bluuebunny/crossref_metadata_2025_split huggingface dataset:
The mitochondrial UPR induced by ATF5 attenuates intervertebral disc degeneration via cooperating with mitophagy
Authors: Xu Wen-Ning , Zheng Huo-Liang , Yang Run-Ze , Sun Yuan-Fang , Peng Bi-Rong , Song Jian , Jiang Sheng-Dan , Zhu Li-Xin 
Published: November 2023

Abstract
Intervertebral disc degeneration (IVDD) is an aging disease that results in a low quality of life and heavy socioeconomic burden. The mitochondrial unfolded protein response (UPRmt) is involved in various aging-related diseases. Our study aims to investigate the role and underlying mechanism of UPRmt in IVDD. Nucleus pulposus (NP) cells were treated by IL-1β and nicotinamide riboside (NR) served as UPRmt inducer to treat NP cells. TUNEL assay, Western blot and Flow cytometry were used to determine the apoptosis of NP cells. Detection of ATP, NAD + and NADH were used to determine the function of mitochondria. MRI, Safranin O-fast green staining and Immunohistochemical examination were used to determine the degree of IVDD in vivo. In the present study, we discovered that the level of UPRmt was significantly lower in the human tissue of patients with IVDD than in healthy controls. In vitro, UPRmt and mitophagy levels were promoted in NP cells after IL-1β treatment. Upregulation of UPRmt by NR and Atf5 overexpression inhibited the apoptosis of NP cells induced by IL-1β treatment and further improved mitophagy. Silencing of Pink1 reversed the protective effects of NR and inhibited mitophagy induced by the UPRmt. In vivo, NR might attenuate the degree of IDD by activating the UPRmt in rats. In summary, the UPRmt was involved in IVDD by regulating Pink1-induced mitophagy. Mitophagy induced by the UPRmt might be a potential therapeutic target for IVDD.
Association between visual functions and qualitative and quantitative Optical Coherence Tomography parameters in Malaysian Eyes with typical neovascular age related macular degeneration: A pilot study
Authors: Ghoshal Rituparna , Ghosh Somnath , Sharanjeet Sharanjeet-Kaur , Fadzil Norliza Mohamad , Ngah Nor Fariza , Aziz Roslin Azni Binti Abd 
Published: November 2023

Abstract
Purpose
None of the previous studies established a strong relationship between them. Thus, the aim of the present pilot research was to evaluate the detailed visual functions and qualitative and quantitative OCT parameters and to measure the correlation between them.
Methods
Patients diagnosed as naïve neovascular AMD were recruited from a public hospital of Malaysia. Best corrected distance visual acuity, near visual acuity, reading speed and contrast sensitivity were assessed. Several quantitative and qualitative morphological parameters were evaluated using the spectral-domain OCT. A semi auto method of image analysis was employed.
Results
Fifteen newly diagnosed typical neovascular AMD eyes were evaluated in this study. Mean (± SD) distance visual acuity, near visual acuity, contrast sensitivity and reading speed were recorded as 0.92 ± 0.39, 0.80 ± 0.38, 0.75 ± 0.39, 70.02 ± 14 respectively. Average retinal thickness, central thickness and centre maximum thickness showed good correlation (r = > 0.05) with distance visual acuity, near visual acuity and contrast sensitivity. Similarly, centre minimum thickness showed good correlation (r = > 0.50) with distance visual acuity. An intact external limiting membrane and photoreceptors inner and outer segment showed better visual functions.
Conclusion
The present pilot study reported morphological and visual functions of Malaysian typical neovascular AMD eyes. All the visual functions of the study eyes showed significant impairment. Some of the OCT parameters showed good correlation with visual functions. Thus, regardless of small sample size, the present pilot study generated new knowledge and understanding on this area. Future research with large sample is recommended.
Multimodal Protein Representation Learning and Target-aware Variational Auto-encoders for Protein-binding Ligand Generation
Authors: Ngo Nhat Khang , Hy Truong Son 
Published: November 2023

Abstract
Without knowledge of specific pockets, generating ligands based on the global structure of a protein target plays a crucial role in drug discovery as it helps reduce the search space for potential drug-like candidates in the pipeline. However, contemporary methods require optimizing tailored networks for each protein, which is arduous and costly. To address this issue, we introduce TargetVAE, a target-aware variational auto-encoder that generates ligands with desirable properties including high binding affinity and high synthesizability to arbitrary target proteins , guided by a multimodal deep neural network built based on geometric and sequence models, named Protein Multimodal Network (PMN), as the prior for the generative model. PMN unifies different representations of proteins (e.g., primary structure-sequence of amino acids, 3D tertiary structure, and residue-level graph) into a single representation. Our multimodal architecture learns from the entire protein structure and is able to capture their sequential, topological, and geometrical information by utilizing language modeling, graph neural networks and geometric deep learning. We showcase the superiority of our approach by conducting extensive experiments and evaluations, including predicting protein-ligand binding affinity in PBDBind v2020, DAVIS and KIBA datasets as well as the assessment of generative model quality, ligand generation for unseen targets, and docking score computation. Empirical results demonstrate the promising and competitive performance of our proposed approach. Our software package is publicly available at https://github.com/HySonLab/ Ligand Generation
Global Soft Pooling Adaptive Attention Network for Single Aerial Image-Based 3D Outdoor Scene Reconstruction
Authors: Wang Wenju , Li Wei , Yan Ruipeng 
Published: November 2023

Abstract

In the realm of outdoor scene 3D reconstruction from a solitary RGB aerial image, a persistent challenge pertains to the issue of inadequate reconstruction accuracy. In this article, we introduce a novel approach, namely, the Global Soft Pooling Adaptive Attention Network, designed to facilitate high-precision 3D scene reconstruction in outdoor environments. This network primarily comprises two distinct attention network modules: the Global Soft Pooling Dynamic Convolutional Attention and the Three-Head Adaptive Graph Attention. The Global Soft Pooling Attention Network employs a stem_conv and four MBdyconv components for the extraction of multi-scale image features. It harnesses global soft pooling techniques, integrating both channels fusion and spatial attention mechanisms, thereby enabling the precise acquisition of composite features. These features are subsequently assigned to initialize mesh vertices. The Three-Head Adaptive Graph Attention Network leverages three sets of adaptive 1D convolutions to derive 3D vertex features, taking into account the weights of neighboring vertices. A linear layer is employed to compute the vertex coordinate offsets (denoted as "ΔV"), which are then utilized to refine the initial mesh vertices, ultimately achieving an enhanced mesh model. When evaluated on the publicly available SensatUrban dataset, our proposed method demonstrates impressive performance metrics, achieving a reconstruction performance index of 0.96 for l2 and 1.68 for l3. Experimental results unequivocally demonstrate that our approach outperforms existing deep learning methodologies, establishing itself as the state-of-the-art solution for outdoor 3D scene reconstruction.
Geochemical Evaluation of Pinghu Formation Source Rocks for Hydrocarbon Potential in East China Sea of Xihu Depression
Authors: Cui Zhihua , Taiwo Olusoji Lawrence , Aaron Peace Mawo 
Published: November 2023

Abstract
The Xihu Depression in the East China Sea Basin (ECSB) is a potential petroleum accumulation area, but its Pinghu Formation is poorly understood and requires more geochemical evidence. This study aims to evaluate the organic matter abundance and hydrocarbon potential of source rocks of typical lithologies of mudstone, carbonaceous mudstone and coal. The results show that mudstone source rocks have a broad total organic carbon (TOC) range, with nearly 35% exceeding 1.0% and averaging 1.03%, indicating relatively high organic content. Carbonaceous mudstone and coal and samples exhibit high TOC, ranging from 5.0% to 72.9% and 31.7% to 72.9%, and with average 12.6% and 51.3%, suggesting significant hydrocarbon generation potential. This formation exhibits high organic richness, especially in coal and carbonaceous mudstone, comparable to top source rocks in other Chinese land basins. This supports that mudstone source rocks have a low organic matter abundance and moderate hydrocarbon potential due to their thickness, whereas carbonaceous mudstone and coal showcase higher organic richness with significant hydrocarbon potential. This study provides new geochemical data and insights on the Pinghu Formation and its exploration potential, particularly by enhancing the previously overlooked but noteworthy evidence related to mudstone.
Prediction of heavy-section ductile iron fracture toughness based on machine learning
Authors: Song Liang , Zhang Hongcheng , Zhang Junxing , Guo Hai 
Published: November 2023

Abstract
The preparation process and composition design of heavy-section ductile iron are the key factors affecting its fracture toughness. These factors are challenging to address due to the long casting cycle, high cost and complex influencing factors of this type of iron. In this paper, 18 cubic physical simulation test blocks with 400 mm wall thickness were prepared by adjusting the C, Si and Mn contents in heavy-section ductile iron using a homemade physical simulation casting system. Four locations with different cooling rates were selected for each specimen, and 72 specimens with different compositions and cooling times of the heavy-section ductile iron were prepared. Six machine learning-based heavy-section ductile iron fracture toughness predictive models were constructed based on measured data with the C content, Si content, Mn content and cooling rate as input data and the fracture toughness as the output data. The experimental results showed that the constructed bagging model has high accuracy in predicting the fracture toughness of heavy-section ductile iron, with a coefficient of coefficient (R2) of 0.9990 and a root mean square error (RMSE) of 0.2373. Therefore, the design requirements of high fracture toughness heavy-section ductile iron, such as nuclear spent fuel storage and transportation containers, wind power generation bases and high-speed railroads, are satisfied.
Yield productivity enhancement through reduced plant spacing and pruning tolerance of Jatropha hybrids
Authors: Arunyanark Anuruck , Foytong Kanniga , Jompuk Choosak , Srini Peerasak , Tanya Patcharin 
Published: November 2023

Abstract
Reducing plant spacing and pruning Jatropha hybrids may increase yield. The study aimed to investigate the effect of reduced plant spacing on yield productivity, assess pruning tolerance, and discover the relationship between yield and growth traits of Jatropha hybrids. Fourteen Jatropha hybrid genotypes evaluated yield with narrow and standard plant spacing for two years. After the first year, the Jatropha hybrid plants were hard-pruned and allowed to regrow in the second year. It found that although narrower plant spacing might reduce Jatropha hybrid growth and yield per plant, increasing plant density by reducing plant spacing could increase fruit yield, seed yield, and oil yield by up to 65.46%, 64.73%, and 63.25%, respectively, when compared to standard spacing. Furthermore, hard pruning could improve the growth of Jatropha hybrids, and pruning tolerance varied between genotypes. Under narrow spacing, KUJL110 and KUJL70 had the highest yields after pruning, and KUJL110, KUJL30, and KUJL23 had the highest pruning tolerance index (PTI). It discovered a correlation (ranging from 0.49** to 0.86**) between yield traits and plant height, canopy width, and the number of secondary branches. Additionally, a correlation (ranging from 0.51** to 0.83**) was found between oil content and shelling, as well as 100 seed weight. As a result, these traits may serve as an indirect tool for selecting Jatropha genotypes with high-yield traits.
Appropriate choice of Capacitive sensor bandwidth
Authors: Ghemari Zine , Belkhiri Salah , Saad Salah 
Published: November 2023

Abstract
To optimize the accuracy of a capacitive sensor, a suitable choice of frequency margin is essential. The frequency margin refers to the difference between the resonant frequency of the sensor and the operating frequency.
The choice of frequency margin should consider the material properties of the target being sensed. Different materials have varying dielectric constants, which affect their capacitance. A wider frequency margin may be required for materials with high dielectric constants to ensure accurate measurements.
Preliminary establishment and validation of the inversion method for growth and remodeling parameters of patient-specific abdominal aortic aneurysms
Authors: Peng Chen , He Wei , Luan Jingyang , Yuan Tong , Fu Weiguo , Shi Yun , Wang Shengzhang 
Published: November 2023

Abstract
Background
Traditional medical imaging studies and biomechanical researches have limitations in analyzing the long-term evolution process of AAA (Abdominal Aortic Aneurysm, AAA). The HCMT (Homogenized Constrained Mixture Theory, HCMT) allows for quantitative analysis of the changes of the three-dimensional morphology and composition of AAA. However, the accuracy of HCMT still requires further clinical verification.
Objective
This study aims to establish a patient-specific AAA growth model based on HCMT, simulate the long-term G&R (Growth and Remodeling G&R) process of AAA, and validate the feasibility and accuracy of the method using two additional AAA cases with 5 follow-up data.
Methods
The media and adventitia of the aorta were modeled as mixtures composed of elastin, collagen fibers, and SMC (smooth muscle cells, SMC). The strain energy function was used to describe the continuously generation and degradation of the mixture during the AAA G&R process. Multiple sets of growth parameters were applied to finite element simulations, and the simulation results were compared with the follow-up data for gradually selecting the optimal growth parameters. Two additional AAA patients with different growth rates were used for validating the method, the optimal growth parameters were obtained using the first two follow-up imaging data, and the growth model was applied to simulate the subsequent four time points. The differences between the simulated diameters and the follow-up diameters of AAA were compared to validate the accuracy of the growth model.
Results
The growth parameters, especially the stress-mediated substance deposition gain factor Kσi, is highly related to the AAA G&R process. When setting the optimal growth parameters to simulate AAA growth, the proportion of simulation results within the distance of less than 0.5 mm from the follow-up model is above 80%. For the validating cases, during the 5 follow-up processes, the mean difference rates between the simulated diameter and the real-world diameter are within 2.5%, which basically meets the clinical demand for quantitatively predicting the AAA growth in maximum diameters.
Conclusion
This study simulated the growth process of AAA, and validated the accuracy of this growth model. This method was proved to be used to predict the G&R process of AAA caused by dynamic changes in the mixtures of the AAA vessel wall at a long-term time scale, assisting accurately and quantitatively predicting the multi-dimensional morphological development and mixtures evolution process of AAA in clinic.
Comparative transcriptomic study on the ovarian cancer between chicken and human
Authors: Zhu Guoqiang , Wang Xinglong , Wang Yajun , Huang Tianjiao , Zhang Xiao , He Jiliang , Shi Ningkun , Chen Juntao , Zhang Mao , Li Juan 
Published: November 2023

Abstract

Background
The laying hen is the only spontaneous model of ovarian tumor. But no studies have systematically compared the molecular mechanisms of ovarian cancer in hens and women.
Methods
We performed RNA sequencing of nine chicken ovarian tumor samples and four normal ovarian samples, which has been deposited in the Gene Expression Omnibus under accession number GSE246604. Together with five public datasets (GSE21706, GSE40376, GSE18520, GSE27651, GSE66957), we conducted a comparative transcriptomics study.
Results
In our RNA-seq data, a total of 549 and 2654 differentially expressed genes were identified in early-stage ovarian cancer vs. normal and late-stage ovarian cancer vs. normal, respectively. And molecular signals from nine cancer hallmarks, twenty-five KEGG pathways, and three hundred and sixty-nine GO pathways exhibited abnormalities in ovarian cancer compared to normal ovaries. In the comparative transcriptomics analysis, we have uncovered the conservation of eighty-one pathways between chicken and human using gene set enrichment analysis (GSEA). Moreover, a total of one hundred seventy-four genes were identified for the core enrichment of these pathways.
Conclusions
We are the first to report the differential expression profiles of ovarian cancer in early and late stages in domestic chickens, which contributes to our understanding of the development of ovarian cancer in domestic chickens. Through comparative transcriptome analysis, we also disclosed for the first time molecular pathways and core genes of ovarian cancer shared between hens and women, which informs model animal studies and gene-targeted drug development.
The Gut Microbiome in End-stage Lung Disease and Lung Transplantation
Authors: Zhang Shuyan , Swarte J. Casper , Gacesa Ranko , Knobbe Tim J. , Kremer Daan , Jansen Bernadien H. , Borst Martin H. , Harmsen Hermie J.M. , Erasmus Michiel E. , Verschuuren Erik A.M. , Bakker Stephan J.L. , Gan C. Tji , Weersma Rinse K. , Björk Johannes R. 
Published: November 2023

Abstract

Background
Gut dysbiosis has been associated with impaired outcomes in liver and kidney transplant recipients but the gut microbiome of lung transplant recipients has not been previously studied.
Methods
We assessed the gut microbiome in 64 faecal samples from end-stage lung disease patients before transplantation and 219 samples from lung transplant recipients after transplantation using metagenomic sequencing. To identify dysbiotic microbial signatures, we analysed 243 faecal samples from age-, sex- and BMI-matched healthy controls. By unsupervised clustering, we identified five groups of lung transplant recipients using different combinations of immunosuppressants and antibiotics and analysed them in relation to the gut microbiome. Finally, we investigated the gut microbiome composition of lung transplant recipients in different chronic lung allograft dysfunction stages and longitudinal gut microbiome changes after transplantation.
Results
We found 108 species (58.1%) in end-stage lung disease patients and 139 species (74.7%) in lung transplant recipients that were differentially abundant compared with healthy controls, with several species exhibiting sharp longitudinal increases from before to after transplantation. Different combinations of immunosuppressants and antibiotics were associated with specific gut microbial signatures. We found that the gut microbiome of lung transplant recipients in chronic lung allograft dysfunction (CLAD) stage 0 was more similar to healthy controls compared to those in CLAD stage 1. Finally, the gut microbial diversity of lung transplant recipients remained lower than the average gut microbial diversity of healthy controls up to more than 20 years post-transplantation.
Conclusions
Gut dysbiosis, already present before lung transplantation was exacerbated following lung transplantation, including decreased microbial diversity, reduced abundances of important metabolic pathways and higher prevalence of antibiotic resistance genes and virulence factors.
Study on the Effect of Cinder Ash as Auxiliary Additive Mineral in Hydrated Lime Treatment for Expansive Subgrade Soil for Road Construction
Authors: Bassa Abrham , Bekele Belay 
Published: November 2023

Abstract
Expansive soils are one of a major challenging soil for road construction in all over the world, the swelling and shrinkage behavior of expansive soil response to changes in moisture content and as a consequence it's leading to pavement failure. From the chemical additives, hydrated lime is one of a common improver used to stabilize expansive soils, but the use of it can be expensive and lead economical limitation and also require a long curing time. A Cinder ash is both a naturally and industrially byproduct available mineral which has been the most likely auxiliary additive mineral for hydrated lime stabilization of expansive soils. This research work is designed to analyze the improvement of the problematic sub-grade soil with the conjugation of random distributed local natural cinder ash in the proportion of 20 to 35% with a 2 to 5% proportion of hydrated lime. The subgrade soil treated with the conjugation of cinder ash and hydrated lime indicated appropriate improvement in the engineering properties of the soil compared to the native subgrade soil. However, the test result showed a reduction in moisture content, swelling properties, and liquid limit, which were noted in all cinder ash and hydrated lime composites. The samples of soil and cinder ash are collected from Wolaita region Kindo Didaye Woreda Belle Keble of Ethiopia. The MDD, OMC, CBR, and UCS values of the untreated soil were 1.429g/cc, 25.71%, 2.85% and 36.5kpa respectively. The method of characterization is done as per AAS HTO and ASTM test methods, which are recommended by the Ethiopian Road Authority (ERA). The proportion used to treat expansive subgrade soil for characterization was, 20%, 25%, 30%, and 35% for cinder ash, and 2%, 3%, 4%, and 5%, for hydrated lime are used accordingly. The analysis presented that, MDD increased and OMC decreased with increased percent of cinder ash and hydrated lime. The three-point soaked CBR test indicated that the value increased from 2.7–12.8%, this result shows that the CBR value is increased by 374% from the native soil CBR value when the expansive soil is treated with the mixture of 35% of cinder ash and 5% of hydrated lime. 4.54 kg surcharged swell value is decreased from 3.56–0.38% as a percent of 20 to 35 of cinder ash and 2 to 5 percent of hydrated lime are conjugated on an expansive soil. Besides, the developed simple linear regression analysis of a statistical model indicated a good agreement with the experimental study. Results from the current study concluded that stabilizing problematic subgrade soil with cinder ash and the hydrated lime mix was an economical and environmentally friendly investigation method to improve expansive subgrade soil. It can be shown from the conducted experimental results, developed excel graphs, and statistical model, the improvement method formed conjugation with successful environmental grip between cinder ash and hydrated lime composite was obtained.