bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated analysis of Single-cell RNA-seq,Mendelian randomization and eQTL reveals immune cell-related nomogram model and subtypes in periodontitis Running title: Immune Cell Subtypes and Nomogram Model in Periodontitis
Authors: Qiu Xuedi , Yang Fan , Li Chenxi , Wang Jian , Yuan Yawen , Guo Chao 
Published: November 2024

Abstract

Background
Periodontitis is a prevalent chronic inflammatory disease characterized by immune cell dysregulation and tissue destruction. This study integrates single-cell RNA sequencing (scRNA-seq), Mendelian randomization (MR), and expression quantitative trait loci (eQTL) analyses to uncover immune cell subtypes, causal genes, and develop a predictive nomogram model for periodontitis.
Methods
We analyzed scRNA-seq data to identify differentially expressed genes (DEGs) and immune cell subtypes in periodontitis. MR analysis was conducted to determine causal relationships between immune cell gene expression and periodontitis risk, utilizing eQTL data. Gene ontology (GO) and pathway enrichment analyses were performed to understand functional implications. Additionally, CellChat trajectory analysis explored intercellular communication. A nomogram model was constructed to predict periodontitis risk based on immune-related DEGs.
Results
The integrated analysis identified 23 distinct immune cell clusters and seven hub genes (ANXA1, ARL4C, CD79B, LRRC25, NKG7, SLC11A1, and VIM) that were causally linked to periodontitis. Pathway enrichment analysis revealed their involvement in key immune regulatory mechanisms. A robust nomogram model based on these DEGs was developed and validated, demonstrating high predictive accuracy for periodontitis risk. Immune subtypes were further characterized, revealing distinct roles in disease progression.
Conclusion
This study highlights the crucial role of immune cell subpopulations and hub genes in the pathophysiology of periodontitis. The nomogram model offers a novel tool for predicting periodontitis risk and identifying potential therapeutic targets. These findings provide valuable insights into immune-related mechanisms and potential interventions for periodontitis.
CCR4a promotes metastasis and invasion of ovarian cancer by downregulating LRRC4 via PI3K/AKT Signaling Pathway Activation
Authors: Wen Fang , yu hang , zhang jingkaiwen , Yang Hanlin , Dan Zixuan , Luo Hao , zi dan 
Published: November 2024

Abstract

Background
It has been established that CCR4-NOT transcription complex subunit 6 (CCR4a) can promote the growth of some malignancies. Its role and clinical significance in ovarian cancer, however, have not been documented. This article examined the spread of cancer following CCR4a modulation.
Methods
Bioinformatics was used to analyze the prognosis of CCR4a using the KM plot dataset. The CCR4a protein was identified by immunohistochemistry investigation in ovarian cancer tissues. Cellular responses were noted following both up-and-down-regulation of CCR4a. The mechanism was validated using Western blotting and RNA sequencing.
Results
Ovarian cancer metastases were positively correlated with CCR4a expression, and a shorter survival period was linked to higher expression. In contrast, down-regulation of CCR4a inhibits LRRC4 (leucine-rich repeat containing 4), which in turn activates the PI3K/AKT signaling pathway, which in turn promotes cell invasion and migration. In vivo, CCR4a up-regulation increased carcinogenic potential while down-regulation reduced it.
Conclusions
In ovarian cancer tissues, high CCR4a expression suggested reduced survival. In ovarian cancer cells, CCR4a facilitated migration and invasion by downregulating LRRC4 through the stimulation of PI3K/AKT signaling. It may be a useful target for prognostic and diagnostic purposes.
Accurate Cell Instance Segmentation Using a one-shot Generalized segmentation model and Energy Gradient Fields
Authors: Zhao Xinzhuo , Liu Bing , Zheng Lin , Bao Yanqing , Tong Guiyuan , Xue Zhaofeng 
Published: November 2024

Abstract

Cell instance segmentation stands as a pivotal endeavor in genomics research and disease diagnosis. However, achieving precise segmentation poses a significant challenge due to the diverse characteristics of cells, encompassing varied contour shapes, adhesions, and overlapping scenarios. In this paper, we introduce a novel cell segmentation framework that integrates a generalized segmentation model with an energy gradient field to accomplish cell instance segmentation. The architecture comprises two primary components: (1) semantic segmentation of cells using a generalized segmentation model, (2) instance segmentation based on an improved energy gradient field algorithm for addressing overlapping cells. Instead of directly aligning with the object's edge profile as the objective, the energy gradient field method aligns with the gradient field within the object. This approach offers a more refined and nuanced representation of the object's internal structure, enhancing the accuracy and robustness of segmentation outcomes. Our approach presents two key advantages. (1) A one-shot generalized segmentation model was introduced to address the challenge of false-positive cell segmentation, (2)An improved energy gradient field algorithm was utilized to effectively reduce cell over-segmentation. The experimental results show that the proposed method has a mean accuracy (mAP) of 87.48%, F1 Score of 82.57%, and Recall of 76.64%, which are better than other state-of-the-art methods in the cell instance segmentation.
Behavioral and Pathological Characteristics of 5xFAD female mice in the early stage
Authors: Zhu Chenlu , Liu Xuejiao 
Published: November 2024

Abstract

Alzheimer's disease (AD) is a central nervous system degenerative disease with insidious onset and gradual development caused by selective and progressive loss of neurons. The 5xFAD mouse is a relatively mature disease model of AD. However, the behavioral research on 5xFAD female mouse is more focused on the changes of late memory function, and the exploration of its early behavioral and pathological changes is still incomplete. This research aims to explore the changes in memory function, emotional function (including anxiety and depression), motor ability, amyloid plaques, glial cell response and neurogenesis in the hippocampus of female 5xFAD mice in the early stage, laying a foundation for a comprehensive exploration of the disease mechanism of AD. The results of this study found that early 4-month-old female 5xFAD mice mainly showed a decline in memory function without other dysfunction. Accompanied by a large amount of amyloid protein plaques deposited in the hippocampus, it induced the response of microglia and astrocytes, and neurogenesis decreased significantly with age, especially in early female 5xFAD mice, which resulted in a decrease in the number of new neurons. This may be an important reason for the decline in memory function of female 5xFAD mice in the early stage.
Suppression of carpogenic germination and viability of Sclerotinia sclerotiorum sclerotia by biofumigation, biological control and Perlka
Authors: Dassanayaka Madhavi P. , Casonato Seona G. , Jones Eirian 
Published: November 2024

Abstract

Sclerotia play an important role in the disease cycle of Sclerotinia sclerotiorum. Traditional control measures do not effectively suppress germination and viability of sclerotia. This study performed a series of in-vivo bioassays to investigate the effect of biofumigants produced by Brassica juncea ‘Caliente 199’, biological control by Coniothyrium minitans, and Perlkaâ on carpogenic germination and sclerotial viability. Coniothyrium minitans alone or in combination with Perlkaâ resulted in complete inhibition of carpogenic germination and high sclerotial mortality. Perlkaâ treatment in quantities equivalent to field rates of 400 and 300 kg ha-1 resulted in 100% and 77% reduction in sclerotial germination, respectively compared with the untreated control, but viability remained high (³97.5%). Treating the potting mix with plant tissue of ‘Caliente 199’ in quantities equivalent to the field rate of 100 and 75 t ha-1 reduced carpogenic germination by about 46% compared to unamended control but did not result in significant reduction in sclerotial viability. Coniothyrium minitans and Perlkaâ were effective in suppressing carpogenic germination but the suppression achieved with biofumigation was much lower. Coniothyrium minitans with Perlkaâ resulted in high sclerotial mortality, which was not achieved with the Perlkaâ only treatment. These results showed that of the treatments tested, C. minitans able to reduce the carpogenic germination and the viable inoculum. Further studies are needed to assess the effectiveness and potential of integrating with non-pesticide methods to achieve better control of S. sclerotiorum in the field.
The Simulation of the “production-living-ecological” space and ecological effect assessment in the Gansu-Qinghai Contiguous Region of the upper Yellow River
Authors: Tong Huali , Zou Pingju , Zhang Xuan , Li Yijing , Wang Quanwen 
Published: November 2024

Abstract

This study explores changes in production-living-ecological space (PLES) and evaluate its ecological impacts in the Gansu-Qinghai contiguous region of the upper Yellow River. The research aims to clarify the historical trends in PLES transformations by analyzing land use data from 2000 to 2020. Using 2020 land use data as a baseline, we employ the FLUS model to estimate the evolution of the PLES within the study region under the SSP1, SSP2, and SSP5 scenarios from 2030 to 2060, as well as the ecological environmental quality (EEQ) in 2035 for these scenarios. The results of this study show that, (1) Under all the three scenarios, living space within the study area shows an expansionary trend, while ecological space decreases. In the SSP5 scenario, production space area increases, while it diminishes in the other two scenarios. (2) PLES evolution patterns are relatively consistent across the three scenarios. Forest and meadow ecological land predominant, agricultural production and urban living land primarily cluster in the northeastern part, and water ecological land is interspersed throughout the central and southwestern regions. (3) By 2035, the ecological environmental quality index (EEQI) within the research area improves compared to the 2020 baseline of 0.41297, with the projected values of 0.41805(SSP1), 0.41398(SSP2), and 0.41562(SSP5). The study’s conclusions provide valuable insights for the natural environment conservation and land development in the upper Yellow River Basin.
Does manager with E-leadership inspire employee creativity?—A Study on moderating role of promoting regulatory focus and preventing regulatory focus.
Authors: Zhao Liang , Chen Hao , Sun Yichao , Luo Maya , Gao Peng 
Published: November 2024

Abstract

Purpose —
This paper examines the mediating effects of emotional exhaustion and the moderating role of promoting regulatory focus and preventing regulatory focus. Exploring the relationship between emotional exhaustion and the personal trait of regulatory focus in E-Leadership and employee creativity.
Design/methodology/approach
— This study adopted a questionnaire survey method and collected 366 samples. Hierarchical regression analysis and bootstrap method were performed using SPSS 27.0 to test the research hypotheses.
Findings—
The findings showed that:1.E-leadership negatively affects employees' emotional exhaustion.2.E-leadership positively influences employees' creativity. 3.Emotional exhaustion negatively affects employees' creativity. 4.Promoting regulatory focus moderates the negative relationship between E-leadership and Emotional exhaustion.5.Prevention regulatory focus moderates the negative relationship between emotional exhaustion and employee creativity.
Originality/value—
This study enriches the research on the influence mechsanism between E-leadership and employee creativity, and also provides references for leadership practices in the digital age. However, the research has some limitations such as using only cross-sectional data and limited representativeness of the sample. Future studies could consider collecting multi-wave data, expanding the sample size, incorporating other influencing factors, etc. to enhance the rigor of the research.
Genome-wide association study identifies key chromosomal regions in rice promoting the enrichment of diazotrophic iron-reducing bacteria in paddy soil
Authors: Lin Li-Yen , Feng Zhihang , Asano Hikaru , Ohmori Yoshihiro , Ohba Hirotomo , Masuda Yoko , Senoo Keishi , Fujiwara Toru 
Published: November 2024

Abstract

Background and Aim
Overuse of nitrogen fertilizers has led to significant environmental issues. Diazotrophic iron-reducing bacteria (IRB), particularly Anaeromyxobacter and Geobacter, are abundant in paddy soils and may enhance nitrogen fixation when ferric compounds are present. This study investigates the effects of rice cultivation on the abundance of IRB and identifies genetic regions in rice that regulate this process.
Methods
We set up a microcosm system using cups filled with paddy soil, separated by nylon mesh to differentiate rhizosphere and bulk soil. The abundance of IRB in the rhizosphere of 143 japonica rice varieties was evaluated. A genome-wide association study (GWAS) with a unified mixed-model was conducted to identify genomic regions associated with IRB abundance.
Results
Our experiments revealed a weak but significant correlation (r= 0.19, p = 0.022) between rice varieties and IRB abundance. GWAS identified peaks on chromosomes (Chr) 2, 3, 4, 9, 10, and 11. Linkage disequilibrium analysis highlighted regions on Chr3, Chr4, Chr9, Chr10, and Chr11 linked to higher IRB abundance. Notably, chromosome segment substitution line SL609, which incorporates fragments from Nipponbare into Koshihikari, showed increased IRB abundance, confirming the genetic influence from Chr3.
Conclusion
This study demonstrates genetic variation in IRB abundance among japonica rice cultivars and identifies associated genomic regions. These findings enhance our understanding of the genetic factors influencing IRB and offer insights for improving nitrogen acquisition in rice production.
Energy Analysis Approach for Detecting Bolt Loosening
Authors: xingjun wang , wei wang , yongbin shao 
Published: November 2024

Abstract

Bolt connections are integral to civil infrastructure and mechanical assemblies, where bolt loosening poses risks of structural instability and safety issues, potentially causing injuries and financial losses. Monitoring the loosening of bolts can mitigate accident risks, enhance safety, and prevent disasters. Consequently, understanding and identifying bolt connection integrity is a critical aspect of structural research. This study introduces a quantitative approach for detecting bolt loosening through controlled small-ball impacts. By adjusting the bolt torque within a defined range to simulate varying levels of tightness or looseness, a small ball is released from a consistent height to strike the bolt. PZT sensors, mounted on the back of the flange, capture the impact signals, with multiple measurements taken across bolts. Experimental and simulation outcomes show that, under specific conditions, the vibration energy captured increases with higher bolt torque. This method of small-ball impact combined with signal analysis effectively and accurately identifies bolt loosening. The approach provides straightforward data processing, making it well-suited for complex structures with low energy requirements. It is compatible with single or multiple sensors, cost-efficient, fast, and accessible to operators with minimal experience, enabling rapid and extensive detection within confined spaces. This technique, therefore, holds substantial research potential.
Assessing Pain Levels and Quality of Life in Peritoneal Dialysis Patients: A Cross-Sectional Study
Authors: Bdair Amjad , Tamimi Rami , Shratih Ahmad , Abuhalima Dania , Abdalla Mazen , Sarsour Alaa , Jebreen Kamel , Hamdan Zakaria , Nazzal Zaher 
Published: November 2024

Abstract

Background
End-stage renal disease is a significant global health issue, with Peritoneal Dialysis (PD) being a vital treatment modality. The study aims to assess the Quality of Life (QoL) and pain levels in PD patients, exploring potential influencing factors.
Methods
A cross-sectional study was conducted in 2022 involving 76 PD patients at referral tertiary dialysis center in Palestine. The study evaluated patient demographics, clinical data, laboratory measures, quality of life as assessed by the KDQOL-SF36, and pain levels as determined by the Brief Pain Inventory. Statistical analyses, including multivariate linear regression, were employed to identify relevant associations.
Results
This study included 76 PD disease patients, with 68.4% being under the age of 60 and 53.9% being female. Almost one-thirds of the participants (34.0%) reported mild to severe pain, and 23.7% reported low to high interference levels. Pain severity was negatively correlated with supplement doses for both vitamin D3 (p = 0.049) and calcium (p < 0.01). Female patients reported higher pain severity (p = 0.001) and interference (p < 0.007) levels. The study revealed relatively higher QoL in PD patients than other dialysis populations. Factors such as age, comorbid conditions, and duration of dialysis influenced QoL (p < 0.05). Pain severity and interference were negatively correlated with QoL (p = 0.01).
Conclusion
This study provides valuable insights into the QoL and pain experiences of PD patients in Palestine. It underscores the importance of effective pain management strategies and holistic care to improve QoL in this patient population. Addressing psychological and emotional well-being is vital for optimizing treatment adherence and long-term outcomes.
Integrative multi-ethnic Mendelian randomisation identifies tissue- specific causal genes for Coronary Artery Disease and interactions with post-acute Covid
Authors: Jaros Rachel , O’Sullivan Justin M. 
Published: November 2024

Abstract

Coronary artery disease (CAD) is highly heritable and remains the leading cause of mortality worldwide. Understanding the genetic and mechanistic underpinnings of CAD is crucial for early risk assessment and intervention. We conducted a transcriptome-wide Mendelian randomisation (MR) study, utilising unbiased tissue-specific gene regulatory networks, to identify genes causally associated with CAD in European and East Asian populations. We identified 291 tissue and ancestry-specific genes implicated in CAD, including 98 novel protein-coding genes across coronary artery, whole blood, and lung tissues. Genes involved in epigenetic processes (eg PAXBP and KIAA0232) causally associated with CAD. Moreover, we identified genes related to the ubiquitin-proteasome system in the coronary artery and kinase signalling in the lung, as being causally related to CAD. The integration of protein interaction networks identified causal connections between CAD and HDL cholesterol levels, providing novel insights into CAD mechanisms, and potential actionable targets for people with this risk profile. The results also provide intriguing insights into the link between SARS-CoV-2 and CAD, unveiling mechanisms that may underlie the increased risk of cardiovascular disease following SARS-CoV-2 infection. The causal mechanisms we identified emphasise the tissue-agnostic and ancestrally unique pathways that underscore the complex interplay between CAD development, metabolic disturbances, and the immune system. Collectively, our results provide valuable insights into CAD pathogenesis and potential therapeutic targets.
Inactive ryanodine receptors sustain lysosomal availability for autophagy by promoting ER-lysosomal contact site formation
Authors: Vervliet Tim , Loncke Jens , Sever Marko , Ahuja Karan , Haute Chris Van den , Verfaillie Catherine , Tomasic Tihomir , Bultynck Geert 
Published: November 2024

Abstract

Lysosomal and endoplasmic reticulum (ER) Ca2+ release mutually influence each other’s functions. Recent work revealed that ER-located ryanodine receptor (RyR) Ca2+ release channels suppress autophagosome turnover by the lysosomes. In familial Alzheimer’s disease, in which excessive RyR activity and lysosomal dysfunction are early hallmarks, inhibiting RyR restored autophagic flux by normalizing lysosomal vacuolar H+-ATPase (vATPase) levels. However, the mechanisms by which RyR control lysosomal function and how it involves the vATPase remain unknown. In this work we demonstrate for the first time that, RyR directly interact with the ATP6v0a1 subunit of the vATPase, contributing to ER-lysosomal contact site formation. This interaction suppresses RyR-mediated Ca²⁺ release, which impacts the handling of lysosomal cargo. Pharmacological inhibition of RyR activity was sufficient to mimic these effects on lysosomal cargo handling. Further investigation identified endogenous RyR activity in cortical neurons derived from human induced pluripotent stem cells to promote lysosomal exocytosis. Inhibiting this spontaneous RyR activity limits lysosomal exocytosis, thus retaining lysosomes inside cells. The latter increases ER-lysosomal contact site formation, rendering lysosomes more available for autophagic flux. In summary, these findings establish RyRs/ATP6v0a1 complexes as novel ER-lysosomal tethers that dynamically/Ca2+ dependently regulate the intracellular availability of lysosomes to participate in autophagic flux.
The Impact of Composite Laminates: Modelling the Effect of a Round-nosed versus a Flat-ended Impactor at High Impact Energies
Authors: Ding Yuzhe , Johnson Michael S. , Liu Jun , Dear James , Li Jiaqi , Liu Haibao , Kinloch Anthony J. , Dear John P. 
Published: November 2024

Abstract

The present study investigates the effect of the impactor geometry on the impact performance, at relatively high impact energies, of carbon fibre-reinforced polymer (CFRP) laminates with a cross-ply configuration of [02/902], which were manufactured using unidirectional (UD) carbon-fibre epoxy-matrix plies. Drop-weight impact tests were performed using both round-nosed and flat-ended rigid impactors. White light interferometry (WLI), ultrasonic C-scan and scanning electron microscopy (SEM) were employed to assess the relationship between the indentation profile, the delamination footprint and the fracture morphology along the fracture plane. This study focusses on the coupling between the extent of indentation, the loading responses and the associated damage caused in the CFRP. This damage involved both intralaminar damage, including matrix cracking and fibre-kinking and fracture, and interlaminar, i.e. delamination, damage. A major finding was that the flat-ended impactor only caused significant damage to the CFRP panel at the relatively high impact energy of 25 J. At these high impact energies, a compressive kink-band fracture plane occurred around the periphery of the flat-ended impactor near the front surface of the laminate. A previously published numerical model has been extended to account for these experimental observations.