bluuebunny/crossref_metadata_2025 huggingface dataset:
Insecticide resistance management scenarios differ for RNA‐based sprays and traits
Authors: Narva Kenneth , Toprak Umut , Alyokhin Andrei , Groves Russ , Jurat‐Fuentes Juan Luis , Moar William , Nauen Ralf , Whipple Sean , Head Graham
Published: February 2025

RNA‐based bioinsecticides that comprise a dsRNA active ingredient and function by RNA interference (RNAi) are being commercialised as insecticidal traits in transgenic crops and as sprayable biopesticides. These RNAi insecticidal technologies are valuable alternatives to conventional chemical insecticides due to their efficacy, high degree of specificity and favourable human and environmental safety profiles. As with all pesticides, appropriate insect resistance management (IRM) programmes are required to mitigate the selection for resistance in target insect populations and extend product durability in the field. IRM programmes for RNAi products follow the same guidelines that currently exist for insecticidal traits or conventional insecticidal sprays. These guidelines reflect the distinct exposure scenarios for traits versus sprays, that is, continuous exposure when dsRNA is expressed in the crop compared to intermittent exposure when sprayed on foliage. As such, IRM plans for dsRNA traits depend on pyramiding (stacking) non‐cross‐resistant traits along with a refuge of non‐transgenic plants. On the other hand, IRM plans for dsRNA sprays rely on the timing of the application so that only a single generation of the pest is exposed, followed by the use of an insecticide from a different IRAC mode of action group.
A Machine Learning Approach to Build and Evaluate a Molecular Prognostic Model for Endometrial Cancer Based on Tumour Microenvironment
Authors: Wu Di , Yan Zhifeng , Li Mingxia , Wang Mingyang , Meng Yuanguang
Published: February 2025

Endometrial cancer (EC) incidence and the associated tumour burden have increased globally. To build a molecular expression prognostic model based on the tumour microenvironment to guide personalised treatment using a machine learning approach. Two datasets were reviewed, including a training cohort (n = 698) and a testing cohort (n = 151). All patients underwent hysterectomy ± adnexectomy ± lymph nodes dissection between December 2014 and June 2020 at the PLA General Hospital First Medical Center and received necessary and regular follow‐up. We developed novel models using R software to predict factors that affect survival, such as progression‐free survival and overall survival. Then, the model was optimised by evaluating the prediction efficiency in multiple dimensions. Eight hundred and forty‐nine patients with EC were included in the study. Survival‐related influences on EC patients were identified by univariate analysis and cox regression equations. In addition, a nomogram was visualised in conjunction with demographic characteristics and the above meaningful clinicopathological variables. Ultimately, through a comprehensive assessment, a random forest model (RF16) was developed for complementing the findings of the molecular classification of EC. The RF16 not only specifically characterises tumour molecules, but also enhances the generalizability of the model by replacing gene sequencing with immunohistochemistry. This study showed that the machine learning model (RF16) is low‐cost, efficient, and clinically valuable in guiding treatment for EC patients.
Large‐scale movement patterns of European catfish (Silurus glanisL.) in the Scheldt River basin, Belgium
Authors: Franquet Sam , Verhelst Pieterjan , Bervoets Lieven , Baeyens Raf , Vermeersch Sophie , Schoelynck Jonas , Van den Neucker Tom , Pauwels Ine
Published: February 2025

The large‐scale movement behavior of European catfish (Silurus glanis L.) remains poorly understood, despite it being a species of interest for conservation management. We report the movement patterns of 13 native individual catfish, recorded using acoustic telemetry over 160‐km estuarine habitat free of migration barriers in the Scheldt River basin (Belgium). The results show that catfish can travel vast distances of over 10 km with a seasonal pattern of fish moving the largest distances in summer. The wels catfish is often considered a relatively sedentary species; however, our results show that this is not the case in systems where they have the freedom to move over large distances. Knowledge about the large‐scale movement behavior of the wels catfish can be useful for species conservation, as well as pest control. For instance, the effects of migration barriers could be (re)considered in terms of the large movement distances.
Plant viruses convergently target NPR1 with various strategies to suppress salicylic acid‐mediated antiviral immunity
Authors: Jiang Xue , Yang Yingshuai , Li Yong , Wang Yongzhi , Rodamilans Bernardo , Ji Weiqin , Wu Xiaoxia , García Juan Antonio , Wu Xiaoyun , Cheng Xiaofei
Published: February 2025

NONEXPRESSER OF PATHOGENESIS‐RELATED GENES 1 (NPR1), the receptor for salicylic acid (SA), plays a central role in the SA‐mediated basal antiviral responses. Recent studies have shown that two different plant RNA viruses encode proteins that suppress such antiviral responses by inhibiting its SUMOylation and inducing its degradation, respectively. However, it is unclear whether targeting NPR1 is a general phenomenon in viruses and whether viruses have novel strategies to inhibit NPR1. In the present study, we report that two different positive‐sense single‐stranded RNA (+ssRNA) viruses, namely, alfalfa mosaic virus (AMV) and potato virus X (PVX); one negative‐sense single‐stranded RNA (−ssRNA) virus (calla lily chlorotic spot virus, CCSV); and one single‐stranded DNA virus (beet severe curly‐top virus, BSCTV) that also encode one or more proteins that interact with NPR1. In addition, we found that the AMV‐encoded coat protein (CP) can induce NPR1 degradation by recruiting S‐phase kinase‐associated protein 1 (Skp1), a key component of the Skp1/cullin1/F‐box (SCF) E3 ligase. In contrast, the BSCTV‐encoded V2 protein inhibits NPR1 function, probably by affecting its nucleocytoplasmic distribution via the nuclear export factor ALY. Taken together, these data suggest that NPR1 is one of the central hubs in the molecular arms race between plants and viruses and that different viruses have independently evolved different strategies to target NPR1 and disrupt its function.
Inequality and Convergence in Latin American Regional Trade Agreements
Authors: Reinoso Alan Fairlie , Paipay Stacy Alvarado
Published: February 2025

The process of Latin American integration has been characterized by both significant advances and setbacks; it is driven by the potential for economic convergence, which seeks to reduce disparities and asymmetries among the region's countries. This article aims to estimate inequality indexes and assess the presence of convergence within and among Latin American integration blocs—The Pacific Alliance, the Andean Community, and the Southern Common Market. To achieve this goal, measures of inequality—including sigma dispersion, the Gini coefficient, and the Theil index—were calculated for the past 22 years. The findings indicate that inequality has increased throughout most of the studied period, with the Southern Common Market exhibiting the highest levels of inequality, followed by the Andean Community and the Pacific Alliance. Furthermore, the analysis of data from 1990 to 2021 reveals a lack of economic convergence between the Southern Common Market and the Andean Community during periods of unilateral trade liberalization, North–South free trade agreements, and the commodities boom. Similarly, the Pacific Alliance shows no evidence of economic convergence between its member countries. While the bloc's formation in 2012 suggests a possible shift in the trend, this change is insufficient to establish a definitive convergence.
Variations in Design, But Similar Effects: Social Participation in the Andean Community, Mercosur, and the Central American Integration System
Authors: Santos‐Carrillo Francisco , Luciano Bruno Theodoro
Published: February 2025

This article provides a comparative study on the spaces for social participation in different Latin American regional organizations. Departing from an institutionalist approach, we review the structures, processes, and outcomes of civil society participation in regional governance in three representative regional projects—the Andean Community, The Southern Common Market, and the Central American Integration System. The objective of this article is to characterize the variation in the institutional designs of the channels for social participation in Latin American regional organizations, identifying their similarities and differences, patterns, and effects on regional governance and the roles played by civil society organizations in these regionalist processes. We reflect on the relevance of design variations, the reasons for such variation, and their effects on regional governance. We argue that despite some differences in institutional design, with the Central American Integration System developing a supranational logic of membership in contrast to the intergovernmental settings of the other two cases, social participation in the three cases is limited to agenda facilitation, and its effects on regional decision‐making is residual.
Multiple Lineages of Transmissible Neoplasia in the Basket Cockle (C. nuttallii) With Repeated Horizontal Transfer of Mitochondrial DNA
Authors: Yonemitsu Marisa A. , Sevigny Jordana K. , Vandepas Lauren E. , Dimond James L. , Giersch Rachael M. , Gurney‐Smith Helen J. , Abbott Cathryn L. , Supernault Janine , Withler Ruth , Smith Peter D. , Weinandt Sydney A. , Garrett Fiona E. S. , Child Zachary J. , Sigo Robin Little Wing , Unsell Elizabeth , Crim Ryan N. , Metzger Michael J.
Published: February 2025

Transmissible cancers are clonal lineages of neoplastic cells able to infect multiple hosts, spreading through populations in the environment as an infectious disease. Transmissible cancers have been identified in Tasmanian devils, dogs, and bivalves. Several lineages of bivalve transmissible neoplasias (BTN) have been identified in multiple bivalve species. In 2019 in Puget Sound, Washington, USA, disseminated neoplasia was observed in basket cockles (Clinocardium nuttallii), a species that is important to the culture and diet of the Suquamish Tribe as well as other tribes with traditional access to the species. To test whether disseminated neoplasia in cockles is a previously unknown lineage of BTN, a nuclear locus was amplified from cockles from Agate Pass, Washington, and sequences revealed evidence of transmissible cancer in several individuals. We used a combination of cytology and quantitative PCR to screen collections of cockles from 11 locations in Puget Sound and along the Washington coastline to identify the extent of contagious cancer spread in this species. Two BTN lineages were identified in these cockles, with one of those lineages (CnuBTN1) being the most prevalent and geographically widespread. Within the CnuBTN1 lineage, multiple nuclear loci support the conclusion that all cancer samples form a single clonal lineage. However, the mitochondrial alleles in each cockle with CnuBTN1 are different from each other, suggesting mitochondrial genomes of this cancer have been replaced multiple times during its evolution, through horizontal transmission. The identification and analysis of these BTNs are critical for broodstock selection, management practices, and repopulation of declining cockle populations, which will enable continued cultural connection and dietary use of the cockles by Coast Salish Tribes.
Temporal changes in taxonomic and functional alpha and beta diversity across tree communities in subtropical Atlantic forests
Authors: Freitag Kramer Jean M. , Bordin Kauane Maiara , Scarton Bergamin Rodrigo , Klipel Joice , Caroline Picolotto Rayana , Zanini Katia J. , Zwiener Victor P. , Cristina Müller Sandra
Published: February 2025

Biodiversity is changing globally, but how these changes impact the structure of local ecological communities remains uncertain and debated. Understanding whether biodiversity increases, decreases, or remains stable across different scales is essential for predicting and managing these shifts. Here we assessed temporal taxonomic and functional alpha and beta diversity of adult and juvenile tree communities across 11 sites in the subtropical Brazilian Atlantic Forest to infer about trends and drivers of biodiversity change. The tree communities were evaluated for temporal changes in: 1) taxonomic and functional alpha diversity, 2) taxonomic and functional composition (beta diversity), and 3) identifying potential abiotic and biotic drivers of these changes, considering three censuses across a period of 10 years. Our results revealed few changes and little directionality in temporal alpha diversity but evidenced directional changes in temporal beta diversity. Furthermore, the rate of change was slightly similar for adult and juvenile tree communities, considering both temporal alpha and beta diversity. Beta diversity decreased over time, which was more pronounced for taxonomic than functional dissimilarity, suggesting a taxonomic homogenization within these forests. Our findings offer important insights that help clarify the mixed results on biodiversity trends, showing that temporal beta diversity is a more sensitive indicator of community change than temporal alpha diversity. The study highlights species loss or gain, which may influence ecosystem functioning, providing crucial information for conservation and management efforts. With most global time series datasets geographically skewed toward the Northern Hemisphere, studies like ours are increasingly important for providing a more balanced understanding of global biodiversity changes.
Spatially‐discrete disturbance overrides inherent environmental heterogeneity in grazed mixed‐grass prairie
Authors: McGranahan Devan Allen
Published: February 2025

Spatial heterogeneity is described as patchiness, with patches constituting local aggregations of low variability in one or more ecosystem properties. Rangelands are heterogeneous natural ecosystems in which spatial heterogeneity can be attributed to inherent variability due to soils, topography, and hydrology, or disturbances such as fire and grazing. But little research has directly compared the relative contributions of inherent heterogeneity and disturbance to spatial variability. Here, variance partitioning is used to parse the relative contributions of inherent heterogeneity described in soil maps, and disturbance‐driven heterogeneity imposed by patch burns, in grazed mixed‐grass prairie of the US Northern Great Plains. Results support the hypothesis that disturbance‐driven heterogeneity overrides inherent heterogeneity. Specifically, on pastures without patch burns, aboveground plant biomass depended on inherent variability in soil and topographic position; on patch‐burned pastures, aboveground plant biomass was driven by time‐since‐fire and plant successional stages. Variability in forage nutritive composition and the spatial distribution of grazers were also driven by patchiness when imposed by spatially‐discrete fire, while the role of inherent heterogeneity was weak for both. These results provide evidence for a default, often weak bottom–up control of spatial heterogeneity in the absence of spatially‐discrete disturbance that can be overridden by top–down disturbance effects.
Anti‐Müllerian Hormone Concentrations Can Be Reliably Determined by a Single Measurement, Irrespective of Cycle, in Synchronised Ewes During Non‐Breeding Season
Authors: Cetin Nebi , Koca Davut
Published: February 2025

Improvement of yield characteristics in animal breeding is important in terms of increasing animal production and sustainability. Fertility is one of the most important yield traits affecting economic gain in sheep breeding. Anti‐Müllerian Hormone (AMH) is widely recognised as a dependable biomarker for assessing ovarian reserves and fertility potential. The aim of this study was to evaluate the dynamics of AMH during different phases of the sexual cycle in Norduz ewes the non‐breeding season. Additionally, the study sought to assess the effects of age and body condition score (BCS) on AMH concentrations during these phases. A total of 32 Norduz ewes with a body condition score (BCS) of 3–4.5 and aged between 2 and 4 years were used as animal material in the study. All experimental procedures were carried out outside the breeding season and when the ewes were lactating. In all ewes in anestrus, intravaginal sponges (Esponjavet, 60 mg MAP, Hipra, Turkey) were kept in the vagina for 7 days for estrus synchronisation. Intramuscular injections of PMSG (Oviser, 500 IU, Hipra, Turkey) and PGF2α analog (Gestavet, 50 μg, Hipra, Turkey) were administered 48 h prior to sponge removal. Twenty‐four hours after sponge removal, ewes were exposed to the ram for estrus detection. Since 5 ewes did not show estrus, blood samples were collected regularly from animals (n = 27) in which estrus was detected at three different stages: one just before the insertion of vaginal sponges (anestrus), another when heat was detected exposing to the ram (estrus), and the final one 10 days after estrus (diestrus). The serum samples were assessed for the levels of AMH and progesterone through the electrochemiluminessence immunoassay technique (ECLIA). The results of the analyses showed that serum AMH concentration did not vary between anestrus, estrus and diestrus phases of the sexual cycle of Norduz ewes outside the breeding season (p > 0.05). Furthermore, age and BCS had no effect on progesterone and AMH levels in different phases of the sexual cycle (p > 0.05). In conclusion, this study shows that serum AMH levels are constant at any stage of the estrus cycle. This suggests that phenotypic evaluation of ewes can be performed with a single measurement and that AMH is a reproducible and dependable biomarker that can be measured at any stage of the estrus cycle at an arbitrary time point.
Harnessing water and salt synergy: Elevating Panax notoginseng growth and quality under drip irrigation in southwest China
Authors: Mu Tianqi , Ji Chunwei , Zang Zhennan , Wang Yinbo , Yang Qiliang , Liang Jiaping , Wang Haidong , Guo Jinjin , Li Na , Liu Xiaogang
Published: February 2025

Panax notoginseng is primarily cultivated in Yunnan Province, China. However, unsound field management practices aimed at increasing yields lead to imbalanced soil moisture, increased rhizome rot, and reduced crop quality, challenging the sustainable development of the P. notoginseng industry. This experiment proposed a rational water salt management strategy to improve growth and quality, offering guidance for sustainable production. A field experiment was conducted under shaded, rain‐shelter conditions with drip irrigation for 1 year. Two irrigation levels were applied based on field capacity (FC): W1 (irrigation lower limit at 90% FC) and W2 (irrigation lower limit at 80% FC). Additionally, three soil salinity levels were established with electrical conductivity values of E1: 130 μS cm−1, E2: 150 μS cm−1, and E3: 170 μS cm−1. A control group (CK) without salt stress was also included to compare the effects of irrigation and salinity on growth, quality, and productivity. Results showed that the combined water and salt management reduced pathogen abundance. Ectomycorrhizal fungi, promoting plant growth, were detected under W2E2. During the reproductive phase, plant height increased gradually and stabilized by the fruiting stage, while stem diameter initially decreased and then stabilized. Growth indicators peaked during the fruiting stage, with a maximum plant height of 29.87 cm and stem diameter of 4.75 mm. Optimal root characteristics were observed under W2E2, including an average root diameter of 1.06 mm, root volume of 1.17 cm3, root surface area of 54.55 cm2, and root length of 214.11 cm. Leaf characteristics also peaked under W2E2, with an average leaf diameter of 5.02 mm, leaf volume of 30.27 cm3, leaf surface area of 236.08 cm2, and leaf length of 181.57 cm. Maximum chlorophyll content reached 32.38. The transpiration rate, stomatal conductance, and intercellular CO2 concentration were highest under W1. The highest total saponin content of 85,759 μg g−1 was observed under W2E3. According to the comprehensive TOPSIS model index, W2E2 outperformed other treatments. Thus, W2E2 was identified as an effective strategy for promoting the growth and quality of P. notoginseng to alleviate root rot disease.
Special Economic Zone and Local Economic Performance in China: Evidence From Tianjin
Authors: Du Zaichao , Ge Linnan , Li Bing , Pei Pei , Zhou Lei
Published: February 2025

Using China's 2006 national strategy on special economic zone (SEZ) in Tianjin, we quantitatively evaluate the effects of SEZ on local economic performance in China. Due to the fact that Tianjin is the only municipality affected by this policy, we adopt a new and simple‐to‐implement policy evaluation method. The method exploits the economic dependence among different provinces in China and constructs the counterfactual economic growth of Tianjin using data from provinces other than Tianjin. The policy effects are then just the difference between the actual economic growth of Tianjin and the counterfactuals. Using the method, we find that the SEZ policy in 2006 substantially enhanced GDP, investment, employment and export in Tianjin.
Evaluating the Factors and Forecasting Childhood Anemia Through Machine Learning Algorithms
Authors: Salma Nahid , Majahar Ali Majid Khan
Published: February 2025

Anemia, characterized by insufficient hemoglobin levels, affects a significant portion of the global population, both in developed and developing nations, and is one of the most prevalent health conditions worldwide. With timely diagnosis and proper care, the risk of anemia can be reduced, potentially saving many lives. In this context, machine learning (ML) techniques can serve as valuable tools for disease diagnosis. Therefore, the objective of this study was to determine the most effective machine learning approach while considering the risk factors for childhood anemia in Bangladesh. Secondary data from the 2011 Bangladesh Demographic and Health Survey were analyzed, with both filter (chi-square test) and wrapper (Boruta algorithm) feature selection methods used to identify significant factors. The findings revealed that 52.11% of all Bangladeshi children suffered from varying degrees of anemia (mild: 29.72%, moderate: 21.60%, and severe: 0.8%). Nine key variables—children’s fathers’ education, child age, breastfeeding status, mother’s age, mother’s education, toilet type, water source, and the number of children under five years old—were found to be directly linked to anemia. Seven machine learning algorithms (KNN, NB, SVM, RF, Bagging, Gradient Boosting, and XGBoost) were compared based on model evaluation metrics, including accuracy, sensitivity, specificity, precision, Cohen’s Kappa, F1-score, and AUC. The results showed that Gradient Boosting outperformed the other algorithms with 87.46% accuracy, 85.31% sensitivity, 96.56% specificity, 95.35% precision, 0.5713 Kappa, 0.8990 F1-score, and 0.9099 AUC. Random Forest followed closely with 83.13% accuracy, 87.36% sensitivity, 83.01% specificity, 84.10% precision, 0.3601 Kappa, 0.8555 F1-score, and 0.8531 AUC. Support Vector Machine (SVM) showed 84.46% accuracy, 0.3501 Kappa, 0.8046 F1-score, and 0.8264 AUC, while XGBoost demonstrated 75.99% accuracy, 75.87% sensitivity, 76.23% specificity, 82.76% precision, 0.3319 Kappa, 0.7913 F1-score, and 0.7599 AUC. These findings suggest that machine learning techniques—especially Gradient Boosting—can be highly effective for predicting anemia in Bangladeshi children, assisting medical professionals in early detection and intervention. The results of this study are expected to guide policymakers and healthcare providers in improving patient care and advancing Bangladesh’s progress towards achieving the Sustainable Development Goal (SDG) related to health.
An Intelligent Optimization Strategy for Medical Doctor Rostering Using Hybrid Genetic Algorithm-Particle Swarm Optimization in Malaysian Public Hospital
Authors: Zainudin Zanariah , Hasan Shafaatunnur , Mohd Zamry Nurfazrina , Sabri Nor 'Afifah , Jamil Nurul Syafidah , Muslim Norliana Muslim , Mat Jan Nur Amalina , Ibrahim Noraini
Published: February 2025

Comparing manual rostering to automated rostering reveals that manual rostering is typically more challenging, time-consuming, and exhausting for doctors, particularly due to shifting business regulations, a shortage of healthcare professionals, and heavy workloads. During rostering, it is essential to consider both hard and soft constraints to minimize constraint violations, maximize medical doctor satisfaction, and meet all requirements for hard constraints. To address these challenges, this paper proposes Hybrid Genetic Algorithm and Particle Swarm Optimization (Hybrid GA-PSO) to model rostering. In this approach, one set population of working days represents the rostering structure, which is determined using evolutionary-inspired operators, search, and update procedures. Additionally, the paper conducts observations and interviews with relevant personnel in a Malaysian hospital to gather insights and highlight constraints associated with medical doctors rostering. Rostering requirements determine the relative importance of the hard and soft constraints. The results of the research indicate that the Hybrid GA-PSO approach can produce workable rosters that reduce the workload of physicians and shorten the time needed to create rosters by the total violation of both soft and hard constraints and accuracy. It also ensures compliance with both hard and soft criteria and improves rostering accuracy.
Pythagorean Neutrosophic Method Based on the Removal Effects of Criteria (PNMEREC): An Innovative Approach for Establishing Objective Weights in Multi-Criteria Decision-Making Challenges
Authors: Mohammad Kamari Mohammad Shafiq , Md. Rodzi Zahari , Kamis Nor Hanimah
Published: February 2025

In the realm of multi-criteria decision-making (MCDM), the significance of criteria weights cannot be overstated. As a result, researchers have innovated and introduced various approaches aimed at precisely determining these weightings. This paper proposes a novel methodology that combines the Pythagorean neutrosophic set (PNS) with Method Based on the Removal Effects of Criteria (MEREC). This integrated method, PNMEREC seeks to offer a thorough and dependable method for evaluating criteria and establishing weightage in MCDM scenarios. PNS provides a more detailed way of handling uncertainty than traditional fuzzy sets or intuitionistic fuzzy sets by considering truth, indeterminacy, and falsity memberships values for each element, allowing for a wider range of uncertainties to be captured. This paper also introduces 5-point, 9-point, and 11-point PNS linguistic variables that can be utilized to represent evaluations from experts. The newly established linguistic variable scales enable decision-makers to express their criteria with clearer and heightened precision in PNS settings according to their preferences. A comparative analysis is conducted by comparing PNMEREC result with PN-Entropy and PN-Statistical Variance procedure to investigate the performance of the proposed method. The result of comparative analysis indicates that the weights produced by the PNMEREC method exhibit a high degree of reliability and stability, as demonstrated by the significant Pearson correlation coefficient values. Hence, the PNMEREC methodology possesses the capacity to thoroughly capture the determination of criterion weight via a more thorough and nuanced analysis. A sensitivity analysis is also conducted to compare the performance of the PNMEREC method using two distance techniques. The results reveal that the choice of distance technique impacts weight distribution and prioritization. Specifically, PN-Hamming emphasizes sharper distinctions, while PN-Euclidean offers a more balanced allocation.
Enhancing Paddy Production in Malaysia: A Comparative Analysis of Multiple Regression with External Factors
Authors: Mohd Shafri Ahmad Syakir , Mohd Nor Siti Rohani , Siti Mariam Norrulashikin
Published: February 2025

Rice is a basic food that is consumed by almost half of the world's population, especially in Malaysia. Unfortunately, paddy productivity has recently decreased dramatically, which has hampered local rice supply and forced Malaysia to depend on rice from neighbouring nations. Therefore, the modelling of paddy production is important because it provides an insight that ensure a sufficient supply of a locally produced paddy. In this study, several multiple regression models were used to predict paddy production model in Malaysia from 1980 to 2022. The multiple regression models are then compared, and the best model is determined. The regression model used in this study are Multiple Linear Regression (MLR), Multivariate Adaptive Regression Spline (MARS) and Support Vector Regression (SVR). The developed models will be evaluated using RMSE, MAPE and Ljung-Box Test. These are excellent tools for gauging the precision of the fitted model, thus can be used to evaluate the model. Based on the study, the MARS model is better at modelling Malaysian paddy production from 1980 to 2022 since it has the smallest number of measurement errors. Therefore, MARS model is the best regression model to be used to model paddy production in Malaysia compared to MLR and SVR model. Since all the models have autocorrelation, a more effective approach and model can be presented to overcome the autocorrelation issue in the future.
Temporal dynamics of the biofilm-mediated open circuit potentials: Understanding the fundamentals via a combined thermodynamic and kinetic modeling approach
Authors: Pejov Ljupcho , Hristovski Kiril D. , Burge Scott R. , Burge Russell G. , Boscovic Dragan
Published: February 2025

This study provides in-depth insights into the thermodynamics of electrochemical processes that govern the generation and temporal modulation of open-circuit potentials in biofilms and presents the foundation and applications of open-circuit potential methods to study the bioelectrochemical behaviors of biofilms. This investigation was guided by an overarching hypothesis that models should adequately explain the open-circuit potential patterns generated by biofilms when environmental conditions change; and from this work, a generalized model of electrochemical processes endemic to the biofilm electrode was developed and validated. The proposed model accounts for open system thermodynamics and the kinetics of bioelectrochemical transformations, and the model is simplified to enable applicability to a wide range of processes that are possible within biofilms. As such, the model can account for different parameters associated with various biofilm systems and is extendable to include numerous other experimental conditions. The model predictions were compared to the experimental data generated by 48 equidistantly located microbial potentiometric sensor electrodes in a chamber capable of simulating naturally occurring water matrix, which was exposed to environmental conditions. By combining electrochemical-cell thermodynamics and kinetics approaches, the model explained the temporal dependences of the open circuit potentials in aerobic and anaerobic conditions and the interconversion of two regimes commonly observed in natural systems. At the same time, it enables extraction of the relevant kinetic parameters from experimentally measured time evolution of the open circuit potentials.
Changes in the dynamic characteristics of G-protein can alter the immune-protection efficacy of rabies virus vaccine
Authors: Chen Chang-xu , Wang Xi , Su Wen , Tian Yuan , Gao Yu , Liu Dong-lan , Xiang Hong , Liu Bo-chuan , Shi Jin-li , Zhang Yang , Shen Dong , He Wen-zhi , Yang Li , Hong Chao , Wu Fan , Shi Lei-tai , Cun Yi-na , Zhou Jian
Published: February 2025

The efficacy of the G-protein is influenced by N-linked glycosylation, which serves as the sole immunogen of the rabies virus vaccine. However, achieving satisfactory immune-protection efficacy remains challenging, owing to the heterogeneous glycosylation of G-proteins. Within molecular dynamics, examining the impact of N-glycan heterogeneity on the structural characteristics of G-proteins provides insights into the relationship between antigens and the efficacy of rabies virus vaccines. Glycosylation is regulated by host cells. In rabies virus cultured in Vero cells (VRV), all N-glycosylation sites of the G-protein underwent modification. In contrast, rabies virus G-protein cultured in KMB17 cells (human diploid cell vaccine [HDCV]) was only modified by N-glycans at amino acid positions 247 and 319. Furthermore, treatment of VRV with de-glycosylation significantly improved its immune-protective efficacy, whereas de-glycosylation did not alter the immune-protective efficacy of HDCV. To support the impact of glycosylation on VRV efficacy, the structures and dynamics of G-proteins were analyzed using GROMACS. Specifically, the hydrophobicity, flexibility, and radius of gyration of the G-protein trimer in VRV were significantly altered by excessive hydrogen bonds formed by the three-branched hybrid glycan at the aa 319 site. These changes increase the instability of the G-protein trimer and may lead to a decrease in vaccine protective efficacy. Ultimately, we determined that N-glycan heterogeneity affects the immune-protection effect of antigen proteins by altering their dynamic characteristics, enhancing our understanding of the correlation between antigen structural characteristics and efficacy.

IMPORTANCE

N-glycosylation of rabies virus glycoprotein dynamically regulates protein folding, stability, and antigenicity. Therefore, regulation of N-glycan modification is key to improving vaccine stability and protective efficacy. How the type and modification sites of N-glycans affect the protective efficacy of rabies vaccines remains unclear. Our research indicates that there are differences in the protective efficacy of rabies virus G-proteins modified with different N-glycans. Moreover, the modification of the three-branched hybrid glycan at the aa 319 site of G-protein significantly altered the hydrophobicity, flexibility, and radius, and increased its trimeric antigen instability through molecular dynamics demonstrations. These findings update the current understanding of the impact of glycans on vaccine antigenicity and develop a system to evaluate the stability of antigen glycoproteins based on molecular dynamics.
A new bacteriophage infecting
Staphylococcus epidermidis
with potential for removing biofilms by combination with chimeric lysin CHAPSH3b and vancomycin
Authors: Duarte Ana Catarina , Fernández Lucía , Rodríguez Ana , García Pilar
Published: February 2025

Staphylococcus epidermidis
is the cause of serious skin and prosthetic joint infections despite being a common inhabitant of human body surfaces. However, both the rise in antibiotic resistance in this species and its ability to form biofilms are increasingly limiting the available therapeutic options against these illnesses. In this landscape, phage therapy stands out as an interesting alternative to antibiotics. In the present study, we report the isolation and characterization of a novel virulent phage infecting
S. epidermidis
(
Staphylococcus
phage IPLA-AICAT), which belongs to the
Herelleviridae
family. The estimated genome size of this virus is 139,941 bp, and sequence analysis demonstrated the absence of antibiotic resistance genes and virulence factors. This phage infects a high proportion (79%) of clinically relevant
S. epidermidis
strains and exhibits antibiofilm activity. Moreover, a combination of this phage with other antimicrobials, i.e., vancomycin and the lytic protein CHAPSH3b, further improved the reduction in surface-attached bacteria. Notably, the combination of
Staphylococcus
phage IPLA-AICAT (10
9
PFU/mL) and CHAPSH3b (8 µM), originally designed to target
Staphylococcus aureus
, was able to reduce the number of viable cells by 3.06 log units in 5-h-old biofilms. In 24-h-old biofilms, the reduction was also significant after 6 h of treatment (2.06 log units) and 24 h of treatment (2.52 log units). These results confirm our previous data regarding the potential of phage-lysin mixtures against staphylococcal biofilms.

IMPORTANCE

Staphylococcus epidermidis
is one of the main causes to device-associated infections mostly due to its ability to form stable biofilms attached to human tissues. Besides the inherent antimicrobial tolerance of biofilms, this microorganism is also increasingly becoming resistant to standard-of-care antibiotics. To fight against this problem, phage therapy is a viable option to complement the available antibiotics in the treatment of recalcitrant infections. This work describes a new phage infecting
S. epidermidis
clinical strains that is a member of the
Herelleviridae
family and the combination with other antimicrobials to further improve the reduction of biofilms. Together with the significant progress achieved in the development of diagnostic tools, phages and their derived proteins will bring us much closer to a therapeutic landscape in which we are not so heavily reliant on antibiotics to combat bacterial pathogens.
Exploring Suicide Factors in Online Discourse: Sentiment and Thematic Analysis of Reddit
Authors: Dan Evan , Zhu Jianfeng , Jin Ruoming
Published: February 2025

Suicide remains a critical global health issue, with rising numbers claiming more lives each year despite ongoing prevention efforts. Current research has extensively explored factors influencing suicidal tendencies, emphasizing trauma, mental health disorders, and social relationships. However, traditional studies often relied on traditional data sources and often examined risk factors in isolation, which may not fully capture the dynamics observed in social media platforms. To address these limitations, our study utilizes data from r/SuicideWatch and r/Teenagers to analyze the emotional sentiment and explore themes associated with suicidal ideation, with r/Teenagers serving as a comparative reference. By leveraging natural language processing (NLP) techniques and statistical methodologies, including sentiment analysis and BERTopic modeling, we aim to gain deeper insights into the factors contributing to suicidal thoughts. Using TextBlob, our findings reveal a significant difference in sentiment between the two subreddits, with r/SuicideWatch posts predominantly expressing challenges and distressing emotions. Through BERTopic analysis, we identified key themes such as emotional challenges related to romantic relationships, academic pressure, and substance use concerns in r/SuicideWatch, highlighting their strong association with suicidal ideation. While r/Teenagers had some similar themes regarding struggles with loneliness and academics, the topics were focused more on general adolescent concerns. These findings demonstrate that advanced NLP methods can effectively analyze large-scale social media data, providing valuable insights into the multifaceted nature of suicidal ideation and emphasizing the need for targeted intervention strategies. Suggested improvements include enhancing relationship counseling and peer support networks, implementing school-based mental health programs, and leveraging social media for real-time support and awareness campaigns. By understanding the emotional and thematic nuances of online discussions, these strategies can more effectively address the multifaceted factors contributing to mental health challenges and reduce the risk of suicidal behavior.
Evaluating Micro-Insertion as a Method for Teaching Responsible Computing: Results from a Randomized Controlled Experiment
Authors: Brown Noelle , Nurollahian Sara , Wiese Eliane S.
Published: February 2025

While there have been many calls for teaching ethics and responsible computing, it is unclear how responsible computing instruction and technical learning interact. Some instructors even hesitate to include ethics in their courses, fearing it might distract students from learning technical computing content. An approach called
micro-insertion
offers a path to teaching responsible computing while teaching technical content. Micro-insertion situates technical problems in real-world contexts, with frequent, minimally-invasive discussions of potential harms of a computing professional’s technical choices. We conducted a between-subjects laboratory study where 82 post-secondary student participants were randomly assigned to one of two instructional conditions to learn a computing topic. The
technical-only
condition received traditional instruction, while the
micro-insertion
condition learned the same technical material contextualized within a real-world scenario with potential broader ethical or social impacts. Our study design included a pre-test, instruction intervention, immediate post-test, and a two-week delayed post-test. Each test included both technical and contextualized questions, and the instructional time was the same across both conditions. The study revealed no statistically significant differences in learning outcomes between the two conditions. Participants in both conditions improved in solving problems presented both abstractly and contextualized with a real-world narrative. Thus, we did not find evidence that our responsible computing intervention distracted participants from learning the technical topics. Further, participants in the technical-only condition could correctly respond to contextualized questions, suggesting that students might be able to engage with responsible computing micro-insertions without targeted instruction. To more deeply understand students’ reasoning, we conducted follow-up interviews with 13 of the participants. The interviews revealed that participants in both conditions perceived to have learned about responsible computing from the study. However, the depth and quality of participants’ engagement with real-world issues varied significantly, with many only superficially addressing the context and many relying on their own personal experiences as their source of knowledge. We, therefore, encourage future studies to investigate other approaches to responsible computing education to determine which approach results in more meaningful consideration of social and ethical issues and whether that detracts from or supports technical learning.
Culture Conditions Differentially Regulate the Inflammatory Niche and Cellular Phenotype of Tracheo-Bronchial Basal Stem Cells
Authors: Murthy Shubha , Seabold Denise A. , Gautam Lalit K. , Caceres Adrian M. , Sease Rosemary , Calvert Ben A. , Busch Shana M. , Neely Aaron , Marconett Crystal N. , Ryan Amy L.
Published: February 2025

Bronchial epithelial cells derived from the tracheo-bronchial regions of human airways (HBECs) provide a valuable in vitro model for studying pathological mechanisms and evaluating therapeutics. This cell population comprises a mixed population of basal cells (BCs), the predominant stem cell in airways capable of both self-renewal and functional differentiation. Despite their potential for regenerative medicine, BCs exhibit significant phenotypic variability in culture. To investigate how culture conditions influence BC phenotype and function, we expanded three independent BC isolates in three media: airway epithelial cell growth medium (AECGM), dual-SMAD inhibitor (DSI)-enriched AECGM, and Pneumacult Ex plus (PEx+). Analysis through RNA sequencing, immune assays and impedance measurements revealed that PEx+ media significantly drove cell proliferation and a broad pro-inflammatory phenotype in BCs. In contrast, BCs expanded in AECGM, displayed increased expression of structural and extracellular matrix components at higher passage. AECGM increased expression of some cytokines at high passage, while DSI suppressed inflammation implicating the involvement TGF-β in BC inflammatory processes. Differentiation capacity of BCs declined with time in culture irrespective of expansion media. This was associated with an increase in PLUNC expressing secretory cells in AECGM and PEx+ media consistent with the known immune modulatory role of PLUNC in the airways. These findings highlight the profound impact of media conditions on inflammatory niche established by, and function of, in vitro expanded BCs. The broad pro-inflammatory phenotype driven by PEx+ media, in particular, should be considered in the development of cell-based models for airway diseases and therapeutic application.
An Efficient Numerical Method for Nonlinear Time Fractional Hyperbolic Partial Differential Equations Based on Fractional Shehu Transform Iterative Method
Authors: Bekela Alemu Senbeta , Deresse Alemayehu Tamirie
Published: February 2025

In science and engineering, nonlinear time‐fractional partial differential equations (NTFPDEs) are thought to be a useful tool for describing several natural and physical processes. It is tough to come up with analytical answers for these issues. Finding answers to NTFPDEs is therefore a crucial component of scientific study. To solve nonlinear time‐fractional hyperbolic partial differential equations (NTFHPDEs), we provide a novel fractional Shehu transform iterative method (FSTIM) in this work. In this case, the Caputo derivative is used to get the fractional derivative. The method combines two powerful numerical approaches called the fractional Shehu transform and the new iterative method (NIM), also known as the Daftardar‐Gejji and Jafari method. Through the recommended scheme, the linear portion of the problem is resolved by employing the Shehu transform method, while the noise terms from the nonlinear portion of the problem disappear over a successive iteration process of the NIM. The solution of FSTIM is then denoted in a series form, which is convergent to the precise answer of the assumed problem. Using principles from Banach’s spaces, the stability and convergence analysis of the suggested approach are addressed. To confirm the effectiveness and accuracy of the method, three illustrations from NTFHPDEs are presented. The obtained results are compared with the exact solutions and the other numerical results existing in the literature in terms of L∞ and L2 absolute errors. The findings showed that the proposed method outperforms the other numerical techniques in the literature and gives accurate results with a few terms. Therefore, the recommended approach is effective and straightforward and can be applied to other complex nonlinear physical differential equations with fractional order.
Table 4 from A Phase 2 Study of Sotigalimab, a CD40 Agonist Antibody, plus Concurrent Chemoradiation as Neoadjuvant Therapy for Esophageal and Gastroesophageal Junction Cancers
Authors: Ko Andrew H. , Chao Joseph , Noel Marcus S. , Shankaran Veena , Sohal Davendra , Crow Mary , Oberstein Paul E. , Scott Aaron J. , McRee Autumn J. , Rocha Lima Caio Max Sao Pedro , Fong Lawrence , Keenan Bridget P. , Soto Maira , Filbert Erin L. , Hsu Frank J. , Yang Xiaodong
Published: February 2025

Efficacy results
Table 3 from A Phase 2 Study of Sotigalimab, a CD40 Agonist Antibody, plus Concurrent Chemoradiation as Neoadjuvant Therapy for Esophageal and Gastroesophageal Junction Cancers
Authors: Ko Andrew H. , Chao Joseph , Noel Marcus S. , Shankaran Veena , Sohal Davendra , Crow Mary , Oberstein Paul E. , Scott Aaron J. , McRee Autumn J. , Rocha Lima Caio Max Sao Pedro , Fong Lawrence , Keenan Bridget P. , Soto Maira , Filbert Erin L. , Hsu Frank J. , Yang Xiaodong
Published: February 2025

Most common AEs (occurring in ≥10% of subjects) considered related to sotigalimab by the investigator (n = 33)
Table 1 from A Phase 2 Study of Sotigalimab, a CD40 Agonist Antibody, plus Concurrent Chemoradiation as Neoadjuvant Therapy for Esophageal and Gastroesophageal Junction Cancers
Authors: Ko Andrew H. , Chao Joseph , Noel Marcus S. , Shankaran Veena , Sohal Davendra , Crow Mary , Oberstein Paul E. , Scott Aaron J. , McRee Autumn J. , Rocha Lima Caio Max Sao Pedro , Fong Lawrence , Keenan Bridget P. , Soto Maira , Filbert Erin L. , Hsu Frank J. , Yang Xiaodong
Published: February 2025

Patient demographics and baseline tumor characteristics