bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictive biomarkers for anti-TNF alpha therapy in IBD patients
Authors: Kumar Manoj , Murugesan Selvasankar , Ibrahim Nazira , Elawad Mamoun , Al Khodor Souhaila
Published: March 2024

Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition characterized by severe gut inflammation, commonly presenting as Crohn’s disease, ulcerative colitis or categorized as IBD- unclassified. While various treatments have demonstrated efficacy in adult IBD patients, the advent of anti-TNF therapies has significantly revolutionized treatment outcomes and clinical management. These therapies have played a pivotal role in achieving clinical and endoscopic remission, promoting mucosal healing, averting disease progression, and diminishing the necessity for surgery. Nevertheless, not all patients exhibit positive responses to these therapies, and some may experience a loss of responsiveness over time. This review aims to present a comprehensive examination of predictive biomarkers for monitoring the therapeutic response to anti-TNF therapy in IBD patients. It will explore their limitations and clinical utilities, paving the way for a more personalized and effective therapeutic approach.
Redox proteomics of PANC-1 cells reveals the significance of HIF-1 signaling protein oxidation in pancreatic ductal adenocarcinoma pathogenesis
Authors: Tan Chaochao , Chen Lichun , Guan Xiaoyu , Huang Wenyi , Feng Yinhong , Li Ziyi , Wu Ling , Huang Xiangping , Ouyang Qianhui , Liu Sixiang , Huang Ying , Hu Jiliang
Published: March 2024

Background

Protein cysteine oxidation is substantially involved in various biological and pathogenic processes, but its implications in pancreatic cancer development remains poorly understood.

Methods and results

In this study, we performed a global characterization of protein oxidation targets in PDAC cells through iodoTMT-based quantitative proteomics, which identified over 4300 oxidized cysteine sites in more than 2100 proteins in HPDE6c7 and PANC-1 cells. Among them, 1715 cysteine residues were shown to be differentially oxidized between HPDE6c7 and PANC-1 cells. Also, charged amino acids including aspartate, glutamate and lysine were significantly overrepresented in flanking sequences of oxidized cysteines. Differentially oxidized proteins in PANC-1 cells were enriched in multiple cancer-related biological processes and signaling pathways. Specifically, the HIF-1 signaling proteins exhibited significant oxidation alterations in PANC-1 cells, and the reduced PHD2 oxidation in human PDAC tissues was correlated with lower survival time in pancreatic cancer patients.

Conclusion

These investigations provided new insights into protein oxidation-regulated signaling and biological processes during PDAC pathogenesis, which might be further explored for pancreatic cancer diagnosis and treatment.
Low-intensity pulsed ultrasound delays the progression of osteoarthritis by regulating the YAP–RIPK1–NF-κB axis and influencing autophagy
Authors: Pan Chunran , Lu Fan , Hao Xiaoxia , Deng Xiaofeng , Liu Jiawei , Sun Kai , Hou Wenjie , Shang Xingru , Chi Ruimin , Guo Fengjing , Xu Tao
Published: March 2024

Background

Osteoarthritis (OA) is a degenerative disease characterized by chronic inflammation of the joint. As the disease progresses, patients will gradually develop symptoms such as pain, physical limitations and even disability. The risk factors for OA include genetics, gender, trauma, obesity, and age. Unfortunately, due to limited understanding of its pathological mechanism, there are currently no effective drugs or treatments to suspend the progression of osteoarthritis. In recent years, some studies found that low-intensity pulsed ultrasound (LIPUS) may have a positive effect on osteoarthritis. Nonetheless, the exact mechanism by which LIPUS affects osteoarthritis remains unknown. It is valuable to explore the specific mechanism of LIPUS in the treatment of OA.

Methods

In this study, we validated the potential therapeutic effect of LIPUS on osteoarthritis by regulating the YAP–RIPK1–NF-κB axis at both cellular and animal levels. To verify the effect of YAP on OA, the expression of YAP was knocked down or overexpressed by siRNA and plasmid in chondrocytes and adeno-associated virus was injected into the knee joint of rats. The effect of LIPUS was investigated in inflammation chondrocytes induced by IL-1β and in the post-traumatic OA model.

Results

In this study, we observed that YAP plays an important role in the development of osteoarthritis and knocking down of YAP significantly inhibited the inflammation and alleviated cartilage degeneration. We also demonstrated that the expression of YAP was increased in osteoarthritis chondrocytes and YAP could interact with RIPK1, thereby regulating the NF-κB signal pathway and influencing inflammation. Moreover, we also discovered that LIPUS decreased the expression of YAP by restoring the impaired autophagy capacity and inhibiting the binding between YAP and RIPK1, thereby delaying the progression of osteoarthritis. Animal experiment showed that LIPUS could inhibit cartilage degeneration and alleviate the progression of OA.

Conclusions

These results showed that LIPUS is effective in inhibiting inflammation and cartilage degeneration and alleviate the progression of OA. As a result, our results provide new insight of mechanism by which LIPUS delays the development of osteoarthritis, offering a novel therapeutic regimen for osteoarthritis.
An automatic system for recognizing fly courtship patterns via an image processing method
Authors: Chen Ching-Hsin , Lin Yu-Chiao , Wang Sheng-Hao , Kuo Tsung-Han , Tsai Hung-Yin
Published: March 2024

Fruit fly courtship behaviors composed of a series of actions have always been an important model for behavioral research. While most related studies have focused only on total courtship behaviors, specific courtship elements have often been underestimated. Identifying these courtship element details is extremely labor intensive and would largely benefit from an automatic recognition system. To address this issue, in this study, we established a vision-based fly courtship behavior recognition system. The system based on the proposed image processing methods can precisely distinguish body parts such as the head, thorax, and abdomen and automatically recognize specific courtship elements, including orientation, singing, attempted copulation, copulation and tapping, which was not detectable in previous studies. This system, which has high identity tracking accuracy (99.99%) and high behavioral element recognition rates (> 97.35%), can ensure correct identification even when flies completely overlap. Using this newly developed system, we investigated the total courtship time, and proportion, and transition of courtship elements in flies across different ages and found that male flies adjusted their courtship strategy in response to their physical condition. We also identified differences in courtship patterns between males with and without successful copulation. Our study therefore demonstrated how image processing methods can be applied to automatically recognize complex animal behaviors. The newly developed system will largely help us investigate the details of fly courtship in future research.
Maximizing efficiency in sunflower breeding through historical data optimization
Authors: Fernández-González Javier , Haquin Bertrand , Combes Eliette , Bernard Karine , Allard Alix , Isidro y Sánchez Julio
Published: March 2024

Genomic selection (GS) has become an increasingly popular tool in plant breeding programs, propelled by declining genotyping costs, an increase in computational power, and rediscovery of the best linear unbiased prediction methodology over the past two decades. This development has led to an accumulation of extensive historical datasets with genotypic and phenotypic information, triggering the question of how to best utilize these datasets. Here, we investigate whether all available data or a subset should be used to calibrate GS models for across-year predictions in a 7-year dataset of a commercial hybrid sunflower breeding program. We employed a multi-objective optimization approach to determine the ideal years to include in the training set (TRS). Next, for a given combination of TRS years, we further optimized the TRS size and its genetic composition. We developed the Min_GRM size optimization method which consistently found the optimal TRS size, reducing dimensionality by 20% with an approximately 1% loss in predictive ability. Additionally, the Tails_GEGVs algorithm displayed potential, outperforming the use of all data by using just 60% of it for grain yield, a high-complexity, low-heritability trait. Moreover, maximizing the genetic diversity of the TRS resulted in a consistent predictive ability across the entire range of genotypic values in the test set. Interestingly, the Tails_GEGVs algorithm, due to its ability to leverage heterogeneity, enhanced predictive performance for key hybrids with extreme genotypic values. Our study provides new insights into the optimal utilization of historical data in plant breeding programs, resulting in improved GS model predictive ability.
AraDQ: an automated digital phenotyping software for quantifying disease symptoms of flood-inoculated Arabidopsis seedlings
Authors: Lee Jae Hoon , Lee Unseok , Yoo Ji Hye , Lee Taek Sung , Jung Je Hyeong , Kim Hyoung Seok
Published: March 2024

Background

Plant scientists have largely relied on pathogen growth assays and/or transcript analysis of stress-responsive genes for quantification of disease severity and susceptibility. These methods are destructive to plants, labor-intensive, and time-consuming, thereby limiting their application in real-time, large-scale studies. Image-based plant phenotyping is an alternative approach that enables automated measurement of various symptoms. However, most of the currently available plant image analysis tools require specific hardware platform and vendor specific software packages, and thus, are not suited for researchers who are not primarily focused on plant phenotyping. In this study, we aimed to develop a digital phenotyping tool to enhance the speed, accuracy, and reliability of disease quantification in Arabidopsis.

Results

Here, we present the Arabidopsis Disease Quantification (AraDQ) image analysis tool for examination of flood-inoculated Arabidopsis seedlings grown on plates containing plant growth media. It is a cross-platform application program with a user-friendly graphical interface that contains highly accurate deep neural networks for object detection and segmentation. The only prerequisite is that the input image should contain a fixed-sized 24-color balance card placed next to the objects of interest on a white background to ensure reliable and reproducible results, regardless of the image acquisition method. The image processing pipeline automatically calculates 10 different colors and morphological parameters for individual seedlings in the given image, and disease-associated phenotypic changes can be easily assessed by comparing plant images captured before and after infection. We conducted two case studies involving bacterial and plant mutants with reduced virulence and disease resistance capabilities, respectively, and thereby demonstrated that AraDQ can capture subtle changes in plant color and morphology with a high level of sensitivity.

Conclusions

AraDQ offers a simple, fast, and accurate approach for image-based quantification of plant disease symptoms using various parameters. Its fully automated pipeline neither requires prior image processing nor costly hardware setups, allowing easy implementation of the software by researchers interested in digital phenotyping of diseased plants.
Optimization of the selection of suitable harvesting periods for medicinal plants: taking Dendrobium officinale as an example
Authors: Li Peiyuan , shen Tao , Li Li , Wang Yuanzhong
Published: March 2024

Background

Dendrobium officinale is a medicinal plant with high commercial value. The Dendrobium officinale market in Yunnan is affected by the standardization of medicinal material quality control and the increase in market demand, mainly due to the inappropriate harvest time, which puts it under increasing resource pressure. In this study, considering the high polysaccharide content of Dendrobium leaves and its contribution to today’s medical industry, (Fourier Transform Infrared Spectrometer) FTIR combined with chemometrics was used to combine the yields of both stem and leaf parts of Dendrobium officinale to identify the different harvesting periods and to predict the dry matter content for the selection of the optimal harvesting period.

Results

The Three-dimensional correlation spectroscopy (3DCOS) images of Dendrobium stems to build a (Split-Attention Networks) ResNet model can identify different harvesting periods 100%, which is 90% faster than (Support Vector Machine) SVM, and provides a scientific basis for modeling a large number of samples. The (Partial Least Squares Regression) PLSR model based on MSC preprocessing can predict the dry matter content of Dendrobium stems with Factor = 7, RMSE = 0.47, R2 = 0.99, RPD = 8.79; the PLSR model based on SG preprocessing can predict the dry matter content of Dendrobium leaves with Factor = 9, RMSE = 0.2, R2 = 0.99, RPD = 9.55.

Conclusions

These results show that the ResNet model possesses a fast and accurate recognition ability, and at the same time can provide a scientific basis for the processing of a large number of sample data; the PLSR model with MSC and SG preprocessing can predict the dry matter content of Dendrobium stems and leaves, respectively; The suitable harvesting period for D. officinale is from November to April of the following year, with the best harvesting period being December. During this period, it is necessary to ensure sufficient water supply between 7:00 and 10:00 every day and to provide a certain degree of light blocking between 14:00 and 17:00.
Infrared: a declarative tree decomposition-powered framework for bioinformatics
Authors: Yao Hua-Ting , Marchand Bertrand , Berkemer Sarah J. , Ponty Yann , Will Sebastian
Published: March 2024

Motivation

Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.

Methods

We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a generalization of constraint networks. Classic Boolean constraints specify a search space, consisting of putative solutions whose evaluation is performed through a combination of features. Problems are then solved using generic cluster tree elimination algorithms over a tree decomposition of the feature network. Their overall complexities are linear on the number of variables, and only exponential in the treewidth of the feature network. For sparse feature networks, associated with low to moderate treewidths, these algorithms allow to find optimal solutions, or generate controlled samples, with practical empirical efficiency.

Results

Implementing these methods, the Infrared software allows Python programmers to rapidly develop exact optimization and sampling applications based on a tree decomposition-based efficient processing. Instead of directly coding specialized algorithms, problems are declaratively modeled as sets of variables over finite domains, whose dependencies are captured by constraints and functions. Such models are then automatically solved by generic DP algorithms. To illustrate the applicability of Infrared in bioinformatics and guide new users, we model and discuss variants of bioinformatics applications. We provide reimplementations and extensions of methods for RNA design, RNA sequence-structure alignment, parsimony-driven inference of ancestral traits in phylogenetic trees/networks, and design of coding sequences. Moreover, we demonstrate multidimensional Boltzmann sampling. These applications of the framework—together with our novel results—underline the practical relevance of Infrared. Remarkably, the achieved complexities are typically equivalent to the ones of specialized algorithms and implementations.

Availability

Infrared is available at https://amibio.gitlabpages.inria.fr/Infrared with extensive documentation, including various usage examples and API reference; it can be installed using Conda or from source.
The influence of anterior cervical discectomy and fusion surgery on cervical muscles and the correlation between related muscle changes and surgical efficacy
Authors: Sun Chong , Xiang Hongfei , Wu Xiaolin , Chen Bohua , Guo Zhu
Published: March 2024

Background

Anterior cervical discectomy and fusion surgery (ACDF) is a common technique in treating degenerative cervical spondylosis. This study is to evaluate the changes of cervical muscles after ACDF and analyze the correlation between related muscle changes and clinical efficacy.

Methods

Sixty-five postoperative patients (single-level ACDF) with cervical spondylotic myelopathy from January 2013 to December 2022 were analyzed. The measured parameters include: the axial section of longus colli cross-sectional area (AxCSA), the volume of cervical longus, the ratio of long and short diameter line (RLS), the cervical extensor cross-sectional area (CESA), the vertebral body area (VBA), and the CESA/VBA. The visual analog scale (VAS), modified Japanese Orthopedic Association score (mJOA), and neck disability index (NDI) were evaluated. The changes in muscle morphology were analyzed, and the correlation analysis was conducted between morphological changes and function scores.

Results

The postoperative AxCSA of surgical segment (3rd month, 12th month, and the last follow-up) was decreased compared to preoperative (141.62 ± 19.78), and the differences were significant (P < 0.05). The corresponding data reduced to (119.42 ± 20.08) mm2, (117.59 ± 19.69) mm2, and (117.41 ± 19.19) mm2, respectively (P < 0.05). The RLS increased, and the volume of cervical longus decreased significantly after surgery (P < 0.05). Negative correlation was found between postoperative volume of cervical longus and VAS at the 3rd month (r = − 0.412), 12th month (r = − 0.272), and last follow-up (r = − 0.391) (P < 0.05). Negative correlation existed between postoperative volume of cervical longus and NDI at the 3rd month (r = − 0.552), 12th month (r = − 0.293), and last follow-up (r = − 0.459) (P < 0.05).

Conclusion

The volume of cervical longus decreased and its morphology changed after ACDF surgery. The mainly affected muscle was the cervical longus closing to the surgical segment. Negative correlation was found between the postoperative volume of cervical longus and function scores (VAS and NDI).
Exosomes derived from umbilical cord-mesenchymal stem cells inhibit the NF-κB/MAPK signaling pathway and reduce the inflammatory response to promote recovery from spinal cord injury
Authors: Luan Zhiwei , Liu Jingsong , Li Mi , Wang Yangyang , Wang Yansong
Published: March 2024

Spinal cord injury (SCI) is a serious traumatic disease of the central nervous system and leads to incomplete or complete loss of the body’s autonomous motor and sensory functions, seriously endangering human health. Recently, exosomes have been proposed as important substances in cell-to-cell interactions. Mesenchymal stem cell (MSC)-derived exosomes exert good therapeutic effects and play a crucial role in neurological damage repair. However, the detailed mechanisms underlying their effects remain unknown. Herein, we found that compared to SCI rats, those subjected to umbilical cord MSC (UC-MSC)-derived exosomes injection showed an improved motor ability. Nevertheless, the transcriptome of BV2 microglia in different treatment groups indicated that the action pathway of exosomes might be the NF-κB/MAPK pathway. Additionally, exosomes from UC-MSCs could inhibit P38, JNK, ERK, and P65 phosphorylation in BV2 microglia and SCI rat tissues. Moreover, exosomes could inhibit apoptosis and inflammatory reaction and reactive oxygen species (ROS) production of BV2 microglia in vitro and in vivo. In conclusion, UC-MSCs-derived exosomes might protect SCI in rats by inhibiting inflammatory response via the NF-κB/MAPK signaling pathway, representing novel treatment targets or approaches for SCI.
Rejuvenating aged microglia by p16ink4a-siRNA-loaded nanoparticles increases amyloid-β clearance in animal models of Alzheimer’s disease
Authors: Shin Hyo Jung , Kim In Soo , Choi Seung Gyu , Lee Kayoung , Park Hyewon , Shin Juhee , Kim Dayoung , Beom Jaewon , Yi Yoon Young , Gupta Deepak Prasad , Song Gyun Jee , Chung Won-Suk , Lee C. Justin , Kim Dong Woon
Published: March 2024

Age-dependent accumulation of amyloid plaques in patients with sporadic Alzheimer’s disease (AD) is associated with reduced amyloid clearance. Older microglia have a reduced ability to phagocytose amyloid, so phagocytosis of amyloid plaques by microglia could be regulated to prevent amyloid accumulation. Furthermore, considering the aging-related disruption of cell cycle machinery in old microglia, we hypothesize that regulating their cell cycle could rejuvenate them and enhance their ability to promote more efficient amyloid clearance. First, we used gene ontology analysis of microglia from young and old mice to identify differential expression of cyclin-dependent kinase inhibitor 2A (p16ink4a), a cell cycle factor related to aging. We found that p16ink4a expression was increased in microglia near amyloid plaques in brain tissue from patients with AD and 5XFAD mice, a model of AD. In BV2 microglia, small interfering RNA (siRNA)-mediated p16ink4a downregulation transformed microglia with enhanced amyloid phagocytic capacity through regulated the cell cycle and increased cell proliferation. To regulate microglial phagocytosis by gene transduction, we used poly (D,L-lactic-co-glycolic acid) (PLGA) nanoparticles, which predominantly target microglia, to deliver the siRNA and to control microglial reactivity. Nanoparticle-based delivery of p16ink4a siRNA reduced amyloid plaque formation and the number of aged microglia surrounding the plaque and reversed learning deterioration and spatial memory deficits. We propose that downregulation of p16ink4a in microglia is a promising strategy for the treatment of Alzheimer’s disease.
Gli1-mediated tumor cell-derived bFGF promotes tumor angiogenesis and pericyte coverage in non-small cell lung cancer
Authors: Lei Xueping , Li Zhan , Huang Manting , Huang Lijuan , Huang Yong , Lv Sha , Zhang Weisong , Chen Zhuowen , Ke Yuanyu , Li Songpei , Chen Jingfei , Yang Xiangyu , Deng Qiudi , Liu Junshan , Yu Xiyong
Published: March 2024

Background

Tumor angiogenesis inhibitors have been applied for non-small cell lung cancer (NSCLC) therapy. However, the drug resistance hinders their further development. Intercellular crosstalk between lung cancer cells and vascular cells was crucial for anti-angiogenenic resistance (AAD). However, the understanding of this crosstalk is still rudimentary. Our previous study showed that Glioma-associated oncogene 1 (Gli1) is a driver of NSCLC metastasis, but its role in lung cancer cell-vascular cell crosstalk remains unclear.

Methods

Conditioned medium (CM) from Gli1-overexpressing or Gli1-knockdown NSCLC cells was used to educate endothelia cells and pericytes, and the effects of these media on angiogenesis and the maturation of new blood vessels were evaluated via wound healing assays, Transwell migration and invasion assays, tube formation assays and 3D coculture assays. The xenograft model was conducted to establish the effect of Gli1 on tumor angiogenesis and growth. Angiogenic antibody microarray analysis, ELISA, luciferase reporte, chromatin immunoprecipitation (ChIP), bFGF protein stability and ubiquitination assay were performed to explore how Gli1 regulate bFGF expression.

Results

Gli1 overexpression in NSCLC cells enhanced the endothelial cell and pericyte motility required for angiogenesis required for angiogenesis. However, Gli1 knockout in NSCLC cells had opposite effect on this process. bFGF was critical for the enhancement effect on tumor angiogenesis. bFGF treatment reversed the Gli1 knockdown-mediated inhibition of angiogenesis. Mechanistically, Gli1 increased the bFGF protein level by promoting bFGF transcriptional activity and protein stability. Importantly, suppressing Gli1 with GANT-61 obviously inhibited angiogenesis.

Conclusion

The Gli1-bFGF axis is crucial for the crosstalk between lung cancer cells and vascular cells. Targeting Gli1 is a potential therapeutic approach for NSCLC angiogenesis.
Trauma systems in high socioeconomic index countries in 2050
Authors: Gauss Tobias , de Jongh Mariska , Maegele Marc , Cole Elaine , Bouzat Pierre
Published: March 2024

Considerable political, structural, environmental and epidemiological change will affect high socioeconomic index (SDI) countries over the next 25 years. These changes will impact healthcare provision and consequently trauma systems. This review attempts to anticipate the potential impact on trauma systems and how they could adapt to meet the changing priorities. The first section describes possible epidemiological trajectories. A second section exposes existing governance and funding challenges, how these can be met, and the need to incorporate data and information science into a learning and adaptive trauma system. The last section suggests an international harmonization of trauma education to improve care standards, optimize immediate and long-term patient needs and enhance disaster preparedness and crisis resilience. By demonstrating their capacity for adaptation, trauma systems can play a leading role in the transformation of care systems to tackle future health challenges.
The prevalence of sarcopenia in spondyloarthritis patients: a meta-analysis
Authors: Hu Jiawen , Wang Yiwen , Ji Xiaojian , Zhang Yinan , Li Kunpeng , Huang Feng
Published: March 2024

Background

Spondyloarthritis (SpA) is a chronic inflammatory disorder that affects sacroiliac joints and spine, resulting in substantial disability. Sarcopenia, characterized by the loss of muscle mass and function, is a prevalent comorbidity in various chronic diseases. However, the exact prevalence of sarcopenia in SpA patients remains uncertain. The objective of this study is to conduct a systematic review and meta-analysis of the available literature to determine the prevalence of sarcopenia in SpA.

Methods

A comprehensive search was conducted in EMBASE, MEDLINE, WEB OF SCIENCE, and COCHRANE databases to identify relevant studies published up to 2023. Studies investigating the prevalence of sarcopenia in SpA patients were included. Data on study characteristics, participant demographics, diagnostic criteria for sarcopenia, and prevalence rates were extracted. Meta-analysis was performed using a random-effects model to estimate the overall prevalence of sarcopenia in SpA patients.

Results

A total of 16 studies that met the inclusion criteria were included in the systematic review. These studies encompassed a combined sample size of 999 patients with SpA. The meta-analysis findings revealed that the overall prevalence of sarcopenia in SpA patients was 25.0% (95% confidence interval: 0.127 to 0.352). Furthermore, the prevalence of presarcopenia and severe sarcopenia was found to be 21.0% and 8.7%, respectively. Subgroup analysis was conducted to examine different diagnostic criteria, subtypes, and sex of SpA in relation to sarcopenia.

Conclusion

This systematic review and meta-analysis provide a comprehensive overview of the prevalence of sarcopenia in SpA patients. The findings suggest a high prevalence of sarcopenia in SpA patients, emphasizing the need for targeted interventions to prevent and manage sarcopenia. And further research is needed to explore the underlying mechanisms and potential therapeutic strategies for sarcopenia in SpA.
Predictive value of insulin resistance surrogates for the development of diabetes in individuals with baseline normoglycemia: findings from two independent cohort studies in China and Japan
Authors: Shangguan Qing , Liu Qiuling , Yang Ruijuan , Zhang Shuhua , Sheng Guotai , Kuang Maobin , Zou Yang
Published: March 2024

Background

Insulin resistance (IR) plays a crucial role in the occurrence and progression of diabetes. This study aimed to evaluate and compare the predictive value of four IR surrogates, including the triglycerides glucose (TyG) index, TyG and body mass index (TyG-BMI), triglycerides/high-density lipoprotein cholesterol (TG/HDL-C) ratio, and the metabolic score for IR (MetS-IR) for diabetes in two large cohorts.

Methods

A total of 116,661 adult participants from the China Rich Healthcare Group and 15,464 adult participants from the Japanese NAGALA cohort were included in the study. Multivariable Cox proportional hazards models were used to assess the standardized hazard ratio (HR) of the TyG index, TyG-BMI, TG/HDL-C ratio, and MetS-IR directly associated with diabetes. Receiver operating characteristic (ROC) curve and time-dependent ROC curve analysis were performed to evaluate and compare the predictive value of the four IR surrogates for diabetes.

Results

In the two independent cohorts, the average follow-up time was 3.1 years in the China cohort, with 2681(2.30%) incident cases of diabetes recorded, and 6.13 years in the Japan cohort, with 373 incident cases (2.41%) of diabetes recorded. After adjusting for potential confounding factors, we found that among the four IR surrogates, TyG-BMI and MetS-IR showed stronger associations with diabetes. The stronger associations persisted even after further stratification by age, sex, hypertension, and obese subgroups. In terms of diabetes prediction, based on ROC analysis, TyG-BMI demonstrated the highest predictive accuracy for diabetes in the Chinese population, while both TyG-BMI and MetS-IR showed the highest predictive accuracy in the Japanese population. The results of further subgroup ROC analysis confirmed the robustness of these findings. Furthermore, the time-dependent ROC results indicated that among the four IR surrogates, MetS-IR exhibited the highest accuracy in predicting future diabetes at various time intervals in the Japanese population.

Conclusion

Our findings suggest that evaluating TyG-BMI and MetS-IR as IR surrogates may be the most useful for predicting diabetes events and assessing the risk of developing diabetes in East Asian populations.
Bilateral vertebral artery injury leads to brain death following traumatic brain injury: a case report
Authors: Irawany Vera , Nasution Vizzi A. F. , Amalia Noorcahya
Published: March 2024

Background

Vertebral artery injury is a rare condition in trauma settings. In the advanced stages, it causes death.

Case

A 31-year-old Sundanese woman with cerebral edema, C2–C3 anterolisthesis, and Le Fort III fracture after a motorcycle accident was admitted to the emergency room. On the fifth day, she underwent arch bar maxillomandibular application and debridement in general anesthesia with a hyperextended neck position. Unfortunately, her rigid neck collar was removed in the high care unit before surgery. Her condition deteriorated 72 hours after surgery. Digital subtraction angiography revealed a grade 5 bilateral vertebral artery injury due to cervical spine displacement and a grade 4 left internal carotid artery injury with a carotid cavernous fistula (CCF). The patient was declared brain death as not improved cerebral perfusion after CCF coiling.

Conclusions

Brain death due to cerebral hypoperfusion following cerebrovascular injury in this patient could be prevented by early endovascular intervention and cervical immobilisation.
Construction of recombinant fluorescent LSDV for high-throughput screening of antiviral drugs
Authors: Wang Jingyu , Ji Jinzhao , Zhong Yongcheng , Meng Wenxin , Wan Shaobin , Ding Xiaoqing , Chen Zihan , Wu Weiyong , Jia Kun , Li Shoujun
Published: March 2024

Lumpy skin disease virus (LSDV) infection is a major socio-economic issue that seriously threatens the global cattle-farming industry. Here, a recombinant virus LSDV-ΔTK/EGFP, expressing enhanced green fluorescent protein (EGFP), was constructed with a homologous recombination system and applied to the high-throughput screening of antiviral drugs. LSDV-ΔTK/EGFP replicates in various kidney cell lines, consistent with wild-type LSDV. The cytopathic effect, viral particle morphology, and growth performance of LSDV-ΔTK/EGFP are consistent with those of wild-type LSDV. High-throughput screening allowed to identify several molecules that inhibit LSDV-ΔTK/EGFP replication. The strong inhibitory effect of theaflavin on LSDV was identified when 100 antiviral drugs were screened in vitro. An infection time analysis showed that theaflavin plays a role in the entry of LSDV into cells and in subsequent viral replication stages. The development of this recombinant virus will contribute to the development of LSDV-directed antiviral drugs and the study of viral replication and mechanisms of action.
A matter of differentiation: equine enteroids as a model for the in vivo intestinal epithelium
Authors: Windhaber Christina , Heckl Anna , Csukovich Georg , Pratscher Barbara , Burgener Iwan Anton , Biermann Nora , Dengler Franziska
Published: March 2024

Epithelial damage due to gastrointestinal disorders frequently causes severe disease in horses. To study the underlying pathophysiological processes, we aimed to establish equine jejunum and colon enteroids (eqJE, eqCE) mimicking the in vivo epithelium. Therefore, enteroids were cultivated in four different media for differentiation and subsequently characterized histomorphologically, on mRNA and on protein level in comparison to the native epithelium of the same donor horses to identify ideal culture conditions for an in vitro model system. With increasing enterocyte differentiation, the enteroids showed a reduced growth rate as well as a predominantly spherical morphology and less budding compared to enteroids in proliferation medium. Combined or individual withdrawal of stem cell niche pathway components resulted in lower mRNA expression levels of stem cell markers and concomitant differentiation of enterocytes, goblet cells and enteroendocrine cells. For eqCE, withdrawal of Wnt alone was sufficient for the generation of differentiated enterocytes with a close resemblance to the in vivo epithelium. Combined removal of Wnt, R-spondin and Noggin and the addition of DAPT stimulated differentiation of eqJE at a similar level as the in vivo epithelium, particularly with regard to enterocytes. In summary, we successfully defined a medium composition that promotes the formation of eqJE and eqCE consisting of multiple cell types and resembling the in vivo epithelium. Our findings emphasize the importance of adapting culture conditions to the respective species and the intestinal segment. This in vitro model will be used to investigate the pathological mechanisms underlying equine gastrointestinal disorders in future studies.
Pasteurella multocida activates Rassf1-Hippo-Yap pathway to induce pulmonary epithelial apoptosis
Authors: Zhao Guangfu , Tang Yunhan , Liu Xiongli , Li Pan , Zhang Tianci , Li Nengzhang , He Fang , Peng Yuanyi
Published: March 2024

Pasteurella multocida is an opportunistic zoonotic pathogen that primarily causes fatal respiratory diseases, such as pneumonia and respiratory syndromes. However, the precise mechanistic understanding of how P. multocida disrupts the epithelial barrier in mammalian lung remains largely unknown. In this study, using unbiased RNA-seq analysis, we found that the evolutionarily conserved Hippo-Yap pathway was dysregulated after P. multocida infection. Given the complexity of P. multocida infection associated with lung injury and systemic inflammatory processes, we employed a combination of cell culture models, mouse models, and rabbit models to investigate the dynamics of the Hippo-Yap pathway during P. multocida infection. Our findings reveal that P. multocida infection activates the Hippo-Yap pathway both in vitro and in vivo, by upregulating the upstream factors p-Mst1/2, p-Lats1, and p-Yap, and downregulating the downstream effectors Birc5, Cyr61, and Slug. Conversely, pharmacological inhibition of the Hippo pathway by XMU-MP-1 significantly rescued pulmonary epithelial cell apoptosis in vitro and reduced lung injury, systemic inflammation, and mouse mortality in vivo. Mechanistic studies revealed that P. multocida induced up-regulation of Rassf1 expression, and Rassf1 enhanced Hippo-Yap pathway through phosphorylation. Accordingly, in vitro knockdown of Rassf1 significantly enhanced Yap activity and expression of Yap downstream factors and reduced apoptosis during P. multocida infection. P. multocida-infected rabbit samples also showed overexpression of Rassf1, p-Lats1, and p-Yap, suggesting that P. multocida activates the Rassf1-Hippo-Yap pathway. These results elucidate the pathogenic role of the Rassf1-Hippo-Yap pathway in P. multocida infection and suggest that this pathway has the potential to be a drug target for the treatment of pasteurellosis.
An equine iPSC-based phenotypic screening platform identifies pro- and anti-viral molecules against West Nile virus
Authors: Cochet Marielle , Piumi François , Gorna Kamila , Berry Noémie , Gonzalez Gaëlle , Danckaert Anne , Aulner Nathalie , Blanchet Odile , Zientara Stéphan , Donadeu Francesc Xavier , Munier-Lehmann Hélène , Richardson Jennifer , Benchoua Alexandra , Coulpier Muriel
Published: March 2024

Outbreaks of West Nile virus (WNV) occur periodically, affecting both human and equine populations. There are no vaccines for humans, and those commercialised for horses do not have sufficient coverage. Specific antiviral treatments do not exist. Many drug discovery studies have been conducted, but since rodent or primate cell lines are normally used, results cannot always be transposed to horses. There is thus a need to develop relevant equine cellular models. Here, we used induced pluripotent stem cells to develop a new in vitro model of WNV-infected equine brain cells suitable for microplate assay, and assessed the cytotoxicity and antiviral activity of forty-one chemical compounds. We found that one nucleoside analog, 2′C-methylcytidine, blocked WNV infection in equine brain cells, whereas other compounds were either toxic or ineffective, despite some displaying anti-viral activity in human cell lines. We also revealed an unexpected proviral effect of statins in WNV-infected equine brain cells. Our results thus identify a potential lead for future drug development and underscore the importance of using a tissue- and species-relevant cellular model for assessing the activity of antiviral compounds.
What evidence exists on birds and mammals' biodiversity in the Brazilian Atlantic Forest (BAF) agricultural ecosystems? A systematic map protocol
Authors: Casallanovo Fábio , Santos Gustavo Souza , Cione Ana Paola
Published: March 2024

Background

Brazil has one of the planet's greatest biodiversity, with over 20% of the world’s total species. The Brazilian Atlantic Forest (BAF) spans 17 Brazilian states, making it the third-largest biome in Brazil. The BAF is composed of a range of ecological formations, with climatic conditions and landscape diversity that directly contribute to the different structures of the forest. The fragmentation of the original habitats, mainly due to anthropogenic activities, is one of the main causes of biodiversity loss, causing the decline and habitat loss for several species, including birds and mammals. While there has been extensive research on species diversity in forest fragments or protected areas, there is a lack of basic research in agricultural ecosystems. Only 1.5% of the studies on bird occurrence data in the BAF were reported from pasture habitats and 1.4% from exotic tree plantations. To address this gap, the present systematic map protocol aims to carry out a bibliographic survey on the presence of birds and mammals in agricultural landscapes and its adjacent areas of natural vegetation to describe the prevalence of species across different (semi-)natural and anthropogenic habitat types. Collecting this data is important to support environmental management policies to preserve biodiversity in these areas.

Methods

We will conduct a systematic literature review on the biodiversity of birds and mammals in agricultural landscapes within the Brazilian Atlantic Forest as well as adjacent areas of natural vegetation. Our search will cover the following databases, without limiting the year of publication: Web of Knowledge, Scopus, and PubMed. We will also include grey literature such as dissertations and theses, performing the search at the “Biblioteca Digital Brasileira” database. The results will be screened for relevance based on predefined criteria. The screening process will take place in two stages: firstly, the articles will be screened by title and abstract, and then the eligible articles will be screened in full text. Only articles that meet the eligibility criteria will proceed to data extraction. The extracted data will provide the elements to build a systematic map.
Machine learning-driven prognostic analysis of cuproptosis and disulfidptosis-related lncRNAs in clear cell renal cell carcinoma: a step towards precision oncology
Authors: Chen Ronghui , Wu Jun , Che Yinwei , Jiao Yuzhuo , Sun Huashan , Zhao Yinuo , Chen Pingping , Meng Lingxin , Zhao Tao
Published: March 2024

Cuproptosis and disulfidptosis, recently discovered mechanisms of cell death, have demonstrated that differential expression of key genes and long non-coding RNAs (lncRNAs) profoundly influences tumor development and affects their drug sensitivity. Clear cell renal cell carcinoma (ccRCC), the most common subtype of kidney cancer, presently lacks research utilizing cuproptosis and disulfidptosis-related lncRNAs (CDRLRs) as prognostic markers. In this study, we analyzed RNA-seq data, clinical information, and mutation data from The Cancer Genome Atlas (TCGA) on ccRCC and cross-referenced it with known cuproptosis and disulfidptosis-related genes (CDRGs). Using the LASSO machine learning algorithm, we identified four CDRLRs—ACVR2B-AS1, AC095055.1, AL161782.1, and MANEA-DT—that are strongly associated with prognosis and used them to construct a prognostic risk model. To verify the model's reliability and validate these four CDRLRs as significant prognostic factors, we performed dataset grouping validation, followed by RT-qPCR and external database validation for differential expression and prognosis of CDRLRs in ccRCC. Gene function and pathway analysis were conducted using Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) for high- and low-risk groups. Additionally, we have analyzed the tumor mutation burden (TMB) and the immune microenvironment (TME), employing the oncoPredict and Immunophenoscore (IPS) algorithms to assess the sensitivity of diverse risk categories to targeted therapeutics and immunosuppressants. Our predominant objective is to refine prognostic predictions for patients with ccRCC and inform treatment decisions by conducting an exhaustive study on cuproptosis and disulfidptosis.
A non-linear connection between the total cholesterol to high-density lipoprotein cholesterol ratio and stroke risk: a retrospective cohort study from the China Health and Retirement Longitudinal Study
Authors: Xiao Binhui , Cao Changchun , Han Yong , Yang Fangju , Hu Haofei , Luo Jiao
Published: March 2024

Objective

The connection between total cholesterol to high-density lipoprotein cholesterol (TC/HDL-C) ratio and stroke risk is controversial. This study aims to examine the connection between the TC/HDL-C ratio and stroke in middle-aged and older individuals who are part of the China Health and Retirement Longitudinal Study (CHARLS).

Methods

This study conducted a retrospective cohort analysis, enrolling a total of 10,184 participants who met the designated criteria from CHARLS between 2011 and 2012. We then used the Cox proportional-hazards regression model to analyze the relationship between the TC/HDL-C ratio and stroke risk. Using a Cox proportional hazards regression model with cubic spline functions and smooth curve fitting, we were able to identify the non-linear relationship between the TC/HDL-C ratio and stroke occurrence. The sensitivity and subgroup analyses were also performed to investigate the connection between TC/HDL-C ratio and stroke.

Results

This study revealed a statistically significant association between the TC/HDL-C ratio and stroke risk in subjects aged 45 years or older after adjusting for risk factors (HR: 1.05, 95%CI 1.00–1.10, P = 0.0410). Furthermore, a non-linear connection between the TC/HDL-C ratio and stroke risk was detected, with a TC/HDL-C ratio inflection point of 3.71. We identified a significant positive connection between the TC/HDL-C ratio and stroke risk, when the TC/HDL-C ratio was less than 3.71 (HR: 1.25, 95%CI 1.07–1.45, P = 0.0039). However, their connection was not significant when the TC/HDL-C ratio exceeded 3.71 (HR: 1.00, 95%CI 0.94–1.06, P = 0.9232). The sensitivity analysis and subgroup analyses revealed that our findings were well-robust.

Conclusion

Our study demonstrated a positive, non-linear connection between the TC/HDL-C ratio and stroke risk in middle-aged and older individuals. There was a significant positive connection between the TC/HDL-C ratio and stroke risk, when the TC/HDL-C ratio was less than 3.71. The current research can be used as a guideline to support clinician consultation and optimize stroke prevention measures for middle-aged and older adults.
Conservative management by embolization of a ruptured renal arterio-venous malformation (AVM) in Hereditary Hemorrhagic Telangiectasia (HHT)
Authors: L’Huillier Romain , Pagnoux Gaële , Dupuis-Girod Sophie , Stacoffe Nicolas
Published: March 2024

Background

Renal arteriovenous malformation (AVM) in Hereditary Hemorrhagic Telangiectasia (HHT) is uncommon and only few cases have been described, mainly with surgical management because of uncontrolled hematuria.

Case presentation

We managed a 70-year-old patient with HHT who presented with hematuria and left flank pain. Computed Tomography and ultrasound showed left renal AVM of 18 mm with clotting in the urinary tract. An external ureteral catheter was placed during 3 days to allow rinsing and facilitate elimination of clots.

Given the patient's hemodynamic stability, a non-surgical management was chosen. Treatment of the AVM was performed by trans-arterial embolization using micro-coils and ethylene–vinyl alcohol copolymer.

Conclusions

Our case study shows a conservative management by embolization of ruptured left renal AVM revealed by hematuria in a 70-year-old patient with HHT.