bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global, regional, and national health inequalities in hepatitis B virus-related liver cancer in 204 countries, 1990-2021
Authors: Wu Dongjie , Guo Ziwei , Liu Jing , Wang Liang , Yang Lan , Mao Runhan , Lu Yanping , Lyu Wenliang 
Published: October 2024

Abstract

Background
Hepatitis B virus-related liver cancer (HBV-LC) is a significant public health challenge, particularly in low- and middle-income countries. Despite advancements in vaccination and antiviral therapies, global disparities persist.
Objective
This study provides a comprehensive analysis of the global, regional, and national burden of HBV-LC from 1990 to 2021 and projects future trends to 2036, using data from the Global Burden of Disease (GBD) 2021 study.
Methods
Data on prevalence, incidence, mortality, and disability-adjusted life years (DALYs) were extracted from GBD 2021. Joinpoint regression was used to analyze trends, and Bayesian age-period-cohort (BAPC) models were employed to forecast future burden.
Results
In 2021, an estimated 288,106 global cases of HBV-LC were reported, with an age-standardized prevalence rate (ASPR) of 3.32 per 100,000 people. The global incidence rate (ASIR) was 2.37 per 100,000, while the mortality rate (ASMR) was 2.09 per 100,000. From 1990 to 2021, the ASIR declined by 0.22%, and the DALYs decreased by 0.79 years per 100,000. The highest burden was observed in East Asia and the High-income Asia Pacific region, while the lower SDI regions experienced more significant mortality. Projections from the BAPC model indicate continued declines in both ASIR and ASMR through 2036, particularly among females.
Conclusion
This study highlights a global reduction in the HBV-LC burden over the past three decades, yet significant disparities remain between regions. Future efforts should focus on expanding access to vaccination and antiviral therapies in low-SDI areas to further mitigate the disease burden.
SMARCAL1: a DNA repair protein recruited to double-strand breaks at stalled replication forks to promote genome stability through a homologous recombination pathway
Authors: Safa Amin , Cárdenas Paula P , Perrig Melina Soledad , Chaparro-García Rebeca , Román-Ortiz Elena , Sánchez-Ramón Silvia , Diego Rebeca Pérez , Recio María J. 
Published: October 2024

Abstract

To create an exact copy of the entire genome, replication should be completed promptly and accurately. However, obstacles can arise during replication that can cause genotoxic fork stalling. The DNA damage response pathway plays a crucial role in preventing fork collapse by stabilizing the stalled fork, regulating DNA repair, and promoting replication restart. There are multiple pathways to recover stalled replication forks, including double-strand break (DSB)-mediated recovery. SMARCAL1, a damage-binding protein involved in stabilizing stalled replication forks during DNA repair, is recruited to replication forks via interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells; however, the process by which it promotes DSB repair is poorly understood. Here, we present cellular and biochemical evidence that SMARCAL1 c.1920_1921insG frameshift mutation impairs SMARCAL1 protein expression causing defects in DNA damage response and hypersensitivity to several genotoxic agents that cause DSBs and replication fork collapse in a patient with Schimke immuno-osseous dysplasia. We analyzed the role of SMARCAL1 in the two major DNA DSB repair pathways, homologous recombination (HR) and nonhomologous end-joining (NHEJ). γ-H2AX foci repair kinetics analysis and survival experiments performed in SMARCAL1-deficient fibroblasts point to an essential role for SMARCAL1 in repairing DSBs generated in the S/G2 phase cell cycle as a result of oxidative damage and replication stress. The contribution to survival of SMARCAL1-dependent DSB rejoining in the S/G2 phase cell cycle suggests that SMARCAL1 is a novel damage repair protein involved in the HR pathway.
Spatial Analysis of Urban Expansion and Temperature Dynamics in the Kolkata Metropolitan Area
Authors: Saha Gourab , Das Dipendra Nath , Banerjee Anushna , Singh Piyush 
Published: October 2024

Abstract

Urbanization in Southeast Asia, particularly in India, has witnessed rapid growth driven by demographic, economic, and socio-political factors. Kolkata, as a prominent urban center, exemplifies this trend, experiencing substantial urban expansion and consequent changes in land use and land cover (LULC), leading to elevated Land Surface Temperature (LST) levels. This study investigates the spatio-temporal dynamics of land transformation and its influence on LST distribution in Kolkata and its suburban areas over 22 years (2000–2022). Using remote sensing and GIS techniques, we analyze Landsat data to assess LULC changes and their correlation with LST. Additionally, we examine seasonal LST variations in relation to land use characteristics, employing various spectral indices. The findings reveal significant LULC alterations, including the reduction of green spaces and the expansion of built-up areas, contributing to higher LST levels and the development of Urban Heat Island (UHI) effects. This research underscores the adverse implications of escalating LST on urban environmental quality and public health. Additionally. it emphasizes the importance of environmental sustainability initiatives in urban planning to mitigate UHI impacts and enhance residents' well-being. The methodological advancements presented here hold promise for ongoing monitoring of environmental quality and urban heat dynamics, aiding future decision-making processes.
Tenofovir Alafenamide versus Entecavir in the Treatment of Renal Safety in Patients with Chronic Hepatitis B: An Observational Study
Authors: Zhou ding ying , Zhong Lianghui , Mao Yaqian , Zhang Lunli , Zhong Yuanbin 
Published: October 2024

Abstract

Background and aims: Urinary α1-microglobulin (α1-MG), β2-microglobulin (β2-MG), urinary N-acetyl-β-glucosaminidase (NAG) and retinol-binding protein (RBP) have predictive effects on renal tubular injury, the purpose of this study is to investigate whether the renal tubular abnormalities in chronic hepatitis B (CHB) patients during long-term entecavir (ETV) treatment cloud be improved after altering to tenofovir alafenamide(TAF).
Methods：This study included 224 CHB patients of abnormal renal tubular markers from June 2022 to September 2023, of which 122 patients continuing ETV and 102 patients of altering to TAF for 6 months. Propensity score matching was used to analyze the differences of renal tubular indexes between the continuing ETV treatment and altering to TAF treatment.
Results: A 1:1 propensity score match yielded 62 patients in each treatment group.The baseline characteristics, the ratio of complete virology respond,liver blood phosphorus, the estimated glomerular filtration rate (eGFR), α1-MG, β2-MG, NAG, RBP were comparable between the two groups. After 6 months, the level of eGFR(ETV:101.5mL/(min*1.73m2),TAF:100.1mL/(min*1.73m2),p>0.05),RBP(△ETV -0.159 △TAF -0.213,p>0.05), the ratio of complete virology response(ETV 87.1% TAF 91.9%,P< 0.05) were statistically different.The difference ratio of α1-MG, β2-MG, NAG, blood phosphorus was statistically significant（p<0.05）。TAF decreased more than ETV in α1-MG, β2-MG, NAG indicators(△ETV: -4.016, -0.373,-0.852, △TAF: -12.050, -1.272, -5.583），TAF increased less than ETV in blood phosphorus (△ETV +0.019, △TAF -0.286）。
Conclusion: Altering to TAF of CHB patients with renal tubular abnormalities after long-term use of ETV , the treatment efficacy and renal tubular damage can be improved, indicating that TAF has better renal safety than ETV.
Ki-67 expression in anti-programmed cell death protein-1 antibody-bound CD8+ T cells as a predictor of clinical benefit
Authors: Tsurui Toshiaki , Hosonuma Masahiro , Sasaki Aya , Maruyama Yuuki , Amari Yasunobu , Funayama Eiji , Tajima Kohei , Toyoda Hitoshi , Isobe Junya , Yamazaki Yoshitaka , Baba Yuta , Shida Midori , Udaka Yuko , Mura Emiko , Suzuki Risako , Iriguchi Nana , Ishiguro Tomoyuki , Hirasawa Yuya , Ohkuma Ryotaro , Shimokawa Masahiro , Ariizumi Hirotsugu , Kubota Yutaro , Horiike Atsushi , Wada Satoshi , Kuramasu Atsuo , Tsuji Mayumi , Kiuchi Yuji , Tsunoda Takuya , Yoshimura Kiyoshi 
Published: October 2024

Abstract

Aims
Developing predictive biomarkers for immune checkpoint inhibitors (ICIs) is important. Programmed cell death protein-1 (PD-1) receptor occupancy by anti-PD-1 antibodies on circulating T cells varies among patients. However, the association between the exhaustion of these antibody-bound T cells and the clinical efficacy of ICIs remains unknown. Therefore, the present study was aimed at evaluating this association.
Methods
This prospective cohort study included patients with advanced non-small cell lung cancer (NSCLC) and esophageal squamous cell carcinoma (ESCC) who received pembrolizumab therapy. Peripheral blood samples were collected during the second cycle of chemotherapy. We analyzed the relationship between exhaustion markers in pembrolizumab-bound (PB) T cells and clinical response.
Results
A total of 21 patients were analyzed, including 12 patients with NSCLC and 9 patients with ESCC. The expression of Ki-67 in PB-CD8+ TCM and TEM was negatively correlated with both clinical response and overall survival.
Conclusion
The expression of Ki-67 of PB-CD8+ TCM and TEM can serve as a predictive biomarker for the clinical benefit of pembrolizumab therapy. Our study suggests that analyzing antibody-bound T cells could be a novel approach to predict the clinical outcomes of PD-1 blockade therapy.
Improving the accuracy of pose prediction by incorporating symmetry-related molecules
Authors: Hima Sree , Remya Chandran , Dileep K. V. 
Published: October 2024

Abstract

Accurate prediction of biologically relevant binding poses is crucial for the success of computer-aided drug development. In this study, we describe a general strategy to enhance the precision of pose prediction in molecular docking by incorporating symmetry-related molecules (SRMs). Our objective was to demonstrate the significant impact of SRMs on the accuracy of pose prediction. To achieve this, we evaluated our method on high-quality protein-ligand complex structures, focusing on the presence and absence of SRMs during molecular docking studies. We have extracted the co-crystal ligands from the selected crystal structure and were redocked in presence and absence of SRM to assess their influence. Additionally, we calculated the free energy of the docked poses using the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) method, comparing the results in the presence and absence of SRMs. The findings revealed that redocking performed in the presence of SRMs significantly improved the prediction of biologically significant/crystallographically relevant poses. Consequently, our proposed strategy offers a robust method for enhancing pose prediction in current molecular docking programs, potentially leading to more effective and reliable drug development processes.
REMFLOW: RAG-Enhanced Multi-Factor Rainfall Flooding Warning in Sponge Airports via Large Language Model
Authors: Wang Gelan , Liu Yu , Liu Shukai , Zhang Ling , Yang Liqun 
Published: October 2024

Abstract

The integration of rainfall flooding data, particularly with the development and application of the Storm Water Management Model (SWMM), has significantly enhanced the predictive capabilities of flood warning systems. However, existing models often lack relevant environmental context, leading to the incorporation of external knowledge bases. Previous machine learning approaches have primarily focused on structured knowledge, neglecting unstructured data and high-dimensional semantic information. To address these issues, we propose REMFLOW, a Retrieval-Augmented Generation (RAG) framework designed to improve the analysis and application of multi-factor rainfall flooding data. We employ an embedding model to encode time-series flood data, which is then stored in a knowledge base. Simultaneously, a Large Language Model (LLM) is used to encode multi-factor rainfall flooding data and retrieve relevant knowledge. Subsequently, an adaptive context fusion mechanism is applied to integrate the extracted knowledge and generate the final outputs. Experimental results from various rainfall flooding prediction tasks demonstrate that the REMFLOW framework significantly outperforms baseline models in the precise predictive analysis of multi-factor rainfall flooding data, highlighting its effectiveness.
Mode shapes and sensitivity analysis of torsional vibrations in overhang- and T-shaped microcantilevers
Authors: Dat Le Tri , Pham Vinh N.T. , Vy Nguyen Duy , Payam Amir F. 
Published: October 2024

Abstract

The torsional mode of atomic force microscope (AFM) cantilevers has been extensively employed in a range of sensitive measurements. However, the use of approximate frequencies and mode shapes for overhang-shaped cantilevers often leads to discrepancies between theoretical predictions and experimental results. In this study, we performed detailed calculations of the frequency and mode shapes for width-varying cantilevers, enabling the determination of any higher-order mode. Modal sensitivities were then calculated based on the obtained mode shapes. We observed clear changes in mode shapes and frequencies, with mode shapes exhibiting multiple maxima as the overhang length increased. Notably, effective tuning of the frequency was demonstrated by adjusting the overhang length. The relationship between modal sensitivity and the coupling strength between the cantilever and a surface was elucidated, showing consistency with results from other groups. This work provides valuable guidance for experimentalists in selecting optimal geometric parameters for cantilevers to target specific frequencies.
Spatial patterns and conservation gaps of Fritillaria species in China
Authors: Ullah Fazal , Saqib Saddam , Temur Asatulloev , Xiong You-Cai 
Published: October 2024

Abstract

The genus Fritillaria, a well-known Chinese traditional medicine used for over 2000 years, is primarily distributed across the temperate regions of China and is one of the threatened genera due to climate change, habitat loss, and excessive harvesting. These perennial bulbous plants are important for their ornamental beauty and traditional medicinal uses. To provide a scientific guide for Fritillaria conservation, this study explores the diversity patterns of 21 species across China using three diversity indices (species richness (SR), weighted endemism (WE), and β-diversity) with a spatial resolution of 100 X 100 km2. The top 5% richness and complementary algorithms were used to identify diversity hotspots and conservation gaps were recognized by overlapping the diversity hotspots with Chinese nature reserves. Our results indicate that Fritillaria SR and WE are high in central and southwestern China, particularly in Sichuan and Yunnan provinces. The β-diversity is scattered across these regions, suggesting different species compositions among grid cells. We identified 145 grids as diversity hotspots for Fritillaria species in China, with significant overlap in Sichuan and Yunnan. The first-level diversity hotspots include over 70% of the Endangered (EN) and Vulnerable (VU) Fritillaria species and are the priority areas for conservation. However, only 24% of the diversity hotspots fall within nature reserves, and many regions, especially in Zhejiang, Guizhou, and Fujian, have less than 20% of diversity hotspots covered by protected areas. Using multiple diversity indices and algorithms, our study identifies critical diversity hotspots and conservation gaps for Fritillaria species in China. These findings provide a scientific basis for targeted conservation strategies to protect these valuable plants and their habitats, particularly in regions with high biodiversity and significant conservation gaps.
Imbalance in Redox Homeostasis is Associated with Neurodegeneration in the Murine Model of Tay-Sachs Disease
Authors: Basırlı Hande , Ateş Nurselin , Seyrantepe Volkan 
Published: October 2024

Abstract

Background
Tay-Sachs disease is a type of neurodegenerative disorder with a build-up of GM2 ganglioside in the brain, which results in progressive central nervous system dysfunction. Our group recently generated Hexa-/-Neu3-/- mice, a murine model with neuropathological abnormalities similar to the infantile form of Tay-Sachs disease. Previously, we reported progressive neurodegeneration with neuronal loss in the brain sections of Hexa-/-Neu3-/- mice. However, the relationship of the severity of neurodegeneration to imbalance in redox homeostasis has not been clarified in Hexa-/-Neu3-/- mice. Here, we evaluated whether neurodegeneration is associated with oxidative stress in the tissues and cells of Hexa-/-Neu3-/- mice and neuroglia cells from Tay-Sachs patients.
Methods and Results
In four brain regions and fibroblasts of 5-month-old WT, Hexa-/-, Neu3-/-, and Hexa-/-Neu3-/- mice and human neuroglia cells, apoptosis and oxidative stress-related markers were evaluated using Western blot, RT-PCR, and immunohistochemistry analyses. We further analyzed oxidative stress levels using flow cytometry analyses. We discovered neuronal death, alterations in intracellular ROS levels, and damaging effects of oxidative stress, especially in the cerebellum and fibroblasts of Hexa-/-Neu3-/- mice.
Conclusions
Our results showed that alteration in redox homeostasis might be related to neurodegeneration in the murine model of Tay-Sachs Disease. These findings suggest that targeting the altered redox balance and increased oxidative stress might be a rational therapeutic approach for alleviating neurodegeneration and treating Tay-Sachs disease.
Comparative Evaluation of the Effects of Diclofenac Sodium and Vitamin D Supplementation on Symptoms in Individuals With Myofascial Pain and Vitamin D Deficiency
Authors: KAHRAMAN Nazlı Hilal , TUNÇ Serap KESKİN 
Published: October 2024

Abstract

Background: Temporomandibular joint disorders are significant health issues characterized by dysfunctions in the masticatory muscles and the temporomandibular joint. These disorders are often associated with stress, oral parafunctions, and habits such as bruxism. Treating bruxism and other parafunctional habits can reduce symptoms of myofascial pain. While the etiology of bruxism remains unclear, psychological factors like stress and anxiety, along with central nervous system, are thought that it will provoke. Additionally, a significant relationship has been reported between low serum vitamin D levels and bruxism.
Methods: The aim of this study is to comparatively evaluate the effectiveness of nonsteroidal anti-inflammatory drug treatment and vitamin D supplementation on symptoms in individuals with myofascial pain and vitamin D deficiency. Two different treatment methods were applied to the patients. One group received medical treatment with diclofenac sodium and an occlusal splint. The other group received vitamin D supplementation and an occlusal splint. The patients' mouth opening and pain scores were evaluated.
Results: The results obtained are homogeneous in both groups.
Conclusions: Vitamin D may serve as an alternative with anti-inflammatory and analgesic effects compared to NSAIDs.
Trial registration: This study was approved by the Van Yüzüncü Yıl University Faculty of Medicine Clinical Research Ethics Committee (May 18, 2022, decision no: 05).
Computational modeling of vaccination strategies for infectious disease control: Insights from network-based simulations
Authors: Branda Francesco , Veltri Pierangelo , Chiodo Francesco , Ciccozzi Massimo , Scarpa Fabio , Guzzi Pietro Hiram 
Published: October 2024

Abstract

Background Computational modeling of disease transmission is crucial for understanding the dynamics of infectious outbreaks and assessing the effectiveness of control measures. These models offer valuable insights into the factors influencing disease spread, enabling public health authorities to develop effective containment strategies. Vaccination is among the most impactful interventions in controlling disease transmission and has proven essential in preventing the spread of contagious diseases such as measles. However, recent trends indicate a concerning decline in the fraction of vaccinated individuals in various populations, increasing the risk of outbreaks.
Methods In this study, we utilize computational simulations on graph-based models to analyze how vaccination affects the spread of infectious diseases. By representing populations as networks in which individuals (nodes) are connected by potential transmission pathways (edges), we simulate different vaccination coverage scenarios and assess their impact on disease propagation. Our simulations incorporate high and low vaccination coverage to reflect real-world trends and explore various conditions under which disease transmission can be effectively blocked.
Results The results demonstrate that adequate vaccination coverage is critical for halting outbreaks, with a marked reduction in disease transmission observed as the fraction of vaccinated individuals increases. Conversely, insufficient vaccination rates lead to widespread outbreaks, underscoring the importance of maintaining high vaccination levels to achieve herd immunity and prevent resurgence. These findings highlight the vital role of vaccination as a preventative tool and emphasize the potential risks posed by declining vaccination rates.
Conclusion This study provides a deeper understanding of how vaccination strategies can mitigate the spread of infectious diseases and serves as a reminder of the importance of maintaining robust immunization programs to protect public health.
Savannah Bengal Tiger Optimization (SBTO): A Novel Metaheuristic Algorithm for Constrained Optimization Problems
Authors: Sun Yujing , Xu Xingguo 
Published: October 2024

Abstract

This paper introduces a novel optimizer based on animal survival experiments called Savannah Bengal Tiger Optimization (SBTO). Inspired by the survival behavior of Bengal tigers on the African savannah, SBTO aims to address continuous complex constrained optimization problems. SBTO simulates the group hunting behavior of Bengal tigers and integrates the support of Kalman filters, employing three strategies: prey search, stealth approach, and hunting. The prey search strategy reflects SBTO's exploration capabilities, while the stealth approach and hunting strategies primarily demonstrate its exploitation capabilities. Compared to other metaheuristic algorithms, SBTO has an advantage in population distribution, maintaining good exploration performance while performing exploitation, which helps the algorithm escape local optima in a timely manner. Finally, SBTO was experimentally evaluated against 10 popular algorithms and recently proposed algorithms on CEC2017, CEC2020, CEC2022 test functions, and 9 engineering problems. The results indicate that SBTO achieved the best fitness ratio of 27/30, 8/10, and 8/12 in the test functions, with Wilcoxon rank-sum tests showing significance proportions of 260/300, 89/100, and 104/120, respectively. In the 9 engineering problems, SBTO obtained the best average and optimal fitness in 7 problems, demonstrating exceptional performance in constrained optimization problems and complex multi-modal functions. The source code for SBTO is publicly available at https://www.mathworks.com/matlabcentral/fileexchange/172500-sbto.