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Wholly defined ex vivo expansion conditions for biliary tree stem cell (BTSC) organoids were established, consisting of a defined proliferative medium (DPM) used in combination with soft hyaluronan hydrogels. The DPM consisted of commercially available Kubota's Medium (KM), to which a set of small molecules, particular paracrine signals, and heparan sulfate (HS) were added. The small molecules used were DNA methyltransferase inhibitor (RG108), TGF- β Type I receptor inhibitor (A83-01), adenylate cyclase activator (Forskolin), and L-type Ca2+ channel agonist (Bay K8644). A key paracrine signal proved to be R-spondin 1 (RSPO1), a secreted protein that activates Wnts. Soluble hyaluronans, 0.05 % sodium hyaluronate, were used with DPM to expand monolayer cultures. Expansion of organoids was achieved by using DPM in combination with embedding organoids in Matrigel that was replaced with a defined thiol-hyaluronan triggered with PEGDA to form a hydrogel with a rheology [G*] of less than 100 Pa. The combination is called the BTSC-Expansion-Glycogel-System (BEX-gel system) for expanding BTSCs as a monolayer or as organoids. The BTSC organoids were expanded more than 3000-fold ex vivo in the BEX-gel system within 70 days while maintaining phenotypic traits indicative of stem/progenitors. Stem-cell-patch grafting of expanded BTSC organoids was performed on the livers of Fah-/- mice with tyrosinemia and resulted in the rescue of the mice and restoration of their normal liver functions. The BEX-gel system for BTSC organoid expansion provides a strategy to generate sufficient numbers of organoids for the therapeutic treatments of liver diseases.

Fibrolamellar carcinoma (FLC) is a rare but fatal cancer that occurs primarily in young people. There are currently no known effective treatments, although several promising treatments appear to be in development. Genetic studies have confirmed that almost all FLC tumors have a fusion protein marker (DNAJB1-PRKACA) encoded by a fusion gene (DNAJB1-PRKACA); It is currently accepted as a diagnostic criterion for FLCs. Several research teams have established patient-derived xenograft (PDX) FLC models using immunocompromised animals as hosts and patient tissue samples (tumors or ascites) as primary sources for PDX-derived organoids. These FLC organoids are composed of FLC epithelia, endothelial progenitor cells, and stellate cells. CRISPR/Cas9 was used as a gene editing technique to modify mature hepatocytes to obtain ex vivo FLC-like cells expressing the fusion gene and/or other mutated genes associated with FLCs. Although these models simulate some but not all FLC features. Drug screening using these models has not proven effective in identifying clinically useful treatments. Genetic studies comparing FLCs to normal maturing endodermal cell lineages have shown that FLCs share genetic signatures not with hepatocytes, but with subpopulations of biliary tree stem cells (BTSCs), hepato/pancreatic stem/progenitor cells that consistently reside in peribiliary glands (PBGs) located in the biliary tree and are sources of stem cells for the formation and postnatal regeneration of the liver and pancreas. Therefore, it is expected that models of BTSCs, instead of hepatocytes may prove more useful. In this review, we summarize the status of the various FLC models and their features, applications, and limitations. They provide opportunities to understand the cause and characteristics of this deadly disease and are models from which effective treatments can be identified.

Camellia oleifera is a kind of high-quality oil supply species. Its seeds contain rich unsaturated fatty acids and antioxidant active ingredients, which is a kind of high-quality edible oil. In this study, we used bioinformatics methods to decipher a hexaploid Camellia oil tree’s mitochondrial (mt) genome based on second-generation sequencing data. A 709,596 bp circular map of C. oleifera mt genome was found for the first time. And 74 genes were annotated in the whole genome. Mt genomes of C. oleifera and three Theaceae species had regions with high similarity, including gene composition and gene sequence. At the same time, five conserved gene pairs were found in 20 species. In all of the mt genomes, most of nad genes existed in tandem pairs. In addition, the species classification result, which, according to the gene differences in tandem with nad5 genes, was consistent with the phylogenetic tree. These initial results provide a valuable basis for the further researches of Camellia oleifera and a reference for the systematic evolution of plant mt genomes.

The direct feeding value of distillers grains is low due to the presence of higher cellulose, lignin and anti-nutritional factors such as mannan and xylan. In this study, complex enzymes and probiotic flora based on “probiotic enzyme synergy” technology were used to produce fermented distillers grains. The optimal substrate ratio, moisture content, fermentation time and temperature were determined. Subsequently, scale-up experiments were conducted to determine the performance of fermented feed. The results showed that multi-probiotic (Lactobacillus casei, Bacillus subtilis, Saccharomyces cerevisiae, and Aspergillus oryzae) cooperated with complex enzymes (glucanase, mannanase, xylanase) showed excellent fermentation effect, crude protein, trichloroacetic acid soluble protein and fat increased by 31.25, 36.68, and 49.11% respectively, while crude fiber, acidic fiber and neutral fiber decreased by 34.24, 26.91, and 33.20%, respectively. The anti-nutritional factors mannan and arabinoxylan were reduced by 26.96 and 40.87%, respectively. Lactic acid, acetic acid, and propionic acid in the fermented organic acids increased by 240.93, 76.77, and 89.47%, respectively. Butyric acid increased significantly from scratch, and the mycotoxin degradation effect was not significant. This study provides a potential approach for high-value utilization of distillers grains.

This study focused on developing an effective cell wall-breaking method for Phaffia rhodozyma, followed by utilizing subcritical fluid extraction to isolate, extract, and concentrate astaxanthin from the complex fermentation products of P. rhodozyma. A comprehensive comparison of seven distinct methods for disrupting cell walls, including dimethyl sulfoxide treatment, lactic acid treatment, sodium hydroxide treatment, β-glucanase enzymatic digestion, β-mannanase enzymatic digestion, and a combined enzymatic treatment involving both β-mannanase and β-glucanase was conducted. The results identified the lactic acid method as the most effective in disrupting the cell walls of P. rhodozyma. The software, Design Expert, was used in the process of extracting astaxanthin from cell lysates using a subcritical extraction method. Through fitting analysis and response surface optimization analysis by Design Expert, the optimal extraction conditions were determined as follows: an extraction temperature of 41 °C, extraction frequency of two times, and extraction time of 46 min. These parameters facilitated the efficient extraction, concentration, and enrichment of astaxanthin from P. rhodozyma, resulting in an astaxanthin concentration of 540.00 mg/L. This result can establish the foundation for its high-value applications.

Spacetime wormholes are evidently an essential component of the construction of a time machine. Within the context of general relativity, such objects require, for their formation, exotic matter—matter that violates at least one of the standard energy conditions. Here, we explore the possibility that higher-curvature gravity theories might permit the construction of a wormhole without any matter at all. In particular, we consider the simplest form of a generalized quasi topological theory in four spacetime dimensions, known as Einsteinian Cubic Gravity. This theory has a number of promising features that make it an interesting phenomenological competitor to general relativity, including having non-hairy generalizations of the Schwarzschild black hole and linearized equations of second order around maximally symmetric backgrounds. By matching series solutions near the horizon and at large distances, we find evidence that strong asymptotically AdS wormhole solutions can be constructed, with strong curvature effects ensuring that the wormhole throat can exist.

We evaluate here the quantum gravity partition function that counts the dimension of the Hilbert space of a simply connected spatial region of a fixed proper volume in the context of Lovelock gravity, generalizing the results for Einstein gravity. It is found that there are sphere saddle metrics for a partition function at a fixed spatial volume in Lovelock theory. Those stationary points take exactly the same forms as in Einstein gravity. The logarithm of Z corresponding to a zero effective cosmological constant indicates that the Bekenstein–Hawking entropy of the boundary area and that corresponding to a positive effective cosmological constant points to the Wald entropy of the boundary area. We also show the existence of zeroth-order phase transitions between different vacua, a phenomenon distinct from Einstein gravity.

Camellia oleifera is a woody edible oil species with late self-incompatibility characteristics. Previous transcriptome analysis showed that genes involved in jasmonic acid signal transduction were significantly different in self-and cross-pollinated pistils of Camellia oleifera. To investigate the relationship between jasmonate signal and self-incompatibility by studying the core genes of jasmonate signal transduction. The results showed that exogenous JA and MeJA at 1.0 mM significantly inhibited pollen tube germination and pollen tube elongation. and JA up-regulated CoCOI1, CoJAZ1, and CoMYC, the core genes of jasmonate signal transduction. Subcellular localization indicated that CoCOI1 and CoJAZ1 were located in the nucleus and CoMYC2 in the endoplasmic reticulum. The three genes exhibited tissue-specific expression pattern. CoCOI1 was significantly expressed in pollen, CoJAZ1 was significantly expressed in ovary, CoMYC2 was significantly expressed in filaments, but not in pollen. Furthermore, CoJAZ1 and CoMYC2 were highly expressing at 24 h in self-pollinated styles. These results suggested that JA signal transduction of C. oleifera was involved in the process of self-pollination, and thus in the process of plant defense. When pollen tubes grew slowly in the style, ovary may receive JA signal, which initiates the molecular mechanism of inhibiting the growth of self-pollinating pollen tubes.

IntroductionSelf-incompatibility (SI) is an important strategy for plants to maintain abundant variation to enhance their adaptability to the environment. Camellia oleifera is one of the most important woody oil plants and is widely cultivated in China. Late acting self-incompatibility (LSI) in C. oleifera results in a relatively poor fruit yield in the natural state, and understanding of the LSI mechanism remains limited. MethodsTo better understand the molecular expression and gene coexpression network in the LSI reaction in C. oleifera, we conducted self- and cross-pollination experiments at two different flower bud developmental stages (3–4 d before flowering and 1 d before flowering), and cytological observation, fruit setting rate (FSR) investigation and RNA-Seq analysis were performed to investigate the mechanism of the male −female interaction and identify hub genes responsible for the LSI in C. oleifera.ResultsBased on the 21 ovary transcriptomes, a total of 7669 DEGs were identified after filtering out low-expression genes. Weighted gene coexpression network analysis (WGCNA) divided the DEGs into 15 modules. Genes in the blue module (1163 genes) were positively correlated with FSR, and genes in the pink module (339 genes) were negatively correlated with FSR. KEGG analysis indicated that flavonoid biosynthesis, plant MAPK signaling pathways, ubiquitin-mediated proteolysis, and plant-pathogen interaction were the crucial pathways for the LSI reaction. Fifty four transcription factors (TFs) were obtained in the two key modules, and WRKY and MYB were potentially involved in the LSI reaction in C. oleifera. Network establishment indicated that genes encoding G-type lectin S-receptor-like serine (lecRLK), isoflavone 3’-hydroxylase-like (CYP81Q32), cytochrome P450 87A3-like (CYP87A3), and probable calcium-binding protein (CML41) were the hub genes that positively responded to the LSI reaction. The other DEGs inside the two modules, including protein RALF-like 10 (RALF), F-box and pectin acetylesterase (MTERF5), might also play vital roles in the LSI reaction in C. oleifera.DiscussionOverall, our study provides a meaningful resource for gene network studies of the LSI reaction process and subsequent analyses of pollen−pistil interactions and TF roles in the LSI reaction, and it also provides new insights for exploring the mechanisms of the LSI response.

Visfatin, a multifunctional adipocytokine, is particularly important in the regulation of apoptosis and inflammation through an unidentified mechanism. Clarifying the control mechanisms of visfatin on inflammation and apoptosis in RAW264.7 cells and mice immunological organs was the goal of the current investigation. In order to create a pathophysiological model, the RAW264.7 cells were stimulated with 200 ng/mL visfatin and 20 μg/mL lipopolysaccharide (LPS), either separately or combined. The effects of exogenous visfatin on inflammation and apoptosis in RAW264.7 cells were investigated by flow cytometry assay, RNA-seq analysis and fluorescence quantitative PCR. According to the findings, exogenous visfatin exhibits dual effects on inflammation by modulating the expression of IL-1α, TNFRSF1B, and LIF as well as taking part in various signaling pathways, including the MAPK and Rap1 signaling pathways. By controlling the expression levels of Bcl2l1, Bcl2a1a, and Fas and primarily participating in the PI3K/AKT signaling pathway and Hippo signaling pathway, exogenous visfatin can inhibit apoptosis in RAW264.7 cells. The visfatin inhibitor FK866 was used to further confirm the effects of visfatin on inflammation and apoptosis in mice immune organs. Subsequently, mice spleen and thymus were collected. It is interesting to note that in LPS-treated mice, suppression of endogenous visfatin might worsen the immune system’s inflammatory response and even result in rapid mortality. Additionally, endogenous visfatin promotes the apoptosis in mice immune organs by regulating the expression levels of Bcl2l1, Fas, Caspase 3, Bcl2a1a, and Bax. Together, these results imply that visfatin is a multifaceted molecule that regulates inflammation and apoptosis in RAW264.7 cells and mice immunological organs by taking part in a variety of biological processes and regulating the amounts of associated cytokines expression. Our findings offer additional understandings of how visfatin affects apoptosis and inflammation.

The Camellia oil tree (Camellia oleifera Abel.) is an important nonwood forest species in China, and the majority of its cultivars are late-acting self-incompatibility (LSI) types. Although several studies have examined the mechanism of LSI, the process is quite complicated and unclear. In this study, pollen tube growth and fruit setting of two Camellia oil tree cultivars Huashuo (HS) and Huajin (HJ) were investigated after non and self-pollination, and transcriptomic analysis of the ovaries was performed 48 h after self-pollination to identify the potential genes implicated in the LSI of Camellia oil trees. The results showed that the fruit set of HS was significantly higher than that of HJ after self-pollination. Transcriptomic analysis revealed that plant hormone signal transduction, the phosphatidylinositol signaling system, ATP-binding cassette (ABC) transporters, reactive oxygen species (ROS) metabolism, and Ca2+ signaling were mainly contributed in the LSI of reaction of Camellia oil tree. Moreover, nine RNase T2 genes were identified from the transcriptome analysis, which also showed that CoRNase7 participated in the self-incompatibility reaction in HS. Based on phylogenetic analysis, CoRNase6 was closely related to S-RNase from coffee, and CoRNase7 and CoRNase8 were closely related to S-RNase from Camellia sinensis. The 9 RNase T2 genes successfully produced proteins in prokaryotes. Subcellular localization indicated that CoRNase1 and CoRNase5 were cytoplasmic proteins, while CoRNase7 was a plasma membrane protein. These results screened the main metabolic pathways closely related to LSI in Camellia oil tree, and SI signal transduction might be regulated by a large molecular regulatory network. The discovery of T2 RNases provided evidence that Camellia oil tree might be under RNase-based gametophytic self-incompatibility.

Background Caseinolytic protease P (ClpP), which is located on the inner mitochondrial membrane, degrades mitochondrial proteins damaged by oxidative stress. The role of ClpP varies among tumor types. However, the expression pattern and biological functions of ClpP in breast cancer (BC) have not yet been investigated. Methods The Cancer Genome Atlas (TCGA) and Kaplan Meier-plotter database were used to analyze the expression level of ClpP in BC tissues, relationships with clinicopathological characteristics, and the influence on the prognosis of BC. Protein and mRNA expression levels of ClpP in BC cell lines and tissues were detected by quantitative real-time PCR, western blot and immunohistochemical (IHC) analyses. The colony formation assay, transwell assay and flow cytometric analysis were performed to assess various functions of ClpP. Western blot analysis was also conducted to determine the mechanism of ClpP. Results ClpP expression was markedly increased in BC cells and tissues. High expression of ClpP was significantly correlated with the T stage, estrogen receptor (ER) expression, and poor recurrence-free survival (RFS) in TCGA and Kaplan Meier-plotter database. ClpP silencing significantly inhibited proliferation, migration, invasion, and promoted apoptosis of BC cells, which resulted in suppression of the Src/PI3K/Akt signaling pathway. The gain-of-function assay confirmed partial these results.

Titanium alloy chemical milling wastewater contains a significant amount of ethylene glycol monobutyl ether (EGBE), which is toxic and difficult to be degraded by microorganisms, and the emission will lead to severe environmental pollution. To solve this problem, the electrocatalytic oxidation method was employed to remove EGBE in the wastewater, in which a porous Ti4O7/Ti electrode were prepared and employed as the anode, while stainless steel acted as the cathode. The effects of current density, interelectrode distance, and stirring mode on the COD removal rate were also investigated. Results show that the COD of the wastewater significantly decreases from 12410 to 15 mg L−1 after 16 h of electrolysis at 10 mA cm−2 and electrode spacing of 1.0 cm as well as aeration stirring at 100 mL min−1. Moreover, pilot-plant scale testing reveals that the COD decreasing from 11980 to 183 mg L−1 after 24 h of electrolysis. Consequently, the utilization of porous Ti4O7/Ti electrode as anode in the electrocatalytic oxidation method presents significant potential in removal of EGBE in aviation industry wastewater.

Abstract Alkaline hydrogen evolution reaction (HER) for scalable hydrogen production largely hinges on addressing the sluggish bubble‐involved kinetics on the traditional Ni‐based electrode, especially for ampere‐level current densities and beyond. Herein, 3D‐printed Ni‐based sulfide (3DPNS) electrodes with varying scaffolds are designed and fabricated. In situ observations at microscopic levels demonstrate that the bubble escape velocity increases with the number of hole sides (HS) in the scaffolds. Subsequently, we conduct multiphysics field simulations to illustrate that as the hole shapes transition from square, pentagon, and hexagon to circle, where a noticeable reduction in the bubble‐attached HS length and the pressure balance time around the bubbles results in a decrease in bubble size and an acceleration in the rate of bubble escape. Ultimately, the 3DPNS electrode with circular hole configurations exhibits the most favorable HER performance with an overpotential of 297 mV at the current density of up to 1000 mA cm−2 for 120 h. The present study highlights a scalable and effective electrode scaffold design that promotes low‐cost and low‐energy green hydrogen production through the ampere‐level alkaline HER.

BackgroundThe accurate diagnosis of thyroid nodules with indeterminate cytology, particularly in the atypia of undetermined significance (AUS) category, remains challenging. This study aims to predict the risk of malignancy in AUS nodules by comparing two machine learning (ML) and three conventional logistic regression (LR) models.MethodsA retrospective study on 356 AUS nodules in 342 individuals from 6728 patients who underwent thyroid surgery in 2021. All the clinical, ultrasonographic, and molecular data were collected and randomly separated into training and validation cohorts at a ratio of 7: 3. ML (random forest and XGBoost) and LR (lasso regression, best subset selection, and backward stepwise regression) models were constructed and evaluated using area under the curve (AUC), calibration, and clinical utility metrics.ResultsApproximately 90% (321/356) of the AUS nodules were malignant, predominantly papillary thyroid carcinoma with 68.6% BRAF V600E mutations. The final LR prediction model based on backward stepwise regression exhibited superior discrimination with AUC values of 0.83 (95% CI: 0.73-0.92) and 0.80 (95% CI: 0.67-0.94) in training and validation, respectively. Well calibration, and clinical utility were also confirmed. The ML models showed moderate performance. A nomogram was developed on the final LR model.ConclusionsThe LR model developed using the backward stepwise regression, outperformed ML models in predicting malignancy in AUS thyroid nodules. The corresponding nomogram based on this model provides a valuable and practical tool for personalized risk assessment, potentially reducing unnecessary surgeries and enhancing clinical decision-making.

BackgroundMigraine risk factors are associated with migraine susceptibility, yet their mechanisms are unclear. Evidence suggests a role for inflammatory proteins and immune cells in migraine pathogenesis. This study aimed to examine the inflammo-immune association between eight migraine risk factors and the disorder.MethodsThis study utilized inverse variance weighted (IVW) method and colocalization analysis to explore potential causal relationships between eight migraine risk factors, migraine, 731 immune cells, and 91 circulating inflammatory proteins. Mediation Mendelian randomization (MR) was further used to confirm the mediating role of circulating inflammatory proteins and immune cells between the eight migraine risk factors and migraine.ResultsMigraine risk factors are linked to 276 immune cells and inflammatory proteins, with cigarettes smoked per day strongly co-localized with CD33-HLA DR+ cells. Despite no co-localization, 23 immune cells/inflammatory proteins relate to migraine. Depression, all anxiety disorders, and sleep apnea are correlated with migraine, and all anxiety disorders are supported by strong co-localization evidence. However, the mediating effect of inflammatory proteins and immune cells between eight migraine risk factors and migraine has not been confirmed.ConclusionWe elucidate the potential causal relationships between eight migraine risk factors, migraine, immune cells, and inflammatory proteins, enhancing our understanding of the molecular etiology of migraine pathogenesis from an inflammatory-immune perspective.

Abstract Background Inflammatory bowel disease (IBD) has been associated with lipid-lowering drugs in observational studies. Drug-target Mendelian randomization (MR) was utilized in this study to examine the causal relationship between lipid-lowering drugs and incidence of IBD, aiming to identify new preventive uses for the drugs. Methods We identified instrumental variables for three classes of lipid-lowering drugs: HMGCR inhibitors, PCSK9 inhibitors, and NPC1L1 inhibitors, using data from the Global Lipids Genetics Consortium. Summary statistics of IBD were obtained from UK Inflammatory Bowel Disease Genetics. The summary-data-based MR (SMR) and the inverse-variance weighted (IVW) MR were used for analysis. Sensitivity analyses were performed by conventional MR methods. Results The SMR analysis showed no significant genetic association between increased gene expression of HMGCR, PCSK9, and NPC1L1 and IBD, Crohn’s disease (CD) and ulcerative colitis (UC). According to IVW-MR analysis, increased HMGCR expression is associated with a reduced risk of IBD (OR = 0.73, 95% confidence interval (CI) 0.59–0.90, P = 0.003) and CD (OR = 0.75, 95% CI 0.57–0.97, P = 0.03), but not with UC. Additionally, increased NPC1L1 gene expression was associated with elevated risk of IBD (OR = 1.60, 95% CI 1.07–2.40, P = 0.023), but not with CD and UC. However, no significant causal relationships were found between PCSK9 gene expression and IBD, CD, and UC. The sensitivity analysis demonstrated no evidence of heterogeneity or pleiotropy among the reported results. Conclusions The heightened expression of genetic variations in HMGCR inhibitor targets could potentially reduce the risk of IBD and CD, while genetic variation in the expression of NPC1L1 targets was positively associated with IBD.

Aims: The formation of anti-drug antibodies (ADAs) during anti-tumor necrosis factor (anti-TNF) therapy is reported to lead to reducing serum drug levels, which may bring about a loss of response to treatment. Previous research has suggested an association between specific antibiotic classes and ADA formation during anti-TNF therapy. However, there are few studies specifically examining this association in Chinese inflammatory bowel disease (IBD) patients. Therefore, our study aimed to evaluate the possible effect of antibiotic use on ADA formation to anti-TNF therapy in Chinese patients with IBD.Methods: A total of 166 patients with IBD, including 149 with Crohn’s disease (CD) and 17 with ulcerative colitis (UC), were included in this retrospective analysis. These patients were initially treated with anti-TNF therapy (infliximab or adalimumab) after January 2018 and reviewed with available ADA levels before October 2023. After univariable analysis of all the variables, a multivariate Cox proportional hazards model was used to assess the association between antibiotic use and ADA development.Results: Among 166 IBD patients treated with infliximab (108/166, 65.1%) or adalimumab (58/166, 34.9%), 31 patients (18.7%) were measured as positive ADA levels. Cox proportional hazard model demonstrated an increased risk of ADA formation in IBD patients who used β-lactam-β-lactamase inhibitor combinations (BL-BLIs) (HR = 5.143, 95%CI 1.136–23.270, p = 0.033), or nitroimidazoles (HR = 4.635, 95%CI 1.641–13.089, p = 0.004) during 12 months before the ADA test. On the contrary, a reduced risk was noted in patients treated with fluoroquinolones (HR = 0.258, 95% CI 0.072–0.924, p = 0.037). Moreover, the median serum infliximab or adalimumab concentration in patients with positive ADA levels was significantly lower than that in patients with negative ADA levels (infliximab: 0.30 vs. 1.85 μg/mL, p < 0.0001; adalimumab: 0.45 vs. 7.55 μg/mL, p = 0.0121).Conclusion: ADA development is associated with various antibiotic classes. BL-BLIs and nitroimidazoles might increase the risk of ADA formation during anti-TNF therapy in Chinese IBD patients, while the treatment with fluoroquinolones could probably reduce such risk. There were certain limitations in the retrospective analysis of the study, therefore, the results are just for reference, and other studies are needed to further confirm our findings.

Abstract Background To study the dentoskeletal characteristics and the degree of compensations in skeletal Class I adults with unilateral posterior crossbite (UPCB). Methods A sample of 40 adults was chosen for this cross-sectional study. 20 skeletal Class I adults with UPCB (mean age: 22.20 ± 2.88 years), were compared to 20 skeletal Class I adults with normal occlusion (mean age: 27.56 ± 5.76 years). The respective dentoskeletal measurements were made on cross-sectional images from cone-beam computed tomography scans. Results Skeletally, both groups showed significant differences (P 0.05). For dental variables on the second premolar and first molar, the UPCB group showed greater linear and angular differences when compared to the control group (P

Background: The BRAFV600E mutation is a valuable indicator for thyroid cancer diagnosis. This study aimed to develop a deep convolutional neural network (DCNN) model based on ultrasound images to predict the BRAFV600E mutation status of thyroid nodules. Methods: The ultrasound images were obtained from four hospitals between January 2017 and January 2022. We trained and validated the DCNN model based on the primary set from center 1 (979 images, 528 patients). The DCNN network consists of Conv block, Downsample block, Gaussian error linear unit, Global Average Polling, and Full Connected. The predictive performance of this model was evaluated by using areas under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity in four independent test sets from center 1 to center 4 (531 images, 282 patients). Heatmaps were used to visualize the most predictive regions of each image. Specimens obtained through fine‐needle aspiration or surgery were used to detect the BRAFV600E mutation. Results: The DCNN model achieved encouraging predictive performance by fivefold cross‐validation (AUC 0.95) in the primary set. This performance was further confirmed in the independent internal test set (AUC 0.93) and three independent external test sets (AUC 0.84–0.88). The deep learning score revealed significant differences between BRAFV600E‐mutant and BRAFV600E‐wild‐type groups (all test sets p < .001). The heatmaps visualized the most predictive region located inside or alongside the thyroid nodules. Conclusion: A DCNN model with encouraging predictive performance was developed based on ultrasound images to predict the BRAFV600E mutation status of thyroid nodules.

Abstract Background Ubiquitylation is an important post-translational modification of proteins that not only plays a central role in cellular coding, but is also closely associated with the development of a variety of diseases. The specific selection of substrate by ligase E3 is the key in ubiquitylation. As various high-throughput analytical techniques continue to be applied to the study of ubiquitylation, a large amount of ubiquitylation site data, and records of E3-substrate interactions continue to be generated. Biomedical literature is an important vehicle for information on E3-substrate interactions in ubiquitylation and related new discoveries, as well as an important channel for researchers to obtain such up to date data. The continuous explosion of ubiquitylation related literature poses a great challenge to researchers in acquiring and analyzing the information. Therefore, automatic annotation of these E3-substrate interaction sentences from the available literature is urgently needed. Results In this research, we proposed a model based on representation and attention mechanism based deep learning methods, to automatic annotate E3-substrate interaction sentences in biomedical literature. Focusing on the sentences with E3 protein inside, we applied several natural language processing methods and a Long Short-Term Memory (LSTM)-based deep learning classifier to train the model. Experimental results had proved the effectiveness of our proposed model. And also, the proposed attention mechanism deep learning method outperforms other statistical machine learning methods. We also created a manual corpus of E3-substrate interaction sentences, in which the E3 proteins and substrate proteins are also labeled, in order to construct our model. The corpus and model proposed by our research are definitely able to be very useful and valuable resource for advancement of ubiquitylation-related research. Conclusion Having the entire manual corpus of E3-substrate interaction sentences readily available in electronic form will greatly facilitate subsequent text mining and machine learning analyses. Automatic annotating ubiquitylation sentences stating E3 ligase-substrate interaction is significantly benefited from semantic representation and deep learning. The model enables rapid information accessing and can assist in further screening of key ubiquitylation ligase substrates for in-depth studies.

Monoclonal immunoglobulin produced by clonal plasma cells is the main cause in multiple myeloma and monoclonal gammopathy of renal significance. Because of the complicated purification method and the low stoichiometry of purified protein and glycans, site-specific N-glycosylation characterization for monoclonal immunoglobulin is still challenging. To profile the site-specific N-glycosylation of monoclonal immunoglobulins is of great interest. Therefore, in this study, we presented an integrated workflow for micro monoclonal IgA and IgG purification from patients with multiple myeloma in the HYDRASYS system, in-agarose-gel digestion, LC-MS/MS analysis without intact N-glycopeptide enrichment, and compared the identification performance of different mass spectrometry dissociation methods (EThcD-sceHCD, sceHCD, EThcD and sceHCD-pd-ETD). The results showed that EThcD-sceHCD was a better choice for site-specific N-glycosylation characterization of micro in-agarose-gel immunoglobulins (~2 μg) because it can cover more unique intact N-glycopeptides (37 and 50 intact N-glycopeptides from IgA1 and IgG2, respectively) and provide more high-quality spectra than sceHCD, EThcD and sceHCD-pd-ETD. We demonstrated the benefits of the alternative strategy in site-specific N-glycosylation characterizing micro monoclonal immunoglobulins obtained from bands separated by electrophoresis. This work could promote the development of clinical N-glycoproteomics and related immunology.

Abstract Background Lymphangioleiomyomatosis (LAM) is a rare, low-grade multisystem neoplastic disease. Most LAM patients are at a high risk of losing lung function at an accelerated rate and developing progressive dyspnea. Recently, several studies have reported their experience with pharmacological treatments for LAM. Therefore, we conducted a systematic review and meta-analysis to assess the efficacy and safety of these therapies. Methods PubMed (Medline), EMBASE, Cochrane Library, Web of Science and EBSCO Host were searched (until March 31, 2019) for eligible prospective studies regarding LAM patients treated with pharmacological treatments. Random effect models were used for quantitative analysis. Results Fourteen prospective studies regarding five pharmacological treatments (including sirolimus, everolimus, doxycycline, triptorelin, and a combination therapy of sirolimus and hydroxychloroquine) were enrolled in our systematic review, and ten of them were used for the meta-analysis. Seven prospective studies reported that sirolimus was effective at improving or stabilizing lung function and alleviating renal angiomyolipoma (AML) in LAM patients. Subsequent quantitative analyses showed that during sirolimus treatment, the pooled values of lung function and 6-min walk distance (6MWD) were not significantly changed (P > 0.05), with the pooled response rate of AML being 0.62 (95% confidence intervals [CIs]: 0.43 to 0.82, I 2 = 65%). Regarding everolimus, three prospective studies reported similar effects to those of sirolimus with regard to preserving lung function and reducing AMLs. The meta-analysis showed that the changes in lung function during everolimus treatment were not statistically significant (P > 0.05), while the pooled response rate of AML was 0.78 (95% CI: 0.68 to 0.88, I 2 = 8%). Neither the qualitative nor the quantitative results confirmed the benefits of doxycycline or triptorelin treatment, and the effects of the combination therapy were unclear in LAM patients. Most of the adverse events during pharmacological treatments were low or moderate grade and tolerable. Conclusions Overall, sirolimus and everolimus were recommended for the treatment of LAM because they could stabilize lung function and alleviate renal AML. Doxycycline and triptorelin were not recommended for the treatment of LAM because no beneficial outcomes were consistently observed. The efficacy and safety of combination therapy remain to be further explored.

Human spermatozoa proteomics exposed to some physical, biological or chemical stressors is being explored. However, there is a lack of optimized sample preparation methods to achieve in-depth protein coverage for sperm cells. Meanwhile, it is not clear whether antibiotics can regulate proteins to affect sperm quality. Here, we systematically compared a total of six different protein extraction methods based the combination of three commonly used lysis buffers and physical lysis strategies. The urea buffer combined with ultrasonication (UA-ultrasonication) produced the highest protein extraction rate, leading to the deepest coverage of human sperm proteome (5685 protein groups) from healthy human sperm samples. Since the antibiotics, amoxicillin and clarithromycin, have been widely used against H. pylori infection, we conduct a longitudinal study of sperm proteome via data-independent acquisition tandem mass spectrometry (DIA-MS/MS) on an infected patient during on and off therapy with these two drugs. The semen examination and morphological analysis were performed combined with proteomics analysis. Our results indicated that antibiotics may cause an increase in the sperm concentration and the rate of malformed sperm and disrupt proteome expression in sperm. This work provides an optimized extraction method to characterize the in-depth human sperm proteome and to extend its clinical applications.