bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tbxt alleviates senescence and apoptosis of nucleus pulposus cells through Atg7 mediated autophagy activation during intervertebral disc degeneration
Authors: yue Caichun , Wu Yinghui , Xia Yanzhang , Xin Tianwen , Gong Yuhao , Tao Linfeng , Shen Cong , Zhu Yue , Shen Minghong , Wang Donglai , Shen Jun 
Published: October 2023

Abstract

Intervertebral disc degeneration (IDD) is a significant cause of low back pain, characterized by excessive senescence and apoptosis of nucleus pulposus cells (NPCs). However, the precise mechanisms behind this senescence and apoptosis remains unclear. This study aimed to investigate the role of Tbxt in IDD both in vitro and in vivo, using a hydrogen peroxide (H2O2)-induced NPCs senescence and apoptosis model, as well as a rat acupuncture IDD model. Firstly, the expression of p16 and cleaved-caspase 3 significantly increased in degenerated human NPCs, accompanied by a decrease in Tbxt expression. Knockdown of Tbxt exacerbated senescence and apoptosis in the H2O2-induced NPCs degeneration model. Conversely, upregulation of Tbxt alleviated these effects induced by H2O2. Mechanistically, bioinformatic analysis revealed that the direct downstream target genes of Tbxt were highly enriched in autophagy-related pathways and overexpression of Tbxt significantly activated autophagy in NPCs. Moreover, the administration of the autophagy inhibitor, 3-methyladenine, impeded the impact of Tbxt on the processes of senescence and apoptosis in NPCs. Further investigation revealed that Tbxt enhances autophagy by facilitating the transcription of ATG7 through its interaction with a specific motif within the promoter region. In conclusion, this study suggests that Tbxt mitigates H2O2-induced senescence and apoptosis of NPCs by activating ATG7-mediated autophagy.
Hairy root induction and plant regeneration techniques in Brassicaceae for biotechnological applications
Authors: Jedličková Veronika , Štefková Marie , Mandáková Terezie , López Juan Francisco Sánchez , Sedláček Marek , Lysak Martin A. , Robert Hélène S. 
Published: October 2023

Abstract
Background
Hairy roots constitute a valuable tissue culture system for species that are difficult to propagate through conventional seed-based methods. Moreover, the generation of transgenic plants can be facilitated by employing carefully designed hormone-containing media.
Results
We initiated hairy root formation in the rare crucifer species Asperuginoides axillaris via an injection-based protocol and successfully regenerated plants from established hairy root lines. Our study confirms the genetic stability of both hairy roots and their derived regenerants and highlights their utility as a permanent source of mitotic chromosomes for cytogenetic investigations. Additionally, we have developed an effective embryo rescue protocol to circumvent seed dormancy issues in A. axillaris seeds. By using inflorescence primary stems of Arabidopsis thaliana and Cardamine hirsuta as starting material, we also established hairy root lines, that were subsequently used for regeneration studies.
Conclusion
We developed efficient hairy root transformation and regeneration protocols for various crucifers, namely A. axillaris, A. thaliana, and C. hirsuta. Hairy roots and derived regenerants can serve as a continuous source of plant material for molecular and cytogenetic analyses.
Augmented drug combination dataset to improve the performance of machine learning models predicting synergistic anticancer effects
Authors: Liu Mengmeng , Srivast Gopal , Ramanujam J. , Brylinski Michal 
Published: October 2023

Abstract
Combination therapy has gained popularity in cancer treatment as it enhances the treatment efficacy and overcomes drug resistance. Although machine learning (ML) techniques have become an indispensable tool for discovering new drug combinations, the data on drug combination therapy currently available may be insufficient to build high-precision models. We developed a data augmentation protocol to unbiasedly scale up the existing anti-cancer drug synergy dataset. Using a new drug similarity metric, we augmented the synergy data by substituting a compound in a drug combination instance with another molecule that exhibits highly similar pharmacological effects. Using this protocol, we were able to upscale the AZ-DREAM Challenges dataset from 8,798 to 6,016,697 drug combinations. Comprehensive performance evaluations show that Random Forest and Gradient Boosting Trees models trained on the augmented data achieve higher accuracy than those trained solely on the original dataset. Our data augmentation protocol provides a systematic and unbiased approach to generating more diverse and larger-scale drug combination datasets, enabling the development of more precise and effective ML models. The protocol presented in this study could serve as a foundation for future research aimed at discovering novel and effective drug combinations for cancer treatment.
CGB5 Proves to be a Promising Predictive and Immunotherapeutic Indicator across Pan-Cancer
Authors: Chen Shuni , Yu Weifeng , He Guihua , Zhong Zishao , Huang Suiping 
Published: October 2023

Abstract
CGB5 plays an important factor in numerous different cancers and is strongly associated with patient prognosis. Unfortunately, there is currently no data, however, on whether CGB5 plays a role in pan-cancer diseases. Research on CGB5 in pan-cancer has been conducted through multiple websites and public databases, including TCGA, HPA, UALCAN, cbiopportal Platform, UALCAN, GSCA, Kaplan-Meier Plotter, TIMER, TISIDB, SangerBox Website, and metscape. The genomic, transcriptomic, epigenetic, immune microenvironmental, and clinical prognostic significance of CGB5 across pan-cancer is investigated with the resulting outcome. CGB5 expression in gastric cancer was further detected, and the potential mechanism of its influence on prognosis was elucidated. This study found that abnormal CGB5 expression in pan carcinoma is correlated with a poorer prognosis. Aberrant CGB5 expression is potentially linked to gene mutations, copy number variation (CNV), and DNA methylation. In addition, this study revealed a robust association between the expression of CGB5 and immune cell infiltration across various types of cancer, with differences in cell type and level among distinct tumor types. In addition, the present investigation has shown that A strong association has been detected between the upregulation of CGB5 expression and immune cell infiltration in various forms of cancer, with differences in the different tumor types in the type and level of immune cell infiltration. Our further cell experiments also confirmed the upregulation of CGB5 within the context of gastric cancer. In conclusion, it has been noted that CGB5 expression exhibited a substantial rise across wide types of malignancies, and this upregulation was shown to exhibit a significant association with the prognosis of individuals who have cancer. Further studies showed that CGB5 expression in tumors affects the tumor immune microenvironment and promotes tumorigenesis. We also explored CGB5 expression in gastric cancer and clarified its potential prognostic mechanism. It reveals CGB5's significance in cancer diagnosis and treatment.
Water footprint of flooded rice cultivation in subtropical climate in extreme southern Brazil
Authors: Morais Francisco Alexandre , Marcolini Elio , Santos Rafael Nunes , Mello Ivo , Pereira Marco Alésio Figueiredo 
Published: October 2023

Abstract
Due to projections of world population growth, the concern with water resources is becoming increasingly urgent. Thus, the use of water contabilization indicators, such as the water footprint, can be useful in the pursuit of sustainability. Rice is one of the most consumed foods in the world, Brazil is the 9th biggest producer and the largest producer outside the Asian continent. The state of Rio Grande do Sul (RS), in Brazil, is responsible for about 70% of the national production. Since there is little information on the water footprint of rice cultivation in this state, this study aims to: quantify the rice yield through field experiments (2020/2021 and 2021/2022 harvest) in the municipality of Cachoeirinha- RS, measurement and segment the crop water requirement and the water footprint of flooded rice through remotely obtained meteorological data and presents a critical analysis on the accounting of the water footprint of this crop. On the mean of the two harvests, the water footprint was 443.0 m³ t− 1 (62.1% green water footprint and 37.9% blue water footprint). The crop water demand was 5763.3 m³ ha− 1. The yield was 13.010 t ha− 1. Under experimental conditions, the water footprint is in the optimal range of maximum technical and economic efficiency. The inclusion or not of return flow in accounting for the water footprint of flooded rice cultivation is a highly relevant inconsistency. Another inconsistency is the lack of isonomy in gray water footprint accounting because of the variable "maximum allowable concentration of the critical pollutant".
The Bayesian Parametric Survival Approach to Predicting Time to Death of Children Under Five year with Acute Pneumonia in Jigjiga University Referal Hospital
Authors: Mengistie Dagne Tesfaye , Marine Buzuneh Tesfa 
Published: October 2023

Abstract

Introduction Pneumonia is one of the most common causes of death and serious illness among children below the age of five in underdeveloped nations, including Ethiopia. However, there is a scarcity of data on this dangerous condition among particularly sensitive and vulnerable children living in peri-urban environments. Establishing the proportion of cases of pneumonia as well as understanding the risk factors can be crucial for successful prevention and reaction. Methods: A retrospective cohort analysis was carried out, with 451 child pneumonia patients from Jigjiga University reference hospital provided as samples. The Cox proportional hazard model, the parametric AFT model, and the Bayesian parametric survival model have been applied, each of which employed a different model selection approach. Result: among covariates, Female pneumonia patients had an acceleration factor of 1.48 with [95% CI: 0.556, 0.741], co-morbidity had an acceleration factor of 1.26 with [95% CI: 0.740, 1.416], severe acute malnutrition had an acceleration factor of 0.26 with [95% CI: 1.609, 6.890], and anemia status had an acceleration factor of 0.89 with [95% CI: -1.1, -0.5357]. On the basis of DIC, the Bayesian lognormal parametric model was selected. Conclusion: At a 5% level of significance, sex, residency, comorbidities, Severe Acute Malnutrition (SAM), age, anemia status, delivery palace, season, and weight were all strongly associated with the patient's overall survival time. In all health facilities, physicians, clinicians, and health extension workers need to concentrate on preventing anemia, severe acute malnutrition, morbidity, and mortality from pneumonia through the delivery of health promotion to the community based on the understood risk factors.
Finite element analysis of basicervical femoral neck fracture treated with proximal femoral bionic nail
Authors: Cheng Xiaodong , Yang Yanjiang , Zhu Jian , Li Guimiao , Chen Wei , Wang Juan , Zhang Qi , Zhang Yingze 
Published: October 2023

Abstract
Background:Dynamic hip screws (DHS) and proximal femoral nail anti-rotation (PFNA) were recommended for basicervical femoral neck fracture (BFNF), however, with high rate of postoperative femoral neck shortening. The Proximal Femoral Bionic Nail (PFBN) was designed to decrease the postoperative complications associated with DHS and PFNA. The aim of this study is to compare the biomechanical characters of DHS, PFNA, and PFBN for fixation of BFNF.
Methods: Using finite element analysis, we created a three-dimensional model of the BFNF for this investigation. The PFBN group, the PFNA group and the DHS+DS group, were our three test groups. For each fracture group, the von Mises stress and displacements of the femur and internal fixation components were measured under 2100 N axial loads.
Results: The PFBN group demonstrated the lowest stress on the implants, significantly lower than the PFNA and DHS+DS groups. In terms of stress on the implants, the PFBN group exhibited the best performance, with the lowest stress concentration at 112.0 MPa, followed by the PFNA group at 124.8 MPa and the DHS+DS group at 149.8 MPa. The PFBA group demonstrated the smallest displacement at the fracture interface, measuring 0.21 mm, coupled with a fracture interface pressure of 17.41 MPa, signifying excellent stability.
Conclusions: Compared with DHS and PFNA, PFBN has advantages in stress distribution and biological stability. We believe the concept of triangle fixation will be helpful to reduce femoral neck shortening associated with DHS and PFNA, and thus improve the prognosis of BFNF.
Synergistic activity of gold nanoparticles with Amphotericin B on persister cells of Candida tropicalis biofilms
Authors: Silva M. A. da , Andrada K. F. Crespo , Torales M. Maldonado , Hughess I. Manrrique , Páez P. , Paraje M.G. 
Published: October 2023

Abstract
Aim: The antifungal activity was studied on sessile and persister cells (PCs) of Candida tropicalis biofilms of gold nanoparticles (AuNPs) stabilized with cetyltrimethylammonium bromide (CTAB-AuNPs) and those conjugated with cysteine, in combination with Amphotericin B (AmB).
Materials/methods: The PC model was used and synergistic activity was tested by the checkerboard assay. Biofilms were studied by crystal violet and scanning electron microscopy.
Results/Conclusions: After the combination of both AuNPs and AmB the biofilm biomass was reduced, with significant differences in architecture being observed with a reduced biofilm matrix. In addition, the CTAB-AuNPs-AmB combination significantly reduced PCs. Understanding how these AuNPs aid in the fight against biofilms and the development of new approaches to eradicate PCs has relevance for chronic infection treatment.
First-principles study of shear deformation on Mg adsorption by monolayer SnS 2
Authors: Ma Mengting , Liu Guili , Wei Ran , Su Dan , Yang Zhonghua , Zhang Guoying 
Published: October 2023

Abstract
Context
In this study, the effects of different shear deformations on the structural stability, electronic structure, and optical properties of the Mg atom adsorption system of S vacancy defect SnS2 are systematically investigated based on density functional theory. It is shown that the presence of S-vacancy defects makes the band gap value of the system significantly smaller than that of a perfect SnS2 monolayer, and the SnS2 system changes from a direct band gap semiconductor to an indirect band gap semiconductor. The optimal adsorption position of Mg atoms in the S-vacancy defects SnS2 system is above the S atom when the adsorption energy is the largest and the system is the most stable. The density of states of the adsorption system is predominantly contributed by the S-3p and Sn-5s orbital electrons. The imposition of shear deformation leads to the introduction of certain impurity energy levels in the adsorption system, and the gap in the density of states near the Fermi energy level decreases. The charge transfer indicates that 0.96e of electrons are transferred from Mg atoms to S atoms at the surface of the adsorption system. The absorption and reflection peaks of the S-vacancy SnS2 adsorption system with Mg atoms were red-shifted and appeared in the ultraviolet region as compared to the intrinsic SnS2. This improves the utilization of the adsorption system for ultraviolet light to a great extent.
Methods
The model calculations in this paper are performed using the CASTEP module of the Material Studio (MS) software based on the first principles of Density Functional Theory (DFT) [21] for plane wave artifacts. Geometrical optimization and computational procedures are used to calculate the exchange correlation energy using the Perdew-Burke-Ernzerhof (PBE) generalized function [22] of the Generalized gradient approximation (GGA). The Monkhorst-Pack method [23] was used to rationalize the sampling of the highly symmetric k-points in the Brillouin zone. The grid of k-points is set to be 6 × 6 × 1. The plane-wave truncation energy is set to be 400 eV. The energy convergence criterion is 1.0 × 10− 5 eV. The residual stress of all atoms is 0.01 eV/Å. A vacuum layer with a thickness of 15 Å is set up in the z-direction, which ensures that the interactions of the system along the z-axis between the top and the bottom layers can be ignored during the whole simulation process.A 3 × 3 × 1 single-layer of SnS2 containing 27 atoms is used as a model for the calculations. The intrinsic SnS2 contains 9 Sn atoms and 18 S atoms.
Associations of White Blood Cell Counts and Cytokine Levels with Lumbar Disc Degeneration Pre- and Post-Spine Surgery: A Retrospective Analysis from a Single Center
Authors: Lu Jiawei , Guo Youfeng , Guo Kai , Wang Feng , Zeng Jianhua , Hu Tao , Wu Desheng 
Published: October 2023

Abstract
Objective:
This study aimed to investigate the associations between white blood cell (WBC) counts, Monocytes, Neutrophils, cytokine levels including IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12P70, IL-17, IFN-α, IFN-γ, and TNF-α, and lumbar disc degeneration before and after spine surgery.
Methods:
A retrospective analysis was conducted on a cohort of 131 patients diagnosed with disc degeneration disease, comprising 62 males and 69 females. Parameters assessed included age, BMI, WBC counts, and cytokine concentrations. Cumulative grade was ascertained by aggregating the Pfirrmann grades for all lumbar spine intervertebral discs. The severity of disc degeneration was grouped according to the median score of the population. The corresponding T-test or William rank sum test was used to assess differences between groups.
Results:
Prior to surgery, females exhibited a higher age, greater Pfirrmann score (20.3±0.41), and elevated IL-8 level (31.3±12.22) compared to males. Patients with a higher cumulative Pfirrmann score (≥19) were characterized by advanced age (68.52±0.90), elevated counts of monocytes (0.49±0.02), WBC (6.40±0.23), neutrophils (4.02±0.19), and reduced IL-12p70 concentration (25.83±7.32). On the third post-operative day, significant changes were observed in monocytes, WBC, neutrophils, IL-1β, IL-6, IL-8, IL-10, and IL-12p70 levels, with no discernible variation related to the Pfirrmann score. Among the assessed cytokines, only IL-6 exhibited a significant correlation (r=0.20, p=0.02) with the increase in monocytes.
Conclusion:
Monocytes, neutrophils, WBC counts, and IL-12p70 were intricately associated with the grade of disc degeneration. Furthermore, the third day post-surgery saw surges in monocytes, neutrophils, WBC, IL-1β, IL-6, IL-8, and IL-10, with only IL-6 presenting a notable correlation with the elevation in monocytes.
Three-dimensional Visualization of Thyroid Ultrasound Images Based on Multi-scale Features Fusion and Hierarchical Attention
Authors: Mi Junyu , Wang Rui , Feng Qian , Han Lin , Zhuang Yan , Chen Ke , Chen Zhong , Hua Zhan , Luo Yan , Lin Jiangli 
Published: October 2023

Abstract
Background
The incidence of thyroid disorders is increasing every year. Three-dimensional visualization of the thyroid gland and its surrounding tissues based on free-arm ultrasound scanning videos is essential for identifying the thyroid and related tissues in the neck and screening for associated diseases. However, the key to achieving 3D visualization lies in the multi-target segmentation of neck tissues. Currently, the accuracy of multi-target segmentation for thyroid ultrasound images are unsatisfactory.
Method
Therefore, in order to enhance the multi-target segmentation accuracy for the thyroid and its surrounding tissues and improve the 3D visualization, in this paper we proposed PA-Unet++. Pyramid pooling module helps in the segmentation of multi-organization with different sizes by integrating multi-scale feature information. Additionally, attention gating mechanism is applied to each decoding layer to progressively highlight the target tissue and suppress the representation of background pixels.
Results
With 4600 images containing 23,000 annotated regions are divided into training and test sets at a ratio of 9:1, the results show that: compared with the results of U-net++, the Dice of our model increased from 78.78–81.88% (+ 3.10%), the mIOU increased from 73.44–80.35% (+ 6.91%), the PA index increased from 92.95–94.79% (+ 1.84%).
Conclusions
This indicates that PA-Unet + + has a higher accuracy for segmentation of multiple tissues in thyroid ultrasound images. The segmentation results can optimize the 3D visualization.
Factors Associated with Work Engagement Among Specialty Nurses in China: A Latent Profile Analysis
Authors: Xu Lichun , Lin Liyu , Guan Aixuan , Wang Qingqing , Lin Weicong , Lin Feng , Li Jing 
Published: October 2023

Abstract
Background: In recent years, specialty nurses' work engagement has received much attention because of its positive impact on nurses and hospitals. Therefore, knowing more about it and its influencing factors can help nurse managers improve nurses' physical and mental health and the quality of care in hospitals. The purpose of this study was to explore the current status and analyze the potential profiles and population characteristics of specialized nurses in China.
Methods: This was a cross-sectional study with data collected from April 13 to July 23, 2023. Convenience sampling method was used to select 724 nurses from 22 hospitals in Xiamen, China as study subjects, and self-administered general information questionnaires and work engagement scales were used to conduct surveys, to study the potential characteristics of work engagement of specialized nurses using latent profile analysis, and to determine the factors influencing their potential characteristics using univariate and binary logistic regression analyses.
Results: The total score of specialty nurses' work engagement was divided into 2 potential profiles: low engagement and high engagement. The results of binary logistic regression analysis showed that whether or not to participate in nurse-led clinics, career satisfaction, and title were the main influencing factors for the potential profile categories of specialty nurses' work engagement in Xiamen.
Conclusion: Xiamen, China has a high level of investment in the work of specialized nurses. In the future, we can strengthen the construction of nurse-led clinics, and at the same time establish an effective career development support mechanism, so as to improve investment in the work of specialized nurses and promote the development of specialized nurses.