from overscreening and derive the excitonic Bloch equations. These equations describe the time-evolution of coherent, irreducible, and incoherent excitons during and after the optical excitation. They are applicable beyond the linear regime, and predict that the total number of excitons is preserved when the external fields are switched off.