Growth Curves of Subependymal Giant Cell Tumors in Tuberous Sclerosis Complex

BACKGROUND AND PURPOSE

Growth of subependymal giant cell tumor and subependymal nodules has not been well-characterized. The purpose of this study was to determine whether growth curves can differentiate subependymal giant cell tumors from subependymal nodules.

MATERIALS AND METHODS

Brain MR imaging of patients with tuberous sclerosis complex were retrospectively reviewed from 2002 to 2018. All lesions in the region of the foramen of Monro were measured. Lesions were categorized on the basis of maximal diameter at the most recent scan: small lesions (<1 cm), indeterminate lesions (>1 cm), and resected lesions (>1 cm and surgically resected). Growth velocity and acceleration on serial imaging were analyzed, and growth rates were calculated between 0 and 20 years of age and compared among the 3 categories.

RESULTS

Forty-one patients were analyzed. The average age at the earliest scan was 5.9 (SD = 5.7) years. One hundred twenty-six small, 27 indeterminate, and 10 resected lesions were measured. Subependymal giant cell tumors grew faster than indeterminate lesions between 6 and 15 years of age. Indeterminate lesions grew faster than small lesions at 0-10 years of age. Resected lesions showed increased velocity and acceleration of growth compared with indeterminate lesions and small lesions on serial imaging.

CONCLUSIONS

Growth differentiates subependymal nodules and subependymal giant cell tumors within the first 20 years of life, and the use of velocity and acceleration of growth may refine the diagnostic criteria of subependymal giant cell tumors. Additionally, 6-15 years of age may be an important period to monitor subependymal giant cell tumors at the foramen of Monro because increased growth may help to identify subependymal giant cell tumors that will continue to grow and result in obstructive hydrocephalus.

Consensus-based clustering of single cells by reconstructing cell-to-cell dissimilarity

The development of single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) technology has led to great opportunities for the identification of heterogeneous cell types in complex tissues. Clustering algorithms are of great importance to effectively identify different cell types. In addition, the definition of the distance between each two cells is a critical step for most clustering algorithms. In this study, we found that different distance measures have considerably different effects on clustering algorithms. Moreover, there is no specific distance measure that is applicable to all datasets. In this study, we introduce a new single-cell clustering method called SD-h, which generates an applicable distance measure for different kinds of datasets by optimally synthesizing commonly used distance measures. Then, hierarchical clustering is performed based on the new distance measure for more accurate cell-type clustering. SD-h was tested on nine frequently used scRNA-seq datasets and it showed great superiority over almost all the compared leading single-cell clustering algorithms.

[Introduction of World Health Organization Strategies and the Technical Advisory Committee actions on viral hepatitis control and status of the elimination of viral hepatitis in China]

Viral hepatitis has been causing big threat to public health globally. The number of annual deaths caused by hepatitis surpassed the deaths caused by AIDS, tuberculosis, and malaria. World Health Organization (WHO) issued the global health sector strategy on viral hepatitis 2016-2020 (GHSS) to control its epidemic. It established the Strategies and Technical Advisory Committee on HIV, viral hepatitis, and sexually transmitted infections (STAC). This paper summarizes the GHSS goals and the keynote of the 2020 STAC meeting, analyzes the challenges and opportunities faced by China in eliminating viral hepatitis, and provides the comments on the papers on this issue, which could guide further actions.

[Analysis on hepatitis B cases reported from surveillance points in China, 2019]

Objective: To understand the characteristics of hepatitis B cases reported through the National Notifiable Disease Reported System (NNDRS) of China in 2019, analyze the quality of hepatitis B reporting. Methods: The survey forms and reporting cards of hepatitis B cases in 200 surveillance points in China in 2019 were collected from NNDRS, the completeness rate of the reporting card was calculated, and the reported hepatitis B cases were verified based on the diagnostic criteria (WS 299-2008). The clinical types of the cases after verification were compared with the reported ones, the consistency was evaluated with Kappa test. The reasons for the inconsistent clinical types of the cases were analyzed. Results: In 2019, a total of 64 686 hepatitis B cases were reported through NNDRS. Acute, chronic and unclassified hepatitis B cases accounted for 5.8%, 92.4% and 1.8%, respectively. The average age of reported cases was 47 (47±15) years, and males accounted for 64.4%. The average level of alanine aminotransferase was 214.2 (214.2±1 253.4) U/L. The reported cases mainly worked in agriculture, forestry, animal husbandry, fishery, and water conservancy (50.6%, 32 722). The proportions of cases reported from the eastern, western and central regions were 42.5% (27 501),22.1% (14 315) and 35.4% (22 870), respectively. The consistent rate of the clinical types between the reported cases and the verified cases was 58.8%, with a Kappa value of 0.15. For the 39 271 cases confirmed as acute and chronic hepatitis B cases in the reporting cards, the consistent rate of the clinical types between the reported cases and the verified cases was 96.9%, with a Kappa value of 0.73. In 94.5% (24 267/25 681) of the cases with inconsistent clinical types, the reporting card information were incomplete. Conclusion: The diagnosis of hepatitis B has been improved in the hepatitis B surveillance in China, but it is necessary to improve the completeness of the reporting cards of hepatitis B cases to NNDRS.

[Cost-benefit analysis of the hepatitis B vaccination to prevent mother-to-child transmission strategies in China, 1992-2019]

Objective: To make a cost-benefit analysis of the hepatitis B vaccination (HepB) to prevent mother-to-child transmission (PMTCT) strategies in China, 1992-2019. Methods: We built a decision analytic-Markov model to estimate the birth cohorts of 1992-2019. The parameters in our model were referred from literature, published yearbooks, and data from Chinese Center for Disease Control and Prevention. We conducted a univariate sensitivity analysis to test the robustness of the model. Results: For the 28 birth cohorts, the Chinese government has invested 37.43 billion RMB Yuan in direct costs and 47.61 billion RMB Yuan in societal costs on HepB vaccination and HBV prevention of mother to child transmission (PMTCT). And we estimated that about 50 million chronic HBV infections and 12.5 million premature deaths due to HBV-related diseases would be averted. China would save 2.89 trillion RMB Yuan and 6.92 trillion RMB Yuan for the direct and societal medical burden on HBV-related conditions. The direct and societal net benefit was 2.85 trillion RMB yuan 6.87 trillion RMB yuan, respectively. The direct and societal benefit-cost ratios (BCRs) were 77.21 and 145.29, respectively. Conclusion: The strategies of HepB vaccination for HBV PMTCT prevention were cost-effective in China during 1992-2019.

[Estimation of incidence of viral hepatitis B and analysis on case characteristics in China,2013-2020]

Objective: To understand the epidemiological characteristics of hepatitis B in China, evaluate the performance of elimination hepatitis B in China and provide scientific evidence for the prevention and control of hepatitis B. Methods: An analysis was conducted by using the data of hepatitis B cases reported to the National Notifiable Disease Reporting System (NNDRS) from the areas with low, moderate and high hepatitis B prevalence in China from 2013 to 2020, and the information about the diagnoses of the hepatitis B cases were collected, the incidence of hepatitis B was estimated according to the reporting and diagnosis information and the characteristics of acute and chronic hepatitis B were compared. Results: A total of 27 013 hepatitis B cases were reported to NNDRS, including 4 070 acute cases, 21 971 chronic cases and 972 unclassified cases. Among the reported acute hepatitis B cases, 69.9% (2 845/4 070) were confirmed. Among the reported chronic hepatitis B cases, 89.0% (19 548/21 971) were confirmed, and 2.1% (452/21 971) were confirmed as acute cases. It was estimated that the incidence of acute hepatitis B was 4.6/100 000 and the incidence of chronic hepatitis B cases was 54.5/100 000. The case number of acute hepatitis B in age group 31-45 years was highest, accounting for 35.3% (1 164/3 297). The case number of acute hepatitis B in children under 15 years old was lowest, accounting for 0.4% (13/3 297). The case number of chronic hepatitis B in age group 46-60 years was highest, accounting for 34.4% (7 211/20 932). Conclusions: The incidence of acute hepatitis B was in decrease and the incidence of chronic of hepatitis B was in increase in China year by year. It is important to strengthen the standardized diagnosis and treatment of chronic hepatitis B to decrease the morbidity and mortality of hepatitis B. At the same time, it is necessary to standardize the management and reporting of hepatitis B cases reported to NNDRS to improve the accuracy of the reporting of hepatitis B.

[Hesitancy of parents towards vaccines in national immunization program in three regions in China: a cross-sectional study]

Objective: To investigate the incidence and determinants of vaccine hesitancy towards national immunization program in China and understand the current status of parents' hesitancy to different vaccines used in national immunization program. Methods: A cross-sectional survey was conducted in Beijing, Sichuan and Gansu. The methods of proportional probability sampling and convenience sampling were used to select the eligible study subjects for questionnaire surveys. Results: A total of 3 592 parents were enrolled in the study, in whom 38.22% fully accepted all the vaccines, 59.35% agreed to let their children to receive all the vaccines but showed slight concern, and 2.42% had hesitancy to the vaccines. The vaccine with the most hesitancy was polio vaccine (0.89%), followed by diphtheria pertussis tetanus vaccine (0.70%) and hepatitis A vaccine (0.64%). The dominant reason for vaccine hesitancy was the risk-benefit perception of vaccination (31.03%), followed by the low awareness of the parents (21.84%) and the inconvenience caused by distance and time (21.84%). Conclusions: The incidence of vaccine hesitancy towards national immunization program was low in parents in China, but over 50% of the parents showed concern to the vaccines. It is essential to improve the service quality of national immunization program and strengthen the health education about the vaccination to reduce the incidence of vaccine hesitancy in parents.

Achieving Cycling Durability of Lithium-Sulfur Batteries via Capturing Polysulfides through a Three-Dimensional Interconnected Carbon Network Anchored with Ultrafine FeS Nanoparticles

Shuttle effect has always been a critical obstacle to the application of lithium-sulfur (Li-S) batteries for leading to unstable cycle performance and a short lifespan. To solve this problem, a particular strategy is put up to relieve shuttle effect by capturing soluble polysulfides through a three-dimensional interconnected carbon network. Due to the uniformly anchored ultrafine FeS nanoparticles on a 3D interconnected carbon network, the material could lock soluble polysulfides on the cathode side and promote electrochemical conversion reactions among sulfur species. By optimizing the active site exposure of FeS and designing a hierarchical porous and multichannel structure to ensure rapid migration of ions and electrons at the same time, the interlayer can effectively suppress the shuttle effect and enhance sulfur utilization. Thus, the Li-S battery presents excellent cycling stability and rate capability, namely, a reversible specific capacity of 560 mAh g^-1 at 2.0 C over 500 cycles with a decay rate of 0.012% per cycle and a specific capacity of 597 mAh g^-1 at a 5.0 C current rate. This study offers a promising strategy for designing the structure of an interlayer to achieve long-cycle stable Li-S batteries.

[Development and outlook on human challenge trial of vaccine]

Human challenge trial (HCT) is a test in which human volunteers are intentionally infected with pathogens in order to evaluate the efficacy of candidate preventive or therapeutic drugs. During the COVID-19 pandemic, the HCT of vaccines has aroused people's attention due to its significant advantages over clinical trial. This paper introduces the concept, development and application of HCT, the advantages and limitations of HCT for vaccine evaluation, and the consideration of future HCT of COVID-19 vaccine in China.

[Efficacy of intravascular ultrasound-guided rotational atherectomy combined with cutting balloon for pretreatment of severe coronary artery calcified lesions]

OBJECTIVE

To investigate the efficacy and safety of intravascular ultrasound (IVUS)-guided rotational atherectomy (RA) combined with cutting balloon for pretreatment of severe calcified lesions in the coronary artery before stent placement.

METHODS

A total of 120 patients with severe coronary artery calcifications detected by IVUS that required percutaneous coronary intervention (PCI) were recruited from our hospital between January, 2016 to January, 2019. The patients were randomized into two groups for pretreatment of the lesions with semicompliant balloon (SB group, 60 cases) or RA combined with CB (RA+CB group, 60 cases), and drug-eluting stents were implanted after the procedure. The immediate success rate of PCI, vascular parameters detected by IVUS after PCI, and the rates of residual stenosis < 10% were compared between the two groups. The incidences of intraoperative complications and major adverse cardiac events (MACE) within 24 months after the surgery were also observed in the two groups.

RESULTS

The immediate success rate was significantly higher in RA+CB group than in SB group (P=0.032). After pretreatment and stent placement, the minimum stent lumen diameter (P=0.035), minimum stent lumen cross-sectional area (P=0.029), immediate lumen acquisition, immediate lumen cross-sectional area acquisition and the rate of residual stenosis < 10% were all significantly higher in RA+CB group than in SB group (P < 0.001). The patients in RA+ CB group showed obviously less residual stenosis of lumen cross-sectional area than those in SB group after the surgery (χ²= 7.859, P=0.005). The incidences of intraoperative complications (χ²=5.997, P=0.014) and MACE within 24 months after the operation (χ²=4.285, P=0.038) were significantly lower in RA+CB group than in SB group.

CONCLUSION

For patients with severe coronary artery calcifications eligible for PCI, RA combined with CB angioplasty can significantly improve the success rate of immediate PCI, expand the lumen diameter and cross-sectional area of the stent after PCI, enhance immediate lumen gain, and reduce the incidence of intraoperative complications and MACE after the operation.

Sequence-specific minimizers via polar sets

Motivation

Minimizers are efficient methods to sample k-mers from genomic sequences that unconditionally preserve sufficiently long matches between sequences. Well-established methods to construct efficient minimizers focus on sampling fewer k-mers on a random sequence and use universal hitting sets (sets of k-mers that appear frequently enough) to upper bound the sketch size. In contrast, the problem of sequence-specific minimizers, which is to construct efficient minimizers to sample fewer k-mers on a specific sequence such as the reference genome, is less studied. Currently, the theoretical understanding of this problem is lacking, and existing methods do not specialize well to sketch specific sequences.

Results

We propose the concept of polar sets, complementary to the existing idea of universal hitting sets. Polar sets are k-mer sets that are spread out enough on the reference, and provably specialize well to specific sequences. Link energy measures how well spread out a polar set is, and with it, the sketch size can be bounded from above and below in a theoretically sound way. This allows for direct optimization of sketch size. We propose efficient heuristics to construct polar sets, and via experiments on the human reference genome, show their practical superiority in designing efficient sequence-specific minimizers.

Availability and implementation

A reference implementation and code for analyses under an open-source license are at https://github.com/kingsford-group/polarset.

Supplementary information

Supplementary data are available at Bioinformatics online.

TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs

RNA-seq technology is widely employed in various research areas related to transcriptome analyses, and the identification of all the expressed transcripts from short sequencing reads presents a considerable computational challenge. In this study, we introduce TransRef, a new computational algorithm for accurate transcriptome assembly by redefining a novel graph model, the neo-splicing graph, and then iteratively applying a constrained dynamic programming to reconstruct all the expressed transcripts for each graph. When TransRef is utilized to analyze both real and simulated datasets, its performance is notably better than those of several state-of-the-art assemblers, including StringTie2, Cufflinks and Scallop. In particular, the performance of TransRef is notably strong in identifying novel transcripts and transcripts with low-expression levels, while the other assemblers are less effective.

[Relationship between age at menarche and obesity in women]

Objective: To explore the relationship between age at menarche and general obesity (based on BMI) and central obesity (based on WC or WHtR) in middle-aged and elderly women in China. Methods: A total of 6 363 women from the China Health and Retirement Longitudinal Study were included. Restricted cubic splines based on binary logistic regressions were used to analyze the relationship between age at menarche and the risk of obesity. Age at menarche was divided into four groups: ≤13, 14- (control group), 16- , and ≥18 years old. Binary logistic regressions were applied to analyze the relationship between the continuous or grouped variable of age at menarche and the risk of obesity. Results: After adjusting potential confounders, the age at menarche showed a negative linear relationship with the risk of general obesity and central obesity. The risk for obesity based on BMI, WC and WHtR significantly decreased by 6% (OR=0.94, 95%CI: 0.90-0.99), 4% (OR=0.96, 95%CI: 0.92-1.00), and 6% (OR=0.94, 95%CI: 0.90-0.99) for each 1 year increase in age at menarche. Compared with participants who had menarche at age 14- years old, the risk for obesity based on BMI (OR=0.71, 95%CI: 0.55-0.91), WC (OR=0.75, 95%CI: 0.62-0.92) and WHtR (OR=0.76, 95%CI: 0.61-0.96) significantly decreased by 29%, 25%, and 24% in participants who had menarche at age ≥18 years old. Conclusions: There was a negative linear relationship between age at menarche and the risk for general obesity and central obesity in middle-aged and elderly women in China. Older age at menarche might be negatively associated with risk for obesity in middle-aged and elderly women.

A further survey of the quantitative trait loci affecting swine body size and carcass traits in five related pig populations

Breeding for good meat quality performance while maintaining large body size and desirable carcass traits has been the major challenge for modern swine selective breeding. To address this goal, in the present work we studied five related populations produced by two commercial breeds (Berkshire and Duroc) and two Chinese breeds (Licha black pig and Lulai black pig). A single-trait GWAS performed on 20 body size and carcass traits using a self-developed China Chip-1 porcine SNP50K BeadChip identified 11 genome-wide significant QTL on nine chromosomes and 22 suggestive QTL on 15 chromosomes. For the 11 genome-wide significant QTL, eight were detected in at least two populations, and the rest were population-specific and only mapped in Shanxia black pig. Most of the genome-wide significant QTL were pleiotropic; for example, the QTL around 75.65 Mb on SSC4 was associated with four traits at genome-wide significance level. After screening the genes within 50 kb of the top SNP for each genome-wide significant QTL, NR6A1 and VRTN were chosen as candidate genes for vertebrae number; PLAG1 and BMP2 were identified as candidate genes for body size; and MC4R was the strong candidate gene for body weight. The four genes have been reported as candidates for thoracic vertebrae number, lumbar vertebrae number, carcass length and body weight respectively in previous studies. The effects of VRTN on thoracic vertebrae number, carcass length and body length have been verified in Shanxia black pig. Therefore, the VRTN genotype could be used in gene-assisted selection, and this could accelerate genetic improvement of body size and carcass traits in Shanxia black pig.

FEGS: a novel feature extraction model for protein sequences and its applications

BACKGROUND

Feature extraction of protein sequences is widely used in various research areas related to protein analysis, such as protein similarity analysis and prediction of protein functions or interactions.

RESULTS

In this study, we introduce FEGS (Feature Extraction based on Graphical and Statistical features), a novel feature extraction model of protein sequences, by developing a new technique for graphical representation of protein sequences based on the physicochemical properties of amino acids and effectively employing the statistical features of protein sequences. By fusing the graphical and statistical features, FEGS transforms a protein sequence into a 578-dimensional numerical vector. When FEGS is applied to phylogenetic analysis on five protein sequence data sets, its performance is notably better than all of the other compared methods.

CONCLUSION

The FEGS method is carefully designed, which is practically powerful for extracting features of protein sequences. The current version of FEGS is developed to be user-friendly and is expected to play a crucial role in the related studies of protein sequence analyses.

[Clinical and genetic studies on 76 patients with hydrocephalus caused by methylmalonic acidemia combined with homocysteinuria]

Objective: To analyze the clinical features, genetic characteristics, treatment and follow-up results of patients with hydrocephalus caused by methylmalonic acidemia combined with homocysteinuria, and to discuss the optimal strategies for assessing and treating such patients. Methods: From January 1998 to December 2020, 76 patients with hydrocephalus due to methylmalonic acidemia combined with homocysteinuria in the Department of Pediatrics in 11 hospitals including Peking University First Hospital were diagnosed by biochemical, genetic analysis and brain imaging examination. The patients were divided into operation-group and non-operation-group according to whether they underwent ventriculoperitoneal shunt. The clinical features, laboratory examinations, genotype, and follow-up data were retrospectively analyzed. Data were compared between the two groups using rank sum test, and categorical data were compared using χ² test. Results: Among the 76 patients (51 male, 25 female), 5 were detected by newborn screening, while 71 were diagnosed after clinical onset, 68 cases (96%) had early-onset, 3 cases (4%) had late-onset. The most common clinical manifestations of 74 cases with complete data were psychomotor retardation in 74 cases (100%), visual impairment in 74 cases (100%), epilepsy in 44 cases (59%), anemia in 31 cases (42%), hypotonia or hypertonia in 21 cases (28%), feeding difficulties in 19 cases (26%) and disturbance of consciousness in 17 cases (23%). Genetic analysis was performed in 76 cases, all of whom had MMACHC gene variations, including 30 homozygous variations of MMACHC c.609G>A. The most common variations were c.609G>A (94, 62.7%), followed by c.658_660del (18, 12.0%), c.567dupT (9, 6.0%) and c.217C>T (8, 5.3%). Therapy including cobalamin intramuscular injection, L-carnitine and betaine were initiated immediately after diagnosis. A ventriculoperitoneal shunt operation was performed in 41 cases (operation group), and 31 patients improved after metabolic intervention (non-operation group). There was no significant difference in the age of onset, the age of diagnosis, the blood total homocysteine, methionine, and urinary methylmalonic acid concentration between the two groups (all P>0.05). The symptoms of psychomotor development, epilepsy, and visual impairments improved gradually after a long-term follow-up in the operation group. Conclusions: Hydrocephalus is a severe complication of methylmalonic acidemia combined with homocysteinuria. The most common clinical manifestations are psychomotor retardation, visual impairment, and epilepsy. It usually occurs in early-onset patients. Early diagnosis and etiological treatment are very important. Hydrocephalus may improve after metabolic intervention in some patients. For patients with severe ventricular dilatation, prompt surgical intervention can improve the prognosis.

[The quotations of Yijing Dazhi from the Danxi Yi An]

The Yijing Dazhi (, Great Illustrated Directions on Medical Classics) was written by Haiyan He Yue in the Ming Dynasty. This book cited some sections from the Danxi Yi An ( , Danxi's Medical Cases), and some cases in this book were new discoveries. Using the method of philology, this paper compared the cited sections from the Danxi Yi An () in The Yijing Dazhi with the medical records in Danxi Yi An (), Gezhi Yu Lun (, Further Discourses on the Properties of Things), Danxi Zuanyao (, Collected Essentials of Master Danxi's Medical Book), and Danxi Zhifa Xinyao (, Heart and Essentials of Danxi's Treatment Methods). It found that Danxi Yi An() and Danxi Yi An () are actually two individual books. In addition, the contents of Yijing Dazhi cited from Danxi Yi An () are well preserved and have important reference value for collating the medical records of Zhu Danxi in other relevant medical archives.

Gut Barrier Proteins Mediate Liver Regulation by the Effects of Serotonin on the Non-Alcoholic Fatty Liver Disease

Serotonin (5-hydroxytryptamine, 5-HT) has been recognized as a potent pro-inflammatory mediator. Increasing the bioavailability and preventing the formation of 5-HT can reduce the inflammatory response in the body. Moreover, 5-HT is considered as an important central physiologic mediator of intestinal function by regulating intestinal motility, permeability, and other functions. The dysfunction of intestinal serotonergic system causes intestinal barrier damage and further leads to the increase of bacterial endotoxin (LPS) translocation into the liver, which contributes to the development of non-alcoholic fatty liver disease (NAFLD). In addition, increasing the expression of serotonin reuptake transporter (SERT) and decreasing the expression of tryptophan hydroxylase1 (TPH1) can relieve the symptoms of NAFLD. Tryptophan (TRP), as a precursor of 5-HT synthesis, plays an important role in gut homeostasis and energy metabolism. Previous studies have found that TRP supplementation aggravates fatty liver degeneration by producing 5-HT, which activates mTOR signaling pathway in mice fed a high fat and high fructose diet. However, recent researches reveal that TRP supplementation stabilizes the intestinal barrier damage by increasing the expression of occludin and reduces the accumulation of fatty acids in liver. Although the effects of TRP supplementation on NAFLD are not clear and the specific mechanism needs to be further explored. A better understanding of the mechanisms of 5-HT on the liver and gut may open new therapeutic strategies in NAFLD.

[Initial exploration of transfusion-free liver transplantation]

Objective: To evaluate the effect of transfusion-free techniques on the prognosis of liver transplant patients. Methods: The recipients of adult liver transplantation at Tianjin First Central Hospital from August to December 2019 were included in the clinical observation. Liver transplantation without allogeneic blood transfusion was performed through anesthesia management techniques such as acute hemodilution or phlebotomy without volume replacement,maintaining decreased baseline central venous pressure and cell saver. According to the actual results,the patients were divided into two groups: transfusion-free group(n=21) and allogeneic transfusion group(n=28). There were 13 males and 8 females aged of (56.3±11.6) years in the transfusion-free group;and there were 16 males and 12 females aged (54.3±14.2)years in the allogeneic transfusion group. The transplant recipients who had not adopted transfusion management strategy from January to July 2019 were included as control group(27 males and 13 females,aged of (58.9±14.1)years). The clinical data of patients in perioperative period were collected to compare whether there were differences in the recovery of liver function and early complications among the three groups, one-way ANOVA test, rank-sum test, and χ² test were used for data analysis. Results: The amount of intraoperative blood loss in both the transfusion-free group and the transfusion group was less than that in the control group((454.2±271.3)ml vs.(673.6±333.4)ml vs.(890.3±346.7)ml;q=-6.342,-5.286,both P<0.05).The duration of stay in ICU of the transfusion-free group was less than that of the transfusion group and control group((36.4±9.1)hours vs.(44.3±14.9)hours vs.(58.2±21.1)hours;q=-4.432,-3.824,both P<0.05).The mean ALT level at 7 days after operation was significantly lower in the transfusion-free group than in the control group((56.8±32.1)U/L vs.(89.6±45.6)U/L;q=-3.358,P<0.05). Conclusions: The improvement of multi-disciplinary transfusion management technology aimed at transfusion-free liver transplantation can effectively reduce intraoperative hemorrhage and help to avoid surgical transfusion. Transfusion-free liver transplantation is beneficial to the early postoperative recovery,and its long-term clinical significance is worthy of further clinical research.

Exact transcript quantification over splice graphs

Background

The probability of sequencing a set of RNA-seq reads can be directly modeled using the abundances of splice junctions in splice graphs instead of the abundances of a list of transcripts. We call this model graph quantification, which was first proposed by Bernard et al. (Bioinformatics 30:2447–55, 2014). The model can be viewed as a generalization of transcript expression quantification where every full path in the splice graph is a possible transcript. However, the previous graph quantification model assumes the length of single-end reads or paired-end fragments is fixed.

Results

We provide an improvement of this model to handle variable-length reads or fragments and incorporate bias correction. We prove that our model is equivalent to running a transcript quantifier with exactly the set of all compatible transcripts. The key to our method is constructing an extension of the splice graph based on Aho-Corasick automata. The proof of equivalence is based on a novel reparameterization of the read generation model of a state-of-art transcript quantification method.

Conclusion

We propose a new approach for graph quantification, which is useful for modeling scenarios where reference transcriptome is incomplete or not available and can be further used in transcriptome assembly or alternative splicing analysis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13015-021-00184-7.

Tumor-derived exosomal miR-103a-2-5p facilitates esophageal squamous cell carcinoma cell proliferation and migration

OBJECTIVE

This study aimed to identify the different expression of microRNAs (miRNAs) in the plasma derived exosomes of patients with esophageal squamous cell carcinoma (ESCC).

PATIENTS AND METHODS

A total of 9 patients with ESCC and 9 patients with benign diseases were involved. miRNA sequencing was performed to screen differential expression of microRNAs in plasma exosomes between patients with ESCC and controls. The function of miRNA on proliferation and migration abilities was determined by CCK-8 analysis, wound scratch and transwell test. Predicted target genes were screened by databases and confirmed by RT-qPCR.

RESULTS

We identified a total of 10 miRNAs (7 upregulated and 3 downregulated) that were differentially expressed in plasma exosomes between patients with ESCC and control patients (fold change, FC ≥ 2.0 or ≤ -2.0, p ≤ 0.05) by miRNA sequencing. Ten miRNAs were detected by qRT-PCR to verify the results of the miRNA sequencing. MiR-103a-2-5p demonstrated the most significant differential expression in both exosomes of ESCC cell lines and plasma of patients as compared with control patients and was therefore selected for subsequent functional experiments. Overexpression of miR-103a-2-5p promoted proliferation and migration in TE-1 cells, whereas inhibition of miR-103a-2-5p suppressed proliferation and migration in KYSE-150 cells. Exosomes extracted from the cells transfected with miR-103a-2-5p mimics significantly increased the proliferation and migration of two ESCC cell lines. Two genes, CDH11 and NR3C1 were identified as predicted targets of miR-103a-2-5p by the bioinformatics tools TargetScan, MiRanda, and mirDIP and RT-qPCR.

CONCLUSIONS

Our results shed light on how exosomal miR-103a-2-5p can promote proliferation and migration of ESCC cells and may represent a potential target for ESCC therapies.