bluuebunny/crossref_metadata_2025_split huggingface dataset:
SEQSIM – A novel bioinformatics tool for comparisons of promoter regions – a case study of calcium binding protein spermatid associated 1 (CABS1)
Authors: Santos Joy Ramielle L. , Sun Weijie , Befus A. Dean , Marcet-Palacios Marcelo 
Published: December 2024

Abstract

Background
Understanding transcriptional regulation requires an in-depth analysis of promoter regions, which house vital cis-regulatory elements such as core promoters, enhancers, and silencers. Despite the significance of these regions, genome-wide characterization remains a challenge due to data complexity and computational constraints. Traditional bioinformatics tools like Clustal Omega face limitations in handling extensive datasets, impeding comprehensive analysis. To bridge this gap, we developed SEQSIM, a sequence comparison tool leveraging an optimized Needleman-Wunsch algorithm for high-speed comparisons. SEQSIM can analyze complete human promoter datasets in under an hour, overcoming prior computational barriers.
Results
Applying SEQSIM, we conducted a case study on CABS1, a gene associated with spermatogenesis and stress response but lacking well-defined functions. Our genome-wide promoter analysis revealed 41 distinct homology clusters, with CABS1 residing within a cluster that includes promoters of genes such as VWCE, SPOCK1, and TMX2. These associations suggest potential co-regulatory networks. Additionally, our findings unveiled conserved promoter motifs and long-range regulatory sequences, including LINE-1 transposable element fragments shared by CABS1 and nearby genes, implying evolutionary conservation and regulatory significance.
Conclusions
These results provide insight into potential gene regulation mechanisms, enhancing our understanding of transcriptional control and suggesting new pathways for functional exploration. Future studies incorporating SEQSIM could elucidate co-regulatory networks and chromatin interactions that impact gene expression.
Integrating Anisotropic Heat Flow and Transformer Encoders in Convolutional Neural Network for Skin Cancer Classification
Authors: Aburass Sanad , Rumman Maha Abu , Huneiti Ammar 
Published: December 2024

Abstract

The early detection and classification of skin cancer are pivotal in improving patient outcomes and reducing healthcare burdens. However, traditional deep learning models in dermatological diagnostics often struggle with the nuanced differentiation of skin lesions. This paper introduces a novel approach, integrating an Advanced Heat Flow Layer into deep learning architectures for skin cancer classification, this method is centered on the principles of anisotropic diffusion, distinguishing itself from conventional image processing techniques by selectively smoothing image areas while preserving critical edge details, essential for accurate lesion identification. In our research, we utilized the Ham10000 dataset, enriched with data augmentation to simulate real-world variability, we conducted a comprehensive comparison of our model, featuring the Advanced Heat Flow Layer, against several benchmark deep learning models, including Sobel Edge Detection Layer. Our model, integrated with various layers of DenseNet121, consistently outperformed these benchmarks across key metrics such as accuracy, precision, recall, F1 score, and AUC, particularly with augmented data, this indicates a significant enhancement in the model's ability to generalize and maintain critical diagnostic features under diverse conditions. Our code is available at, https://github.com/sanadv/SkinCancerClassificationModels/blob/main/Models.ipynb
Predictors of heatwave risk perception and care adaptation among Nepalese pregnant women: Baseline assessment of a longitudinal concurrent cohort
Authors: Rhomberg Ariane , Schröders Julia , Vaezghasemi Masoud , KC Ashish 
Published: December 2024

Abstract

Background- Heatwaves have detrimental effects on maternal and neonatal health, increasing the risk for maternal complications, preterm birth, and neonatal mortality. There is an urgent need to explore pregnant women’s heatwave risk perceptions and adaptive measures. This study uses the Health Belief Model (HBM) to investigate pregnant women’s perception of heatwave risks and related prevention and mitigation strategies and identifies barriers to the adoption of such behaviours.
Methods- Using a concurrent cohort design, a baseline assessment was conducted through semi-structured interviews with 745 pregnant women in a heat prone district in Nepal. The interviews collected socio-demographic information and assessed the five HBM constructs of heatwave risk perception using a Likert scale. Heat maps were created to visualise perceptions, and Principal Component Analysis was undertaken to create a nominal scale score for each construct. Crude and adjusted linear regressions were performed to assess associations of socio-demographic characteristics and HBM constructs.
Results- Among the pregnant women, 68% perceived dehydration due to heatwave as a risk to their pregnancy, and 37% perceived sunburn as a risk to foetal health. In terms of perceived benefit, 34% agreed that staying in an air-conditioned environment could reduce their chances of suffering during a heatwave. Adjusted linear regression showed that wealthier women perceived higher vulnerability (adj. β=0.14, 95% CI: 0.07, 0.21; p<0.001) and severity (adj.β=0.16, 95% CI: 0.08, 0.23; p<0.001), and reported more barriers (adj. β=0.16, 95%CI: 0.08, 0.23; p<0.001). Conversely, urban residents had significantly lower perceived vulnerability (adjusted β = -0.32, 95% CI: -0.41, -0.24; p < 0.001) and severity (adj. β = -0.34, 95%CI: -0.42, -0.25; p < 0.001), fewer barriers (adj. β = -0.34, 95%CI: -0.42,-0.25; p<0.001), and perceived more benefits (adj. β = 0.31, 95%CI: 0.22, 0.39; p<0.001) from heat stress prevention and mitigation strategies compared to their rural counterparts.
Conclusion- To promote adaptive behaviours in this vulnerable population and strengthen maternal and foetal resilience against the growing threat of heatwaves, we recommend focusing on closing knowledge, availability, and accessibility gaps, particularly among pregnant women of lower economic status in rural areas.
Comparison study of Sargassum Vulgare and Padina Pavonica of Persian Gulf extracts for their bioactive compounds, antioxidant activity, and sun protection factor to improve UV absorption
Authors: Nabizade Nafise , Zarei-Ahmady Amanollah , Shushizadeh Mohammad Reza , RajabZadehGhatrami Ebrahim , Golfakhrabadi Fereshteh 
Published: December 2024

Abstract

This research paper investigates the bioactive compounds, antioxidant activity, and sun protection factor (SPF) in ethanolic extracts from two brown algae, Sargassum vulgare (S. vulgare) and Padina pavonica (P. pavonica), collected from the Persian Gulf. Through qualitative and quantitative tests, various bioactive compounds such as phenols, flavonoids, proteins, and carbohydrates were identified. The antioxidant activity was measured via 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and Ferric reducing antioxidant power (FRAP) methods. SPF values were evaluated for different concentrations of ethanolic extracts. Notably, P. pavonica exhibited higher SPF values than S. vulgare, with an optimal concentration of 4 mg/mL for both species. The findings underscore the potential of these algae extracts as natural ingredients in cosmetic and sun protection products, bolstered by their significant antioxidant and photoprotective properties.
Occurrence of geospatial clustering of anopheline mosquitoes in a settlement in Epe, Nigeria
Authors: Bello Abdulrahman Babatunde , Hassan Adesola Adebolade , Popoola Kabir Olajide Kehinde 
Published: December 2024

Abstract

Targeted mosquito control programmes to areas with high abundance and clustering maximises intervention effectiveness. The distribution pattern of Anopheles mosquito larvae was investigated for the presence of clustering distribution patterns using Global Moran’s Index (GMI) spatial autocorrelation and clustering and outlier analysis, in Epe and Orimedu. Each study area was systematically stratified into 12 settlements. Stratified random technique was used to select two georeferenced sampling stations from each settlement and subsequently imported into ArcGIS environment for overlaying on the land use land cover map of the study areas. Larval abundance varied across the sampling stations in Epe (603±160) and Orimedu (531±248). Larval abundance was 53% and 55% in upper altitude stations in Epe and Orimedu respectively. Anopheles larval clustering was observed in only Sagidan settlement in Epe, GMI = 0.43, p<0.05 but not in any of Orimedu settlements, GMI = -0.093, p>0.05. The observed spatial variability in Anopheles larvae in the study area is independent of presence of clustering. The clustering distribution pattern of Anopheles larvae observed in Epe may be attributed to the relatively heterogeneous nature of the terrain and highly varied altitude. Consequently, Epe will require a targeted approach in the allocation of malaria vector control intervention.
Integration of RNA Editing with Multiomics Data Improves Machine Learning Models for Predicting Drug Responses in Breast Cancer Patients
Authors: Bernal Yanara A. , Blanco Alejandro , Oróstica Karen , Delgado Iris , Armisén Ricardo 
Published: December 2024

Abstract

Background: The integration of conventional omics data such as genomics and transcriptomics data into artificial intelligence models has advanced significantly in recent years; however, their low applicability in clinical contexts, due to the high complexity of models, has been limited in their direct use inpatients. We integrated classic omics, including DNA mutation and RNA gene expression, added a novel focus on promising omics methods based on A>I(G) RNA editing, and developed a drug response prediction model.
Methods: We analyzed 104 patients from the Breast Cancer Genome-Guided Therapy Study (NCT02022202). This study was used to train (70%) with 10-fold cross-validation and test (30%) the drug response classification models. We assess the performance of the random forest (RF), generalized linear model (GLM), and support vector machine (SVM) with the Caret package in classifying therapy response via various combinations of clinical data, tumoral and germline mutation data, gene expression data, and RNA editing data via the LASSO and PCA strategies.
Results: First, we characterized the cohort on the basis of clinical data, mutation landscapes, differential gene expression, and RNAediting sites in 69 nonresponders and 35 responders to therapy. Second, regarding the prediction models, we demonstrated that RNA editing data improved or maintained the performance of the RF model for predicting drug response across all combinations. To select the final model, we compared the F1 score between models with different data combinations, highlighting an F1 score of 0.96 (95% CI: 0.957--0.961) and an AUC of 0.922, using LASSO for feature selection. Finally, we developed a nonresponse risk score on the basis of features that contributed to the selected model, focusing on three RNA-edited sites in the genes KDM4B, miRNA200/TTLL10-AS1, and BEST1. The score was created to facilitate the clinical translation of our findings, presenting a probability of therapy response according to RNA editing site patterns.
Conclusion: Our study highlights the potential of RNA editing as a valuable addition to predictive modeling for drug response in patients with breast cancer. The nonresponse risk score could represent a tool for clinical translation, offering a probability-based assessment of therapy response. These findings suggest that incorporating RNA editing into predictive models could enhance personalized treatment strategies and improve decision-making in oncology.
Spatial Autocorrelation and Predictive Modeling of COVID-19 Vaccine Coverage in Thailand (2021–2022)
Authors: Muntaphan Sarayu , Sornlorm Kittipong 
Published: December 2024

Abstract

The COVID-19 pandemic posed significant challenges globally, with vaccine distribution being a critical factor for recovery. Despite achieving vaccination targets, Thailand faced disparities in vaccine coverage across regions. This study aims to investigate the spatial patterns and predictive determinants of COVID-19 vaccine coverage during 2021–2022 using spatial analysis techniques, including autocorrelation and regression models. Moran’s I and LISA showed significant positive spatial autocorrelation in vaccine coverage in 2021 (0.427) and 2022 (0.467). High-High clusters were found to be predominantly located in the Eastern region. The Spatial Error Model was the most suitable for predictions. In 2021, vaccine coverage was associated with population density, nighttime light, public transport, income, medical personnel, COVID-19 cases, and deaths (R² = 0.699). In 2022, key factors were the elderly population, nighttime light, internet access, and medical personnel (R² = 0.610). We conclude that in 2021, COVID-19 vaccine availability saw limited vaccine quantities distributed unevenly. Areas with substantial economic growth, high COVID-19 incidence rates, and a significant presence of medical personnel tended to have higher COVID-19 vaccine coverage. In 2022, vaccine availability improved with extensive distribution and community-level services targeting vulnerable groups, supported by online decision-making tools and a reservation system.
Efficiency of antiangiogenic therapy for choroidal neovascularization in children
Authors: Katargina L. A. , Denisova E. V. , Osipova N. A. , Kiseleva Ya. A. 
Published: December 2024

Choroidal neovascularization (CNV) in children is a rare but functionally significant complication of a wide range of fundus diseases. Data on the effectiveness of antiangiogenic therapy for CNV of various etiologies in ophthalmopediatrics are scarce.Purpose of the study is to analyze the effectiveness of antiangiogenic therapy for CNV in children.Material and methods. A retrospective analysis of the results of treatment of active CNV was performed in 54 children (59 eyes). All patients underwent intravitreal injection of antiangiogenic drug (ranibizumab, aflibercept or brolucizumab). In addition to standard ophthalmologic examination, children underwent optical coherence tomography (OCT) and OCT angiography (OCTA) of the macular area and optic nerve head at diagnosis and dynamically after treatment.Results. In 51 children (56 eyes), persistent suppression of CNV activity was achieved, in 3 children the drug administration was continued on an “as needed” basis. The number of anti-VEGF drug injections ranged from 1 to 7 (on average, 1.6 ± 1.3), while 8 children (8 eyes, 13.6 %) required more than 2 injections of the drug, in 6 of them the main disease was inflammatory lesion of the uveal tract and retina. The best corrected visual acuity in 20 children (20 eyes, 33.9 %) increased by 0.03–0.4, in 30 children (35 eyes, 59.3 %) it remained stable, in 4 children (4 eyes, 6.8 %) it decreased by 0.05–0.6. Conclusion. Anti-VEGF therapy is an effective method for treating CNV in children. Further studies are needed to identify risk factors and develop treatment regimens for refractory cases of CNV.
Evaluation the tissue inhibitor of matrix metalloproteinases first type concentration in various platelet-related products
Authors: Chentsova E. V. , Borovkova N. V. , Sirotkina K. V. , Beznos O. V. , Makarov M. S. , Ponomarev I. N. , Storozheva M. V. 
Published: December 2024

Purpose: to evaluate the content of tissue inhibitor of matrix metalloproteinase type 1 (TIMP-1) in platelet preparations obtained in different methods.Material and methods. Platelet-rich plasma (PRP), platelet-poor plasma, and a suspension of platelets washed from plasma (WP) were isolated from the blood of 10 volunteer donors, and a morphofunctional analysis of platelets was performed. After that, a platelet lysate was prepared from PRP, WP, and platelet-poor plasma. The concentration of TIMP-1 in the lysates was determined using enzyme immunoassay.Results. The level of TIMP-1 in the lysates of PRP and WP did not differ significantly; in platelet-poor plasma, the level of TIMP-1 was significantly lower than in the lysates of PRP and WP (p = 0.003). In all types of preparations, the concentration of TIMP-1 was 2-4 times higher than similar values in the blood serum of healthy people, as reported in other studies. A weak correlation was found between the TIMP-1 concentration and the platelet number in PRP, and there was no correlation between the content of platelets with granules and the TIMP-1 level in the lysates. The presence of leukocytes in the initial PRP also did not affect the TIMP level in the final lysates. A strong correlation was found between the TIMP-1 concentration in the WP lysate and in platelet-poor plasma, as well as a direct correlation between the total platelet content and the TIMP-1 level in the PRP lysate.Conclusions. Preparations with high concentrations of TIMP-1 can be obtained both from concentrated platelet suspensions and from platelet-poor plasma. To optimize the method, it is necessary to study the effect of platelet preparations with TIMP on various biological models.
Analysis of Scientific Literacy of Senior High School Students in Relation to Global Warming as a Socio-Scientific Issue
Authors: Hernani Hernani , Depi Siska Sintia , Hidayat Lina Nurlina , Nurhadi Atep Rian , Supriatna Asep , Tias Bachrul , Wafi Wulanda 
Published: December 2024

The low scientific literacy skills of Indonesian students should be a serious concern for all science educators. Scientific literacy skills can be improved in contextual learning related to nature and social contexts that occur in the environment around students. This study aims to develop the science literacy of high school students through the application of Problem Based Learning model on the topic of global warming. This study used a quantitative approach with descriptive methods, with participants of 24 students in one of the high schools in Bandung City. The research instrument used is a science literacy test question in the form of descriptions, which consists of 3 domains, namely context, content, and science competence, in addition, student handouts is also used to provide an overview of the PBL learning process containing the applied science literacy. The result shows students performed Moderately in three PISA-based competencies including (i) explaining scientific phenomena, (ii) evaluating and designing scientific investigations, and (iii) analyzing evidence and data scientifically for decision-making and action.
Transformation of persistent organic micropollutants by UV and UV/H2O2 in wastewater treatment plant effluent
Authors: Thor Jan , Dittmann Daniel , Meyer Andreas , Zeeshan Muhammad , Johne Steffen , Reynaert Eva , Ruhl Aki Sebastian 
Published: December 2024

ABSTRACT

Photochemical and advanced oxidation processes (AOPs) are promising options to simultaneously disinfect wastewater treatment plant (WWTP) effluent and degrade organic micropollutants (OMPs). In the present study, kinetic experiments with UV alone (254 or 254+185 nm) and the combination of UV and hydrogen peroxide (H2O2) as an AOP were conducted in WWTP effluent (with and without ultrafiltration) to assess the degradation of 24 OMPs, 13 of which were examined for the first time, in a flow-through batch reactor setup. Four parameters were systematically varied to quantify their impacts on OMP degradation: H2O2 concentrations, UV source, water matrix, and flow rate. Most of the studied OMPs (e.g., trimethylammonium, 1,3-di-o-tolylguanidine, carbamazepine) were only significantly degraded in the presence of UV radiation and H2O2. The highest pseudo-first-order rate constants were found for diclofenac, acesulfame, diatrizoate, and sulfamethoxazole. The experiment with the highest degradation also showed the strongest abatement of UV absorbance at 254 nm. Only three of the 24 substances (cyanoguanidine, melamine, and oxipurinol) were not degraded; UV alone even increased their concentrations. Overall, upgrading a UV disinfection to an AOP using H2O2 allows the degradation of a wide range of OMPs, making it an interesting process for water reuse.
Pardon my trench: reflections on the uptake of trenchless technologies in the Norwegian water sector
Authors: Rokstad Marius Møller , Bruaset Stian , Skaar Bjørn Solnes , Borgen Eirik Otnæs , Tscheikner-Gratl Franz 
Published: December 2024

ABSTRACT
Trenchless pipe renewal can be a more cost-, time- and environmentally effective alternative to traditional open-cut replacement. It reduces service disruptions for surrounding infrastructures and is often cheaper, especially when extensive excavation works are necessary, particularly in cold climates, like Norway, where trenches are traditionally deep due to frost security requirements. Still, the uptake of trenchless technologies is still limited in the Norwegian market. In this study, interviews were conducted with representative actors in the Norwegian water industry (water utilities, contractors, and consultants), with the aim of revealing how the technology for renewal of pipes is selected in the planning phase and identifying hindering and enabling factors for trenchless technology uptake in the market. Factors identified include market conservativism, lack of trust between stakeholders, missing guidelines about the distribution of risk, lack of knowledge/specialization in utilities and consultant offices, and issues pertaining to the project delivery method and tendering process. These factors indicate which measures could be implemented to increase the uptake of trenchless technologies in the Norwegian and similar markets. Suggested measures include strengthening the position of stakeholder independent trade organization, facilitating cooperation between smaller utilities and adapting the tendering process to better reflect the requirements of the projects.
Preparation and Evaluation of Ni/NiAl2O4 Core/Shell Nanostructures in
Non-ionic Surfactant-based Vesicle
Authors: Pardakhty Abbas , Rajaei Peyman , Ranjbar Mehdi , Ohadi Mandana 
Published: December 2024

Background:
Non-ionic surfactant-based vesicles (niosomes) as coherent and selforganization
capability structures form organized core/shell nanostructures.

Objective:
In this academic research, Ni/NiAl2O4 core/shell nanostructures were successfully synthesized
with the ultrasound-assisted direct micelle (UADM) method and these structures were used as a
delivery system for minoxidil drugs.

Method:
The synthesis conditions for producing Ni/NiAl2O4 core/shell structures were optimized
using a design of experiments (DOE) approach. Process control was systematically examined
through analysis of variance (ANOVA) and response surface methodology (RSM). The Ni/NiAl2O4,
core/shell nanostructures, underwent characterization using various techniques such as SEM (scanning
electron microscopy), TEM (transmission electron microscopy), AFM (atomic force microscopy),
FT-IR (Fourier-transform infrared spectroscopy), TGA (thermogravimetric analysis), BET analysis,
differential thermal analysis (DTA), and nitrogen adsorption isotherms. The in vitro release of
minoxidil from the Ni/NiAl2O4 core/shell nanostructures was studied using UV-vis spectroscopy at a
wavelength of 486 nm.

Results:
Results indicated an encapsulation efficiency (EE%) of around 74% after 150 minutes. Furthermore,
the loading efficiency of minoxidil in niosomes modified with Ni/NiAl2O4 core/shell
nanostructures was calculated to be approximately 99.83% at 486 nm.

Conclusion:
Overall, this research lays a foundational framework for developing innovative nanomaterials
with tailored properties for advanced delivery systems and other novel applications.