[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.