Application of deep learning to auto-delineation of target volumes and organs at risk in radiotherapy

The technological advancement heralded the arrival of precision radiotherapy (RT), thereby increasing the therapeutic ratio and decreasing the side effects from treatment. Contour of target volumes (TV) and organs at risk (OARs) in RT is a complicated process. In recent years, automatic contouring of TV and OARs has rapidly developed due to the advances in deep learning (DL). This technology has the potential to save time and to reduce intra- or inter-observer variability. In this paper, the authors provide an overview of RT, introduce the concept of DL, summarize the data characteristics of the included literature, summarize the possible challenges for DL in the future, and discuss the possible research directions.

[Research of the certified reference material of mecury in lyophilized bovine blood]

Objective: To develop a reference material for the analysis of mercury in freeze-dried bovine blood. Methods: The whole blood of the bovine was collected, mercury standard solution was added, After mixing, packaging and freeze-drying. Two concentration levels of reference materials were prepared. The homogeneity and stability were evaluated by t-test and F-test methods respectively. The uncertainty in preparation, long-term stability, short-term stability and fixed value were evaluated Evaluation and assignment of reference materials. The research products were fixed value and were analyzed by two methods and fixed value in 9 laboratories and the uncertainty during development was analyzed. Results: The reference material has good uniformity and can be kept stably for 12 months at -20 ℃; When transported at ≤35 ℃, the quantity value is stable within 7 days; After re dissolution, it can be stored at 4 ℃ for 5 days; The values are 9.4 respectively μg/L and 29.2 μg/L, and the uncertainty is ±1.1 respectively μg/L and ±2.3 μg/L (k=2) . Conclusion: The indexes of reference materials for mercury composition analysis in freeze-dried bovine blood meet the requirements of technical specifications and have certain application value.

P–602 Pregnancy outcomes of progestin primed ovarian stimulation protocol, GnRH antagonist protocol and GnRH agonist protocol for young patients undergoing PGT-M

Study question

To investigate the pregnancy outcomes of progestin primed ovarian stimulation protocol, GnRH antagonist protocol and GnRH agonist protocol for young patients undergoing preimplantation genetic testing for monogenic gene diseases.

Summary answer

PPOS protocol could reduce the normal chromosome formation and further development potential of embryos, suggesting that the PPOS protocol should be used cautiously.

What is known already

GnRH antagonist protocol (GnRHant) and GnRH agonist protocol (GnRHa) have been used in clinic for many years as routine regimens, and their ovarian stimulation effects and pregnancy outcomes have been confirmed by a large number of literatures. As a new protocol in recent years, the reports of pregnancy outcomes of progestin primed ovarian stimulation protocol (PPOS) are inconsistent.

Study design, size, duration

This retrospective cohort study was performed in a reproduction center from a tertiary hospital between September 2018 and November 2020 which included 147 young patients (<35 year old) undergoing preimplantation genetic testing for monogenic gene diseases (PGT-M) after stimulated by progestin primed ovarian stimulation protocol (n = 44), GnRH antagonist protocol (n = 60) or GnRH agonist protocol (n = 43).

Participants/materials, setting, methods

This study included 147 young patients (<35 year old) undergoing preimplantation genetic testing for monogenic gene diseases (PGT-M) after stimulated by progestin primed ovarian stimulation protocol (PPOS, n = 44), GnRH antagonist protocol (GnRHant, n = 60) or GnRH agonist protocol (GnRHa, n = 43). The primary outcomes were normal karyotype embryo rate and live birth rate. The embryological and clinical outcomes were measured.

Main results and the role of chance

Basic characteristics such as infertility duration, age, and body mass index (BMI) were comparable in study groups. No significant difference was found in the number oocytes retrieved or viable embryos between the groups.

Normal karyotype embryo rate of PPOS protocol was significantly lower than GnRHant and GnRHa protocol (57.6% for PPOS vs 76.0% for GnRHant vs 67.3% for GnRHa).

No significant difference were found in chemical pregnancy rate (77.3% for PPOS vs 73.3% for GnRHant vs 74.4% for GnRHa) or clinical pregnancy rate (69.8% for PPOS vs 71.7% for GnRHant vs 72.5% for GnRHa). While live birth rate of PPOS protocol was significantly lower than GnRHant and GnRHa protocol ( 45.5% for PPOS vs 58.3% for GnRHant vs 72.2% for GnRHa).

Limitations, reasons for caution

This is a preliminary study which needs to be further confirmed by large-scale clinical studies.

Wider implications of the findings: Although this is a preliminary study which needs to be further confirmed by large-scale clinical studies, the current results suggest that the application of PPOS should be cautious.

Trial registration number

-

Genome-wide epistatic interactions of litter size at birth in Chinese indigenous pigs

Improving litter size at birth (TNB) and the number of piglets born alive (NBA) are the main breeding goals related to litter traits, which are economically important. A better understanding of genetic architecture underlying TNB and NBA traits could increase pig production efficiency. However, most previous studies on these traits focus on additive genetic effects, while epistatic interactions underlying TNB and NBA traits has not yet been well investigated, which are essential to understand how traits-related genes interact. Herein, we conducted genome scans of epistatic interactions underlying TNB and NBA traits in a total of 150 Chinese indigenous pigs (75 Jinhua and 75 Shengxian Spotted pigs) with high throughput genomic data. Based on SNPs with high interaction values and connectivity scores, we identified eight promising candidate genes (AKT2, TSC1, MTOR, PIK3R5, TIAM1, FGF14, RALB and ROR2) potentially associated with litter traits in pigs. Moreover, the underlying pathways, e.g., calcium ion transport, pointed out their roles in litter size-related traits. Our findings provide new insight into genetic architecture of litter traits in pigs and will benefit economic profits in pig production.

[Design, screening and antibacterial activity evaluation of the novel antibacterial peptide KR-1]

OBJECTIVE

To design novel antimicrobial peptides with high activity and low toxicity and evaluate their effect against Streptococcus mutans and other oral bacteria for prevention and treatment of dental caries.

OBJECTIVE

We synthesized two antimicrobial peptides (KR-1 and KR-2) using Dhvar4 (a histatins5 mimic) as the template. The antimicrobial peptides with high activity and low toxicity were screened using minimal inhibitory concentration (MIC) test, hemolysis test, and CCK-8 assay. Streptococcus mutans biofilms cultured in 96-well plates were divided into experimental group (KR-1) and positive control group (CHX) and treated with concentration gradients (0.6×, 0.8×, 1× and 2× MICs) of KR-1 and CHX, respectively. Crystal violet staining was used for quantitative analysis of the changes of the biofilms after the treatments. The structural changes of the biofilms were observed with laser confocal microscopy after KR-1 treatment at 10 × MIC. The antimicrobial activity of KR-1 against oral Streptococcus was analyzed based on the time required for sterilization after KR-1 treatment.

OBJECTIVE

The MIC of KR-1 and KR-2 for S. mutans was 3.2 μmol/L and 12.8 μmol/L, respectively. Under the effective concentration, KR-1 and KR-2 resulted in hemolysis rates of 0.35% and 48.8% in rabbit red blood cells and lowered the survival rates of gingival fibroblasts to 88.7% and 21.94%, respectively. KR-1 treatment significantly reduced biofilm formation with a minimum biofilm inhibition concentration (MBIC₅₀) lower than 1.92 μmol/L, and showed an even stronger antimicrobial than CHX at the concentration of 2.56 μmol/L (P=0.001). Confocal laser scanning microscopy revealed that the biofilm structure became loosened after KR-1 treatment, which was capable of killing about 90% of the bacteria within 5 min.

OBJECTIVE

The antimicrobial peptide KR-1 has a stronger antibacterial activity and a low toxicity with a good inhibitory effect against S. mutans biofilm.

Distinct Regionalization Patterns of Cortical Morphology are Associated with Cognitive Performance Across Different Domains

Cognitive performance in children is predictive of academic and social outcomes; therefore, understanding neurobiological mechanisms underlying individual differences in cognition during development may be important for improving quality of life. The belief that a single, psychological construct underlies many cognitive processes is pervasive throughout society. However, it is unclear if there is a consistent neural substrate underlying many cognitive processes. Here, we show that a distributed configuration of cortical surface area and apparent thickness, when controlling for global imaging measures, is differentially associated with cognitive performance on different types of tasks in a large sample (N = 10 145) of 9-11-year-old children from the Adolescent Brain and Cognitive DevelopmentSM (ABCD) study. The minimal overlap in these regionalization patterns of association has implications for competing theories about developing intellectual functions. Surprisingly, not controlling for sociodemographic factors increased the similarity between these regionalization patterns. This highlights the importance of understanding the shared variance between sociodemographic factors, cognition and brain structure, particularly with a population-based sample such as ABCD.

LncRNA NORAD stimulates proliferation and migration of renal cancer via activating the miR-144-3p/MYCN axis

OBJECTIVE

The purpose of this study was to clarify the potential role of long non-coding RNA (lncRNA) NORAD in the development of renal cancer.

PATIENTS AND METHODS

Expression levels of NORAD, miR-144-3p, and MYCN in renal cancer tissues and cell lines were detected. After overexpression of NORAD, proliferative and migratory changes in ACHN and A498 cells were evaluated by Cell Counting Kit-8 (CCK-8) and transwell assay, respectively. Thereafter, Luciferase assay was conducted to determine the interaction in the NORAD/miR-144-3p/MYCN axis. Besides, its biological function in influencing phenotype changes of renal cancer cells was finally demonstrated by rescue experiments.

RESULTS

The results manifested that NORAD and MYCN were upregulated, while miR-144-3p was downregulated in renal cancer tissues. Overexpression of NORAD stimulated proliferative and migratory potentials in ACHN and A498 cells, which were partially abolished by co-overexpression of miR-144-3p. Moreover, NORAD/miR-144-3p/MYCN axis was found to be responsible for stimulating the malignant development of renal cancer.

CONCLUSIONS

LncRNA NORAD stimulates proliferative and migratory potentials in renal cancer by sponging miR-144-3p to upregulate MYCN.

[Ion chromatography for the determination of ethylamine in the workplace air]

Objective: To establish a method for the determination of ethylamine in the air of the workplace by ion chromatography. Methods: In August 2020, ethylamine in the air of the workplace was adsorbed by a basic silica gel tube, and ultrasonically desorbed with a 1 mmol/L sulfuric acid solution, and then qualitatively and quantitatively determined by ion chromatography. Results: The linear range of the method was 0.014-50 μg/ml, and the linear equation of the standard curve was y=0.1243x+0.0429, the correlation coefficient was r=0.9997. The detection limit of the method was 4.29 μg/L, and the lower limit of quantification was 14.29 μg/L. The lowest quantitative concentration was 0.012 mg/m(3) (in term of sampling 6.0 L) . The average desorption efficiency of the method was 97.31%, the precision was 1.00%-1.68%, and the standard recovery rate was 96.33%-99.61%. Conclusion: This method is fast, sensitive and accurate, and can be used for the determination of ethylamine in the air of workplace.

Multi-scale modeling for systematically understanding the key roles of microglia in AD development

Alzheimer's disease (AD) is the leading cause of age-related dementia, affecting over 5 million people in the United States. Unfortunately, current therapies are largely palliative and several potential drug candidates have failed in late-stage clinical trials. Studies suggest that microglia-mediated neuroinflammation might be responsible for the failures of various therapies. Microglia contribute to Aβ clearance in the early stage of neurodegeneration and may contribute to AD development at the late stage by releasing pro-inflammatory cytokines. However, the activation profile and phenotypic changes of microglia during the development of AD are poorly understood. To systematically understand the key role of microglia in AD progression and predict the optimal therapeutic strategy in silico, we developed a 3D multi-scale model of AD (MSMAD) by integrating multi-level experimental data, to manipulate the neurodegeneration in a simulated system. Based on our analysis, we revealed that how TREM2-related signal transduction leads to an imbalance in the activation of different microglia phenotypes, thereby promoting AD development. Our MSMAD model also provides an optimal therapeutic strategy for improving the outcome of AD treatment.

Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges

The rapid development of single-cell technologies allows for dissecting cellular heterogeneity at different omics layers with an unprecedented resolution. In-dep analysis of cellular heterogeneity will boost our understanding of complex biological systems or processes, including cancer, immune system and chronic diseases, thereby providing valuable insights for clinical and translational research. In this review, we will focus on the application of machine learning methods in single-cell multi-omics data analysis. We will start with the pre-processing of single-cell RNA sequencing (scRNA-seq) data, including data imputation, cross-platform batch effect removal, and cell cycle and cell-type identification. Next, we will introduce advanced data analysis tools and methods used for copy number variance estimate, single-cell pseudo-time trajectory analysis, phylogenetic tree inference, cell-cell interaction, regulatory network inference, and integrated analysis of scRNA-seq and spatial transcriptome data. Finally, we will present the latest analyzing challenges, such as multi-omics integration and integrated analysis of scRNA-seq data.

[Predictive value of quantitative electroencephalogram in the poor outcome of children with non-traumatic disturbance of consciousness in pediatric intensive care unit]

Objective: To explore the predictive value of quantitative electroencephalogram (qEEG) in the poor outcome of children with non-traumatic disturbance of consciousness (DoC) in the pediatric intensive care unit (PICU). Methods: A prospective study was conducted. From January 2019 to May 2019, a total of 62 patients aged from 1 month to 11 years with non-traumatic DoC in the PICU of the First Affiliated Hospital of Bengbu Medical College were enrolled. Bedside monitoring with NicoletOne monitor was performed within 24 hours after admission, and qEEG parameters, including amplitude-integrated electroencephalogram (aEEG), relative alpha variability (RAV), relative band power (RBP), and spectral entropy (SE) were recorded. The state of consciousness was assessed with modified pediatric Glasgow coma scale (MPGCS) before monitoring. According to the pediatric cerebral performance category score at 1 year after discharge, the enrolled subjects were divided into good and poor outcome groups. The association between these variables and the poor outcome was analyzed by univariate and multivariate logistic regression analysis, and the predictive performance was analyzed by receiver operator characteristic (ROC) curve. Results: There were 39 males and 23 females, with the age of 12.0 (5.8, 24.0) months. Fifty patients (81%) were in the good outcome group and 12 patients (19%) in the poor outcome group. The univariate Logistic regression analysis showed that age (OR=1.037, 95%CI 1.001-1.074, P=0.041), severe abnormal aEEG (OR=128.000, 95%CI 10.274-1 594.656, P<0.01), RAV (OR=0.877, 95%CI 0.810-0.949, P=0.001), SE (OR=0.892, 95%CI 0.814-0.978, P=0.015), and MPGCS score (OR=0.511, 95%CI 0.349-0.747, P=0.001) were significantly associated with the poor outcome. However, the multivariate Logistic regression analysis showed that only severe abnormal aEEG (OR=315.692, 95%CI 6.091-16 362.298, P=0.004) and RAV (OR=0.808, 95%CI 0.664-0.983, P=0.033) were significantly associated with the poor outcome. The area under the curve (AUC) of the aEEG and RAV in predicting the poor outcome were 0.848 (95%CI 0.735-0.927, P<0.01) and 0.847 (95%CI 0.733-0.926, P<0.01), respectively. The optimal cut-off value was severe abnormal for the aEEG and 38% for the RAV, with sensitivity of 67% and 83%, specificity of 98% and 84%, positive predictive value of 89% and 55%, negative predictive value of 92% and 95%, and Youden index of 0.647 and 0.673, respectively. The AUC of the novel combined index of aEEG and RAV for predicting the poor outcome was 0.974 (95%CI 0.898-0.998, P<0.01). Conclusions: The aEEG and RAV are reliable predictors for the poor outcome of children with non-traumatic DoC, and the novel combined index of aEEG and RAV can improve the predictive performance. The qEEG can be used as a routine method for outcome assessment due to its good objectivity.

Autophagy activators stimulate the removal of advanced glycation end products in human keratinocytes

BACKGROUND

The accumulation of advanced glycation end products (AGEs) can impact cellular homoeostasis and protein structure, thus is implicated in numerous skin conditions including yellow, dull appearance. AGE formation is irreversible; thus, understanding of the recycling process of AGEs in the skin is critical for addressing skin appearance conditions.

OBJECTIVE

To determine whether (i) accumulation of AGEs occurs in dull appearance group among young population (age 20-29) (ii) in vitro autophagy stimulation results in reduction of AGEs in keratinocytes.

METHODS

Facial cheek biopsies were collected from Chinese women (age 20-50) exhibiting either dull or non-dull appearing skin. Histological assessment of glycation was performed for representative subjects among the 20-29 years sub-group by immunofluorescence staining of AGEs. LC-MS methods and keratinocyte cell culture were used to assess impact of autophagy modulators and skin care materials on carboxymethyl lysine (CML) amount, a representative AGE.

RESULTS

Notable amounts of AGEs were observed in the epidermal samples among young females. Interestingly, the amount of AGEs was significantly higher among the dull skin appearance group. Treatment of keratinocytes with glyceraldehyde (GLA) enhanced CML in the cells, and postglycation treatment with autophagy activators reduced CML. Two skin care materials, Nymphaea alba flower extract (a.k.a. white water lily extract) and sucrose dilaurate, were identified based from in vitro autophagy activation and found to reduce CML in keratinocytes.

CONCLUSION

We found AGEs accumulate in the facial epidermis even among young people, correlating to a yellow and dull appearance. We also demonstrated in vitro activation of autophagy can reduce AGEs in keratinocytes, and autophagy activating skin care materials, N. alba flower extract and sucrose dilaurate, also reduce AGEs in the keratinocyte in vitro model. These data suggest epidermal AGEs contribute to the dull skin appearance, and autophagy activators may provide an effective solution to improve dull appearance by removing and recycling the accumulated glycation in the skin.

Effect of lncRNA AK023948 on rats with postmenopausal osteoporosis via PI3K/AKT signaling pathway

OBJECTIVE

To investigate the effect of long non-coding ribonucleic acid (lncRNA) AK023948 (AK0) on rats with postmenopausal osteoporosis via the phosphoinositide 3-kinase/protein kinase B (PI3K/AKT) signaling pathway.

MATERIALS AND METHODS

Firstly, postmenopausal osteoporosis rat models were established to obtain osteoblasts. The phosphorylation level of AKT was analyzed by controlling the expression of AK0 gene in osteoblasts. Finally, XTT was used to analyze the proliferation of osteoblasts and the messenger ribonucleic acid (mRNA) expression level of caspase in AK0 gene knockout (KO) rat model.

RESULTS

In the bone tissue of postmenopausal osteoporosis rats, the levels of phospho-PI3K (p-PI3K), p-Akt, and p-phosphoinositide-dependent kinase-1(PDK1) were significantly decreased (p<0.05). In rat model osteoblasts, the overexpression of AK0 gene upregulated the phosphorylation level of AKT, while the interference with small interfering RNA (siRNA) in AK0 gene decreased that of AKT. Knocking out AK0 gene led to the down-regulation of phosphorylation level of AKT in cells. Moreover, if the AK0 gene was re-expressed in the KO rat model cells, the phosphorylation level of AKT was restored to a certain extent, but still lower than that after the overexpression of AK0 gene. Although the proliferation rate of osteoblasts in estrogen deficiency-related osteoporosis rats was low, the growth rate of osteoblasts with AK0 KO was remarkably lower than that in blank control group (p<0.05). It was also found that there was a certain correlation between AK0 gene and osteoblast apoptosis.

CONCLUSIONS

LncRNA AK0 can regulate the phosphorylation level of AKT in osteoblasts of rats with estrogen deficiency-related osteoporosis through the PI3K/AKT signaling pathway, thus regulating the proliferation of osteoblasts. It is speculated that lncRNA AK0 may be an important factor in regulating the PI3K/AKT signaling pathway.