bluuebunny/crossref_metadata_2025 huggingface dataset:
Vitamin D binding protein correlate with estrogen increase after administration of human chorionic gonadotropin but do not affect ovulation, embryo, or pregnancy outcomes
Authors: Chen Huijun , Yao Jianghui , Hu Liang , Liu Yvonne , Hocher Johann-Georg , Zhang Xiaoli , Hasan Ahmed A. , Lin Ge , Gong Fei , Hocher Berthold
Published: May 2024

Background

Vitamin D binding protein (DBP) might increase substantially after ovarian stimulation and hence could be associated with IVF/ICSI outcomes because it determines the fraction of free bioavailable 25(OH) vitamin D. In this study, we aim to determine whether DBP is associated with E2 level after ovarian stimulation and IVF/ICSI outcomes.

Design

Post-hoc analysis of a prospective observational cohort.

Setting

Single-center study.

Participants

2569 women receiving embryo transfer.

Intervention

None.

Main outcome measures

The main outcomes were oocyte and embryo quality as well as pregnancy outcomes.

Results

DBP concentration correlates with E2 on hCG day (=day of inducing ovulation with hCG; correlation coefficient r = 0.118, P<0.001) and E2 x-fold change to baseline level (r = 0.108, P<0.001). DBP is also positively correlated with total 25(OH)D (r = 0.689, R2 = 0.475, P<0.001) and inversely with free 25(OH)D (r=-0.424, R2=0.179, P<0.001), meaning that E2-stimulated DBP synthesis results in a decrease of free 25(OH)D during ovarian stimulation. However, such alteration does not affect IVF/ICSI outcomes when considering confounding factors, such as the number and quality of oocytes nor embryo quality as well as pregnancy outcomes.

Conclusion

DBP concentration correlates with the degree of E2 increase after ovarian stimulation. DBP is also positively correlated with total 25(OH)D and inversely with free 25(OH)D, suggesting that the proportion of free 25(OH)D decreases during ovarian stimulation caused by E2-stimulated DBP synthesis. However, such alteration does not affect clinical IVF/ICSI outcomes.
Cardiometabolic risk factors in MASLD patients with HCC: the other side of the coin
Authors: Meroni Marica , Longo Miriam , Dongiovanni Paola
Published: May 2024

Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) constitutes the commonest cause of chronic liver disorder worldwide, whereby affecting around one third of the global population. This clinical condition may evolve into Metabolic Dysfunction-Associated Steatohepatitis (MASH), fibrosis, cirrhosis and hepatocellular carcinoma (HCC), in a predisposed subgroup of patients. The complex pathogenesis of MASLD is severely entangled with obesity, dyslipidemia and type 2 diabetes (T2D), so far so nutritional and lifestyle recommendations may be crucial in influencing the risk of HCC and modifying its prognosis. However, the causative association between HCC onset and the presence of metabolic comorbidities is not completely clarified. Therefore, the present review aimed to summarize the main literature findings that correlate the presence of inherited or acquired hyperlipidemia and metabolic risk factors with the increased predisposition towards liver cancer in MASLD patients. Here, we gathered the evidence underlining the relationship between circulating/hepatic lipids, cardiovascular events, metabolic comorbidities and hepatocarcinogenesis. In addition, we reported previous studies supporting the impact of triglyceride and/or cholesterol accumulation in generating aberrancies in the intracellular membranes of organelles, oxidative stress, ATP depletion and hepatocyte degeneration, influencing the risk of HCC and its response to therapeutic approaches. Finally, our pursuit was to emphasize the link between HCC and the presence of cardiometabolic abnormalities in our large cohort of histologically-characterized patients affected by MASLD (n=1538), of whom 86 had MASLD-HCC by including unpublished data.
A method for reducing torque ripple of switched reluctance motor based on partitioned TSF
Authors: Hui Cai , Yanjie Han , Yinbin Pan , Tao Zean
Published: May 2024

In this paper, a new torque sharing function control strategy is proposed to reduce the torque ripple. The traditional torque ripple methods, such as exponential and linear torque allocation strategies, the torque generation capacity of each phase and the power limitation of the power converter is not taken into account, in this paper, the communication region is divided into three intervals by establishing a new partitioning standard. According to the re-established reference function of torque generation, the torque deviation caused by phase current tracking error is compensated according to the torque generation capacity. Both optimization of torque ripple suppression and copper loss minimization are taken into consideration in this paper. To verify the validity and performances of the proposed TSF methods, simulations and experiments have been implemented in a 12/8 structure Switched Reluctance Motor prototype. This method can be applied to other switched reluctance motors with different topologies. Result shows lower current tracking error and better performance of torque ripple minimization compared with the conventional two-interval compensation method.
Geographic variation in genetic composition, sexual communication and mating compatibility of the False Codling Moth, Thaumatotibia leucotreta for optimisation of area-wide control
Authors: Aigbedion-Atalor Pascal , Heiduk Annemarie , Upfold Jennifer , Shuttleworth Adam , Moore Sean , Hill Martin , Coombes Candice
Published: May 2024

Intraspecific variation in sex pheromones is a driver of reproductive isolation and speciation in insects. The False Codling Moth (FCM) Thaumatotibia leucotreta (Lepidoptera: Tortricidae) is a quarantine pest endemic to sub-Saharan Africa (SSA). The currently available precision control measures for FCM use female sex pheromone components to lure males into traps. However, the existing data on the composition of the female sex pheromone, especially the isomer ratios of the main pheromone component (E/Z)-8-dodecenyl acetate, are inconsistent for populations in SSA. This inconsistency led to speculation about possible reproductive isolation between geographically separated FCM populations and the potential need for local adjustment of pheromone-based FCM control tools. This, however, requires a comparative evaluation of geographic variation in FCM sexual communication and inter-population mating compatibility. We therefore investigated genetic isolation and mating compatibility between five geographically isolated FCM populations in South Africa and analysed the ratio of (E)- and (Z)-8-dodecenyl acetate in females from these populations. The five studied populations were found to form three genetically distinct groups with high genetic distances between each other. Mating compatibility tests showed that mating is possible across these groups, however, males preferred females of their own population when given choices; without a choice, males successfully mated with and transferred spermatophores to females from all other populations. The ratio of (E)- and (Z)-8-dodecenyl acetate was similar (c. 4:1) across the populations, indicating that this main female pheromone component does not cause the observed intra-population mating preferences. It remains to be investigated if qualitative/quantitative variation in other sex pheromone components influences intra-population recognition in South African FCM, providing a base for the development of regionally-specific lures for area-wide control programmes.
Genetically predicted asthma and the risk of abnormal spermatozoa
Authors: Li Zhichao , Teng Zhihai , Han Zhenwei , Zhang Yanping , Wang Yaxuan
Published: May 2024

Background

Several previous animal and human studies have found a strong association between asthma and spermatozoa quality, but whether these associations are causal or due to bias remains to be elucidated.

Methods

We performed a two-sample Mendelian randomization (MR) analysis to assess the causal effect of genetically predicted asthma on the risk of abnormal spermatozoa. Asthma, childhood-onset asthma (COA), and adult-onset asthma (AOA) (sample sizes ranging from 327,670 to 408,442) were included as the exposures. Genetic information for abnormal spermatozoa was obtained from a genome-wide association study (GWAS) comprising 209,921 participants. In univariable MR (UVMR) analysis, the inverse variance weighted (IVW) method was conducted as the primary method, with the MR Egger and weighted median used as supplementary methods for causal inference. Sensitivity analyses, including the Cochran Q test, Egger intercept test, MR-PRESSO, and leave-one-out analysis, were performed to verify the robustness of the MR results. Multivariable MR (MVMR) was conducted to evaluate the direct causal effects of asthma on abnormal spermatozoa risk.

Results

UVMR detected causal associations between genetically predicted asthma and an increased risk of abnormal spermatozoa (OR: 1.270, 95% CI: 1.045–1.545, p = 0.017). Moreover, we found that AOA (OR: 1.46, 95% CI: 1.051, 2.018, p = 0.024) has positive causal effects on the risk of abnormal spermatozoa rather than COA (p = 0.558). Sensitivity analysis found little evidence of bias in the current study (p > 0.05). MVMR further confirmed that asthma directly affected the risk of abnormal spermatozoa.

Conclusion

Our MR study suggested that genetically predicted asthma could be associated with an increased risk of abnormal spermatozoa, and similar results were obtained in AOA. Further studies are warranted to explain the underlying mechanisms of this association and may provide new avenues for prevention and treatment.
High-throughput sequencing for plant virology diagnostics and its potential in plant health certification
Authors: Maina Solomon , Donovan Nerida J. , Plett Krista , Bogema Daniel , Rodoni Brendan C.
Published: May 2024

High-throughput sequencing (HTS) technologies have revolutionized plant virology through simultaneous detection of mixed viral infections. HTS advances have uncovered and improved understanding of virus biology, ecology, and evolution which is vital for viral disease management. Plant viruses continue to threaten global agricultural productivity and strict quarantine measures are essential to prevent the introduction and spread of virulent viruses around the world. The gradual decrease in HTS operational costs, including improved computational systems and automation through robotics, has facilitated the adoption of this tool for plant diagnostics, including its use in surveillance and quarantine programs. However, the speed of technology advancements and distinct HTS chemistries, laboratory procedures, data management, and bioinformatic analyses have proven challenging. In addition, the lack of viral species reference sequences, compared with the estimated number of distinct viral taxa, makes classification and identification of novel viruses difficult. There is a need for standardized HTS testing, especially within plant health programs. In this review, we consider the application of HTS in plant virology, explore the technical challenges faced and the opportunities for HTS in plant health certification. We propose standards for overcoming current barriers and for ensuring reliable and reproducible results. These efforts will impact global plant health by reducing the risk of introduction and the spread of damaging novel viruses.
Exosomal ROR1 in peritoneal fluid identifies peritoneal disseminated PDAC and is associated with poor survival
Authors: Mittelstädt Anke , Anthuber Anna , David Paul , Podolska Malgorzata , Bénard Alan , Brunner Maximilian , Krautz Christian , Jacobsen Anne , Denz Axel , Weber Klaus , Merkel Susanne , Hackner Danilo , Buniatov Timur , Roßdeutsch Lotta , Klösch Bettina , Swierzy Izabella , Hansen Frederik J. , Strobel Deike , Zopf Yurdagül , Baur Jan-Ole , Van Deun Jan , Immanuel Geppert Carol , Gießl Andreas , Lettmaier Sebastian , Semrau Sabine , Grützmann Robert , Kouhestani Dina , Weber Georg F.
Published: May 2024

Background

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer and peritoneal dissemination is one major cause for this poor prognosis. Exosomes have emerged as promising biomarkers for gastrointestinal cancers and can be found in all kinds of bodily fluids, also in peritoneal fluid (PF). This is a unique sample due to its closeness to gastrointestinal malignancies. The receptor tyrosine kinase-like orphan receptor 1 (ROR1) has been identified as a potential biomarker in human cancers and represents a promising target for an immunotherapy approach, which could be considered for future treatment strategies. Here we prospectively analyzed the exosomal surface protein ROR1 (exo-ROR1) in PF in localized PDAC patients (PER-) on the one hand and peritoneal disseminated tumor stages (PER+) on the other hand followed by the correlation of exo-ROR1 with clinical-pathological parameters.

Methods

Exosomes were isolated from PF and plasma samples of non-cancerous (NC) (n = 15), chronic pancreatitis (CP) (n = 4), localized PDAC (PER-) (n = 18) and peritoneal disseminated PDAC (PER+) (n = 9) patients and the surface protein ROR1 was detected via FACS analysis. Additionally, soluble ROR1 in PF was analyzed. ROR1 expression in tissue was investigated using western blots (WB), qPCR, and immunohistochemistry (IHC). Exosome isolation was proven by Nano Tracking Analysis (NTA), WB, Transmission electron microscopy (TEM), and BCA protein assay. The results were correlated with clinical data and survival analysis was performed.

Results

PDAC (PER+) patients have the highest exo-ROR1 values in PF and can be discriminated from NC (p <0.0001), PDAC (PER-) (p <0.0001), and CP (p = 0.0112). PDAC (PER-) can be discriminated from NC (p = 0.0003). In plasma, exo-ROR1 is not able to distinguish between the groups. While there is no expression of ROR1 in the exocrine pancreatic tissue, PDAC and peritoneal metastasis show expression of ROR1. High exo-ROR1 expression in PF is associated with lower overall survival (p = 0.0482).

Conclusion

With exo-ROR1 in PF we found a promising diagnostic and prognostic biomarker possibly discriminating between NC, PDAC (PER-) and PDAC (PER+) and might shed light on future diagnostic and therapeutic concepts in PDAC.
Exosomes derived from miR-146a-overexpressing fibroblast-like synoviocytes in cartilage degradation and macrophage M1 polarization: a novel protective agent for osteoarthritis?
Authors: Wang Huan , Zhang Yue , Zhang Chengfei , Zhao Yan , Shu Jun , Tang Xuezhang
Published: May 2024

Introduction

Pathological changes in the articular cartilage (AC) and synovium are major manifestations of osteoarthritis (OA) and are strongly associated with pain and functional limitations. Exosome-derived microRNAs (miRNAs) are crucial regulatory factors in intercellular communication and can influence the progression of OA by participating in the degradation of chondrocytes and the phenotypic transformation in the polarization of synovial macrophages. However, the specific relationships and pathways of action of exosomal miRNAs in the pathological progression of OA in both cartilage and synovium remain unclear.

Methods

This study evaluates the effects of fibroblast-like synoviocyte (FLS)-derived exosomes (FLS-Exos), influenced by miR-146a, on AC degradation and synovial macrophage polarization. We investigated the targeted relationship between miR-146a and TRAF6, both in vivo and in vitro, along with the involvement of the NF-κB signaling pathway.

Results

The expression of miR-146a in the synovial exosomes of OA rats was significantly higher than in healthy rats. In vitro, the upregulation of miR-146a reduced chondrocyte apoptosis, whereas its downregulation had the opposite effect. In vivo, exosomes derived from miR-146a-overexpressing FLSs (miR-146a-FLS-Exos) reduced AC injury and chondrocyte apoptosis in OA. Furthermore, synovial proliferation was reduced, and the polarization of synovial macrophages shifted from M1 to M2. Mechanistically, the expression of TRAF6 was inhibited by targeting miR-146a, thereby modulating the Toll-like receptor 4/TRAF6/NF-κB pathway in the innate immune response.

Discussion

These findings suggest that miR-146a, mediated through FLS-Exos, may alleviate OA progression by modulating cartilage degradation and macrophage polarization, implicating the NF-κB pathway in the innate immune response. These insights highlight the therapeutic potential of miR-146a as a protective agent in OA, underscoring the importance of exosomal miRNAs in the pathogenesis and potential treatment of the disease.
CAP2 contributes to Parkinson’s disease diagnosed by neutrophil extracellular trap-related immune activity
Authors: Li Xiaohe , Luo Meiling , Xu Hangrui , Jia Lei , Liang Yanan , Xu Qianxi , Wang Yonghui
Published: May 2024

Introduction

Neutrophil extracellular traps (NETs) constitute a crucial element of the immune system, and dysfunction in immune responses is implicated in the susceptibility and progression of Parkinson's disease (PD). Nevertheless, the mechanism connecting PD and NETs remains unclear. This study aims to uncover potential NETs-related immune biomarkers and elucidate their role in PD pathogenesis.

Methods

Through differential gene analysis of PD and NETs in GSE7621 datasets, we identified two PD subtypes and explored potential biological pathways. Subsequently, using ClusterWGCNA, we pinpointed pertinent genes and developed clinical diagnostic models. We then optimized the chosen model and evaluated its association with immune infiltration. Validation was conducted using the GSE20163 dataset. Screening the single-cell dataset GSE132758 revealed cell populations associated with the identified gene.

Results

Our findings identified XGB as the optimal diagnostic model, with CAP2 identified as a pivotal gene. The risk model effectively predicted overall diagnosis rates, demonstrating a robust correlation between infiltrating immune cells and genes related to the XGB model.

Discussion

In conclusions, we identified PD subtypes and diagnostic genes associated with NETs, highlighting CAP2 as a pivotal gene. These findings have significant implications for understanding potential molecular mechanisms and treatments for PD.
Real-world outcomes of chemotherapy plus immune checkpoint inhibitors versus chemotherapy alone in advanced, unresectable, and recurrent intrahepatic cholangiocarcinoma
Authors: Madzikatire Tinotenda Blessing , Heng Shan , Gu HongYi , Shan YunFeng , Lin EnHua , Banda Joshua , Debora Asta , Madziva Brandon Anotida , Bowa Mutale Jaeste , Mudhuri Munyaradzi Godfrey , Bwalya Canol
Published: May 2024

Background

There are limited treatment options available to improve the prognosis of patients with advanced or metastatic cholangiocarcinoma particularly intrahepatic cholangiocarcinoma (iCCA). This study aimed to evaluate the efficacy and safety of combining chemotherapy plus anti-PD-1/L1 drugs compared to chemotherapy alone in advanced, unresectable, and recurrent intrahepatic cholangiocarcinoma patients.

Methods

Patients with advanced, unresectable, or recurrent iCCA who received chemotherapy combined with PD-1/PD-L1 inhibitors or chemotherapy alone were retrospectively screened and analyzed. The primary outcomes were overall survival (OS) and progression-free survival (PFS). The secondary outcomes were overall response rate (ORR), disease control rate (DCR), and safety.

Results

81 eligible patients were included in the study (chemotherapy plus anti-PD-1/L1 group n=51, and chemotherapy-alone group n=30). The median OS was 11 months for the chemotherapy plus anti-PD-1/L1 group, significantly longer than the 8 months in the chemotherapy-alone group, with a hazard ratio (HR) of 0.53 (95% CI 0.30–0.94, P = 0.008). The median PFS of 7 months in the chemotherapy plus anti-PD-1/L1 group was significantly longer than the 4 months in the chemotherapy-alone group, with HR of 0.48 (95% CI 0.27–0.87); P = 0.002). Similarly, the combined therapy group showed a higher ORR (29.4%) and DCR (78.4%) compared to 13.3% and 73.3% in the chemotherapy-alone group, respectively. More grade 3–4 treatment-related adverse effects were recorded in the chemotherapy plus anti-PD-1/L1 group (66.7%) compared to the chemotherapy-alone group (23.3%), however, they were manageable and tolerable.

Conclusion

Chemotherapy plus anti-PD-1/L1 represents a more effective and tolerable treatment option for advanced, unresectable, and recurrent iCCA patients compared to chemotherapy alone.
Genetically predicted N-methylhydroxyproline levels mediate the association between naive CD8+ T cells and allergic rhinitis: a mediation Mendelian randomization study
Authors: Chen Zhengjie , Suo Ying , Du Xintao , Zhao Xiaoyun
Published: May 2024

Background

Allergic rhinitis (AR), a prevalent chronic inflammatory condition triggered by immunoglobulin E (IgE), involves pivotal roles of immune and metabolic factors in its onset and progression. However, the intricacies and uncertainties in clinical research render current investigations into their interplay somewhat inadequate.

Objective

To elucidate the causal relationships between immune cells, metabolites, and AR, we conducted a mediation Mendelian randomization (MR) analysis.

Methods

Leveraging comprehensive publicly accessible summary-level data from genome-wide association studies (GWAS), this study employed the two-sample MR research method to investigate causal relationships among 731 immune cell phenotypes, 1400 metabolite levels, and AR. Additionally, employing the mediation MR approach, the study analyzed potential mediated effect of metabolites in the relationships between immune cells and AR. Various sensitivity analysis methods were systematically employed to ensure the robustness of the results.

Results

Following false discovery rate (FDR) correction, we identified three immune cell phenotypes as protective factors for AR: Naive CD8br %CD8br (odds ratio (OR): 0.978, 95% CI = 0.966–0.990, P = 4.5×10–4), CD3 on CD39+ activated Treg (OR: 0.947, 95% CI = 0.923–0.972, P = 3×10–5), HVEM on CD45RA- CD4+ (OR: 0.967, 95% CI = 0.948–0.986, P = 4×10–5). Additionally, three metabolite levels were identified as risk factors for AR: N-methylhydroxyproline levels (OR: 1.219, 95% CI = 1.104–1.346, P = 9×10–5), N-acetylneuraminate levels (OR: 1.133, 95% CI = 1.061–1.211, P = 1.7×10–4), 1-stearoyl-2-arachidonoyl-gpc (18:0/20:4) levels (OR: 1.058, 95% CI = 1.029–1.087, P = 5×10–5). Mediation MR analysis indicated a causal relationship between Naive CD8br %CD8br and N-methylhydroxyproline levels, acting as a protective factor (OR: 0.971, 95% CI = 0.950–0.992, P = 8.31×10–3). The mediated effect was -0.00574, accounting for 26.1% of the total effect, with a direct effect of -0.01626. Naive CD8+ T cells exert a protective effect on AR by reducing N-methylhydroxyproline levels.

Conclusion

Our study, delving into genetic information, has substantiated the intricate connection between immune cell phenotypes and metabolite levels with AR. This reveals a potential pathway to prevent the onset of AR, providing guiding directions for future clinical investigations.
Tidal zone effects on the diet composition of leaf-eating crabs in natural mangrove communities: a stable isotope analysis
Authors: Lu Xiaoyan , Gu Xuan , Zhang Lin , Zhang Jinhan , Wang Wenqing , Wang Mao
Published: May 2024

Background

In natural mangrove communities, mangrove species are often distributed zonally. Leaf-eating crabs are one of the most abundant and iconic arboreal brachyurans in mangrove forests, but variation in the composition of crab diets in different mangrove tidal zones is unknown.

Methods

To determine the contributions of mangrove leaves and other organic carbon (C) sources to leaf-eating crab diets, dual stable C and nitrogen (N) isotope signatures (δ13C and 1δ5N) were used in a Bayesian stable isotope mixing model. We conducted experiments at various tidal levels in the Dongzhaigang Bay National Natural Reserve in China. We analyzed δ13C and δ15N of leaf-eating crabs, mangrove leaves, sediment organic matter (SOM), and animal tissues (prey).

Results

The food composition of the dominant crab species, Parasesarma continentale, exhibited significant differences among the four tidal zones. From the margin to the high tide zone, the main food source shifted from predominantly mangrove leaves and SOM to primarily SOM and animal tissues. We observed a significant negative relationship between the C/N ratios of mangrove leaves and the proportion of leaves consumed by leaf-eating crabs. Additionally, as the tidal level increased, the C/N ratio of mangrove leaves also increased, whereas the proportion of leaves consumed by crabs decreased.

Conclusion

Leaf-eating crab diets vary significantly across tidal zones, highlighting the importance of considering tidal zone differentiation when studying consumer diets in mangrove ecosystems.
Long-term annual trawl data show shifts in cephalopod community in the western Barents sea during 18 years
Authors: Golikov Alexey V. , Jørgensen Lis L. , Sabirov Rushan M. , Zakharov Denis V. , Hoving Henk-Jan
Published: May 2024

Climate change is threatening marine ecosystems on a global scale but particularly so in the Arctic. As a result of warming, species are shifting their distributions, altering marine communities and predator-prey interactions. This is known as the Atlantification of the Arctic. Warming may favor short-lived, opportunistic species such as cephalopods, marine mollusks that previously have been hypothesized to be winners in an ocean of change. To detect temporal regional trends in biodiversity, long-term annual surveys in hotspots of climate change are an unparalleled source of data. Here, we use 18 years of annual bottom trawl data (2005–2022) to analyse cephalopods in the western Barents Sea. More specifically, our research goals are to assess temporal trends in cephalopod fauna composition, abundance and biomass, and to relate these trends to climate change in the western Barents Sea. Main changes in cephalopod diversity and distribution occurred in mid-2000s and early 2010s, which corresponds with a period of warming in the Arctic since the late 1990s/early 2000s. Repeated increased occurrence of the boreal-subtropical cephalopods was recorded from 2005–2013 to 2014–2022. Moreover, the abundance of cephalopods in the area (in general and for most taxa) increased from 2005–2013 to 2014–2022. These observations suggest that the cephalopod community of the Barents Sea is subjected to Atlantification since the 2005–2013 period. This corresponds with previously reported evidence of the Atlantification in fishes and benthic invertebrates in the Barents Sea and benthic invertebrates. ‘Typical’ Arctic cephalopod species such as Bathypolypus spp., Gonatus fabricii and Rossia spp., however, are still much more abundant in the western Barents Sea compared to the deep-sea and the boreal-subtropical species. We also found indirect indications for body-size reduction in Bathypolypus spp. from 2005–2013 to 2014–2022. Overall, the temporal trends in the Barents Sea cephalopod fauna provide evidence for changing marine communities in the Arctic.
USNet: underwater image superpixel segmentation via multi-scale water-net
Authors: Wang Chuhong , Duan Wenli , Luan Chengche , Liang Junyan , Shen Lengyu , Li Hua
Published: May 2024

Underwater images commonly suffer from a variety of quality degradations, such as color casts, low contrast, blurring details, and limited visibility. Existing superpixel segmentation algorithms face challenges in achieving superior performance when directly applied to underwater images with quality degradation. In this paper, to alleviate the limitations of superpixel segmentation when applied to underwater scenes, we propose the first underwater superpixel segmentation network (USNet), specifically designed according to the intrinsic characteristics of underwater images. Considering the quality degradation, we propose a multi-scale water-net module (MWM) aimed at enhancing the quality of underwater images before superpixel segmentation. The degradation-aware attention (DA) mechanism is then created and incorporated into MWM to solve light scattering and absorption, which can decrease object visibility and cause blurred edges. By effectively directing the network to prioritize locations that exhibit a considerable decrease in quality, this method enhances the visibility of those specific areas. Additionally, we extract the deep spatial features using the coordinate attention method. Finally, these features are fused with the shallow spatial information using the dynamic spatiality embedding module to embed comprehensive spatial features. Training and testing were conducted on the SUIM dataset, the underwater change detection dataset, and UIEB dataset. Experimental results show that our method achieves the best scores in terms of achievable segmentation accuracy, undersegmentation error, and boundary recall evaluation metrics compared to other methods. Both quantitative and qualitative evaluations demonstrate that our method can handle complicated underwater scenes and outperform existing state-of-the-art segmentation methods.
Swelling pressure of phyllite residual soil during saturation
Authors: Zhang Qin , Qin Liuyang , Tang Hao , Yan Mengqiu , Ji Jingru , Yang Wenzhou , Yan Rongtao
Published: May 2024

Phyllite residual soil is a typical regional soil formed from the weathering of phyllite rock formations, characterized by poor engineering properties. The swelling pressure could pose a threat to roadbed stability and other geological engineering disasters during the rainy season. Therefore, studying the swelling pressure of phyllite residual soil is critical for ensuring the sustainable development of both human society and the natural environment. In this study, a series of swelling pressure tests were conducted on the phyllite residual soil to determine its swelling pressure, and nuclear magnetic resonance (NMR) test was applied to assess the evolution of soil fabric in both the initial unsaturated state and saturated state. The results indicate that the swelling rate of phyllite residual soil is negatively correlated with the initial water content and positively correlates with the dry density. The denser or drier the phyllite residual soil is in its initial state, the higher the equilibrium swelling pressure will be. The analysis of T2 distribution curves reveals that during the wetting process in phyllite residual soil, water fills micropores prior to macropores until water fills up all pores.
A nomogram for predicting survival in patients with gastrointestinal stromal tumor: a study based on the surveillance, epidemiology, and end results database
Authors: Li Xiaxi , You Lijuan , Liu Qinghua , He Wenhua , Cui Xiaobing , Gong Wei
Published: May 2024

Purpose

The objective of this investigation was to construct and validate a nomogram for prognosticating cancer-specific survival (CSS) in patients afflicted with gastrointestinal stromal tumor (GIST) at 3-, 5-, and 8-years post-diagnosis.

Methods

Data pertaining to patients diagnosed with GIST were acquired from the Surveillance, Epidemiology, and End Results (SEER) database. Through random selection, a training cohort (70%) and a validation cohort (30%) were established from the patient population. Employing a backward stepwise Cox regression model, independent prognostic factors were identified. Subsequently, these factors were incorporated into the nomogram to forecast CSS rates at 3-, 5-, and 8-years following diagnosis. The nomogram’s performance was assessed using indicators such as the consistency index (C-index), the area under the time-dependent receiver operating characteristic curve (AUC), the net reclassification improvement (NRI), the integrated discrimination improvement (IDI), calibration curves, and decision-curve analysis (DCA).

Results

This investigation encompassed a cohort of 3,062 GIST patients. By analyzing the Cox regression model within the training cohort, nine prognostic factors were identified: age, sex, race, marital status, AJCC (American Joint Committee on Cancer) stage, surgical status, chemotherapy status, radiation status, and income status. The nomogram was subsequently developed and subjected to both internal and external validation. The nomogram exhibited favorable discrimination abilities, as evidenced by notably high C-indices and AUC values. Calibration curves confirmed the nomogram’s reliability. Moreover, the nomogram outperformed the AJCC model, as demonstrated by enhanced NRI and IDI values. The DCA curves validated the clinical utility of the nomogram.

Conclusion

The present study has successfully constructed and validated the initial nomogram for predicting prognosis in GIST patients. The nomogram’s performance and practicality suggest its potential utility in clinical settings. Nevertheless, further external validation is warranted.
Diagnosis of hemidiaphragm paralysis: refine ultrasound criteria
Authors: Boussuges Alain , Fourdrain Alex , Leone Marc , Brioude Geoffrey , Menard Amelie , Zieleskiewicz Laurent , Delliaux Stephane , Gouitaa Marion , Dutau Hervé , Brégeon Fabienne
Published: May 2024

Background

Ultrasound has demonstrated its interest in the analysis of diaphragm function in patients with respiratory failure. The criteria used to diagnose hemidiaphragm paralysis are not well defined.

Methods

The aim of this observational retrospective study was to describe the ultrasound findings in 103 patients with diaphragm paralysis, previously diagnosed by conventional methods after various circumstances such as trauma or surgery. The ultrasound study included the recording of excursions of both diaphragmatic domes and the measurement of inspiratory thickening.

Results

On paralyzed hemidiaphragm, thickening was less than 20% in all patients during deep inspiration. Thinning was recorded in 53% of cases. In some cases, the recording of the thickening could be difficult. The study of motion during voluntary sniffing reported a paradoxical excursion in all but one patient. During quiet breathing, an absence of movement or a paradoxical displacement was observed. During deep inspiration, a paradoxical motion at the beginning of inspiration followed by a reestablishment of movement in the cranio-caudal direction was seen in 82% of cases. In some patients, there was a lack of movement followed, after an average delay of 0.4 s, by a cranio-caudal excursion. Finally, in 4 patients no displacement was recorded. Evidence of hyperactivity (increased inspiratory thickening and excursion) of contralateral non-paralyzed hemidiaphragm was observed.

Conclusion

To accurately detect hemidiaphragm paralysis, it would be interesting to combine the ultrasound study of diaphragm excursion and thickening. The different profiles reported by our study must be known to avoid misinterpretation.
Irisin alleviated the reproductive endocrinal disorders of PCOS mice accompanied by changes in gut microbiota and metabolomic characteristics
Authors: Yang Meina , Deng Hongxia , Zhou Siyu , Lu Danhua , Shen Xiaoyang , Huang Lu , Chen Yan , Xu Liangzhi
Published: May 2024

Introduction

Folliculogenesis and oligo/anovulation are common pathophysiological characteristics in polycystic ovary syndrome (PCOS) patients, and it is also accompanied by gut microbiota dysbiosis. It is known that physical activity has beneficial effects on improving metabolism and promoting ovulation and menstrual cycle disorder in PCOS patients, and it can also modulate the gastrointestinal microbiota in human beings. However, the mechanism remains vague. Irisin, a novel myokine, plays a positive role in the mediating effects of physical activity.

Methods

Mice were randomly divided into the control group, PCOS group and PCOS+irisin group. PCOS model was induced by dehydroepiandrosterone (DHEA) and high-fat diet (HFD). The PCOS+irisin group was given irisin 400μg/kg intraperitoneal injection every other day for 21 days. The serum sex hormones were measured by radioimmunoassay. Hematoxylin and Eosin (H&E) Staining and immunohistochemistry (IHC) were conducted on ovarian tissue. The feces microbiota and metabolomic characteristics were collected by 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC–MS).

Results

In this study, we demonstrated that irisin supplementation alleviated reproductive endocrine disorders of PCOS mice, including estrous cycle disturbance, ovarian polycystic degeneration, and hyperandrogenemia. Irisin also improved the PCOS follicles dysplasia and ovulation disorders, while it had no significant effect on the quality of oocytes. Moreover, irisin could mitigate the decreased bacteria of Odoribacter and the increased bacteria of Eisenbergiella and Dubosiella in PCOS mice model. Moreover, irisin could alleviate the increased fecal metabolites: Methallenestril and PS (22:5(4Z,7Z,10Z,13Z,16Z)/ LTE4).

Conclusion

These results suggest that irisin may alleviate the status of PCOS mice model by modulating androgen-induced gut microbiota dysbiosis and fecal metabolites. Hence, our study provided evidence that irisin may be considered as a promising strategy for the treatment of PCOS.
Widely targeted metabolomics analysis of Sanghuangporus vaninii mycelia and fruiting bodies at different harvest stages
Authors: Qi Yue , Guo Xiao-Ying , Xu Xin-Yue , Hou Jian-Xuan , Liu Shi-Lai , Guo Hong-Bo , Xu Ai-Guo , Yang Rui-Heng , Yu Xiao-Dan
Published: May 2024

Sanghuangprous vaninii is a medicinal macrofungus cultivated extensively in China. Both the mycelia and fruiting bodies of S. vaninii have remarkable therapeutic properties, but it remains unclear whether the mycelia may serve as a substitute for the fruiting bodies. Furthermore, S. vaninii is a perennial fungus with therapeutic components that vary significantly depending on the growing year of the fruiting bodies. Hence, it is critical to select an appropriate harvest stage for S. vaninii fruiting bodies for a specific purpose. With the aid of Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), metabolomics based on ultra-high performance liquid chromatography coupled to triple quadrupole mass spectrometry (UHPLC-QQQ-MS) was used to preliminarily determine 81 key active metabolites and 157 active pharmaceutical metabolites in S. vaninii responsible for resistance to the six major diseases. To evaluate the substitutability of the mycelia and fruiting bodies of S. vaninii and to select an appropriate harvest stage for the fruiting bodies of S. vaninii, we analyzed the metabolite differences, especially active metabolite differences, among the mycelia and fruiting bodies during three different harvest stages (1-year-old, 2-year-old, and 3-year-old). Moreover, we also determined the most prominent and crucial metabolites in each sample of S. vaninii. These results suggested that the mycelia show promise as a substitute for the fruiting bodies of S. vaninii and that extending the growth year does not necessarily lead to higher accumulation levels of active metabolites in the S. vaninii fruiting bodies. This study provided a theoretical basis for developing and using S. vaninii.
Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture
Authors: Chen Mingfei , Acharya Shwetha M. , Yee Mon Oo , Cabugao Kristine Grace M. , Chakraborty Romy
Published: May 2024

The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.
Cross-species transmission of a novel bisegmented orfanplasmovirus in the phytopathogenic fungus Exserohilum rostratum
Authors: Jia Jichun , Nan Linjie , Song Zehao , Chen Xu , Xia Jinsheng , Cheng Lihong , Zhang Baojun , Mu Fan
Published: May 2024

Mycoviruses have been found in various fungal species across different taxonomic groups, while no viruses have been reported yet in the fungus Exserohilum rostratum. In this study, a novel orfanplasmovirus, namely Exserohilum rostratum orfanplasmovirus 1 (ErOrfV1), was identified in the Exserohilum rostratum strain JZ1 from maize leaf. The complete genome of ErOrfV1 consists of two positive single-stranded RNA segments, encoding an RNA-dependent RNA polymerase and a hypothetical protein with unknown function, respectively. Phylogenetic analysis revealed that ErOrfV1 clusters with other orfanplasmoviruses, forming a distinct phyletic clade. A new family, Orfanplasmoviridae, is proposed to encompass this newly discovered ErOrfV1 and its associated orfanplasmoviruses. ErOrfV1 exhibits effective vertical transmission through conidia, as evidenced by its 100% presence in over 200 single conidium isolates. Moreover, it can be horizontally transmitted to Exserohilum turcicum. Additionally, the infection of ErOrfV1 is cryptic in E. turcicum because there were no significant differences in mycelial growth rate and colony morphology between ErOrfV1-infected and ErOrfV1-free strains. This study represents the inaugural report of a mycovirus in E. rostratum, as well as the first documentation of the biological and transmission characteristics of orfanplasmovirus. These discoveries significantly contribute to our understanding of orfanplasmovirus.
Bioinformatics study of the potential therapeutic effects of ginsenoside Rh3 in reversing insulin resistance
Authors: Wang Yayun , Wu Dongming , Wang Yongxin , Sun Jingwen , Wang Xiaona , Huang Yanqin , Sun Mingliang
Published: May 2024

Background

In recent years, the incidence of insulin resistance is increasing, and it can cause a variety of Metabolic syndrome. Ginsenosides have been clinically proven to improve fat metabolism and reduce insulin resistance, but their components and mechanism of action are still unclear.

Objective

Ginsenoside, a bioactive compound derived from ginseng, exhibits significant potential in treating obesity, diabetes, and metabolic disorders. Despite evidence supporting its efficacy in ameliorating insulin resistance (IR) in obesity, the specific bioactive components and underlying mechanisms remain obscure. In this study, we endeavored to elucidate the potential molecular targets and pathways influenced by ginsenoside Rh3 (GRh3) to ameliorate IR in liver tissue. We employed a comprehensive approach that integrates system pharmacology and bioinformatics analysis.

Materials and methods

Our methodology involved the identification of candidate targets for GRh3 and the profiling of differentially expressed genes (DEGs) related to IR in individuals with insulin resistance. The coalescence of candidate targets and DEGs facilitated the construction of a “GRh3-targets-disease” network for each tissue type, ultimately yielding 38 shared target genes. Subsequently, we conducted pathway enrichment analysis, established protein-protein interaction (PPI) networks, and identified hub targets among the GRh3 targets and IR-related DEGs. Additionally, we conducted animal experiments to corroborate the role of these hub targets in the context of GRh3.

Results

Our investigation identified a total of 38 overlapping targets as potential candidates. Notably, our analysis revealed crucial hub targets such as EGFR, SRC, ESR1, MAPK1, and CASP3, alongside implicated signaling pathways, including those related to insulin resistance, the FoxO signaling pathway, the PPAR signaling pathway, and the IL-17 signaling pathway. This study establishes a robust foundation for the mechanisms underlying GRh3’s efficacy in mitigating IR. Furthermore, these results suggest that GRh3 may serve as a representative compound within the ginsenoside family.

Conclusion

This study elucidates the potential molecular targets and associated pathways through which GRh3 ameliorates IR, showcasing its multifaceted nature, spanning multiple targets, pathways, and mechanisms. These findings establish a robust foundation for subsequent experimental inquiries and clinical applications.
A complementary approach for neocortical cytoarchitecture inspection with cellular resolution imaging at whole brain scale
Authors: Liu Zhixiang , Feng Zhao , Liu Guangcai , Li Anan , Gong Hui , Yang Xiaoquan , Li Xiangning
Published: May 2024

Cytoarchitecture, the organization of cells within organs and tissues, serves as a crucial anatomical foundation for the delineation of various regions. It enables the segmentation of the cortex into distinct areas with unique structural and functional characteristics. While traditional 2D atlases have focused on cytoarchitectonic mapping of cortical regions through individual sections, the intricate cortical gyri and sulci demands a 3D perspective for unambiguous interpretation. In this study, we employed fluorescent micro-optical sectioning tomography to acquire architectural datasets of the entire macaque brain at a resolution of 0.65 μm × 0.65 μm × 3 μm. With these volumetric data, the cortical laminar textures were remarkably presented in appropriate view planes. Additionally, we established a stereo coordinate system to represent the cytoarchitectonic information as surface-based tomograms. Utilizing these cytoarchitectonic features, we were able to three-dimensionally parcel the macaque cortex into multiple regions exhibiting contrasting architectural patterns. The whole-brain analysis was also conducted on mice that clearly revealed the presence of barrel cortex and reflected biological reasonability of this method. Leveraging these high-resolution continuous datasets, our method offers a robust tool for exploring the organizational logic and pathological mechanisms of the brain’s 3D anatomical structure.