Association analyses between the variants of SNAP25, SV2C and ST3GAL2 and the efficacy of botulinum toxin A in the treatment of the primary Meige syndrome

Objective

Individual differences were observed in the clinical efficacy of Botulinum toxin A (BoNT-A) in the treatment of the primary Meige syndrome. Our study aimed to explore the potential associations between the clinical efficacy of BoNT-A in the treatment of the primary Meige syndrome and variants of SNAP25, SV2C and ST3GAL2, which are involving in the translocation of the BoNT-A in vivo.

Methods

Patients with the primary Meige syndrome treated with BoNT-A were enrolled. Clinical efficacy was evaluated by the maximum improvement rate of motor symptoms and the duration of efficacy. Variants of SNAP25, SV2C and ST3GAL2 were obtained by Sanger sequencing. Another cohort diagnosed with primary cervical dystonia was also enrolled in the replication stage.

Results

Among the 104 primary Meige syndrome patients, 80 patients (76.9%) had a good efficacy (the maximum improvement rate of motor symptoms ≥30%) and 24 (23. 1%) had a poor (the maximum improvement rate of motor symptoms <30%). As to the duration of efficacy, 52 patients (50.0%) had a long duration of efficacy (≥4 months), and 52 (50.0%) had a short (<4 months). In terms of primary Meige syndrome, SNAP25 rs6104571 was found associating with the maximum improvement rate of motor symptoms (Genotype: P = 0.02, OR = 0.26; Allele: P = 0.013, OR = 0.29), and SV2C rs31244 was found associating with the duration of efficacy (Genotype: P = 0.024, OR = 0.13; Allele: P = 0.012, OR = 0.13). Besides, we also conducted the association analyses between the variants and BoNT-A-related adverse reactions. Although, there was no statistical difference between the allele of SV2C rs31244 and BoNT-A-related adverse reactions, there was a trend (P = 0.077, OR = 2.56). In the replication stage, we included 39 patients with primary cervical dystonia to further expanding the samples' size. Among the 39 primary cervical dystonia patients, 25 patients (64.1%) had a good efficacy (the maximum improvement rate of motor symptoms ≥50%) and 14 (35.9%) had a poor (the maximum improvement rate of motor symptoms <50%). As to the duration of efficacy, 32 patients (82.1%) had a long duration of efficacy (≥6 months), and 7 (17.9%) had a short (<6 months). Integrating primary Meige syndrome and primary cervical dystonia, SV2C rs31244 was still found associating with the duration of efficacy (Genotype: P = 0.002, OR = 0. 23; Allele: P = 0.001, OR = 0. 25).

Conclusion

In our study, SNAP25 rs6104571 was associated with the maximum improvement rate of motor symptoms in patients with primary Meige syndrome treated with BoNT-A, and patients carrying this variant had a lower improvement rate of motor symptoms. SV2C rs31244 was associated with duration of treatment in patients with primary Meige syndrome treated with BoNT-A and patients carrying this variant had a shorter duration of treatment. Patients with primary Meige syndrome carrying SV2C rs31244 G allele have an increase likelihood of BoNT-A-related adverse reactions. Involving 39 patients with primary cervical dystonia, the results further verify that SV2C rs31244 was associated with duration of treatment and patients carrying this variant had a shorter duration of treatment.

Effectiveness and tolerability of programmed cell death protein-1 inhibitor + chemotherapy compared to chemotherapy for upper gastrointestinal tract cancers

BACKGROUND

The combination of programmed cell death protein-1 (PD-1) inhibitor and chemotherapy is approved as a standard first- or second-line treatment in patients with advanced oesophageal or gastric cancer. However, it is unclear whether this combination is superior to chemotherapy alone.

AIM

To assess the comparative effectiveness and tolerability of combining PD-1 inhibitors with chemotherapy vs chemotherapy alone in patients with advanced gastric cancer, gastroesophageal junction (GEJ) cancer, or oesophageal carcinoma.

METHODS

We searched the PubMed and Embase databases for studies that compared the efficacy and tolerance of PD-1 inhibitors in combination with chemotherapy vs chemotherapy alone in patients with advanced oesophageal or gastric cancer. We employed either random or fixed models to analyze the outcomes of each clinical trial, encompassing data on overall survival (OS), progression-free survival (PFS), objective response rate, and adverse events (AEs).

RESULTS

Nine phase 3 clinical trials (7016 advanced oesophageal and gastric cancer patients) met the inclusion criteria. Our meta-analysis demonstrated that the pooled PD-1 inhibitor + chemotherapy group had a significantly longer OS than the chemotherapy-alone group [hazard ratio (HR) = 0.76, 95% confidence interval (CI): 0.71-0.81]; the pooled PFS result was consistent with that of OS (HR = 0.67, 95%CI: 0.61-0.74). The count of patients achieving an objective response in the PD-1 inhibitor + chemotherapy group surpassed that of the chemotherapy-alone group [odds ratio (OR) = 1.86, 95%CI: 1.59-2.18]. AE incidence was also higher in the combination-therapy group than in the chemotherapy-alone group, regardless of whether ≥ grade 3 only (OR = 1.30, 95%CI: 1.07-1.57) or all AE grades (OR = 1.88, 95%CI: 1.39-2.54) were examined. We performed a subgroup analysis based on the programmed death-ligand 1 (PD-L1) combined positive score (CPS) and noted extended OS and PFS durations within the CPS ≥ 1, CPS ≥ 5, and CPS ≥ 10 subgroups of the PD-1 inhibitor + chemotherapy group.

CONCLUSION

In contrast to chemotherapy alone, the combination of PD-1 inhibitor and chemotherapy appears to present a more favorable option for initial or subsequent treatment in patients with gastric cancer, GEJ tumor, or oesophageal cancer. This holds true particularly for individuals with PD-L1 CPS scores of ≥ 5 and ≥ 10.

Automated identification of protein expression intensity and classification of protein cellular locations in mouse brain regions from immunofluorescence images

Knowledge of protein expression in mammalian brains at regional and cellular levels can facilitate understanding of protein functions and associated diseases. As the mouse brain is a typical mammalian brain considering cell type and structure, several studies have been conducted to analyze protein expression in mouse brains. However, labeling protein expression using biotechnology is costly and time-consuming. Therefore, automated models that can accurately recognize protein expression are needed. Here, we constructed machine learning models to automatically annotate the protein expression intensity and cellular location in different mouse brain regions from immunofluorescence images. The brain regions and sub-regions were segmented through learning image features using an autoencoder and then performing K-means clustering and registration to align with the anatomical references. The protein expression intensities for those segmented structures were computed on the basis of the statistics of the image pixels, and patch-based weakly supervised methods and multi-instance learning were used to classify the cellular locations. Results demonstrated that the models achieved high accuracy in the expression intensity estimation, and the F1 score of the cellular location prediction was 74.5%. This work established an automated pipeline for analyzing mouse brain images and provided a foundation for further study of protein expression and functions.

Evaluation of therapeutic benefits of botulinum toxin for foot dystonia associated with Parkinson's disease

BACKGROUND

Foot dystonia occurs in patients with Parkinson's disease (PD) and leads to pain, malformation, and difficulty with walking. Botulinum toxin injections may be effective for foot dystonia, but the extent of improvement and effects on motor function are unclear.

METHODS

In this study, we performed botulinum toxin injections for foot dystonia in 25 patients with PD. At 3 weeks and 3 months post-infection, we assessed changes in plantar pressure distribution utilizing the Pressure Plate system; dystonia using the Modified Ashworth Spasm score; pain using the visual analog scale (VAS) score; and lower extremity function using the Calf-raise Senior (CRS) test, Timed Up and Go (TUG) test, and gait parameters (eg, stride length, step length).

RESULTS

We found improved Modified Ashworth Spasm score (p < 0.01) and VAS score (p < 0.01) post-injection. CRS test score (3 weeks, p = 0.006; 3 months, p = 0.068), stride length (3 weeks, p = 0.012; 3 months, p = 0.715), and step length (3 weeks, p = 0.011; 3 months, p = 0.803) also improved. Plantar pressure distribution improved after botulinum toxin injection (metatarsal 1, 3 weeks, p = 0.031; 3 months, p = 0.144; metatarsal 2, 3 weeks, p = 0.049; 3 months, p = 0.065; metatarsal 3, 3 weeks, p = 0.002; 3 months, p = 0.017; metatarsal 4, 3 weeks, p = 0.017; 3 months, p = 0.144; medial heel, 3 weeks, p = 0.01; 3 months, p = 0.395; lateral heel, 3 weeks, p = 0.035; 3 months, p = 0.109).

CONCLUSION

Botulinum toxin injection for foot dystonia in patients with PD can reduce spasms and pain and normalize plantar pressure distribution, which improves balance and lower extremity function.

[Research progress of vaccination status, efficacy and safety in children with tumor]

Malignant tumors in children are one of the most important diseases that threaten the health and quality of life of children and are the second most common cause of death in children.With the continuous improvement and progress of treatment technology, the long-term survival rate of children with tumor has been significantly improved, but both the disease itself and the treatment can impair the immune function of children, which makes them vulnerable to various infectious diseases and secondary serious complications, and even become a source of infection, endangering the health of others. Vaccination is the most cost-effective measure to prevent infectious diseases. For children with normal immune functions, the benefits of vaccination usually outweigh the disadvantages. However, there is a lack of detailed data on the vaccination situation, efficacy and safety of vaccine use for such immunocompromised tumor survivors, and there are no authoritative and uniform vaccination recommendations. This article reviewed and summarized the literature and consensus of some domestic and foreign scholars on current status of post-treatment vaccination status, efficacy and safety of vaccination for children with tumors after treatment, with the aim of providing a reference for the practice in this field in China.

6-Aza-2-Thiothymine-Capped Gold Nanoclusters as Robust Antimicrobial Nanoagents for Eradicating Multidrug-Resistant Escherichia coli Infection

Multidrug-resistant bacterial infections, especially those caused by multidrug-resistant Escherichia coli (E. coli) bacteria, are an ever-growing threat because of the shrinking arsenal of efficacious antibiotics. Therefore, it is urgently needed to develop a kind of novel, long-term antibacterial agent effectively overcome resistant bacteria. Herein, we present a novel designed antibacterial agent-6-Aza-2-thiothymine-capped gold nanoclusters (ATT-AuNCs), which show excellent antibacterial activity against multidrug-resistant E. coli bacteria. The prepared AuNCs could permeabilize into the bacterial cell membrane via binding with a bivalent cation (e.g., Ca2+), followed by the generation of reactive oxygen species (e.g., •OH and •O2-), ultimately resulting in protein leakage from compromised cell membranes, inducing DNA damage and upregulating pro-oxidative genes intracellular. The AuNCs also speed up the wound healing process without noticeable hemolytic activity or cytotoxicity to erythrocytes and mammalian tissue. Altogether, the results indicate the great promise of ATT-AuNCs for treating multidrug-resistant E. coli bacterial infection.

[Effectiveness of 13-valent pneumococcal conjugate vaccine against invasive disease caused by serotype 19A in children: a meta-analysis]

Objective: Using Meta-analysis to evaluate the vaccine effectiveness of 13-valent pneumococcal conjugate vaccine (PCV13) against invasive Streptococcus pneumoniae disease (IPD) caused by serotype 19A in children <5 years old. Methods: "Streptococcus pneumoniae infection""invasive pneumococcal disease""13-valent pneumococcal polysaccharide conjugate vaccine""PCV13""effectiveness""infant""child" and related terms were searched from China National Knowledge Infrastructure (CNKI), WANFANG DATA, PubMed, SCOPUS and Web of science with no limited on language, region and research institution. The retrieval time was limited from January 2010 to February 2023 and cohort study, case-control study and randomized controlled trial were included. Data were extracted from eligible studies by two independent reviewers, and after study quality assessment by NOS scale, Meta-analysis was completed using Stata 16.0 software. Results: A total of 2 340 related literatures were searched, and 10 literatures were finally included, including 5 case-control studies and 5 indirect cohort studies, which showed good literature quality. The vaccine effectiveness against serotype 19A IPD of PCV13 in children was 83.91% (95%CI: 78.92%-88.89%), and the subgroup analysis (P=0.240) showed there was no significant difference among the case-control study (VE=87.34%, 95%CI:79.74%-94.94%) and the indirect cohort study (VE=81.30%, 95%CI:74.69%-87.92%). The funnel plot and Egger test suggested that the possibility of publication bias was small. Conclusion: The present evidence indicates that PCV13 has a good vaccine effectiveness against serotype 19A IPD in children, and it is recommended to further increase the vaccination rate of PCV13 to reduce the disease burden of IPD in children <5 years old.

[Risk factors of systemic allergic reactions caused by subcutaneous allergen immunotherapy]

Objective: To investigate the incidence and risk factors of systemic allergic reactions induced by subcutaneous immunotherapy (SCIT) in patients undergoing SCIT injections in Peking Union Medical College Hospital (PUMCH). Methods: This is a single center retrospective cohort study. Using the outpatient information system of PUMCH, the demographic information and injection-related reaction data of patients undergoing SCIT injection in Allergy Department of PUMCH from December 2018 to December 2022 were retrospectively analyzed to count the incidence and risk factors of systemic allergic reactions caused by SCIT. Mann-Whitney nonparametric test or chi-square test was used for single-factor analysis, and multiple logistic regression was used for multiple-factor analysis. Results: A total of 2 897 patients received 18 070 SCIT injections in Allergy Department during the four years, and 40 systemic allergic reactions occurred, with the overall incidence rate of 0.22%. The incidence of systemic allergic reaction was 0.37% when using imported dust mite preparation and 0.15% when using domestic multi-component allergen preparation. The risk factors significantly related with SCIT-induced systemic allergic reactions in patients using imported dust mite preparation were age less than 18 years old (OR=3.186,95%CI: 1.255-8.085), highest injection concentration (OR value could not be calculated because all patients with systemic reactions were injected with highest concentration), and large local reaction in previous injection (OR=22.264,95%CI: 8.205-60.411). The risk factors for SCIT-induced systemic allergic reactions in patients using domestic allergen preparation were 5 or more types of allergens (OR=3.455,95%CI: 1.147-10.402), highest injection concentration (OR=3.794,95%CI: 1.226-11.740) and large local reaction in previous injection (OR=63.577,95%CI: 22.248-181.683). However, SCIT injection in pollen allergic patients during the pollen season did not show a correlation with systemic allergic reaction. Conclusion: The incidence of SCIT-induced systemic allergic reactions was low in the Chinese patient population of this study. Patients with one or more risk factors, such as multiple allergen injection, highest injection concentration, large local reaction in previous injection, should be given high attention and vigilance against systemic allergic reactions.

Phylogeny and species diversity of the genus Helvella with emphasis on eighteen new species from China

Helvella is a widespread, frequently encountered fungal group appearing in forests, but the species diversity and molecular phylogeny of Helvella in China remains incompletely understood. In this work, we performed comprehensive phylogenetic analyses using multilocus sequence data. Six datasets were employed, including a five-locus concatenated dataset (ITS, nrLSU, tef1-α, rpb2, hsp), a two-locus concatenated dataset (ITS, nrLSU), and four single-locus datasets (ITS) that were divided based on the four different phylogenetic clades of Helvella recognized in this study. A total of I 946 sequences were used, of which 713 were newly generated, including 170 sequences of ITS, 174 sequences of nrLSU, 131 sequences of tef1-α, 107 sequences of rpb2 and 131 sequences of hsp. The phylogeny based on the five-locus concatenated dataset revealed that Helvellas. str. is monophyletic and four phylogenetic clades are clearly recognized, i.e., Acetabulum clade, Crispa clade, Elastica clade, and Lacunosa clade. A total of 24 lineages or subclades were recognized, II of which were new, the remaining 13 corresponding with previous studies. Chinese Helvella species are distributed in 22 lineages across four clades. Phylogenetic analyses based on the two-locus concatenated dataset and four single-locus datasets confirmed the presence of at least 93 phylogenetic species in China. Among them, 58 are identified as known species, including a species with a newly designated lectotype and epitype, 18 are newly described in this paper, and the remaining 17 taxa are putatively new to science but remain unnamed due to the paucity or absence of ascomatal materials. In addition, the Helvella species previously recorded in China are discussed. A list of 76 confirmed species, including newly proposed species, is provided. The occurrence of H. crispa and H. elastica are not confirmed although both are commonly recorded in China. Citation: Mao N, Xu YY, Zhang YX, Zhou H, Huang XB, Hou CL, Fan L (2023). Phylogeny and species diversity of the genus Helvella with emphasis on eighteen new species from China. Fungal Systematics and Evolution 12: 111-152. doi: 10.3114/fuse.2023.12.08.

Development and validation of a nomogram for predicting internal mammary sentinel node metastasis in breast cancer patients

OBJECTIVE

Internal mammary nodes are important in breast cancer prognosis, but their diagnosis is often missed in clinical practice, leading to inaccurate staging and treatment. We developed a validated nomogram to predict the presence of internal mammary sentinel nodes (IMSN) metastasis.

METHODS

A total of 864 sequential IMSN biopsy procedures from a prospective studies database of 1505 cases were used for model development and validation. Multivariable logistic regression was performed on 519 sequential IMSN biopsy procedures from multi-center data between August 2018 and July 2022 to predict the presence of IMSN metastasis. A nomogram was developed based on the logistic regression model and subsequently applied to 345 sequential IMSN biopsy procedures from single-center data between November 2011 and July 2018. The model's discrimination was assessed using the area under the receiver operating characteristic curve.

RESULTS

The overall frequency of IMSN metastasis was 17.0% in our study. A predictive model for IMSN metastasis was constructed using tumor size, tumor location, lymphovascular invasion, the number of positive axillary nodes (P < 0.05 for all variables in multivariate analysis), and histological grade (P < 0.05 only in univariate analysis). The nomogram was accurate, with a concordance index of 0.84 in the bootstrapping analysis and an area under the receiver operating characteristic curve of 0.80 in the validation population.

CONCLUSION

Our nomogram provides an accurate and validated multivariable predictive model for estimating the individual likelihood of having IMSN metastasis. This may be useful for personalized treatment decisions regarding internal mammary radiotherapy in breast cancer patients.

Effect of CICARE communication nursing model combined with motivational psychological intervention in patients with post-intensive care unit syndrome

BACKGROUND

Post-intensive care syndrome (PICS) is a term used to describe a constellation of new or worsened dysfunctions in the physical, cognitive, or mental health status of critically ill patients after their discharge from the intensive care unit (ICU). These dysfunctions persist beyond the acute phase of illness and have a significant impact on both the patient and their family. Connect, Introduce, Communicate, Ask, Respond, Exit (CICARE) communication advocates that patients should be respected and accepted when receiving medical services. Clinicians should attach importance to the communication mode of feelings, including connection, introduction, communication, ask, response, and exit 6 steps.

AIM

To assess the impact of CICARE communication on the reduction of anxiety, depression, and post-traumatic stress disorder (PTSD) symptoms in patients transitioning from the ICU to other care settings.

METHODS

This prospective, randomized, controlled study was performed between October 2021 and March 2023. Intensive Care Unit Memory Tool was used to evaluate patients' ICU memory. The Hospital Anxiety and Depression Scale was employed to determine the presence of anxiety or depression symptoms. Impact of Event Scale-Revised was utilized to assess the presence of PTSD. All data were processed and analyzed using R language software version 4.1.0. The measurement data were expressed as mean ± SD, and the t test was used. The count data were analyzed by the χ2 test and expressed as [n (%)].

RESULTS

In total, 248 subjects were included in this study. Among them, 206 were successfully followed up for three months after transfer from the ICU, and 42 cases were lost to follow-up. There was no significant difference in the composition of ICU memory between the two groups. The application of the CICARE communication nursing model combined with the motivational psychological intervention nursing model, as well as the adoption of only the motivational psychological intervention nursing model, demonstrated favorable effects on PICS. Both groups of patients showed a reduction in anxiety scores, depression scores, and PTSD scores following the implementation of these two nursing models. However, it is noteworthy that the experimental group exhibited greater improvements compared to the control group.

CONCLUSION

Our findings suggest that CICARE communication nursing mode may have good influence on relieving PICS.

BaLa5V2O3N7: a novel anti-perovskite oxynitride for electrode applications

The exploration of transition metal oxynitrides has garnered significant interest due to their intriguing property diversity. Herein, we present a promising new transition metal oxynitride BaLa5V2O3N7, which features an anti-perovskite structure type. This unique structural configuration endows the material with remarkable conductivity, particularly at low temperatures, paving the way for the material to be used in a wide range of technological applications.

[Long-term trend analysis of liver cancer survival rate in Qidong region, Jiangsu Province, 1972-2019]

Objective: To analyze the incidence and survival rate of liver cancer cases in the entire population in the Qidong region from 1972 to 2019, so as to provide a basis for prognosis evaluation, prevention, and treatment. Methods: The observed survival rate (OSR) and relative survival rate (RSR) of 34 805 cases of liver cancer in the entire Qidong region population from 1972 to 2019 were calculated using Hakulinen's method with SURV3.01 software. Hakulinen's likelihood ratio test was used for statistical analysis. Age-standardized relative survival (ARS) was calculated using the International Cancer Survival Standard. The Joinpoint regression analysis was performed with Joinpoint 4.7.0.0 software to calculate the average annual percentage change (AAPC) of the liver cancer survival rate. Results: 1-ASR increased from 13.80% in 1972-1977 to 50.20% in 2014-2019, while 5-ASR increased from 1.27% in 1972-1977 to 27.64% in 2014-2019. The upward trend of RSR over eight periods was statistically significant (χ (2) = 3045.29, P < 0.001). Among them, male 5-ASR was 0.90%, 1.80%, 2.33%, 4.92%, 5.43%, 7.05%, 10.78%, and 27.78%, and female 5-ASR was 2.33%, 1.51%, 3.35%, 3.92%, 3.84%, 7.18%, 11.45%, and 29.84%, respectively. There was a statistically significant difference in RSR between males and females (χ (2) = 45.68, P < 0.001). The 5-RSR for each age group of 25-34 years old, 35-44 years old, 45-54 years old, 55-64 years old, 65-74 years old, and 75 years old were 4.92%, 5.29%, 8.17%, 11.70%, 11.63%, and 9.60%, respectively. There were statistically significant differences in RSR among different age groups (χ (2) = 501.29, P < 0.001). The AAPC in Qidong region from 1972 to 2019 for 1-ARS, 3-ASR, and 5-ARS were 5.26% (t = 12.35, P < 0.001), 8.10% (t = 15.99, P < 0.001), and 8.96 % (t = 16.06, P < 0.001), respectively. The upward trend was statistically significant in all cases. The AAPC of 5-ARS was 9.82% in males (t = 14.14, P < 0.001), and 8.79% in females (t = 11.48, P < 0.001), and the upward trend was statistically significant in both. The AAPC of 25-34 years old, 35-44 years old, 45-54 years old, 55-64 years old, 65-74 years old, and 75 years old were 5.37% (t = 5.26, P = 0.002), 5.22% (t = 5.66, P = 0.001), 7.20% (t = 6.88, P < 0.001), 10.00% (t = 12.58, P < 0.001), 9.96% (t = 7.34, P < 0.001) and 8.83% (t = 3.51, P = 0.013), and the upward trend was statistically significant. Conclusion: The overall survival rate of registered cases of liver cancer in the Qidong region's entire population has greatly improved, but there is still much room for improvement. Hence, constant attention should be paid to the study on preventing and treating liver cancer.

Amelioratory effects of astragaloside IV on hepatocarcinogenesis via Nrf2-mediated pSmad3C/3L transformation

BACKGROUND

Phosphorylated Smad3 isoforms are reversible and antagonistic, and the tumour-suppressive pSmad3C can shift to an oncogenic pSmad3L signal. In addition, Nrf2 has a two-way regulatory effect on tumours, protecting normal cells from carcinogens and promoting tumour cell survival in chemotherapeutics. Accordingly, we hypothesised that the transformation of pSmad3C/3L is the basis for Nrf2 to produce both pro- and/or anti-tumourigenic effects in hepatocarcinogenesis. Astragaloside IV (AS-IV), the major component of Astragalus membranaceus, exerts anti-fibrogenic and carcinogenic actions. Lately, AS-IV administration could delay the occurrence of primary liver cancer by persistently inhibiting the fibrogenesis and regulating pSmad3C/3 L and Nrf2/HO-1 pathways synchronously. However, effect of AS-IV on hepatocarcinogenesis implicated in the bidirectional cross-talking of pSmad3C/3 L and Nrf2/HO-1 signalling, especially which one contributes palpably than the other still remains unclear.

PURPOSE

This study aims to settle the above questions by using in vivo (pSmad3C^+/- and Nrf2^-/- mice) and in vitro (plasmid- or lentivirus- transfected HepG2 cells) models of HCC.

STUDY DESIGN AND METHODS

The correlation of Nrf2 to pSmad3C/pSmad3L in HepG2 cells was analysed by Co-immunoprecipitation and dual-luciferase reporter assay. Pathological changes of Nrf2, pSmad3C, and pSmad3L in human HCC patients, pSmad3C^+/- mice, and Nrf2^-/- mice were gauged by immunohistochemical, haematoxylin and eosin staining, Masson, and immunofluorescence assays. Finally, western blot and qPCR were used to verify the bidirectional cross-talking of pSmad3C/3L and Nrf2/HO-1 signalling protein and mRNA in vivo and in vitro models of HCC.

RESULTS

Histopathological manifestations and biochemical indicators revealed that pSmad3C^+/- could abate the ameliorative effects of AS-IV on fibrogenic/carcinogenic mice with Nrf2/HO-1 deactivation and pSmad3C/p21 transform to pSmad3L/PAI-1//c-Myc. As expected, cell experiments confirmed that upregulating pSmad3C boosts the inhibitory activity of AS-IV on phenotypes (cell proliferation, migration and invasion), followed by a shift of pSmad3L to pSmad3C and activation of Nrf2/HO-1. Synchronously, experiments in Nrf2^-/- mice and lentivirus-carried Nrf2shRNA cell echoed the results of pSmad3C knockdown. Complementarily, Nrf2 overexpression resulted in the opposite result. Furthermore, Nrf2/HO-1 contributes to AS-IV's anti-HCC effect palpably compared with pSmad3C/3L.

CONCLUSION

These studies highlight that harnessing the bidirectional crosstalk pSmad3C/3 L and Nrf2/HO-1, especially Nrf2/HO-1 signalling, acts more effectively in AS-IV's anti-hepatocarcinogenesis, which may provide an important theoretical foundation for the use of AS-IV against HCC.

[Read-through circular RNA rt-circ-HS promotes hypoxia inducible factor 1α expression and renal carcinoma cell proliferation, migration and invasiveness]

OBJECTIVE

To identify and characterize read-through RNAs and read-through circular RNAs (rt-circ-HS) derived from transcriptional read-through hypoxia inducible factor 1α (HIF1α) and small nuclear RNA activating complex polypeptide 1 (SNAPC1) the two adjacent genes located on chromosome 14q23, in renal carcinoma cells and renal carcinoma tissues, and to study the effects of rt-circ-HS on biological behavior of renal carcinoma cells and on regulation of HIF1α.

METHODS

Reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing were used to examine expression of read-through RNAs HIF1α-SNAPC1 and rt-circ-HS in different tumor cells. Tissue microarrays of 437 different types of renal cell carcinoma (RCC) were constructed, and chromogenic in situ hybridization (ISH) was used to investigate expression of rt-circ-HS in different RCC types. Small interference RNA (siRNA) and artificial overexpression plasmids were designed to examine the effects of rt-circ-HS on 786-O and A498 renal carcinoma cell proliferation, migration and invasiveness by cell counting kit 8 (CCK8), EdU incorporation and Transwell cell migration and invasion assays. RT-PCR and Western blot were used to exa-mine expression of HIF1α and SNAPC1 RNA and proteins after interference of rt-circ-HS with siRNA, respectively. The binding of rt-circ-HS with microRNA 539 (miR-539), and miR-539 with HIF1α 3' untranslated region (3' UTR), and the effects of these interactions were investigated by dual luciferase reporter gene assays.

RESULTS

We discovered a novel 1 144 nt rt-circ-HS, which was derived from read-through RNA HIF1α-SNAPC1 and consisted of HIF1α exon 2-6 and SNAPC1 exon 2-4. Expression of rt-circ-HS was significantly upregulated in 786-O renal carcinoma cells. ISH showed that the overall positive expression rate of rt-circ-HS in RCC tissue samples was 67.5% (295/437), and the expression was different in different types of RCCs. Mechanistically, rt-circ-HS promoted renal carcinoma cell proliferation, migration and invasiveness by functioning as a competitive endogenous inhibitor of miR-539, which we found to be a potent post-transcriptional suppressor of HIF1α, thus promoting expression of HIF1α.

CONCLUSION

The novel rt-circ-HS is highly expressed in different types of RCCs and acts as a competitive endogenous inhibitor of miR-539 to promote expression of its parental gene HIF1α and thus the proliferation, migration and invasion of renal cancer cells.

[Application of augmented reality navigation in laparoscopic and robot-assisted liver surgery]

In recent years, laparoscopic surgery and robotic surgery have been widely used, and various intraoperative image navigation systems have also developed rapidly. However, the liver itself has a complex vessel and duct system, which increase the difficulty of liver surgery. The augmented reality image navigation system combines the three-dimensional reconstructed image of the liver with the real liver anatomy, which presents the specific relationship between the tumor location and the surrounding vessels for the surgeon. Compared with other intraoperative image navigation methods, augmented reality has its unique advantages. This paper provides an overview of current advances in registration technology in augmented reality image navigation system, and focuses on its applications in liver surgery, including laparoscopic surgery and robotic surgery. Finally, the technological problems and difficulties still faced at present are summarized, and future directions worth studying in this field are proposed.

Resistance to antibody-drug conjugates in breast cancer: mechanisms and solutions

Antibody-drug conjugates (ADCs) are a rapidly developing therapeutic approach in cancer treatment that has shown remarkable activity in breast cancer. Currently, there are two ADCs approved for the treatment of human epidermal growth factor receptor 2-positive breast cancer, one for triple-negative breast cancer, and multiple investigational ADCs in clinical trials. However, drug resistance has been noticed in clinical use, especially in trastuzumab emtansine. Here, the mechanisms of ADC resistance are summarized into four categories: antibody-mediated resistance, impaired drug trafficking, disrupted lysosomal function, and payload-related resistance. To overcome or prevent resistance to ADCs, innovative development strategies and combination therapy options are being investigated. Analyzing predictive biomarkers for optimal therapy selection may also help to prevent drug resistance.

Primary malignant melanoma of the esophagus: A case report

BACKGROUND

Primary malignant melanoma of the esophagus (PMME) is a rare malignant disease whose clinical and molecular pathological features, origin and pathogenesis, diagnosis and treatment have not been elucidated.

CASE SUMMARY

In this paper, we report a case of a 73-year-old male with PMME. The patient complained of progressive dysphagia accompanied by substantial weight loss. Gastroscopy revealed a purple black bulging-type mass in the lower esophagus with easy bleeding on contact and scattered satellite lesions in the stomach. Histopathological biopsy revealed melanocytes in the esophageal mucosa. Physical examination and multidisciplinary consultation led to diagnostic exclusion of melanoma originating in other organs, such as the skin. Through this case report and literature review, we aimed to describe the clinical and molecular pathological features of PMME and summarize possible pathways of pathogenesis as well as cutting-edge therapeutic advances.

CONCLUSION

PMME is a rare malignancy of the esophagus with a poor prognosis. Clinicians should raise their awareness and be able to identify early lesions.

Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning

With the improvement of single-cell measurement techniques, there is a growing awareness that individual differences exist among cells, and protein expression distribution can vary across cells in the same tissue or cell line. Pinpointing the protein subcellular locations in single cells is crucial for mapping functional specificity of proteins and studying related diseases. Currently, research about single-cell protein location is still in its infancy, and most studies and databases do not annotate proteins at the cell level. For example, in the human protein atlas database, an immunofluorescence image stained for a particular protein shows multiple cells, but the subcellular location annotation is for the whole image, ignoring intercellular difference. In this study, we used large-scale immunofluorescence images and image-level subcellular locations to develop a deep-learning-based pipeline that could accurately recognize protein localizations in single cells. The pipeline consisted of two deep learning models, i.e. an image-based model and a cell-based model. The former used a multi-instance learning framework to comprehensively model protein distribution in multiple cells in each image, and could give both image-level and cell-level predictions. The latter firstly used clustering and heuristics algorithms to assign pseudo-labels of subcellular locations to the segmented cell images, and then used the pseudo-labels to train a classification model. Finally, the image-based model was fused with the cell-based model at the decision level to obtain the final ensemble model for single-cell prediction. Our experimental results showed that the ensemble model could achieve higher accuracy and robustness on independent test sets than state-of-the-art methods.

[Analysis of the effects of low/intermediate dose of coagulation factor Ⅷ on 30 adult patients with severe hemophilia A in a single center]

Objective: To evaluate the clinical effects of low- and intermediate-dose factor Ⅷ (F Ⅷ) prophylaxis in Chinese adult patients with severe hemophilia A. Methods: Thirty adult patients with severe hemophilia A who received low- (n=20) /intermediate-dose (n=10) F Ⅷ prophylaxis at Nanjing Drum Tower Hospital affiliated with Nanjing University Medical College were included in the study. The annual bleeding rate (ABR), annual joint bleeding rate (AJBR), number of target joints, functional independence score of hemophilia (FISH), quality of life score, and health status score (SF-36) before and after preventive treatment were retrospectively analyzed and compared. Results: The median follow-up was 48 months. Compared with on-demand treatment, low- and intermediate-dose prophylaxis significantly reduced ABR, AJBR, and the number of target joints (P<0.05) ; the improvement in the intermediate-dose prophylaxis group was better than that in the low-dose prophylaxis group (P<0.05). Compared with on-demand treatment, the FISH score, quality of life score, and SF-36 score significantly improved in both groups (P<0.05), but there was no significant difference between the two groups (P>0.05) . Conclusion: In Chinese adults with severe hemophilia A, low- and intermediate-dose prophylaxis can significantly reduce bleeding frequency, delay the progression of joint lesions, and improve the quality of life of patients as compared with on-demand treatment. The improvement in clinical bleeding was better with intermediate-dose prophylaxis than low-dose prophylaxis.

Modulating tumour vascular normalisation using triptolide-loaded NGR-functionalized liposomes for enhanced cancer radiotherapy

Radiotherapy is an effective therapy in tumour treatment. However, the characteristics of the tumour microenvironment, including hypoxia, low pH, and interstitial fluid pressure bring about radioresistance. To improve the anti-tumour effect of radiotherapy, it has been demonstrated that antiangiogenic therapy can be employed to repair the structural and functional defects of tumour angiogenic vessels, thereby preventing radioresistance or poor therapeutic drug delivery. In this study, we prepared triptolide (TP)-loaded Asn-Gly-Arg (NGR) peptide conjugated mPEG2000-DSPE-targeted liposomes (NGR-PEG-TP-LPs) to induce tumour blood vessel normalisation, to the end of increasing the sensitivity of tumour cells to radiotherapy. Further, to quantify the tumour vessel normalisation window, the structure and functionality of tumour blood vessels post NGR-PEG-TP-LPs treatment were evaluated. Thereafter, the anti-tumour effect of radiotherapy following these treatments was evaluated using HCT116 xenograft-bearing mouse models based on the tumour vessel normalisation period window. The results obtained showed that NGR-PEG-TP-LPs could modulate tumour vascular normalisation to increase the oxygen content of the tumour microenvironment and enhance the efficacy of radiotherapy. Further, liver and kidney toxicity tests indicated that NGR-PEG-TP-LPs are safe for application in cancer treatment.

[Long-term trend of colorectal cancer survival rate in Qidong, 1972-2016]

Objective: The survival of colorectal cancer in Qidong City, Jiangsu Province from 1972 to 2016 was analyzed to provide a basis for the evaluation of prognosis and the formulation of prevention and control measures. Methods: Colorectal cancer data were obtained from the Qidong Cancer Registration and Reporting System, and the follow-up was up to December 31, 2021. The observed survival rate (OSR) and relative survival rate (RSR) were calculated by SURV 3.01 software, and the trend test was performed by Hakulinen's likelihood ratio test. The Joinpoint regression model was used to calculate the average annual percentage change (AAPC) of survival, and the ARIMA model was used to predict the trend of colorectal cancer survival. Results: There were 8 637 new cases of colorectal cancer in Qidong from 1972 to 2016. Dividing 1972-2016 into 9 periods at 5-year intervals, the 5-year OSR from 1972-1976 to 2012-2016 increased from 21.86% to 48.86%, and the 5-year RSR increased from 26.45% to 59.91%. The increasing trend of RSR was statistically significant (χ(2)=587.47, P<0.001). From 1972 to 2016, the survival rates of colorectal cancer in different sexes in Qidong were similar, and the 5-year RSR was 44.63% for men and 44.07% for women. Since the 1990s, the 5-year OSR and RSR for men have been lower than those for women. From 1972 to 2016, the 5-year RSR of colorectal cancer in Qidong was significantly improved in the 65-74 and ≥75-year-old groups, but the survival rate of the ≥75-year-old group was still the lowest (36.78%), followed by the 35-44-year-old group ( 43.04%). The time trend showed that the overall AAPC of colorectal cancer 5-year RSR in Qidong from 1972 to 2016 was 2.50% (t=16.45, P<0.001). The upward trend of different sexes was consistent, and the increase was greater in women (AAPC for males=2.18%, AAPC for females=2.54%, both P<0.05). The 5-year RSR of colorectal cancer in each age group showed an upward trend, and the AAPCs of the 35-44, 45-54, 55-64, 65-74, and ≥75-year-old groups were 1.54%, 1.83%, 2.00%, 3.51% and 4.35%, respectively (all P<0.05). The prediction results of colorectal cancer survival rate showed that the 5-year RSR of colorectal cancer in Qidong will increase to 71.62% by 2026. Conclusions: The overall survival rate of colorectal cancer patients in Qidong has been greatly improved, but there is still room for improvement. We should continue to pay attention to the early diagnosis and early treatment of colorectal cancer.

Automated classification of protein expression levels in immunohistochemistry images to improve the detection of cancer biomarkers

Background

The expression changes of some proteins are associated with cancer progression, and can be used as biomarkers in cancer diagnosis. Automated systems have been frequently applied in the large-scale detection of protein biomarkers and have provided a valuable complement for wet-laboratory experiments. For example, our previous work used an immunohistochemical image-based machine learning classifier of protein subcellular locations to screen biomarker proteins that change locations in colon cancer tissues. The tool could recognize the location of biomarkers but did not consider the effect of protein expression level changes on the screening process.

Results

In this study, we built an automated classification model that recognizes protein expression levels in immunohistochemical images, and used the protein expression levels in combination with subcellular locations to screen cancer biomarkers. To minimize the effect of non-informative sections on the immunohistochemical images, we employed the representative image patches as input and applied a Wasserstein distance method to determine the number of patches. For the patches and the whole images, we compared the ability of color features, characteristic curve features, and deep convolutional neural network features to distinguish different levels of protein expression and employed deep learning and conventional classification models. Experimental results showed that the best classifier can achieve an accuracy of 73.72% and an F1-score of 0.6343. In the screening of protein biomarkers, the detection accuracy improved from 63.64 to 95.45% upon the incorporation of the protein expression changes.

Conclusions

Machine learning can distinguish different protein expression levels and speed up their annotation in the future. Combining information on the expression patterns and subcellular locations of protein can improve the accuracy of automatic cancer biomarker screening. This work could be useful in discovering new cancer biomarkers for clinical diagnosis and research.

[Long-term trend of esophageal cancer survival rate in Qidong, 1972-2016]

Objective: To analyze the survival of esophageal cancer cases in Qidong, Jiangsu Province from 1972 to 2016, and provide a basis for the prognosis evaluation and prevention of esophageal cancer patients. Methods: The data of esophageal cancer were obtained from the Qidong Cancer Registration and Reporting System, and the follow-up date ended December 31, 2021. Observed survival rate (OSR) and relative survival rate (RSR) were calculated by SURV 3.01 software, and Hakulinen's likelihood ratio test was used for statistical difference comparison. Joinpoint regression model was used to conduct the average annual percentage change (AAPC) in esophageal cancer survival rate, and the ARIMA model was used to predict the trend of esophageal cancer survival rate. Results: During 1972 to 2016, there were 5 112 new cases of esophageal cancer in Qidong. The OSR of esophageal cancer at 1, 5 and 10 years were 24.43%, 6.93% and 4.43%, and the RSR at 1, 5 and 10 years were 25.88%, 9.35% and 8.34%, respectively. Dividing 1972-2016 into 9 periods, compared with 1972-1976, the 5-year RSR from 2012-2016 increased from 4.47% to 17.85%, and the RSR trend of the 9 periods was statistically significant (χ(2)=263.43, P<0.001). The survival rate of female with esophageal cancer was slightly higher than that of male, however, there was no significant difference in RSR between male and female (χ(2)=9.40, P=0.401). The 5-OSR and 5-RSR for male were 6.73% and 9.11%, and for female were 7.37% and 9.87%, respectively. The 5-RSR for the age groups of 45-54, 55-64, 65-74, and over 75 years old were 11.99%, 11.21%, 8.17% and 7.08%, respectively. There was a statistically significant difference in RSR among different age groups (χ(2)=98.19, P<0.001). The time trend results showed that the overall AAPC of the 5-RSR of esophageal cancer in Qidong from 1972 to 2016 was 3.89% (t=11.98, P<0.001). The 5-RSR uptrend was consistent among different genders, and the uptrend was greater in female (AAPC=4.25% for male, and AAPC=5.72% for female, P<0.05). Furthermore, the 5-RSR of esophageal cancer in all age groups showed an upward trend, and the upward trend was statistically significant in the 55-64-year-old group (AAPC=4.23%, P<0.05) and the 65-74-year-old group (AAPC=6.82%, P<0.05), there was no statistical significance in the 45-54-year-old group (AAPC=2.17%, P>0.05) and more than 75 years old group (AAPC=1.82%, P>0.05). Survival rate prediction of esophageal cancer showed that by 2026, 5-RSR will increase to 24.79%. Conclusions: During 1972 to 2016, the overall survival rate of esophageal cancer in the whole population of Qidong has improved to a certain extent, but there is still a large room for improvement. More emphasis should be continued to strengthen on the early diagnosis and early treatment of esophageal cancer.

GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images

Motivation

Recognition of protein subcellular distribution patterns and identification of location biomarker proteins in cancer tissues are important for understanding protein functions and related diseases. Immunohistochemical (IHC) images enable visualizing the distribution of proteins at the tissue level, providing an important resource for the protein localization studies. In the past decades, several image-based protein subcellular location prediction methods have been developed, but the prediction accuracies still have much space to improve due to the complexity of protein patterns resulting from multi-label proteins and variation of location patterns across cell types or states.

Results

Here, we propose a multi-label multi-instance model based on deep graph convolutional neural networks, GraphLoc, to recognize protein subcellular location patterns. GraphLoc builds a graph of multiple IHC images for one protein, learns protein-level representations by graph convolutions, and predicts multi-label information by a dynamic threshold method. Our results show that GraphLoc is a promising model for image-based protein subcellular location prediction with model interpretability. Furthermore, we apply GraphLoc to the identification of candidate location biomarkers and potential members for protein networks. A large portion of the predicted results have supporting evidence from the existing literatures and the new candidates also provide guidance for further experimental screening.

Availability

The dataset and code are available at: www.csbio.sjtu.edu.cn/bioinf/GraphLoc.

Supplementary information

Supplementary data are available at Bioinformatics online.

[Progress on the diagnosis and therapy about atopic diseases and primary immunodeficiency diseases]

Primary immunodeficiency diseases (PID) is a congenital disease caused by single gene germline mutation related to the immune system. PID patients have immune dysregulation, and are susceptible to infectious diseases, autoimmune diseases, autoimmune diseases, allergic diseases, and malignant tumors. The first symptom of some PID patients is atopic disease, therefore they go to the department of allergy, department of pediatrics and other relevant departments. How to identify and diagnose PID in allergic patients, to reduce diagnosis delay and prevent disease aggravation are the abilities that allergists, pediatricians, and doctors in other relevant departments need to master. This article summarizes the warning signs of PID in allergic patients and the mechanism of allergy combined with PID, and then summarizes the common types of PID in allergic patients, the evaluation, treatment and prevention in patients with PID and allergy.

Latamoxef-induced severe thrombocytopenia during the treatment of pulmonary infection: A case report

BACKGROUND

Latamoxef shows excellent antibacterial activity against anaerobic bacteria such as Bacteroides fragilis. Reports of thrombocytopenic toxicity of latamoxef are limited. This report presents a case of severe thrombocytopenia possibly induced by latamoxef, an infrequent adverse drug reaction in a young patient with tuberculosis and Crohn's disease in China.

CASE SUMMARY

We reported a case of severe thrombocytopenia induced by latamoxef in a 28-year-old man with tuberculosis and Crohn's disease. On admission, the patient presented with a cough productive of bloody sputum, a chest computed tomogram suggested scattered mottled, high-density shadows in both lungs. Laboratory tests indicated a platelet count of 140000/μL. Considered a pulmonary bacterial infection, the patient received anti-infection therapy with latamoxef (dose: 2.0 g) intravenously Q12h. On the 9^th day of treatment, the platelet count decreased to 44000/μL. On the 12^th day, scattered purpura and ecchymosis appeared on the patient’s limbs and trunk, and the platelet count decreased to 9000/μL after latamoxef treatment for 15 d. Three days after discontinuation of latamoxef, the platelet count recovered to 157000/μL, and the area of scattered purpura and ecchymosis on the limbs and trunk decreased. The platelet counts remained in the normal range, and no thrombocytopenia was found at follow-up 15 mo after discharge.

CONCLUSION

For patients treated with latamoxef, platelet counts should be carefully followed, and caregivers should be vigilant for the appearance of scattered ecchymosis.

Individualized risk estimation for postoperative pulmonary complications after hepatectomy based on perioperative variables

BACKGROUND

At present, there is no perfect system to evaluate pulmonary complications of liver surgery using perioperative variables.

AIM

To design and verify a risk assessment system for predicting postoperative pulmonary complications (PPCs) after hepatectomy based on perioperative variables.

METHODS

A retrospective analysis was performed on 1633 patients who underwent liver surgery. The variables were screened using univariate and multivariate analyses, and graded scores were assigned to the selected variables. Logistic regression was used to develop the liver operation pulmonary complication scoring system (LOPCSS) for the prediction of PPCs. The LOPCSS was verified using the receiver operating characteristic curve.

RESULTS

According to the multivariate correlation analysis, the independent factors which influenced PPCs of liver surgery were age [≥ 65 years old/< 65 years old, odds ratio (OR) = 1.926, P = 0.011], medical diseases requiring drug treatment (yes/no, OR = 3.523, P < 0.001), number of liver segments to be removed (≥ 3/≤ 2, OR = 1.683, P = 0.002), operation duration (≥ 180 min/< 180 min, OR = 1.896, P = 0.004), and blood transfusion (yes/no, OR = 1.836, P = 0.003). The area under the curve (AUC) of the LOPCSS was 0.742. The cut-off value of the expected score for complications was 5. The incidence of complications in the group with ≤ 4 points was significantly lower than that in the group with ≥ 6 points (2.95% vs 33.40%, P < 0.001). Furthermore, in the validation dataset, the corresponding AUC of LOPCSS was 0.767.

CONCLUSION

As a novel and simplified assessment system, the LOPCSS can effectively predict PPCs of liver surgery through perioperative variables.

Species diversity, phylogeny, endemism and geography of the truffle genus Tuber in China based on morphological and molecular data

The genus Tuber (Tuberaceae, Pezizales) is an important fungal group of Ascomycota both economically and ecologically. However, the species diversity, phylogenetic relationships, and geographic distribution of Tuber species in China remains poorly understood, primarily because descriptions of many new species relied heavily on morphological features with molecular data either not sought or ignored. The misapplication of European and North American names further added to confusion regarding the taxonomy of Chinese Tuber species. In this study, we examined more than 1 000 specimens from China, and performed a comprehensive phylogenetic analysis for Chinese Tuber species using ITS sequences and multilocus sequence data. To infer the phylogeny of Chinese Tuber spp., 11 molecular datasets were assembled, including a concatenated internal transcribed spacers of the nuc rDNA (ITS), nuc rDNA 28S subunit (LSU), translation elongation factor 1-alpha (tef1-α), and RNA polymerase II subunit (rpb2) dataset as well as 10 ITS datasets (totally including 1 435 sequences from 828 collections with 597 newly generated sequences, and 168 sequences from the types of 63 species). Our phylogenetic tree based on a concatenated multilocus dataset revealed that all Chinese Tuber species nested in nine phylogenetic clades (phylogroups), including Aestivum, Excavatum, Latisporum, Macrosporum, Maculatum, Melanosporum, Puberulum, Rufum and Turmericum. Of these, five phylogroups (Macrosporum, Maculatum, Melanosporum, Puberulum and Rufum) are shared across the continents of Asia, Europe and North America; two phylogroups (Aestivum and Excavatum) are shared by Europe and Asia; and the phylogroups Turmericum and Latisporum are endemic only to Asia. Phylogenetic trees based on 10 ITS datasets confirmed the presence of at least 82 phylogenetic species in China. Of these, 53 are identified as known species, including three new records for China, and 25 species are identified as new to science. Of the new species, nine are described and illustrated in this paper, and the others remain unnamed due to the paucity or absence of ascomatal materials. Accordingly, the confirmed, excluded and doubtful Tuber species in China are discussed. Tuber species showed high endemism. Of the 82 phylogenetic species found in China, 68 species occur only in China, six species are also found in other regions in Asia, and only eight species (T. anniae, T. excelsum-reticulatum, T. formosanum, T. maculatum, T. wenchuanense, Tuber sp. CHN-3, Tuber sp. CHN-10 and Tuber sp. CHN-11) are shared with other continents. Most Tuber species have a small and limited distribution in China, but a few, such as T. formosanum and T. parvomurphium, are widely distributed across China. Some phylogenetically closely related species, such as T. liaotongense and T. subglobosum, as well as T. xuanhuaense and T. lijiangense, show a pattern of allopatric distribution.

Antenna effect of pyridoxal phosphate on the fluorescence of mitoxantrone-silicon nanoparticles and its application in alkaline phosphatase assay

As a kind of sensing and imaging fluorescent probe with the merit of low toxicity, good stability, and environment-friendly, silicon nanoparticles (SiNPs) are currently attracting extensive research. In this work, we obtained mitoxantrone-SiNPs (MXT-SiNPs) with green emission by one-pot synthesis under mild temperature condition. The antenna based on pyridoxal phosphate (PLP) was designed for light-harvesting to enhance the luminescence of MXT-SiNPs and to establish a novel sensing strategy for alkaline phosphatase (ALP). PLP transfers the absorbed photon energy to MXT-SiNPs by forming Schiff base. When PLP is dephosphorized by ALP, the released free hydroxyl group reacts with aldehyde group to form internal hemiacetal, which leads to the failure of Schiff base formation. Based on the relationship between antenna formation ability and PLP hydrolysis degree, the activity of ALP can be measured. A good linear relationship was obtained from 0.2 to 3.0 U/L, with a limit of detection of 0.06 U/L. Furthermore, the sensing platform was successfully used to detect ALP in human serum with recovery of 97.6-106.2%. The rational design of antenna elements for fluorescent nanomaterials can not only provide a new pathway to manipulate the luminescence, but also provide a new direction for fluorescence sensing strategy.

[Advances on the toxicology and molecular mechanisms of different components of ambient fine particulate matter]

Ambient fine particulate matters (PM_2.5) refer to particulate matters with an aerodynamic diameter less than or equal to 2.5 μm. PM_2.5 enter the body through the target organ-lung, and can induce a variety of adverse health effects (such as cardiovascular diseases, diabetes, respiratory diseases, neurodegenerative diseases and adverse birth outcomes). PM_2.5 are known to have complex compositions (including water-soluble/-insoluble components and biological components), diverse sources and capacity of secondary transformation. Numerous epidemiological and toxicological studies indicated that different components of PM_2.5 may induce adverse health effects through different biological mechanisms. In adddition, co-exposure of different components and their interaction should also be considered. Thus here we have systematically reviewed studies in recent years about the toxicological effects and underlying mechanisms of different components of ambient fine particulate matters, including inflammatory response, oxidative stress, endoplasmic reticulum stress, activation of the NF-κB signaling pathway and so on. The information may give some insights into the prevention and treatment of adverse health effects caused by exposure to different components of PM_2.5.

Molecularly Imprinted Polymer-Coated Optical Waveguide for Attogram Sensing

Ultrahigh sensitivity and selectivity are the ultimate goals of sensor development. For such purposes, we propose a sensing platform in which an optical fiber-waveguide-fiber (OFWF) structure is integrated with a molecularly imprinted polymer (MIP). The OFWF works as a highly efficient probe light launcher and signal light collector, and the MIP layer acts as a highly selective and sensitive sensing interface. In the MIP design, a high-molecular refractive index monomer (2-phenylphenoxyethyl acrylate) was copolymerized with a MIP functional monomer (acrylic acid). The resulting high-refractive index MIP layers could effectively extract the probe light from the waveguide and send it to the MIP sensing interface. Moreover, a highly elastic cross-linker (poly(ethylene glycol) 600 diacrylate) was employed to increase the MIP mesh size, which could effectively increase the penetrability of the analyte. Rhodamine B (Rh B) is widely used in the textile industry, and its contamination may lead to serious public health problems. As a proof of concept, the Rh B chromophore was used as a molecular template, and the thin MIP layer was cured on the waveguide surface by utilizing the evanescent wave of the 405 nm propagating light in the waveguide. The MIP-OFWF sensing platform afforded highly selective monitoring of the absorption spectra of the components in a mixture solution of Rh B and methyl blue. It also afforded an extremely low detection limit of approximately 6.5 × 10^-17 g/mL, with an absolute mass of 20-30 ag.

Cellulosic hydrocarbons production by engineering dual synthesis pathways in Corynebacterium glutamicum

Background

Lignocellulose provides the only practical carbohydrates feedstock for sustainable bioproduction of hydrocarbons as future alternative of fossil fuels. Production of hydrocarbons from lignocellulose is achieved by a biorefinery process chain including pretreatment to breakdown the crystalline structure for cellulase-catalyzed hydrolysis, detoxification of inhibitory compounds generated during pretreatment, enzymatic hydrolysis to fermentable monosaccharide sugars, and fermentation to hydrocarbon products. The major barriers on fermentative production of hydrocarbons from lignocellulose include two aspects: one is the inherent stress of pretreatment-derived inhibitors on microbial cells, the other is the toxicity of hydrocarbons to cell membranes. The microbial cell factory should be tolerant to both inhibitor stress and hydrocarbons toxicity.

Results

Corynebacterium glutamicum was selected as the starting strain of hydrocarbons synthesis since it is well adapted to lignocellulose hydrolysate environment. The dual hydrocarbon synthesis pathways were constructed in an industrial C. glutamicum S9114 strain. The first pathway was the regular one in microalgae composed of fatty acyl-acyl carrier protein (fatty acyl-ACP) reductase (AAR) and aldehyde deformylating oxygenase (ADO) with fatty acyl-ACP as precursor. The second pathway was the direct decarboxylation of free fatty acid by fatty acid decarboxylase (OleT) using the rich fatty acids from the disruption of the transcriptional regulator fasR gene. The transmembrane transportation of hydrocarbon products was avoided by secretively expressing the fatty acid decarboxylase (OleT) to the extracellular space. The hydrocarbons generation from glucose reached 29.2 mg/L, in which the direct decarboxylation pathway contributed more than 70% of the total hydrocarbons generation, and the AAR–ADO pathway contributed the rest 30%.

Conclusion

The dual hydrocarbon synthesis pathways (OleT and AAR–ADO pathways) were constructed in the inhibitors tolerant C. glutamicum S9114 strain for hydrocarbon production using lignocellulose feedstock as the starting feedstock. When corn stover was used for hydrocarbons production after dry acid pretreatment and biodetoxification, the hydrocarbons generation reached 16.0 mg/L. This study provided a new strategy for hydrocarbons synthesis using microbial cell factory suitable for lignocellulose feedstock.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02129-7.

Efficacy and practice of facemask use in general population: a systematic review and meta-analysis

In recent decades, respiratory infections, including SARS, HINI and the currently spreading COVID-19, caused by various viruses such as influenza and coronavirus have seriously threatened human health. It has generated inconsistent recommendations on the mandatory use of facemasks across countries on a population level due to insufficient evidence on the efficacy of facemask use among the general population. This meta-analysis aimed to explore (1) the efficacy of facemask use on preventing respiratory infections, and (2) the perceptions, intentions, and practice about facemask use among the general population worldwide. We searched PubMed, MEDLINE, Web of Science, Cochrane, bioRxiv, and medRxiv databases since inception to August 17, 2020. From 21,341 records identified, eight RCTs on facemask in preventing infections and 78 studies on perception, intention, and practice of facemask use among the general population were included in the analysis. The meta-analysis of RCTs found a significant protective effect of facemask intervention (OR = 0.84; 95% CI = 0.71-0.99; I2 = 0%). This protective effect was even more pronounced when the intervention duration was more than two weeks (OR = 0.76; 95% CI = 0.66-0.88; I2 = 0%). The meta-analysis of observational studies on perception, intention, and practice on facemask use showed that 71% of respondents perceived facemasks to be effective for infection prevention, 68% of respondents would wear facemasks, and 54% of respondents wore facemasks for preventing respiratory infections. Differences in perception, intention, and practice behavior of facemask use in different regions may be related to the impact of respiratory infections, regional culture, and policies. The governments and relevant organizations should make effort to reduce the barriers in the use of facemasks.

Efficacy and Safety of Albumin-Bound Paclitaxel Compared to Docetaxel as Neoadjuvant Chemotherapy for HER2-Negative Breast Cancer

Background

Nanoparticle albumin-bound paclitaxel (nab-paclitaxel) as neoadjuvant chemotherapy (NAC) for breast cancer remains controversial. We conducted a retrospective study to compare the efficacy and safety of nab-paclitaxel with those of docetaxel as neoadjuvant regimens for HER2-negative breast cancer.

Methods

In this retrospective analysis, a total of 159 HER2-negative breast cancer patients who had undergone operation after NAC were consecutively analyzed from May 2016 to April 2018. Patients were classified into the nab-paclitaxel group (n = 79, nab-paclitaxel 260 mg/m², epirubicin 75 mg/m², and cyclophosphamide 500 mg/m²) and the docetaxel group (n = 80, docetaxel 75 mg/m², epirubicin 75 mg/m², and cyclophosphamide 500 mg/m²) according to the drug they received for neoadjuvant treatment. The efficacy and adverse events were evaluated in the two groups.

Results

The pathological complete response (pCR)(ypT0/isN0) rate was significantly higher in the nab-paclitaxel group than in the docetaxel group (36.71% vs 20.00%; P = 0.031). The multivariate analysis revealed that therapeutic drugs, lymph node status, and tumor subtype were the most significant factor influencing treatment outcome. At a median follow-up of 47 months, disease-free survival (DFS) was not significantly different in those assigned to nab-paclitaxel compared with docetaxel (82.28% vs 76.25%; P = 0.331). The incidence of peripheral sensory neuropathy in the nab-paclitaxel group was higher than that in the docetaxel group (60.76% vs 36.25%; P = 0.008), while the incidence of arthralgia was observed more frequently in the docetaxel group (57.50% vs 39.97%; P = 0.047).

Conclusions

Compared with docetaxel, nab-paclitaxel achieved a higher pCR rate, especially those patients with triple-negative breast cancer or lymph node negative breast cancer. However, there was no significant difference in DFS between the two groups. This study provides a valuable reference for the management of patients with HER2-negative breast cancer.

[Epidemic characteristics of stomach cancer mortality in Qidong during 1972-2016]

Objective: To describe the epidemic characteristics of stomach cancer mortality in Qidong between 1972 and 2016. Methods: The cancer registry data of stomach cancer death and population during 1972-2016 in Qidong was collected. The mortality of crude rate (CR), China age-standardized rate (CASR), world age-standardized rate (WASR), 35-64 years truncated rate, 0-74 years cumulative rate, cumulative risk, percentage change (PC), annual percent change (APC) were calculated. Results: During 1972-2016, a total of 15 863 (male: 10 114, female: 5 749) deaths occurred attributed to stomach cancer, accounting for 16.04% of all cancers, with CR of 31.37/100 000 (CASR: 12.97/100 000, WASR: 21.39/100 000). The truncated rate of 35-64, cumulative rate of 0-74, and cumulative risk were 28.86/100 000, 2.54%, and 2.51%, respectively. For male, the CR, CASR, WASR were 40.53/100 000, 17.98/100 000, 30.13/100 000, respectively, and for female, the CR, CASR, WASR were 22.45/100 000, 8.52/100 000, 13.92/100 000, respectively. Age-specific mortality analysis showed that the mortality of each age group under 25-year-old group was less than 1/100 000. The CR increased with age. The 50-year-old group reached and exceeded the average mortality of the population, and more than 80-year-old group reached the peak of death. During 1972-2016 in Qidong, The PCs in CR, CASR, and WASR of stomach cancer were 55.43%, -52.02%, -43.60%. The APC were 0.54%, -2.30%, -2.08%, respectively. Period mortality analysis showed that except for the 75-year-old group, the mortality of stomach cancer decreased significantly. Conclusions: The crude mortality of stomach cancer increases slightly in Qidong, while the CASR and WASR decrease significantly. However, stomach cancer is still one of the malignant tumors that most affect health and seriously threat lives.

DULoc: quantitatively unmixing protein subcellular location patterns in immunofluorescence images based on deep learning features

MOTIVATION

Knowledge of subcellular locations of proteins is of great significance for understanding their functions. The multi-label proteins that simultaneously reside in or move between more than one subcellular structure usually involve with complex cellular processes. Currently, the subcellular location annotations of proteins in most studies and databases are descriptive terms, which fail to capture the protein amount or fractions across different locations. This highly limits the understanding of complex spatial distribution and functional mechanism of multi-label proteins. Thus, quantitatively analyzing the multiplex location patterns of proteins is an urgent and challenging task.

RESULTS

In this study, we developed a deep-learning-based pattern unmixing pipeline for protein subcellular localization (DULoc) to quantitatively estimate the fractions of proteins localizing in different subcellular compartments from immunofluorescence images. This model used a deep convolutional neural network to construct feature representations, and combined multiple nonlinear decomposing algorithms as the pattern unmixing method. Our experimental results showed that the DULoc can achieve over 0.93 correlation between estimated and true fractions on both real and synthetic datasets. In addition, we applied the DULoc method on the images in the human protein atlas database on a large scale, and showed that 70.52% of proteins can achieve consistent location orders with the database annotations.

AVAILABILITY AND IMPLEMENTATION

The datasets and code are available at: https://github.com/PRBioimages/DULoc.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Learning protein subcellular localization multi-view patterns from heterogeneous data of imaging, sequence and networks

Location proteomics seeks to provide automated high-resolution descriptions of protein location patterns within cells. Many efforts have been undertaken in location proteomics over the past decades, thereby producing plenty of automated predictors for protein subcellular localization. However, most of these predictors are trained solely from high-throughput microscopic images or protein amino acid sequences alone. Unifying heterogeneous protein data sources has yet to be exploited. In this paper, we present a pipeline called sequence, image, network-based protein subcellular locator (SIN-Locator) that constructs a multi-view description of proteins by integrating multiple data types including images of protein expression in cells or tissues, amino acid sequences and protein-protein interaction networks, to classify the patterns of protein subcellular locations. Proteins were encoded by both handcrafted features and deep learning features, and multiple combining methods were implemented. Our experimental results indicated that optimal integrations can considerately enhance the classification accuracy, and the utility of SIN-Locator has been demonstrated through applying to new released proteins in the human protein atlas. Furthermore, we also investigate the contribution of different data sources and influence of partial absence of data. This work is anticipated to provide clues for reconciliation and combination of multi-source data for protein location analysis.

[Emulation pulmonary nodules localization model:a novel non-invasive localization technique in resection of pulmonary nodules]

Objective: To explore the accuracy and efficiency of a novel 3D-printed emulation localization model of small pulmonary nodules in lung surgery. Methods: From April 2020 to April 2021, a total of 66 patients were selected in the study, who underwent localization and resection of pulmonary nodules with video-assisted thoracoscopic surgery (VATS) guided by the 3D-printed emulation localization model at Department of Thoracic Surgery, West China Hospital of Sichuan University. There were 13 males and 53 females, aged from 25 to 79 (52.7±11.4) years. Of all patients, 24 (36.4%) had single pulmonary nodule, and 42 (63.6%) had synchronous multiple pulmonary nodules. The chest high-resolution CT image data were utilized for digital reconstruction and 3D printing to make a tailored life-size emulation pulmonary nodules localization model, which was used to navigate real-time intraoperative localization of nodules. Clinical data including operative parameters, localization information, resection types and pathological findings of nodules were analyzed. The pulmonary nodules that doctors planned to resect were categorized into two categories:major nodules and additional nodules, according to their presence of invasion and radiological risk factors. The accuracy of localization and resection efficiency of nodules were evaluated in accordance with the categories of the nodules respectively. Results: On the basis of preoperative evaluation, there were 71 major nodules with median maximal diameter of 0.9 (0.6-1.3) cm, and 77 additional nodules with median maximal diameter of 0.5 (0.4-0.7) cm. All patients underwent VATS surgery, 52 of them (78.8%) were treated with uniportal VATS and 14 (21.2%) with triportal VATS. Among the patients with single nodule, 18 segmentectomies and 6 wedge resections were performed; whereas among the patients with multiple nodules, 5 segmentectomies, 14 wedge resections, and 23 combined pulmonary resections (including 2 cases of lobectomy+segmentectomy, 7 cases of lobectomy+wedge resections, and 14 cases of segmentectomy+wedge resections) were achieved. The median operative time was 93 (45-240) min, and the median resection time for all nodules was 51.4 (6.7-147.0) min. All major nodules were successfully resected and visibly dissected after removal, and all additional nodules were successfully resected with 85.7%(66/77) nodules visibly dissected. The accuracy rate of localization of both types of nodules was 100%. All major nodules were malignant, and the malignancy rate of additional nodules was 21.2%(14/66). Conclusion: This novel 3D-printed emulation localization model of small pulmonary nodules proved to be a non-invasive, accurate and efficient technique. Not only that, it has a unique advantage in localization of synchronous multiple pulmonary nodules.

[An analysis of mortality trends for upper gastrointestinal neoplasms in Qidong, 1972-2016]

Objective: To describe the trend of upper gastrointestinal cancer mortality in Qidong between 1972 and 2016, and to provide guidelines for prevention and control measures and strategies. Methods: The upper gastrointestinal data was collected in Qidong cancer registration from 1972 to 2016. Crude mortality rate (CR), China age-standardized rate (CASR), world age-standardized rate (WASR), truncated rate (35-64 years old), cumulative rate (0-74 years old) and cumulative risk were calculated. Annual percent change (APC) was calculated by Joinpoint software. Age-period-cohort model was used to analyze the influence of age, period and birth cohort on the changes in the mortality trend of upper gastrointestinal cancer patients. Results: From 1972 to 2016, there were 20 658 deaths of upper gastrointestinal cancer in Qidong, accounting for 20.89% of all cancer deaths. The CR, CASR, WASR, truncated rate (35-64 years old), cumulative rate (0-74 years old) and cumulative risk were 40.85/100 000, 27.96/100 000, 27.69/100 000, 36.01/100 000, 3.30% and 3.25%, respectively. There were 13 429 male deaths, the CR, CASR, and the WASR were 53.81/100 000, 37.62/100 000, and 39.93/100 000; the female deaths were 7 229, and the CR, CASR, and WASR were 28.23/100 000, 18.87/100 000, 17.25/100 000, respectively. The APCs of the 45-year-old, 55-year-old and 65-year-old age groups were -2.94% (95% CI: -3.32%, -2.56%), -2.94% (95% CI: -3.22%, -2.66%) and -2.04% (95% CI: -2.39%, -1.69%), with significant difference (P<0.05), while without significance of 75-year-old group (P>0.05). From 1972 to 2016, the APCs of CR, CASR, and WASR in the gastrointestinal cancer were 0.65% (95%CI: 0.43%, 0.87%), -2.01% (95%CI: -2.24%, -1.77%) and -2.05% (95%CI: -2.28%, -1.81%). The age-period-cohort model showed that the mortality of upper gastrointestinal cancer was increased with age (P<0.05). Conclusions: The crude mortality of upper gastrointestinal cancer increases slightly in Qidong, while the CASR and WASR decrease significantly. However, with aged tendency of population, the early diagnosis and treatment of upper gastrointestinal cancer is still needed to be paid attention.

Improving Protein Subcellular Location Classification by Incorporating Three-Dimensional Structure Information

The subcellular locations of proteins are closely related to their functions. In the past few decades, the application of machine learning algorithms to predict protein subcellular locations has been an important topic in proteomics. However, most studies in this field used only amino acid sequences as the data source. Only a few works focused on other protein data types. For example, three-dimensional structures, which contain far more functional protein information than sequences, remain to be explored. In this work, we extracted various handcrafted features to describe the protein structures from physical, chemical, and topological aspects, as well as the learned features obtained by deep neural networks. We then used these features to classify the protein subcellular locations. Our experimental results demonstrated that some of these structural features have a certain effect on the protein location classification, and can help improve the performance of sequence-based location predictors. Our method provides a new view for the analysis of protein spatial distribution, and is anticipated to be used in revealing the relationships between protein structures and functions.

Onodera's Prognostic Nutritional Index is a novel and useful prognostic marker for gastrointestinal stromal tumors

BACKGROUND

Immunoinflammatory markers such as the peripheral blood neutrophil-to-lymphocyte ratio (NLR) and the platelet-to-lymphocyte ratio (PLR) have gained considerable attention as prognostic markers in gastrointestinal stromal tumors (GISTs).

AIM

To assess the prognostic value of Onodera’s Prognostic Nutritional Index (OPNI) for GISTs.

METHODS

All patients who had undergone surgical resection for a primary, localized GIST from 2009 to 2016 at our cancer center were initially and retrospectively identified. Recurrence-free survival (RFS) was calculated by the Kaplan-Meier method and compared by the log-rank test. We used multivariate Cox proportional hazard regression models to identify associations with outcome variables.

RESULTS

A total of 235 GISTs were identified and included for analysis under our inclusion criteria. Univariate and multivariate analyses both identified the OPNI as an independent prognostic marker, and the OPNI was associated with the primary site, tumor size, mitotic index, tumor rupture, necrosis, and modified NIH risk classification. Low OPNI (< 51.30; hazard ratio = 5.852; 95% confidence interval: 1.072–31.964; P = 0.0414) was associated with worse RFS. The 2- and 5-year RFS rates of the patients with a low OPNI were 92.83% and 76.22%, respectively, whereas 100% and 98.41% were achieved by the patients with a high OPNI.

CONCLUSION

The preoperative OPNI is a novel and useful prognostic marker for GISTs.

Mental and neurological disorders and risk of COVID-19 susceptibility, illness severity and mortality: A systematic review, meta-analysis and call for action

BACKGROUND

Coronavirus disease 2019 (COVID-19) has evolved into a worldwide pandemic, and has been found to be closely associated with mental and neurological disorders. We aimed to comprehensively quantify the association between mental and neurological disorders, both pre-existing and subsequent, and the risk of susceptibility, severity and mortality of COVID-19.

METHODS

In this systematic review and meta-analysis, we searched PubMed, Web of Science, Embase, PsycINFO, and Cochrane library databases for studies published from the inception up to January 16, 2021 and updated at July 7, 2021. Observational studies including cohort and case-control, cross-sectional studies and case series that reported risk estimates of the association between mental or neurological disorders and COVID-19 susceptibility, illness severity and mortality were included. Two researchers independently extracted data and conducted the quality assessment. Based on I2 heterogeneity, we used a random effects model to calculate pooled odds ratios (OR) and 95% confidence intervals (95% CI). Subgroup analyses and meta-regression analysis were also performed. This study was registered on PROSPERO (registration number: CRD 42021230832).

FINDING

A total of 149 studies (227,351,954 participants, 89,235,737 COVID-19 patients) were included in this analysis, in which 27 reported morbidity (132,727,798), 56 reported illness severity (83,097,968) and 115 reported mortality (88,878,662). Overall, mental and neurological disorders were associated with a significant high risk of infection (pre-existing mental: OR 1·67, 95% CI 1·12-2·49; and pre-existing neurological: 2·05, 1·58-2·67), illness severity (mental: pre-existing, 1·40, 1·25-1·57; sequelae, 4·85, 2·53-9·32; neurological: pre-existing, 1·43, 1·09-1·88; sequelae, 2·17, 1·45-3·24), and mortality (mental: pre-existing, 1·47, 1·26-1·72; neurological: pre-existing, 2·08, 1·61-2·69; sequelae, 2·03, 1·66-2·49) from COVID-19. Subgroup analysis revealed that association with illness severity was stronger among younger COVID-19 patients, and those with subsequent mental disorders, living in low- and middle-income regions. Younger patients with mental and neurological disorders were associated with higher mortality than elders. For type-specific mental disorders, susceptibility to contracting COVID-19 was associated with pre-existing mood disorders, anxiety, and attention-deficit hyperactivity disorder (ADHD); illness severity was associated with both pre-existing and subsequent mood disorders as well as sleep disturbance; and mortality was associated with pre-existing schizophrenia. For neurological disorders, susceptibility was associated with pre-existing dementia; both severity and mortality were associated with subsequent delirium and altered mental status; besides, mortality was associated with pre-existing and subsequent dementia and multiple specific neurological diseases. Heterogeneities were substantial across studies in most analysis.

INTERPRETATION

The findings show an important role of mental and neurological disorders in the context of COVID-19 and provide clues and directions for identifying and protecting vulnerable populations in the pandemic. Early detection and intervention for neurological and mental disorders are urgently needed to control morbidity and mortality induced by the COVID-19 pandemic. However, there was substantial heterogeneity among the included studies, and the results should be interpreted with caution. More studies are needed to explore long-term mental and neurological sequela, as well as the underlying brain mechanisms for the sake of elucidating the causal pathways for these associations.

FUNDING

This study is supported by grants from the National Key Research and Development Program of China, the National Natural Science Foundation of China, Special Research Fund of PKUHSC for Prevention and Control of COVID-19, and the Fundamental Research Funds for the Central Universities.

Nerve bundle formation during the promotion of peripheral nerve regeneration: collagen VI-neural cell adhesion molecule 1 interaction

The formation of nerve bundles, which is partially regulated by neural cell adhesion molecule 1 (NCAM1), is important for neural network organization during peripheral nerve regeneration. However, little is known about how the extracellular matrix (ECM) microenvironment affects this process. Here, we seeded dorsal root ganglion tissue blocks on different ECM substrates of peripheral nerve ECM-derived matrix-gel, Matrigel, laminin 521, collagen I, and collagen IV, and observed well-aligned axon bundles growing in the peripheral nerve ECM-derived environment. We confirmed that NCAM1 is necessary but not sufficient to trigger this phenomenon. A protein interaction assay identified collagen VI as an extracellular partner of NCAM1 in the regulation of axonal fasciculation. Collagen VI interacted with NCAM1 by directly binding to the FNIII domain, thereby increasing the stability of NCAM1 at the axolemma. Our in vivo experiments on a rat sciatic nerve defect model also demonstrated orderly nerve bundle regeneration with improved projection accuracy and functional recovery after treatment with 10 mg/mL Matrigel and 20 μg/mL collagen VI. These findings suggest that the collagen VI-NCAM1 pathway plays a regulatory role in nerve bundle formation. This study was approved by the Animal Ethics Committee of Guangzhou Medical University (approval No. GY2019048) on April 30, 2019.

Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images

Analysis of protein subcellular localization is a critical part of proteomics. In recent years, as both the number and quality of microscopic images are increasing rapidly, many automated methods, especially convolutional neural networks (CNN), have been developed to predict protein subcellular location(s) based on bioimages, but their performance always suffers from some inherent properties of the problem. First, many microscopic images have non-informative or noisy sections, like unstained stroma and unspecific background, which affect the extraction of protein expression information. Second, the patterns of protein subcellular localization are very complex, as a lot of proteins locate in more than one compartment. In this study, we propose a new label-correlation enhanced deep neural network, laceDNN, to classify the subcellular locations of multi-label proteins from immunohistochemistry images. The model uses small representative patches as input to alleviate the image noise issue, and its backbone is a hybrid architecture of CNN and recurrent neural network, where the former network extracts representative image features and the latter learns the organelle dependency relationships. Our experimental results indicate that the proposed model can improve the performance of multi-label protein subcellular classification.