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Glycosylation is one of the most significant and abundant posttranslational modifications in mammalian cells. It mediates a wide range of biofunctions, including cell adhesion, cell communication, immune cell trafficking, and protein stability. Also, aberrant glycosylation has been associated with various diseases such as diabetes, Alzheimer's disease, inflammation, immune deficiencies, congenital disorders, and cancers. The alterations in the distributions of glycan and glycopeptide isomers are involved in the development and progression of several human diseases. However, the microheterogeneity of glycosylation brings a great challenge to glycomic and glycoproteomic analysis, including the characterization of isomers. Over several decades, different methods and approaches have been developed to facilitate the characterization of glycan and glycopeptide isomers. Mass spectrometry (MS) has been a powerful tool utilized for glycomic and glycoproteomic isomeric analysis due to its high sensitivity and rich structural information using different fragmentation techniques. However, a comprehensive characterization of glycan and glycopeptide isomers remains a challenge when utilizing MS alone. Therefore, various separation methods, including liquid chromatography, capillary electrophoresis, and ion mobility, were developed to resolve glycan and glycopeptide isomers before MS. These separation techniques were coupled to MS for a better identification and quantitation of glycan and glycopeptide isomers. Additionally, bioinformatic tools are essential for the automated processing of glycan and glycopeptide isomeric data to facilitate isomeric studies in biological cohorts. Here in this review, we discuss commonly employed MS‐based techniques, separation hyphenated MS methods, and software, facilitating the separation, identification, and quantitation of glycan and glycopeptide isomers. [ABSTRACT FROM AUTHOR]

Green food is well-known for its health benefits, environmental-friendliness, and safety. Current recommender systems used by e-commerce websites usually recommend products based on products' popularity or customers' ratings. However, users' reviews could be more representative of consumers' preferences. In addition, users' review time is not utilized. To reduce the recommendation bias, this study proposes a hybrid recommendation algorithm based on green food reviews and review time. The proposed algorithm combines a content-based recommendation algorithm with a user-based collaborative filtering approach, where affective values of reviews replace ratings and a time impact factor is considered. With the two classical evaluation indices of F1 and Mean Absolute Error (MAE), the experiments show that considering both reviews' sentiments and dynamic changes of individuals' preferences could improve recommendation effectiveness over three other algorithms, which provides a new reference direction for improving existing recommender systems on green food. [ABSTRACT FROM AUTHOR]

Aiming to reduce the gap between in vitro and in vivo environment, a complex culture medium, Plasmax, was introduced recently, which includes nutrients and metabolites with concentrations normally found in human plasma. Herein, to study the influence of this medium on cellular behaviors, we utilized Plasmax to cultivate two cancer cell lines, including one breast cancer cell line, MDA-MB-231BR, and one brain cancer cell line, CRL-1620. Cancer cells were harvested and prepared for transcriptomics and proteomics analyses to assess the discrepancies caused by the different nutritional environments of Plasmax and two commercial media: DMEM, and EMEM. Total RNAs of cells were extracted using mammalian total RNA extract kits and analyzed by next-generation RNA sequencing; proteomics analyses were performed using LC-MS/MS. Gene oncology and pathway analysis were employed to study the affected functions. The cellular invasion and cell death were inhibited in MDA-MB-231BR cell line when cultured in Plasmax compared to DMEM and EMEM, whereas the invasion, migration and protein synthesis of CRL-1620 cell line were activated in Plasmax in relative to both commercial media. The expression changes of some proteins were more significant compared to their corresponding transcripts, indicating that Plasmax has more influence upon regulatory processes of proteins after translation. This work provides complementary information to the original study of Plasmax, aiming to facilitate the selection of appropriate media for in vitro cancer cell studies. [ABSTRACT FROM AUTHOR]

Purpose: To investigate the utility of histogram analysis of zoomed EPI diffusion-weighted imaging (DWI) for predicting the perineural invasion (PNI) status of rectal cancer (RC). Methods: This prospective study evaluated 94 patients diagnosed with histopathologically confirmed RC between July 2020 and July 2021. Patients underwent preoperative rectal magnetic resonance imaging (MRI) examinations, including the zoomed EPI DWI sequence. Ten whole-tumor histogram parameters of each patient were derived from zoomed EPI DWI. Reproducibility was evaluated according to the intra-class correlation coefficient (ICC). The association of the clinico-radiological and histogram features with PNI status was assessed using univariable analysis for trend and multivariable logistic regression analysis with β value calculation. Receiver operating characteristic (ROC) curve analysis was conducted to assess the diagnostic performance. Results: Forty-two patients exhibited positive PNI. The inter- and intraobserver agreements were excellent for the histogram parameters (all ICCs > 0.80). The maximum (p = 0.001), energy (p = 0.021), entropy (p = 0.021), kurtosis (p < 0.001), and skewness (p < 0.001) were significantly higher in the positive PNI group than in the negative PNI group. Multivariable analysis showed that higher MRI T stage [β = 2.154, 95% confidence interval (CI) 0.932–3.688; p = 0.002] and skewness (β = 0.779, 95% CI 0.255–1.382; p = 0.006) were associated with positive PNI. The model combining skewness and MRI T stage had an area under the ROC curve of 0.811 (95% CI 0.724–0.899) for predicting PNI status. Conclusion: Histogram parameters in zoomed EPI DWI can help predict the PNI status in RC. [ABSTRACT FROM AUTHOR]

In the pathogenesis of osteoarthritis, various signaling pathways may influence the bone joint through a common terminal pathway, thereby contributing to the pathological remodeling of the joint. Semaphorins (SEMAs) are cell-surface proteins actively involved in and primarily responsible for regulating chondrocyte function in the pathophysiological process of osteoarthritis (OA). The significance of the SEMA family in OA is increasingly acknowledged as pivotal. This review aims to summarize the mechanisms through which different members of the SEMA family impact various structures within joints. The findings indicate that SEMA3A and SEMA4D are particularly relevant to OA, as they participate in cartilage injury, subchondral bone remodeling, or synovitis. Additionally, other elements such as SEMA4A and SEMA5A may also contribute to the onset and progression of OA by affecting different components of the bone and joint. The mentioned mechanisms demonstrate the indispensable role of SEMA family members in OA, although the detailed mechanisms still require further exploration. [ABSTRACT FROM AUTHOR]

A complex physiological culture medium (Plasmax) was introduced recently, composed of nutrients and metabolites at concentrations normally found in human plasma to mimic the in vivo environment for cell line cultivation. As glycosylation has been proved to be involved in cancer development, it is necessary to investigate the glycan expression changes in media with different nutrients. In this study, a breast cancer cell line, MDA-MB-231BR, and a brain cancer cell line, CRL-1620, were cultivated in Plasmax and commercial media to reveal cell line glycosylation discrepancies prompted by nutritional environments. Glycomics analyses of cell lines were performed using LC-MS/MS. The expressions of multiple fucosylated N-glycans, such as HexNAc4Hex3DeoxyHex1 and HexNAc5Hex3DeoxyHex1, derived from both cell lines exhibited a significant increase in Plasmax. Among the O-glycans, significant differences were also observed. Both cell lines cultivated in EMEM had the lowest amounts of O-glycans expressed. The original work described the development of Plasmax, which improves colony formation, and resulted in transcriptomic and metabolomic alterations of cancer cell lines, while our results indicate that Plasmax can significantly impact protein glycosylation. This study also provides information to guide the selection of media for in vitro cancer cell glycomics studies. [ABSTRACT FROM AUTHOR]

Retention time is the most common and widely used criterion to report the separation of glycans using Liquid Chromatography (LC), but it varies widely across different columns, instruments and laboratories. This variation is problematic when inter-laboratory data is compared. Furthermore, it influences reproducibility and hampers efficient data interpretation. In our endeavor to overcome this variance, we propose the use of the Glucose Unit Index (GUI) on C18 and PGC column-based separation of reduced and permethylated glycans. GUI has previously been utilized for retention time normalization of native and labeled glycans. We evaluated this method with reduced and permethylated glycans derived from model glycoproteins fetuin and ribonuclease B (RNase B), and then implemented it to human blood serum to generate C18 and PGC column-based isomeric glycan libraries. GUI values for glycan compositions were calculated with respect to the glucose units derived from dextrin, which was employed as an elution standard. The GUI values were validated on three different LC systems (UltiMate 3000 Nano UHPLC systems) in two laboratories to ensure the reliability and reproducibility of the method. Applicability on real samples was demonstrated using human breast cancer cell lines. A total of 116 permethylated N-glycans separated on a C18 column and 134 glycans separated on a PGC column were compiled in a library. Overall, the established GUI method and the demonstration of reproducible inter- and intra-laboratory GUI values would aid the future development of automated glycan and isomeric glycan identification methods. [ABSTRACT FROM AUTHOR]

Motor imagery (MI) requires subjects to visualize the requested motor behaviors, which involves a large-scale network that spans multiple brain areas. The corresponding cortical activity reflected on the scalp is characterized by event-related desynchronization (ERD) and then by event-related synchronization (ERS). However, the network mechanisms that account for the dynamic information processing of MI during the ERD and ERS periods remain unknown. Here, we combined ERD/ERS analysis with the dynamic networks in different MI stages (i.e. motor preparation, ERD and ERS) to probe the dynamic processing of MI information. Our results show that specific dynamic network structures correspond to the ERD/ERS evolution patterns. Specifically, ERD mainly shows the contralateral networks, while ERS has the symmetric networks. Moreover, different dynamic network patterns are also revealed between the two types of MIs, in which the left-hand MIs exhibit a relatively less sustained contralateral network, which may be the network mechanism that accounts for the bilateral ERD/ERS observed for the left-hand MIs. Similar to the network topologies, the three MI stages also appear to be characterized by different network properties. The above findings all demonstrate that different MI stages that involve specific brain networks for dynamically processing the MI information. [ABSTRACT FROM AUTHOR]

Glycomics continues to be a highly dynamic and interesting research area due to the need to comprehensively understand the biological attributes of glycosylation in many important biological functions such as the immune response, cell development, cell differentiation/adhesion, and host-pathogen interactions. Although matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) has proven to be suitable for glycomic profiling studies, there is a need for improved sensitivity in the detection of native glycans, which ionize inefficiently. In this study, we investigated the efficiencies of graphene nanosheets (GNs) and carbon nanoparticles (CNPs) as MALDI matrices and co-matrices in glycan profiling. Our results indicated an enhancement of signal intensity by several orders of magnitude upon using GNs and CNPs in MALDI analysis of N-glycans derived from a variety of biological samples. Interestingly, increasing the amounts of CNPs and GNs improved not only the signal intensities but also prompted in-source decay (ISD) fragmentations, which produced extensive glycosidic and cross-ring cleavages. Our results indicated that the extent of ISD fragmentation could be modulated by CNP and GN concentrations, to obtain MS2 and pseudo-MS3 spectra. The results for glycan profiling in high salt solutions confirmed high salt-tolerance capacities for both CNPs and GNs. Finally, the results showed that by using CNPs and GNs as co-matrices, DHB crystal formation was more homogeneous which improved shot-to-shot reproducibility and sensitivity.ᅟ [ABSTRACT FROM AUTHOR]

Viral infection heavily relies on host transfer RNA (tRNA) for viral RNA decoding. Counterintuitively, not all tRNA species based on anticodon are matched to all 64-triplet codons during evolution. Life solves this problem by cognate tRNA species via wobbling decoding. We found that 14 out of 64 tRNA genes in humans and the main avian species (chicken and duck) were parallelly missing, including 8 tRNA-A 34 NN and 6 tRNA-G 34 NN species. By analyzing the conservation of key motifs in tRNA genes, we found that box A and B served as intragenic tRNA promoters were evolutionally conserved among human, chicken, and duck. Thus, decoding viral RNA by similar wobbling strategies and tRNA transcripts may be parallelly used by human, chicken, and duck. We envisioned that many basic mechanisms regarding viral RNA decoding were possibly conserved in these hosts and may consequently promote cross-species infection. Transfer RNAs (tRNAs) are essentially required for gene decoding. Despite the universal nature of genetic codon, not all tRNA genes are common to all organisms. Here, we would like to discuss fundamental problems and possible effects arising from the evolutionarily missing and conserved tRNA genes in human, chicken, and duck (Alkatib et al., 2012 ; Ou et al., 2019 ; Rogalski et al., 2008). Among these three organisms, viruses especially the avian influenza virus can crossly infect (Pepin et al., 2010). For multi-host viruses, similar viral RNA decoding strategies may be parallelly used by different hosts. Because viral cross-species infection heavily relies on host tRNAs of different species for viral RNA decoding (Ou et al., 2020 ; van Weringh et al., 2011). We envisioned that many basic mechanisms regarding viral RNA decoding were possibly conserved in these three hosts and may consequently promote cross-species infection. • 8 tRNA-A 34 NN and 6 tRNA-G 34 NN are concurrently missing in human, chicken, and duck. • Box A and B are evolutionally conserved in human, chicken, and duck. • The box A and B in human, chicken, and duck are TGGNNNAG(A)TGG and GGGTTCGANNCC. [ABSTRACT FROM AUTHOR]

Background: Prostate cancer (PC) is the most frequently diagnosed cancer among men worldwide. The poor prognosis of PC is largely due to late diagnosis of the disease when it has progressed to advanced stages marked by androgen-independence. We interrogated proteomic signatures that embody the transition of PC from an androgen-dependent (AD) to an androgen-independent (AI) state. Methods: We have previously established AD and AI murine PC cell lines, PLum-AD and PLum-AI, respectively, which recapitulate primary and progressive PC at phenotypic and subcellular levels. We statistically surveyed global protein expression profiles in these cell lines. Differential profiles were functionally interrogated by pathways and protein–protein interaction network analyses. Results: Protein expression pattern analysis revealed a total of 683 proteins, among which 99 were significantly differentially altered in PLum-AI cells as compared to PLum-AD cells (45 increased and 54 decreased). Principal component analysis (PCA) revealed that the two different cell lines clearly separated apart, indicating a significant proteome expression difference between them. Four of the proteins (vimentin, catalase, EpCAM, and caspase 3) that were differentially expressed in PLum-AI cells compared to PLum-AD cells were subjected to biochemical validation by Western blotting. Biological process gene ontology (GO) analysis of the differentially expressed proteins demonstrated enrichment of biological functions and pathways in PLum-AI cells that are central to PI3 kinase and androgen receptor pathways. Besides, other relevant biological processes that are enriched in PLum-AI cells included cell adhesion and cell migration processes, cell and DNA damage, apoptosis, and cell cycle regulation. Conclusions: Our protein expression analysis of a murine in vitro model of PC progression identified differential protein spots that denote this progression and that comprise high-potential targets for early treatment of PC with a personalized patient-specific approach. Efforts are underway to functionally assess the potential roles of these proteins as therapeutic targets for PC progression. [ABSTRACT FROM AUTHOR]

Breast cancer brain metastasis has been recognized as one of the central issues in breast cancer research. The elucidation of the processes and pathways that mediate this step will provide important clues for a better understanding of breast cancer metastasis. Increasing evidence suggests that aberrant glycosylation patterns greatly contribute to cell invasion and cancer metastasis. Herein, we combined next-generation RNA sequencing with liquid chromatography-tandem mass spectrometry-based proteomic and N-glycomic analysis from five breast cancer cell lines and one brain cancer cell line to investigate the possible mechanisms of breast cancer brain metastasis. The genes/proteins associated with cell movement were highlighted in breast cancer brain metastasis. The integrin signaling pathway and the up-regulation of α-integrin (ITGA2, ITGA3) were associated with the brain metastatic process. 12 glycogenes showed unique expression in 231BR, which could result in an increase of sialylation during brain metastasis. In agreement with the changes of glycogenes, 60 out of 63 N-glycans that were identified exhibited differential expression among cell lines. The correlation between glycogenes and glycans revealed the importance of sialylation and sialylated glycans in breast cancer brain metastasis. Highly sialylated N-glycans, which were up-regulated in brain-seeking cell line 231BR, likely play a role in brain metastasis. [ABSTRACT FROM AUTHOR]

The interaction between influenza A virus (IAV) and host proteins is an important process that greatly influences viral replication and pathogenicity. PB2 protein is a subunit of viral ribonucleoprotein (vRNP) complex playing distinct roles in viral transcription and replication. BAG6 (BCL2-associated athanogene 6) as a multifunctional host protein participates in physiological and pathological processes. Here, we identify BAG6 as a new restriction factor for IAV replication through targeting PB2. For both avian and human influenza viruses, overexpression of BAG6 reduced viral protein expression and virus titers, whereas deletion of BAG6 significantly enhanced virus replication. Moreover, BAG6-knockdown mice developed more severe clinical symptoms and higher viral loads upon IAV infection. Mechanistically, BAG6 restricted IAV transcription and replication by inhibiting the activity of viral RNA-dependent RNA polymerase (RdRp). The co-Immunoprecipitation assays showed BAG6 specifically interacted with the N-terminus of PB2 and competed with PB1 for RdRp complex assembly. The ubiquitination assay indicated that BAG6 promoted PB2 ubiquitination at K189 residue and targeted PB2 for K48-linked ubiquitination degradation. The antiviral effect of BAG6 necessitated its N-terminal region containing a ubiquitin-like (UBL) domain (17-92aa) and a PB2-binding domain (124-186aa), which are synergistically responsible for viral polymerase subunit PB2 degradation and perturbing RdRp complex assembly. These findings unravel a novel antiviral mechanism via the interaction of viral PB2 and host protein BAG6 during avian or human influenza virus infection and highlight a potential application of BAG6 for antiviral drug development. Author summary: Influenza A virus (IAV) is a major public health threat worldwide. The viral polymerase subunit PB2 of IAV is not only responsible for transcription and replication of viral RNA but also acts as a key determinant for host adaptation, making it a key target of host defense system. In this study, we report BAG6 as a novel negative regulator of viral PB2 protein. It interacts with the N-terminus of PB2 and promotes PB2 ubiquitination at the K189 residue, which is highly conserved in all IAV subtypes, resulting in the competitive inhibition of RdRp assembly and the ubiquitination degradation of PB2. These findings emphasize the potent antiviral activity of BAG6 against both avian and human influenza viruses and provide a detailed insight to facilitate antivirals targeting PB2 protein. [ABSTRACT FROM AUTHOR]

Purpose: To develop a nomogram based on preoperative clinical and magnetic resonance imaging (MRI) features for the microvascular invasion (MVI) status in solitary intrahepatic mass-forming cholangiocarcinoma (sIMCC) and to evaluate whether it could predict recurrence-free survival (RFS). Methods: We included 115 cases who experienced MRI examinations for sIMCC with R0 resection. The preoperative clinical and MRI features were extracted. Independent predictors related to MVI+ were evaluated by stepwise multivariate logistic regression, and a nomogram was constructed. A receiver operating characteristic (ROC) curve was used to assess the predictive ability. All patients were classified into high- and low-risk groups of MVI. Then, the correlations of the nomogram with RFS in patents with sIMCC were analyzed by Kaplan–Meier method. Results: The occurrence rate of MVI+ was 38.3% (44/115). The preoperative independent predictors of MVI+ were carbohydrate antigen 19-9 > 37 U/ml, tumor size > 5 cm, and an ill-defined tumor boundary. Integrating these predictors, the nomogram exerted a favorable diagnostic performance with areas under the ROC curve of 0.767 (95% confidence interval [CI] 0.654–0.881) in the development cohort, and 0.760 (95% CI 0.591–0.929) in the validation cohort. In the RFS analysis, significant differences were observed between the high- and low-risk MVI groups (6-month RFS rates: 64.5% vs. 78.8% and 46.7% vs. 82.4% in the development and validation cohorts, respectively) (P < 0.05). Conclusions: A nomogram based on clinical and MRI features is a potential biomarker of MVI and may be a potent method to classify the risk of recurrence in patients with sIMCC. [ABSTRACT FROM AUTHOR]

A heterogeneous, recoverable catalyst of Co(II)−L@nano−SiO2 (where L=N‐(3‐trioxysilyl‐propyl)‐o‐vanillin imine) was synthesized, and it was thoroughly characterized by EA, ICP, FT‐IR, UV‐vis, TGA, XPS and BET techniques. The catalytic performance of Co(II)−L@nano−SiO2 was investigated in cyclohexene(CyH) oxidation under mild conditions with oxygen as the sole oxidant. The results showed that Co(II)−L@nano−SiO2 exhibited better catalytic activity with the CyH conversion of 61 %, and a total selectivity of 55–60 % for the major products (2‐cyclohexen‐1‐one (CyO) and 2‐cyclohexen‐1‐ol (CyOH)), and there was no significant decrease in activity after five times reused. Furthermore, the overoxidation process was performed by epoxidation of CyO and CyOH. The mechanism involved allylic oxidation and overoxidation was confirmed by DFT calculations in the gas phase and the acetonitrile solvent. [ABSTRACT FROM AUTHOR]

Purpose: This study aimed to establish a nomogram based on preoperative magnetic resonance imaging (MRI) features to predict the very early recurrence (VER, less than 6 months) of intrahepatic mass-forming cholangiocarcinoma (IMCC) after R0 resection. Methods: This study enrolled a group of 193 IMCC patients from our institution between March 2010 and January 2022. Patients were allocated into the development cohort (n = 137) and the validation cohort (n = 56), randomly, and the preoperative clinical and MRI features were collected. Univariate and multivariate stepwise logistic regression assessments were adopted to assess predictors of VER. Nomogram was constructed and certificated in the validation cohort. The performance of the prediction nomogram was evaluated by its discrimination, calibration, and clinical utility. The performance of the nomogram was compared with the T stage of the American Joint Committee on Cancer (AJCC) 8th edition staging system. Results: Fifty-three patients (27.5%) experienced VER of the tumor and 140 patients (72.5%) with non-VER, during the follow-up period. After multivariate stepwise logistic regression, number of lesions, diffuse hypoenhancement on arterial phase, necorsis and suspicious lymph nodes were independently associated with VER. The nomogram demonstrated significantly higher area under the curve (AUC) of 0.813 than T stage (AUC = 0.666, P = 0.006) in the development cohort, whereas in the validation cohort, the nomogram showed better discrimination performance, with an AUC of 0.808 than T stage (0.705) with no significantly difference (P = 0.230). Decision curve analysis reflected the clinical net benefit of the nomogram. Conclusion: The nomogram based on preoperative MRI features is a reliable tool to predict VER for patients with IMCC after R0 resection. This nomogram will be helpful to improve survival prediction and individualized treatment. [ABSTRACT FROM AUTHOR]

Food safety is always a global issue, due to the increased dissemination of antimicrobial resistance and food poisoning related to foodborne bacterial pathogens. The purpose of this study was to assess the risk of potential foodborne bacteria of beef and mutton in retail stores. A total of 134 samples were collected from 24 local markets in Beijing, including raw and cooked beef or mutton, as well as samples derived from the corresponding environment and human beings. We obtained 674 isolates, of which Klebsiella spp. and Staphylococcus spp. were the dominant bacterial species in the meat samples and the environmental samples, respectively. Additionally, environmental bacteria are common in samples from different sources. Based on the results of antimicrobial sensitivity testing, resistance to tetracycline (with a resistance rate of 47.40%), amoxicillin + clavulanate (47.13%) and erythromycin (28.03%) were the major resistant phenotypes. According to the whole genome analysis, the extended spectrum beta-lactamase genes harboured by two K. pneumoniae strains isolated from cooked and raw beef were located on mobile elements. The major toxin genes of Bacillus cereus and adhesion- or invasion-related virulence factors were also shared among isolates from different sources. These factors pose potential risks to public health and need attention. [ABSTRACT FROM AUTHOR]

Objectives: This study aimed to investigate whether a deep learning (DL) model based on preoperative MR images of primary tumors can predict lymph node metastasis (LNM) in patients with stage T1–2 rectal cancer. Methods: In this retrospective study, patients with stage T1–2 rectal cancer who underwent preoperative MRI between October 2013 and March 2021 were included and assigned to the training, validation, and test sets. Four two-dimensional and three-dimensional (3D) residual networks (ResNet18, ResNet50, ResNet101, and ResNet152) were trained and tested on T2-weighted images to identify patients with LNM. Three radiologists independently assessed LN status on MRI, and diagnostic outcomes were compared with the DL model. Predictive performance was assessed with AUC and compared using the Delong method. Results: In total, 611 patients were evaluated (444 training, 81 validation, and 86 test). The AUCs of the eight DL models ranged from 0.80 (95% confidence interval [CI]: 0.75, 0.85) to 0.89 (95% CI: 0.85, 0.92) in the training set and from 0.77 (95% CI: 0.62, 0.92) to 0.89 (95% CI: 0.76, 1.00) in the validation set. The ResNet101 model based on 3D network architecture achieved the best performance in predicting LNM in the test set, with an AUC of 0.79 (95% CI: 0.70, 0.89) that was significantly greater than that of the pooled readers (AUC, 0.54 [95% CI: 0.48, 0.60]; p < 0.001). Conclusion: The DL model based on preoperative MR images of primary tumors outperformed radiologists in predicting LNM in patients with stage T1–2 rectal cancer. Key Points: • Deep learning (DL) models with different network frameworks showed different diagnostic performance for predicting lymph node metastasis (LNM) in patients with stage T1–2 rectal cancer. • The ResNet101 model based on 3D network architecture achieved the best performance in predicting LNM in the test set. • The DL model based on preoperative MR images outperformed radiologists in predicting LNM in patients with stage T1–2 rectal cancer. [ABSTRACT FROM AUTHOR]

Purpose: The aim of this retrospective study was to develop and validate a preoperative nomogram for predicting microvascular invasion (MVI) in patients with intrahepatic mass-forming cholangiocarcinoma (IMCC) based on magnetic resonance imaging (MRI). Methods: In this retrospective study, 224 consecutive patients with clinicopathologically confirmed IMCC were enrolled. Patients whose data were collected from February 2010 to December 2020 were randomly divided into the training (131 patients) and internal validation (51 patients) datasets. The data from January 2021 to November 2021 (42 patients) were allocated to the time-independent validation dataset. Univariate and multivariate forward logistic regression analyses were used to identify preoperative MRI features that were significantly related to MVI, which were then used to develop the nomogram. We used the area under the receiver operating characteristic curve (AUC) and calibration curve to evaluate the performance of the nomogram. Results: Interobserver agreement of MRI qualitative features was good to excellent, with κ values of 0.613–0.882. Multivariate analyses indicated that the following variables were independent predictors of MVI: multiple tumours (odds ratio [OR]) = 4.819, 95% confidence interval [CI] 1.562–14.864, P = 0.006), ill-defined margin (OR = 6.922, 95% CI 2.883–16.633, P < 0.001), and carbohydrate antigen 19–9 (CA 19–9) > 37 U/ml (OR = 2.890, 95% CI 1.211–6.897, P = 0.017). A nomogram incorporating these factors was established using well-fitted calibration curves. The nomogram showed good diagnostic efficacy for MVI, with AUC values of 0.838, 0.819, and 0.874 for the training, internal validation, and time-independent validation datasets, respectively. Conclusion: A nomogram constructed using independent factors, namely the presence of multiple tumours, ill-defined margins, and CA 19–9 > 37 U/ml could predict the presence of MVI. This can facilitate personalised therapeutic strategy and clinical management in patients with IMCC. [ABSTRACT FROM AUTHOR]

Glycosylation is known as a critical biological process that can largely affect the properties and the functions of proteins. Glycan isomers have been shown to be involved in a variety of disease progressions. However, the separation and identification of glycan isomers has been a challenge for years due to the microheterogeneity of glycan isomeric structures. Therefore, effective and stable techniques have been investigated over the last few decades to improve isomeric separations of glycans. RPLC has been widely used in biomolecule analysis because of its extraordinary reproducibility and reliability in retention time and separation resolution. However, so far, no studies have achieved high resolution of glycan isomers using this technique. In this study, we focused on further boosting the isomeric separation of permethylated glycans using a 500 mm reversed-phase LC column. To achieve better resolutions on permethylated glycans, different LC conditions were optimized using glycan standards, including core- and branch-fucosylated N-glycan isomers and sialic acid linked isomers, which were both successfully separated. Then, the optimal separation strategy was applied to achieve separations of N- and O-glycan isomers derived from model glycoproteins, including bovine fetuin, ribonuclease B and κ-casein. Baseline separations were observed on multiple sialylated linkage isomers. However, the separation performance of high-mannose isomers needs further improvement. The reproducibility and stability of this long C18 column was also tested by doing run-to-run, day-to-day and month-to-month comparisons of retention times on multiple glycans and the %RSD was found less than 0.92%. Finally, we applied this approach to separate glycan isomers derived from complex biological samples, including blood serum and cell lines, where baseline separations were attained on several isomeric structures. Compared to the separation efficiency of PGC and MGC columns, the RPLC C18 column provides lower resolution but more robust reproducibility, which makes it a good complementary alternative for isomeric separations of glycans. [ABSTRACT FROM AUTHOR]

The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how—at a biomolecular level—mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the leading causes of food-borne illnesses worldwide. To colonize the gastrointestinal tract, S. Typhimurium produces multiple virulence factors that facilitate cellular invasion. Chitinases have been recently emerging as virulence factors for various pathogenic bacterial species, and the S. Typhimurium genome contains two annotated chitinases: STM0018 (chiA) and STM0233. However, the role of these chitinases during S. Typhimurium pathogenesis is unknown. The putative chitinase STM0233 has not been studied previously, and only limited data exists on ChiA. Chitinases typically hydrolyze chitin polymers, which are absent in vertebrates. However, chiA expression was detected in infection models and purified ChiA cleaved carbohydrate subunits present on mammalian surface glycoproteins, indicating a role during pathogenesis. Here, we demonstrate that expression of chiA and STM0233 is upregulated in the mouse gut and that both chitinases facilitate epithelial cell adhesion and invasion. S. Typhimurium lacking both chitinases showed a 70% reduction in invasion of small intestinal epithelial cells in vitro. In a gastroenteritis mouse model, chitinase-deficient S. Typhimurium strains were also significantly attenuated in the invasion of small intestinal tissue. This reduced invasion resulted in significantly delayed S. Typhimurium dissemination to the spleen and the liver, but chitinases were not required for systemic survival. The invasion defect of the chitinase-deficient strain was rescued by the presence of wild-type S. Typhimurium, suggesting that chitinases are secreted. By analyzing N-linked glycans of small intestinal cells, we identified specific N-acetylglucosamine-containing glycans as potential extracellular targets of S. Typhimurium chitinases. This analysis also revealed a differential abundance of Lewis X/A-containing glycans that is likely a result of host cell modulation due to the detection of S. Typhimurium chitinases. Similar glycomic changes elicited by chitinase deficient strains indicate functional redundancy of the chitinases. Overall, our results demonstrate that S. Typhimurium chitinases contribute to intestinal adhesion and invasion through modulation of the host glycome. Author summary: Salmonella Typhimurium infection is one of the leading causes of food-borne illnesses worldwide. In order for S. Typhimurium to effectively cause disease, it has to invade the epithelial cells lining the intestinal tract. This invasion step allows S. Typhimurium to replicate efficiently, causing further tissue damage and inflammation. In susceptible patients, S. Typhimurium can spread past the intestines and infect peripheral organs. It is essential to fully understand the invasion mechanism used by S. Typhimurium to design better treatments for infection. Here, we demonstrate that the two chitinases produced by S. Typhimurium are involved in this invasion process. We show that S. Typhimurium chitinases interact with surface glycans of intestinal epithelial cells and promote adhesion and invasion. Using a mouse infection model, we show that S. Typhimurium chitinases are required for the invasion of the small intestine and enhance the dissemination of S. Typhimurium to other organs. This study reveals an additional mechanism by which S. Typhimurium invades and causes infection. [ABSTRACT FROM AUTHOR]

A stretchable sensor based on NiO-Ni(OH) 2 /SWCNTs/PDMS was developed and applied for the in situ and real-time monitoring of dopamine released from different cells. [Display omitted] • The NiO-Ni(OH) 2 /SWCNTs/PDMS film is mechanically stable and biocompatible. • The film electrode exhibited superior detection performance for dopamine. • The sensor can in situ monitor dopamine release from deformed cells. As the most abundant catecholamine neurotransmitter in the human brain, dopamine directly facilitates intercellular communication and is closely related to multiple functions of the central nervous system. Here, a flexible and stretchable electrochemical sensor based on NiO-Ni(OH) 2 and single-walled carbon nanotubes (SWCNTs) on flexible poly-dimethylsiloxane (PDMS) substrate was fabricated for the sensitive quantification of dopamine released from different cells. The developed NiO-Ni(OH) 2 /SWCNTs/PDMS film exhibited excellent selectivity and sensitivity to dopamine with a wide linear range from 50 nM to 288 μM and a low detection limit of 12 nM (S/N = 3). The prepared sensor is highly biocompatible, where living cells can grow and proliferate directly on the electrode surface with strong adhesion, allowing for the in situ and real-time tracking dopamine secretion from cells. This work indicated that the flexible NiO-Ni(OH) 2 /SWCNTs/PDMS can serve as an effective sensing platform for monitoring cellular signal molecules released from living cells during mechanical deformation. [ABSTRACT FROM AUTHOR]

• Suspicious lymph nodes, AP enhancement patterns, and bile duct dilatation were independent predictors of OS in solitary IMCC patients. • Suspicious lymph nodes, AP enhancement patterns, and necrosis were independent predictors of RFS in solitary IMCC patients. • The nomograms predicted OS and RFS better than the AJCC staging system. • Risk stratification systems based on the nomograms can classify patients into two risk groups. This study aimed to establish two nomograms for predicting overall survival (OS) and recurrence-free survival (RFS) in patients with solitary intrahepatic mass-forming cholangiocarcinoma (IMCC) based on preoperative magnetic resonance imaging (MRI) features. This retrospective study included 120 consecutive patients who were diagnosed with solitary IMCC. Preoperative MRI and clinical features were collected. Based on the univariate and multivariate Cox regression analyses, two nomograms were constructed to predict OS and RFS, respectively. The effective performance of the nomograms was evaluated using concordance index (C-index). The prognostic stratification systems for OS and RFS were developed and used to classify patients into high- and low-risk groups. Suspicious lymph nodes, arterial phase (AP) enhancement patterns, and bile duct dilatation were independent predictors of OS, while suspicious lymph nodes, AP enhancement patterns, and necrosis were independent predictors of RFS. The nomograms achieved the C-index values of 0.705/0.710 for OS and 0.721/0.759 for RFS in the development/validation cohorts, which were significantly higher than those of the T and TNM stages (P < 0.05). Patients were stratified into high- and low-risk groups, the 1-year OS and RFS rates of high-risk patients were poorer than those of patients with low-risk in the development cohort (OS: 93.5% vs 76.3%, P < 0.001; RFS: 74.5% vs 22.4%, P < 0.001). Similar results were observed in the validation cohort. Two nomograms were constructed based on preoperative MRI features in patients with solitary IMCC for predicting the OS and RFS and facilitate further prognostic stratification. [ABSTRACT FROM AUTHOR]

The P300 event-related potential (ERP) varies across individuals, and exploring this variability deepens our knowledge of the event, and scope for its potential applications. Previous studies exploring the P300 have relied on either electroencephalography (EEG) or functional magnetic resonance imaging (fMRI). We applied simultaneous event-related EEG-fMRI to investigate how the network structure is updated from rest to the P300 task so as to guarantee information processing in the oddball task. We first identified 14 widely distributed regions of interest (ROIs) that were task-associated, including the inferior frontal gyrus and the middle frontal gyrus, etc. The task-activated network was found to closely relate to the concurrent P300 amplitude, and moreover, the individuals with optimized resting-state brain architectures experienced the pruning of network architecture, i.e. decreasing connectivity, when the brain switched from rest to P300 task. Our present simultaneous EEG-fMRI study explored the brain reconfigurations governing the variability in P300 across individuals, which provided the possibility to uncover new biomarkers to predict the potential for personalized control of brain-computer interfaces. • Simultaneous EEG-fMRI is used to study P300 variability during the oddball task. • Network reconfiguration helps to uncover the P300 variability. • Low P300 group shows enhanced connectivity deviating from resting state. • The smaller the network updates, the larger the P300 amplitude. [ABSTRACT FROM AUTHOR]

The success of symbioses between cnidarian hosts (e.g., corals and sea anemones) and micro-algal symbionts hinges on the molecular interactions that govern the establishment and maintenance of intracellular mutualisms. As a fundamental component of innate immunity, glycan-lectin interactions impact the onset of marine endosymbioses, but our understanding of the effects of cell surface glycome composition on symbiosis establishment remains limited. In this study, we examined the canonical N-glycan biosynthesis pathway in the genome of the dinoflagellate symbiont Breviolum minutum (family Symbiodiniaceae) and found it to be conserved with the exception of the transferase GlcNAc-TII (MGAT2). Using coupled liquid chromatography-mass spectrometry (LC-MS/MS), we characterized the cell surface N-glycan content of B. minutum, providing the first insight into the molecular composition of surface glycans in dinoflagellates. We then used the biosynthesis inhibitors kifunensine and swainsonine to alter the glycan composition of B. minutum. Successful high-mannose enrichment via kifunensine treatment resulted in a significant decrease in colonization of the model sea anemone Aiptasia (Exaiptasia pallida) by B. minutum. Hybrid glycan enrichment via swainsonine treatment, however, could not be confirmed and did not impact colonization. We conclude that functional Golgi processing of N-glycans is critical for maintaining appropriate cell surface glycan composition and for ensuring colonization success by B. minutum. [ABSTRACT FROM AUTHOR]

Highly sensitive and specific detection and monitoring of trace norepinephrine (NE) in biological fluids and neuronal cell lines is essential for the investigation of pathogenesis of certain neurological diseases. Herein, we constructed a novel electrochemical sensor for real-time monitoring of NE released by PC12 cells based on glassy carbon electrode (GCE) modified with honeycomb-like nickel oxide (NiO)-reduced graphene oxide (RGO) nanocomposite. The synthesized NiO, RGO and the NiO-RGO nanocomposite were characterized using X-ray diffraction spectrogram (XRD), Raman spectroscopy and scanning electron microscopy (SEM). The porous three-dimensional honeycomb-like structure of NiO and high charge transfer kinetics of RGO endowed the nanocomposite with excellent electrocatalytic activity, large surface area and good conductivity. The developed sensor exhibited superior sensitivity and specificity towards NE in a wide linear range from 20 nM to 14 μM and 14 μM–80 μM, with a low detection limit of 5 nM. The performances of the sensor in terms of excellent biocompatibility and high sensitivity allow it to be successfully employed in the tracking of NE release from PC12 cells under the stimulation of K+, providing an effective strategy for the real-time monitoring of cellular NE. An electrochemical sensor based on honeycomb-like NiO-reduced graphene oxide (RGO) nanocomposite was developed and applied for the real-time tracking of norepinephrine in neuronal cells. [Display omitted] • The synthesized NiO-RGO nanocomposite exhibited large surface area, high conductivity and electrocatalytic activity. • The NiO-RGO/GCE possessed a low detection limit for norepinephrine detection with excellent sensitivity. • The sensor was applied for the real-time monitoring of norepinephrine secreted by PC12 cells. [ABSTRACT FROM AUTHOR]

• Constitutive models of adhesives are characterized by viscoelasticity and hyperelasticity. • Problem of flexible AMOLED module impacted by a steel ball adopts the maximum principal strain theory. • Maybe the impact resistance of AMOLED module decreases when the modulus of the film is increased in the structural optimization. • Critical height test of a falling ball can verify the impact resistance of the module. When the flexible active-matrix organic light-emitting diode (AMOLED) module is subjected to external impact, the key display device is easily damaged, so it is necessary to optimize the module structure to improve the impact resistance of the module. The adhesives in the module make the structural optimization of the module extremely complicated. In this paper, the viscoelastic and hyperelastic constitutive models of adhesives are established, and the method of simplifying the simulation model of the impact test is studied. Through the attenuation of the stress wave in the transmission, the reason why the dead pixels appear in the center of the module impacted by the ball is explained. According to the actual result that the area of dark spots does not expand with time, it is inferred that the AMOLED layer is damaged, and the maximum principal strain of that is extracted for analysis. In order to ensure the impact resistance of the module, the thickness of each layer should be increased to a certain extent. Slightly increasing the modulus of the film on the upper side of the AMOLED layer is likely to reduce the impact resistance of the module, whereas greatly increasing the modulus of that can improve the impact resistance of the module. An experimental method for determining the critical height of the falling ball is proposed, and it proves that the simulation theory and the optimization scheme are reasonable. [ABSTRACT FROM AUTHOR]

Pathogenic bacteria evolve multiple strategies to hijack host cells for intracellular survival and persistent infections. Previous studies have revealed the intricate interactions between bacteria and host cells at genetic, biochemical and even single molecular levels. Mechanical interactions and mechanotransduction exert a crucial impact on the behaviors and functions of pathogenic bacteria and host cells, owing to the ubiquitous mechanical microenvironments like extracellular matrix (ECM) stiffness. Nevertheless, it remains unclear whether and how ECM stiffness modulates bacterial infections and the sequential outcome of antibacterial therapy. Here we show that bacteria tend to adhere to and invade epithelial cells located on the regions with relatively high traction forces. ECM stiffness regulates spatial distributions of bacteria during the invasion through arrangements of F-actin cytoskeletons in host cells. Depolymerization of cytoskeletons in the host cells induced by bacterial infection decreases intracellular accumulation of antibiotics, thus preventing the eradication of invaded bacterial pathogens. These findings not only reveal the key regulatory role of ECM stiffness, but suggest that the coordination of cytoskeletons may provide alternative approaches to improve antibiotic therapy against multidrug resistant bacteria in clinic. [ABSTRACT FROM AUTHOR]

The accurate determination of the nonpolar surface area of glycans is vital when utilizing liquid chromatography/mass spectrometry (LC-MS) for structural characterization. A new approach for defining and computing nonpolar surface areas based on continuum solvation models (CS-NPSA) is presented. It is based on the classification of individual surface elements representing the solvent accessible surface used for the description of the polarized charge density elements in the CS models. Each element can be classified as polar or nonpolar according to a threshold value. The summation of the nonpolar elements then results in the NPSA leading to a very fine resolution of this surface. The further advantage of the CS-NPSA approach is the straightforward connection to standard quantum chemical methods and program packages. The method has been analyzed in terms of the contributions of different atoms to the NPSA. The analysis showed that not only atoms normally classified as nonpolar contributed to the NPSA, but at least partially also atoms next to polar atoms or N atoms. By virtue of the construction of the solvent accessible surface, atoms in the inner regions of a molecule can be automatically identified as not contributing to the NPSA. The method has been applied to a variety of examples such as the phenylbutanehydrazide series, model dextrans consisting of glucose units and biantennary glycans. Linear correlation of the CS-NPSA values with retention times obtained from liquid chromatographic separations measurements in the mentioned cases give excellent results and promise for more extended applications on a larger variety of compounds. Image 1 • New method for calculating the nonpolar surface area. • Automatic quantum chemical calculation and great flexibility. • Important application in liquid chromatography-mass spectrometry applications. • Applications in glycomics and glycoproteomics. [ABSTRACT FROM AUTHOR]

• The novel TGR5 agonists were designed and synthesized. • Compounds 19d and 19e showed excellent agonistic activities against hTGR5. • Compounds 19d and 19e exhibited high selectivity against FXR. • Compounds 19d and 19e suppressed the excursion of glucose levels. • Compound 19d could stimulate GLP-1 secretion by activation of TGR5. TGR5 is emerging as an important and promising target for the treatment of diabetes, obesity and other metabolic syndromes. A series of novel 1-benzyl-1 H -imidazole-5-carboxamide derivatives was designed, synthesized and evaluated in vitro and in vivo. The most potent compounds 19d and 19e exhibited excellent agonistic activities against hTGR5, which was superior to those of the reference drugs INT-777 and LCA. In addition, compounds 19d and 19e exhibited good selectivity against FXR and presented significant glucose-lowering effects in vivo. Compound 19d could stimulate GLP-1 secretion by activating of TGR5. [ABSTRACT FROM AUTHOR]