bluuebunny/crossref_metadata_2025_split huggingface dataset:
The application of induced pluripotent stem cells to assess the toxic effects of environmental contaminants.
Authors: Kadiwala Juned , Ciocan Corina , Shakur Rameen 
Published: July 2024

Abstract

Human exposure to environmental contaminants is inevitable due to lifestyle, geographical proximity to the source, socioeconomic status, and the omnipresence of pollutants. The growing body of literature has advanced our understanding of the potential toxicity of a wide range of contaminants, from pharmaceuticals to nano plastics, however, knowledge gaps still exist. Homosalate (HS) and Triphenyl Phosphate (TPP) are chemical compounds of different commercial products used extensively by consumers. Both chemicals have been detected in the human bloodstream, raising concerns about the potential adverse effects on the cardiovascular system and human health. In this study, we harness the potential of human induced pluripotent stem cell-derived cardiomyocytes (hiPSCs-CMs) as a model to test the effect of these two chemicals on cardiac gene expression profiles, using the quantitative PCR method. Our findings showed that continuous exposure to HS and TPP at 30 and 60 µM doses for 24 hours leads to a dose-dependent significant reduction in the expression of the key cardiac structural and functional genes (TNNT2, TNNC1, MYH-6, MYH-7, MYL-2, ACTN2, and MYBPC3). Thus, this study demonstrated the feasibility of using hiPSCs-CMs as an in vitro model to access cardiotoxic and other functional parameters.
Urine-derived stem cells; A robust platform for generating native or engineered autologous Extracellular Vesicles
Authors: Boysen Anders Toftegaard , Whitehead Bradley , Revenfeld Anne Louise s. , Gupta Dhanu , Petersen Thor , Nejsum Peter 
Published: July 2024

Abstract

Background
Mesenchymal stem cell (MSC) therapy holds great potential as a treatment form, yet efficacy and safety concerns with cell therapy persist. The beneficial effects of MSCs are often attributed to their secretome, including extracellular vesicles (EVs). EVs carry biologically active molecules, protected by a lipid bilayer. However, several barriers hinder large-scale MSC EV production. A serum-free culturing approach is preferred for producing clinical-grade MSC-derived EVs but this can affect the yield and purity. Consequently, new strategies have been explored, including genetically engineering MSCs to alter EV compositions to; enhance potency, increase circulation time, or mediate targeting. However, efficient transfection of MSCs is challenging, and the process can affect MSC phenotype and chromosomal integrity, which are both imperative to preserve in a therapeutic setting. Typical sources of MSC include adipose tissue and bone marrow, which both require invasive extraction procedures. Here, we investigate the use of urine-derived stem cells (USCs) as a non-invasive and inexhaustible source of MSCs for EV production.
Methods
We isolated, expanded, and characterized urine-derived stem cells (USCs) harvested from eight healthy donors at three different time points during the day. We evaluated the number of clones per urination, proliferation capacity and conducted flow cytometry to establish expression of surface markers. EVs were produced in chemically defined media and characterized. PEI/DNA transfection was used to engineer USCs using transposon technology genetically.
Results
There were no observable differences at time points for clone number, doubling time or viability. USCs showed immunophenotypic characteristics of MSCs, such as expression of CD73, CD90 and CD105, with no difference at the different time points, but male donors had reduced CD73 + cells. Expanded USCs were incubated without growth factors or serum for 72 hours without a loss in viability and EVs were isolated. USCs were transfected with high efficiency and after 10 days of selection, pure engineered cell culture was established.
Conclusions
Isolation and expansion of MSCs from urine is non-invasive, robust, and without apparent sex-related differences. The sampling time point did not affect any measured markers or USC isolation potential. USCs offer an attractive production platform for EVs, both native and engineered.
Identiﬁcation of loading source on an inﬁnite elastic beam
Authors: KADRI Mohamed Larbi 
Published: July 2024

Abstract

This paper deals with the reconstruction of an unknown loading source on the topside of aninfinite Bernoulli−Euler beam resting on a Winkler type elastic foundation and subject to appropriateboundary conditions using noise contaminated data measurements of the beam deflection at a finite num-ber of points of the beam. This is an inverse problem that can be recast in the form of a Fredholm integralequation of the first kind which is known to be intrinsically ill-posed and extremely sensitive to high-frequency perturbations. Numerical results obtained using various regularization methods : Tikhonov’sregularization, Truncated Singular Value Decomposition and an optimisation method using Bernsteinpolynomials are discussed. The reconstructions obtained are very satisfactory and give confidence on theapplications of these methods to unknown loads.
Spinal Segmentation Based on Heatmap Regression Positioning and Improved UNet
Authors: Huang Yuyao , Wang Yuhang , He Li , He Zhiqin , Xiao Lin 
Published: July 2024

Abstract

The spine is essential for supporting the human body and maintaining its functions. In primary healthcare settings, radiologist shortages and medical resource scarcity often result in spinal fracture misdiagnoses and oversights. This paper introduces a spinal segmentation method utilizing heat map regression and an enhanced UNet, aiding radiologists in swiftly diagnosing spinal fractures and enhancing diagnostic efficiency. During landmark positioning, this paper presents an M-SCN network structure designed for multi-feature fusion. The LA stage of SCN incorporates multi-level feature outputs, while the SC stage introduces cyclic feature fusion, enhancing the feature extraction method and the selection of the maximum feature values, thereby improving the SCN's capability to capture local and global image features. To enhance positioning accuracy, we propose a graph-structured multi-coordinate point optimization method. A weighted directed graph is constructed, employing the predicted heat map's peak value and the Euclidean distances between points to define unary terms and pairwise weights for graph edges. Finally, the Bellman-Ford algorithm optimizes the coordinate points, significantly enhancing positioning accuracy. Compared to the original SCN network, the M-SCN network reduces the prediction error rate by 4.43%. Addressing the issue of UNet's inability to capture global feature information, which results in incomplete vertebrae segmentation, we introduce a UNet-CB network structure featuring global context attention. ContextBlocks and residual connections are integrated into the UNet BasicBlock to bolster global information capture. Additionally, a central heatmap is introduced to improve individual vertebrae recognition. In the vertebral segmentation experiment, the Dice Similarity Coefficient (DSC) achieved 95.64%, the Maximum Symmetry Surface Distance (MSSD) was 4.862 mm, and accuracy and recall rates were 95.86% and 92.46%, respectively.
Exploring Changes in University Students’ Persuasive Writings with the SFL-based Genre Instruction
Authors: Chen Feng , Foley Joseph , Xiang Peng 
Published: July 2024

Abstract

This study aims to explore the changes students make in their persuasive writing practice with each of the three iterations of the SFL-based (Systemic Functional Linguistics) genre instruction. The random sampling of an intact class of 30 students who were divided into 6 groups from a Chinese university’s English department participated the study. A constructed SFL-based genre teaching model of a four-staged teaching/learning cycle was applied to conduct the teaching instruction. Discourse analysis was used to analyze the group writing compositions. After three iterations of teaching/learning cycle, the data analysis for students’ writing results showed that students improved in following the essential elements of the generic structure of persuasion, and applying some lexicogrammatical features to express the three metafunctions of language in a particular context, even though they still faced challenges in applying some lexical-grammatical features. The findings indicated that this genre-based approach enhanced students’ understanding of genres, and the typical features of explicit teaching, collaborative writing and scaffolding in the SFL-based genre pedagogy helped students write to right.
Break through the thermostability of glucose oxidase in extremely thermal environments with a novel dynamic ensemble design protocol
Authors: Miao Tingwei , Zhi Fengdong , Yang Xin , Yuan Zhaoting , Zhang Chuanxi , Feng Yinghui , Wei Hao , Gao Bei , Zhang Lujia 
Published: July 2024

Abstract

Enhancing the thermostability of glucose oxidase (GOD) is crucial for food science applications. However, traditional design methods based on a single GOD structure are ineffective especially in extreme thermal environments. Here, we established a method for precisely locating residue by analysing the dynamic conformations of GoxM8 (M8) and further enhancing thermostability while maintaining activity. Our novel dynamic ensemble approach, coupled with FireProt computational analyses, was used to obtain the best mutant, V402F, from diverse conformations of M8. The residual activity of V402F was six times that of M8 at 80 ℃ for 2 min, and enzyme activity was even slightly increased. Experimental validation and computational analysis of stability mechanisms demonstrated the deficiencies of previous design strategies for flexible enzymes, proving the validity of our approach. Thus, we present a GOD variant with improved thermostability, as well as a more precise and efficient design strategy for GOD and other flexible enzymes.
Development of a real-time loop-mediated isothermal amplification method with toothpick sampling for non-destructive detection of Ustilago esculenta in Zizania latifolia
Authors: Yamada Ryunosuke , SASAKI Nobumitsu , Komatsu Ken , Mashimo Kouji , Motobayashi Takashi 
Published: July 2024

Abstract

Infection of Zizania latifolia by Ustilago esculenta causes edible stem galls called makomotake. The development of stem galls may be influenced by the fungal colonization level at the seedling stage. To evaluate this possibility, we attempted to develop a real-time loop-mediated isothermal amplification (LAMP) method with toothpick sampling for U. esculenta detection, which allows us to examine non-destructively the relationship between fungal levels in seedlings and makomotake production from the same seedlings. Our method detected U. esculenta efficiently in seedlings that eventually produced makomotake, but did not detect it in those that failed to develop stem galls.
Understanding intraseasonal propagating oscillation in air temperature and its association with heatwaves over Eurasia during boreal summer
Authors: Gong Zhanqiu , Minobe Shoshiro 
Published: July 2024

Abstract

Eurasian heatwaves (HWs), which pose widespread and substantial risks on human livelihoods, have been reported to be related to intraseasonal atmospheric waves. Although previous studies have explored the quasi-stationary nature of these waves, the comprehension of their propagating properties and connection with summer HWs still remains elusive. Therefore, in this study, we aim to investigate the propagating oscillations in air temperature over Eurasia during boreal summer and establish its linkage with HWs. First, we examine eastward propagation signals using complex empirical orthogonal function (CEOF) method. According to the temperature budget analysis, it is found that the advection processes play a critical role in driving this eastward propagation, while the diabatic heating partly compensates. Subsequently, by employing a metric designed to quantify the intensity of propagation, a total of nine years which exhibits the strongest propagating signals are identified. A good association between the HWs and air temperature anomalies estimated by temperature advection can be observed, which indicates a robust linkage. Our results can reinforce the dynamical understanding of summer HWs over Eurasia, and it may also contribute to future monitoring and forecasting capabilities.
Improved damage constitutive modeling of post-peak random failure behavior in quasi-brittle rocks
Authors: Zhang Chao , Ren Shixun , Yu Jin , Su Guoshao , Huang Xiaocheng , Cao Wengui 
Published: July 2024

Abstract

This paper captures the frequently encountered post-peak random failure behaviour of quasi-brittle rocks in conventional triaxial compression. The post-peak theoretical curve of the classic statistical damage constitutive model is essentially regulated by the Weibull distribution parameters m and F0. There exists a one-to-one mapping relationship between the array sets of parameters m and F0 and the confining pressure. However, the peak point method is unable to effectively constrain the post-peak theoretical curve of the model, resulting in the situation that under specific confining pressure, the post-peak theoretical curve of the classic model is unique and stochastic. In order to address this issue, this paper considers the influence of the degradation effect of damaged micro-elements on heterogeneity and proposes a modified damage model based on the classic damage model. A functional hypothesis expression integrating the effects of heterogeneity and stress level is constructed, and an improved statistical damage constitutive model considering the influence of damage threshold is derived. Through case verification and sensitivity analysis of model parameters, the results indicate that compared with the classic model, the model proposed in this paper, with only one additional parameter, can effectively simulate the post-peak random failure behaviour of heterogeneous quasi-brittle rocks under specific confining pressure. A comparison between predictions and published experimental data is claimed to be satisfactory, and it is revealed that the stress drop in the post-peak region of rocks is not completely random but exhibits stochastic characteristics within a certain range.
Action Potential Features: Computation and Spike Sorting of Human C-Nociceptor Action Potentials as obtained via Microneurography Recordings
Authors: Troglio Alina , Konradi Peter , Fiebig Andrea , Garriga Ariadna Pérez , Röhrig Rainer , Dunham James , Kutafina Ekaterina , Namer Barbara 
Published: July 2024

Abstract

Spike sorting represents a persistent challenge in electrophysiology, particularly in extracellular nerve recordings containing signals from several nerve fibers. This issue is exacerbated in microneurography recordings from peripheral unmyelinated afferents in awake humans, which are responsible for pain sensation. This is due to the similarity of spike shapes originating from different fibers, low signal-to-noise ratios, and shape-distorting overlaying signals. Here, we present the first systematic assessment of morphology-based spike sorting in multiple recordings from two microneurography laboratories. We created dedicated ground truth datasets by employing semi-manual labelling methods enabling the comparison of supervised and unsupervised sorting methods for different feature sets. A strong advantage of the supervised approach was observed, while no single feature set showed a global advantage. Further, the high diversity of the results was linked to the per-recording fiber number and spike morphologies. To extend this first systematic assessment of the spike sorting problem in microneurography, our open-source pipeline enables reproducible sortability analysis of any extracellular recordings of neuronal activity if electrical stimulation of the nerve fibers is possible. The achieved advancement of spike sorting for microneurography lays the foundation for gaining insights into the neural coding of pain and itch signals in a clinical context.
Enhanced Triple-branch Network for Generalized Zero-Shot Learning
Authors: Zhu Yifan , Zhou Yuan , Xiang Lei , Duan Haoran , Long Yang 
Published: July 2024

Abstract

Generalized Zero-Shot Learning (GZSL) aims to transfer knowledge from seen data to unseen categories and correctly distinguish both seen and unseen data. Most direct attribute prediction (DAP) methods focus on projecting visual features into attribute space and aligning them with class prototypes. However, domain shifts arise during the dataset acquisition due to camera angles or occlusion. Using the class prototype directly can not accurately represent each sample and will mislead the alignment of visual features and attributes. Moreover, the regularly used visual feature extraction backbone, such as ResNet, is trained on ImageNet, resulting in cross-dataset bias for the GZSL task. Therefore, this paper proposes an Enhanced Triple-branch Network (ETN), which has three branches: Evolving Attribute Feature Learning (EAFL), Cross-dataset Denoising Module (CDM), and Class Prototype Purification (CPP). EAFL progressively refine attribute features by correcting the semantic prototypes and profoundly explores the relationship between individual and group attribute features. CDM uses a mask to mitigate cross-dataset bias between ImageNet and GZSL benchmarks. CPP learns domain shifts of attributes, guaranteeing the predicted attributes align with specific samples.
Furthermore, ETN is conducted on three datasets, demonstrating superior performance compared to some other methods in Generalized Zero-Shot Learning. Specifically, on the SUN dataset, the proposed ETN shows an advantage of $1.5\%$ in the GZSL compared to the second-best method. ETN has demonstrated notable advancements compared to the baseline, achieving improvements of $2.5\%$ and $3.4\%$ on the CUB dataset and AWA2 dataset, respectively. The codes are available at \url{https://github.com/GAInuist/ETN}.
Diverse effects of chronic cobalt supplementation on iron metabolism during erythropoiesis
Authors: Pavlova Ekaterina , Petrova Emilia , Tinkov Alexey A. , Ajsuvakova Olga P. , Rashev Pavel , Vladov Ivelin , Skalny Anatoly V. , Gluhcheva Yordanka 
Published: July 2024

Abstract

Cobalt (Co) is an essential trace element and its cellular uptake occurs in a similar to iron (Fe) profile. The aim was to assess the alterations in iron and Fe regulatory proteins concentrations - transferrin receptor 1 (TfR1), hepcidin and ferritin, and their effect on erythrocyte count (RBCs) in mice following chronic exposure to cobalt chloride (CoCl2). Pregnant ICR mice were subjected to 125 mg/kg body weight CoCl2x6H2O daily 2–3 days prior delivery and treatment continued 90 days after birth. CoCl2 was administrated with drinking water. Pups were sacrificed on postnatal days 18, 30, 45, 60 and 90. Exposure to CoCl2 induced significant accumulation of Co ions in blood sera and RBCs. During long-term exposure the most Co was accumulated in the serum after 30 days of exposure and decreased by day 90 of dosing indicating that serum Co concentration is a reliable marker for recent exposure. Hemoglobin content increased in a time-dependent manner. Co administration significantly elevated serum Fe but decreased it in RBCs. Exposure to Co stimulated Fe storage, enhancing hepcidin production and ferritin concentrations, and reducing TfR1 expression. Chronic exposure to CoCl2 resulted in a lower Fe content of mature mice compared to immature suggesting stimulated Fe release as a possible survival mechanism to counteract the toxic effects of Fe overload.
Genome-wide identification, characterization, and expression analysis of the BTB domain-containing protein gene family in poplar
Authors: Jing Ruotong , Liu Xuan , LI Ruili , Du Liang 
Published: July 2024

Abstract

In recent years, the BTB (Bric-a-brac/Tramtrack/Broad complex) gene family in plants has garnered widespread attention for its regulatory roles in plant growth and development. However, knowledge regarding BTBs in poplar trees remains limited. Here, we identified 89 BTB gene family members across the genome of Populus alba L. Through phylogenetic analysis, these members were classified into seven subfamilies and 16 branches, followed by comprehensive bioinformatics and biological analyses. Structural analysis revealed that poplar BTB gene family exhibits both high conservation and diversity, with distinct gene structures and protein features. Expression pattern analysis demonstrated differential expression of poplar BTB genes across various tissues, hormone treatments, and under drought stress, suggesting their potential roles in poplar growth and development and drought response. This study provides a vital foundation and reference for unraveling the BTB-involved regulatory mechanisms underlying poplar growth and development and drought response.
Improvement of Sperm parameters and Hormonal Receptor Expression in a Rat Model of Testicular Hypoxia Treated with N-acetylcysteine Running title: N-acetylcysteine Improves Sperm Parameters
Authors: Shokoohi Majid , Roshangar Leila , Esfahani Mohammad Hossein Nasr , Soltani Gilda Ghazi , Khaki Amir Afshin , Alihemmati Alireza 
Published: July 2024

Abstract

Testicular tissue hypoxia is a state in which tissues do not receive enough oxygen to meet their demand. One disease known to cause this hypoxic condition is varicocele (VCL), which can negatively impact the testicles and lead to poor sperm quality. Previous research has indicated that antioxidants play a significant role in protecting against the damage resulting from hypoxia. This study aims to identify the potential antioxidant properties of N-acetylcysteine (NAC) on sperm characteristics and hormonal receptor expression within the testes of adult male Wistar rats. The study involved 32 rats randomly assigned to four groups: Sham (control), Varicocele-induced Hypoxia (Hypo), Hypoxia with NAC treatment (Hypo + NAC), and NAC treatment (NAC). The investigation measured serum testosterone, LH, and FSH levels, and evaluated sperm characteristics, histological features, and hormonal gene receptors across the groups. Analysis of the Hypoxia group showed a remarkable increase in serum FSH and LH levels compared to the Sham group (P < 0.05). Hypoxia led to deterioration in sperm quality, testosterone levels, number of germ cells, and hormonal receptor-related genes (P < 0.05). Importantly, NAC treatment improved male fertility by increasing sperm quality and protecting testicular tissues against hypoxia induced by varicocele in the rats.The present study suggests the potential for using NAC to prevent testicular tissue damage caused by testicular hypoxia.