[Progress of circulating tumor DNA in the clinical management of colorectal cancer]

Despite the great progress in the treatment of colorectal cancer (CRC), the current standard treatment protocols still have many limitations, and there is an urgent need for more effective biomarkers for personalized patient treatment. Circulating tumor DNA (ctDNA), as a dynamic, non-invasive liquid biopsy approach, overcomes the limitations of tissue biopsy in detecting tumor heterogeneity and molecular evolution. Current evidence from several studies suggests that ctDNA shows great promise in stratifying recurrence risk, guiding treatment decisions, and monitoring early recurrence. In addition, ctDNA can improve the efficiency of clinical research and drug development. However, the lack of standardisation of pre-ctDNA test variables and analysis procedures and the high technical costs limit its promotion and development. In this review, we summarize the available evidence on ctDNA in the clinical management of CRC and present its limitations and strategies for improvement.

Genomic profiling of pediatric hematologic malignancies and diagnosis of cancer predisposition syndromes: tumor-only versus paired tumor-normal sequencing

Not available.

Effects of oleanolic acid on acute liver injury triggered by lipopolysaccharide in broiler chickens

1. Infectious injury caused by lipopolysaccharide (LPS), a metabolite of gram-negative bacteria, can induce stress responses in animals and is a significant cause of morbidity and mortality in young birds. The purpose of this study was to investigate the effects of dietary supplementation with oleanolic acid (OA) on acute liver injury in broiler chickens challenged with LPS.2. In total, 120 broiler chickens were randomly divided into six groups and fed a basal diet containing 0, 50, 100, or 200 mg/kg OA or 100 mg/kg aureomycin. On d 15, broiler chickens were injected with either LPS or an equivalent volume of normal saline. Six hours after LPS injection, two broiler chicks were randomly selected for sampling in each replicate.3. The results indicated that dietary aureomycin was ineffective in alleviating LSP-associated liver injury, but protected broiler chickens from LPS-induced liver damage. This promoted a significant reduction in the levels of malondialdehyde and an increase in the levels of superoxide dismutase in liver. In addition, OA was found to cause significant reductions in the relative expression of IL-1β, IL-6, and TNF-α in broiler liver tissues, whereas the relative expression of IL-10 was significantly increased.4. In conclusion, oleanolic acid can alleviate oxidative stress and injury in the livers of broiler chickens induced by lipopolysaccharide. Consequently, oleanolic acid has potential utility as a novel anti-inflammatory and antioxidant feed additive.

[Safety of the strategy of minimizing intestinal resection during surgery for pelvic radiation- induced terminal small intestinal stenosis]

Objective: To investigate the efficacy of strategies for minimizing small bowel resection during surgery for pelvic radiation-induced terminal small intestinal stenosis in preventing postoperative complications such as anastomotic leakage and short bowel syndrome. Methods: This was a retrospective cohort study. There are two subtypes of chronic radiation enteritis (CRE) with combined intestinal stenosis and intestinal obstruction: (1) Type I: terminal ileal lesions with a normal ileal segment of 2-20 cm between the ileal lesion and ileocecal junction; and (2) Type II: the lesion is located in the small bowel at a distance from the ileocecal region, usually accompanied by extensive damage to the bowel segments outside the lesion. The indications for minimal bowel resection are as follows: (1) diagnosis of Type I small bowel CRE; (2) absence of radiological evidence of rectosigmoid damage; and (3) absence of colonic obstruction. The contraindications are: (1) stenotic, penetrating lesions of the distal cecum; (2) emergency surgery; (3) recurrence of malignant tumor or history of radiotherapy for recurrent malignant tumor; (4) interval between radiotherapy and surgery <6 months; and (5) history of preoperative small bowel resection or abdominal chemotherapy. Case data of 40 patients with Type I CRE who met the above criteria and had undergone minimal bowel resection between April 2017 and December 2019 were retrospectively analyzed (minimal bowel resection group; including 13 patients from Jinling Hospital, 16 from the Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, and 11 from the Affiliated Hospital of Xuzhou Medical University). Forty patients with Type I CRE who had undergone resection of intestinal stenosis lesions and the ileocecal region between October 2015 and March 2017 were included as historical controls (conventional resection group; all from Jinling Hospital). The specific strategy for minimal bowel resection was one-stage partial ileal resection+ileo anastomosis+protective small bowel stoma. In contrast, conventional resection comprised ileocecal resection+ileocecal-ascending colon anastomosis. Postoperative complications, intraoperative and postoperative recovery, and changes in postoperative quality of life were analyzed in both groups. The severity of postoperative complications was assessed by Clavien-Dindo and the Comprehensive Complication Index (CCI). Karnofsky performance scores (KPS) were used to evaluate the quality of life of patients in the two groups preoperatively and postoperatively. The higher the KPS score, the better the quality of life. Results: Baseline patient characteristics did not differ significantly between the two groups (P>0.05). Compared with the conventional resection group, the length of small bowel resected in the minimal bowel resection group (51 [20-200] cm vs. 91 [60-200] cm, Z=5.653, P<0.001), duration of postoperative total enteral nutrition [9 (3-18) days vs. 12 (4-50) days, Z=2.172, P=0.030], and duration of postoperative hospital stay [17 (9-24) days vs 29 (13-57) days, Z=6.424, P<0.001] were shorter; all of these differences are statistically significant. The overall incidence of postoperative complications was lower in the minimal bowel resection group than in the conventional resection group [20.0% (8/40) vs. 70.0% (28/40), χ2=19.967, P<0.001], These comprised short bowel syndrome [5.0% (2/40) vs. 25.0% (10/40), χ2=6.274, P=0.012], anastomotic leakage or fistula [2.5% (1/40) vs. 22.5% (9/40), χ2=7.314, P=0.014], and pleural effusion [7.5% (3/40) vs. 25.0% (10/40), χ2=4.500, P=0.034], all of which occurred less often in the minimal bowel resection than conventional resection group. The CCI index was also lower in the minimal bowel resection group than in the conventional resection group [CCI>40: 2.5% (1/40) vs. 12.5% (5/40), Z=18.451, P<0.001]. KPS scores were higher in the minimal bowel resection group 1 and 3 months postoperatively than they had been 1 day preoperatively (79.9±4.7 vs. 75.3±4.1, 86.2±4.8 vs. 75.3±4.1, both P<0.05). In the minimal bowel resection group, seven patients were satisfied with their current quality of life and refused to undergo stoma reduction at follow-up and one deferred stoma reduction because of rectal bleeding. The remaining 32 patients underwent stoma reduction 3 to 12 months after surgery, 26 of whom underwent ileo-cecal anastomosis. The remaining six underwent resection of the stoma and anastomosis of the ileum to the ascending colon. Conclusions: The strategy of minimal small bowel resection in patients with radiation-induced bowel injuries reduces the length of resected small bowel, decreases the risk and severity of postoperative complications, and is associated with a better prognosis and quality of life than conventional resection.

The Role of Coronary Artery Calcium Score to Assess Risk of Cardiovascular Disease in Irradiated Esophageal Cancer Patients

PURPOSE/OBJECTIVE(S)

Coronary artery calcium (CAC) score is an important predictive imaging marker of cardiovascular disease (CVD). While studies have found positive association between CAC score and cardiac toxicity in irradiated lung and breast cancer patients, there are no studies assessing CAC scores in esophageal cancer (EC). While a cardiac-gated CT is required for standard Agatston CAC score, visual assessment of CAC via ordinal scoring on non-gated CT has shown good concordance with Agatston score. In this study, we sought to examine whether visual assessment of CAC, measured on standard of care, non-contrast chest CT, predicts the development of adverse cardiovascular events (ACVE) in irradiated EC patients.

MATERIALS/METHODS

This is a single institution retrospective study of EC patients treated with RT from 2010-2021. We included patients with available PET/CT at diagnosis or chest CT simulation scan without contrast, and excluded those with history of percutaneous coronary intervention, coronary bypass surgery, or prior thoracic RT. Pre-treatment characteristics, clinical factors, and grade ≥ 3 (G3+) adverse cardiovascular events (ACVE) (CTCAEv5.0) were evaluated. Visual assessment of CAC was performed using ordinal method (CAC scored from 0 to 12), by a thoracic radiologist. Fine and Gray regression was used to compute hazard ratios for time to first ACVE. Univariate analyses using Cox proportional hazards were used for overall survival (OS). ACVEs were recorded from start of oncologic treatment and OS calculated after completion of RT.

RESULTS

A total of 118 patients were analyzed with a median follow-up of 16 months. Median age was 67 years, 65% male, 43% white, 59% with EC of distal esophagus, and 59% had squamous cell carcinoma. Median mean heart dose was 21.93 Gy (range 0.15-36.94). 24% developed G3+ ACVEs: atrial fibrillation 9%, stroke 6%, heart failure 4%, pulmonary embolism 4%, pericardial effusion 3%, myocardial infarction 2%, heart block 2%, and cardiac death 1%. On univariate analyses, CAC >1 vs. CAC ≤ 1 trended towards increased risk of ACVE (HR = 1.95, 95% CI = 0.89-4.26; p = 0.094), however it is not predictive of OS (HR = 1.31, 95% CI = 0.75-2.30; p = 0.343). Proportion of patients with ACVEs was greater in CAC>1 group (Table). When compared to patients with CAC ≤ 1, those with CAC >1 were older (median age 62 vs 72 years, p = 0.0015), less likely to be never smokers (38% vs 30%, p = 0.0437), and more likely to have hypertension (43% vs 64%, p = 0.0197), and hyperlipidemia (30% vs 47%, p = 0.0557).

CONCLUSION

This is the first study to investigate the relationship between CAC score and ACVEs in EC. While the study was underpowered (likely due to low rates of recorded ACVEs), to detect a significant association between CAC score and ACVEs, there was a trend towards increased risk of ACVEs in patients with a CAC score >1 by visual ordinal scoring. Further prospective evaluation with a larger cohort is warranted.

[Impact of different diagnostic criteria for assessing mild micro-hepatic encephalopathy in liver cirrhosis: an analysis based on a prospective, multicenter, real-world study]

Objective: To compare the differences in the prevalence of mild micro-hepatic encephalopathy (MHE) among patients with cirrhosis by using the psychometric hepatic encephalopathy score (PHES) and the Stroop smartphone application (Encephal App) test. Methods: This prospective, multi-center, real-world study was initiated by the National Clinical Medical Research Center for Infectious Diseases and the Portal Hypertension Alliance and registered with International ClinicalTrials.gov (NCT05140837). 354 cases of cirrhosis were enrolled in 19 hospitals across the country. PHES (including digital connection tests A and B, digital symbol tests, trajectory drawing tests, and serial management tests) and the Stroop test were conducted in all of them. PHES was differentiated using standard diagnostic criteria established by the two studies in China and South Korea. The Stroop test was evaluated based on the criteria of the research and development team. The impact of different diagnostic standards or methods on the incidence of MHE in patients with cirrhosis was analyzed. Data between groups were differentiated using the t-test, Mann-Whitney U test, and χ (2) test. A kappa test was used to compare the consistency between groups. Results: After PHES, the prevalence of MHE among 354 cases of cirrhosis was 78.53% and 15.25%, respectively, based on Chinese research standards and Korean research normal value standards. However, the prevalence of MHE was 56.78% based on the Stroop test, and the differences in pairwise comparisons among the three groups were statistically significant (kappa = -0.064, P < 0.001). Stratified analysis revealed that the MHE prevalence in three groups of patients with Child-Pugh classes A, B, and C was 74.14%, 83.33%, and 88.24%, respectively, according to the normal value standards of Chinese researchers, while the MHE prevalence rates in three groups of patients with Child-Pugh classes A, B, and C were 8.29%, 23.53%, and 38.24%, respectively, according to the normal value standards of Korean researchers. Furthermore, the prevalence rates of MHE in the three groups of patients with Child-Pugh grades A, B, and C were 52.68%, 58.82%, and 73.53%, respectively, according to the Stroop test standard. However, among the results of each diagnostic standard, the prevalence of MHE showed an increasing trend with an increasing Child-Pugh grade. Further comparison demonstrated that the scores obtained by the number connection test A and the number symbol test were consistent according to the normal value standards of the two studies in China and South Korea (Z = -0.982, -1.702; P = 0.326, 0.089), while the other three sub-tests had significant differences (P < 0.001). Conclusion: The prevalence rate of MHE in the cirrhotic population is high, but the prevalence of MHE obtained by using different diagnostic criteria or methods varies greatly. Therefore, in line with the current changes in demographics and disease spectrum, it is necessary to enroll a larger sample size of a healthy population as a control. Moreover, the establishment of more reliable diagnostic scoring criteria will serve as a basis for obtaining accurate MHE incidence and formulating diagnosis and treatment strategies in cirrhotic populations.

The Inactivated ISKNV-I Vaccine Confers Highly Effective Cross-Protection against Epidemic RSIV-I and RSIV-II from Cultured Spotted Sea Bass Lateolabrax maculatus

The genus Megalocytivirus of the family Iridoviridae is composed of two distinct species, namely, infectious spleen and kidney necrosis virus (ISKNV) and scale drop disease virus (SDDV), and both are important causative agents in a variety of bony fish worldwide. Of them, the ISKNV species is subdivided into three genotypes, namely, red seabream iridovirus (RSIV), ISKNV, and turbot reddish body iridovirus (TRBIV), and a further six subgenotypes, RSIV-I, RSIV-II, ISKNV-I, ISKNV-II, TRBIV-I, and TRBIV-II. Commercial vaccines derived from RSIV-I , RSIV-II and ISKNV-I have been available to several fish species. However, studies regarding the cross-protection effect among different genotype or subgenotype isolates have not been fully elucidated. In this study, RSIV-I and RSIV-II were demonstrated as the causative agents in cultured spotted seabass, Lateolabrax maculatus, through serial robust evidence, including cell culture-based viral isolation, whole-genome determination and phylogeny analysis, artificial challenge, histopathology, immunohistochemistry, and immunofluorescence as well as transmission electron microscope observation. Thereafter, a formalin-killed cell (FKC) vaccine generated from an ISKNV-I isolate was prepared to evaluate the protective effects against two spotted seabass original RSIV-I and RSIV-II. The result showed that the ISKNV-I-based FKC vaccine conferred almost complete cross-protection against RSIV-I and RSIV-II as well as ISKNV-I itself. No serotype difference was observed among RSIV-I, RSIV-II, and ISKNV-I. Additionally, the mandarin fish Siniperca chuatsi is proposed as an ideal infection and vaccination fish species for the study of various megalocytiviral isolates. IMPORTANCE Red seabream iridovirus (RSIV) infects a wide mariculture bony fish and has resulted in significant annual economic loss worldwide. Previous studies showed that the phenotypic diversity of infectious RSIV isolates would lead to different virulence characteristics, viral antigenicity, and vaccine efficacy as well as host range. Importantly, it is still doubted whether a universal vaccine could confer the same highly protective effect against various genotypic isolates. Our study here presented enough experimental evidence that a water in oil (w/o) formation of inactivated ISKNV-I vaccine could confer almost complete protection against RSIV-I and RSIV-II as well as ISKNV-I itself. Our study provides valuable data for better understanding the differential infection and immunity among different genotypes of ISKNV and RSIV isolates in the genus Megalocytivirus.

Production and characterization of monoclonal antibodies against mandarinfish ranavirus and first identification of pyloric caecum as the major target tissue

Mandarinfish ranavirus (MRV), also known as a variant of largemouth bass virus (LMBV), is an emerging pathogen in mandarinfish aquaculture. In this study, monoclonal antibodies (mAbs) against MRV were produced and characterized, and 7 mAbs were obtained through Western blotting screening and all 7 mAbs specifically recognized MRV/LMBV but not several piscine iridoviruses as ISKNV, GIV and TFV. By LC MS/MS analysis, the recognized viral proteins by seven mAbs were identified as MRV-pORF47L, MRV-pORF55R, MRV-pORF57L, MRV-pORF77L and MRV-pORF78L, respectively, and all five viral proteins are late expression structural proteins by Western blotting. Based on mAb 1C4, immuno-histochemistry and immuno-histo-fluorescence were performed to re-assess the tissue tropism of MRV. The result showed that abundant reactive signals were observed in infected spleen, kidney as well as intestine and pyloric caecum. Real-time quantitative PCR also demonstrated that spleen as well as pyloric caecum and intestines are the major target tissue upon MRV infection. In infected intestines and pyloric caecum, numerous enlarged, multinucleated cells with intracytoplasmic inclusions were identified as the target cells of MRV, suggesting that MRV serves as a digestive tract pathogen to mandarinfish, which may explain why acute infection of MRV can cause the typical clinicopathology featured by severe ascites.

[Analysis on causes and influencing factors of sudden death on job of workers in a large oil field branch plant during 2014-2020]

Objective: To investigate the epidemiological characteristics of sudden death on job among workers in the large oil field, and to provide scientific basis for dealing with such incidents. Methods: In April 2021, the medical records of employees who died in a large oilfield from 2014 to 2020, and the occupational health examination data in the first year of life were collected, and 85 employees who died suddenly on duty were included in the study. According to whether the employees are exposed to the occupational disease hazards, they are divided into the injured type of work (66 persons) and the non injured type of work (19 persons) . The characteristics of the clinical data of the sudden death employees are analyzed retrospectively. The gender, age, length of service, type of work, distribution of causes of sudden death of the cases are analyzed. The detection of abnormalities in various occupational health examination indicators is analyzed. The chi square test is used to analyze the distribution of the types of work, length of service and abnormal physical examination indicators. Results: Among the 85 employees who died suddenly on duty, the ratio of men and women was 16∶1. The proportion of sudden death among employees aged 40 to 50 years was the highest (54.12%, 46/85) , which was mainly the first-line workers in the affected departments (43.53%, 37/85) and those with 20-30 years of service (57.64%, 49/85) . The main cause of sudden death was cardiogenic sudden death (78.82%, 67/85) . There were statistically significant differences in abnormal rates of blood pressure and blood glucose among workers of different types of work (χ(2)=7.24, 24.22, P<0.05) , and there were statistically significant differences in abnormal rates of blood lipid and blood glucose among workers of different ages of service (χ(2)=12.37, 31.44, P<0.05) Conclusion: Higher risks of sudden death on job are male, older than 40 years old, front-line workers in disaster receiving departments, worked for more than 30 years, and have abnormal cardiovascular indicators. Workers with these high risks are the major target population for the prevention and treatment of sudden death on the job. It's necessary to supervise enterprises to implement protective measures against risk factors, and to strengthen health education and reduce the incidence of cardiovascular and cerebrovascular diseases, in order to reduce the occurrence rate of sudden death in oilfield workers.

RF22 | PSUN318 Hepatocytes Exposed to PFOA Prior to Differentiation Leads to Epigenetic Changes in Genes Linked With NAFLD

Background

Perfluorooctanoic acid (PFOA), is a persistent fluorinated compound with oil and water repelling properties found in cookware, food packaging and municipal water systems. Adult animals exposed to PFOA develop hepatomegaly, fatty liver, peroxisome proliferation, and immunotoxicity. Rodents exposed to PFOA in utero have altered hepatic lipid metabolism, increased hepatic de novo lipogenesis and susceptibility to non-alcoholic fatty liver disease (NAFLD), but underlying molecular mechanisms remain unknown. With increasing rates of obesity, diabetes, and NAFLD it is critical to examine the mechanisms by which in utero exposure to PFOA contributes to the development of metabolic syndrome in offspring.

Objectives

To characterize how PFOA exposure during hepatocyte differentiation leads to the development of NAFLD through alterations in DNA methylation profiles and changes in the availability of transcription factor binding sites.

Methods

HepaRG cells (human-derived hepatocyte progenitor cells) were treated with 0.5uM PFOA or vehicle for 48 hours followed by differentiation. Undifferentiated and differentiated hepatocytes exposed to PFOA were assessed relative to controls (n=4). RNASeq was completed; DESeq2 identified differentially expressed genes via false discovery rate (FDR) of &lt;0.05 after Bonferroni correction. Genome-wide DNA methylation analysis via MethylSeq was completed to identify differentially methylated regions (DMRs) defined as minimum number of CpN =5, absolute change in percent methylation &gt;10%, and FDR of &lt;0.05. Enrichment analysis of transcription factor binding motifs within DMRs and single CpG sites (± 200 bp) was performed using HOMER.

Results

PFOA treatment resulted in decreased expression of the transcription factors early growth response protein 1 (EGR1), nuclear receptor Nur77 (NR4A1), early growth response protein 2 (EGR2), krueppel-like factor 10 (KLF10) and fos-related antigen 1 (FOSL1), which are key genes linked to impaired hepatic insulin signaling, lipid metabolism, steatosis and fibrosis (q&lt;0.05) in undifferentiated hepatocytes. Differentiated hepatocytes showed decreased expression of peroxisome proliferator-activated receptor γ coactivator 1-α (PGC1α), peroxisome proliferator-activated receptor γ (PPARγ), forkhead box protein O1 (FOXO1) and increased expression of pyruvate dehydrogenase kinase isozyme 4 (PDK4), genes linked to regulation of lipid metabolism and insulin signaling (q &lt;0.05). MethylSeq analysis identified changes in DMRs located in exons, introns, and intergenic regions, with 57 DMRs in undifferentiated hepatocytes (46 with gains; 11 with losses; q &lt;0.05) and 75 DMRs in differentiated hepatocytes (32 with gains; 41 with losses; q&lt;0.05). HOMER identified 29 known transcription factor binding motifs with changes in methylation in undifferentiated hepatocytes (p&lt;0.05) and 19 in differentiated hepatocytes after PFOA treatment (p&lt;0.05), with significant changes in the EGR1 consensus sequence identified in both comparisons.

Conclusions

We conclude hepatocyte progenitor cells exposed to low dose PFOA results in changes in DNA methylation and expression of key metabolic genes linked to NAFLD, notably EGR1, a gene previously linked to NAFLD, suggesting PFOA exposure in utero has lasting effects.

Presentation: Sunday, June 12, 2022 12:30 p.m. - 2:30 p.m., Sunday, June 12, 2022 12:48 p.m. - 12:53 p.m.

Novel ATXN1/ATXN1L::NUTM2A fusions identified in aggressive infant sarcomas with gene expression and methylation patterns similar to CIC-rearranged sarcoma

CIC-rearranged sarcomas are newly defined undifferentiated soft tissue tumors with CIC-associated fusions, and dismal prognosis. CIC fusions activate PEA3 family genes, ETV1/4/5, leading to tumorigenesis and progression. We report two high-grade CNS sarcomas of unclear histological diagnosis and one disseminated tumor of unknown origin with novel fusions and similar gene-expression/methylation patterns without CIC rearrangement. All three patients were infants with aggressive diseases, and two experienced rapid disease deterioration and death. Whole-transcriptome sequencing identified an ATXN1-NUTM2A fusion in the two CNS tumors and an ATXN1L-NUTM2A fusion in case 3. ETV1/4/5 and WT1 overexpression were observed in all three cases. Methylation analyses predicted CIC-rearranged sarcoma for all cases. Retrospective IHC staining on case 2 demonstrated ETV4 and WT1 overexpression. ATXN1 and ATXN1L interact with CIC forming a transcription repressor complex. We propose that ATXN1/ATXN1L-associated fusions disrupt their interaction with CIC and decrease the transcription repressor complex, leading to downstream PEA3 family gene overexpression. These three cases with novel ATXN1/ATXN1L-associated fusions and features of CIC-rearranged sarcomas may further expand the scope of "CIC-rearranged" sarcomas to include non-CIC rearrangements. Additional cases are needed to demonstrate if ATXN1/ATXN1L-NUTM2A fusions are associated with younger age and more aggressive diseases.

[Comparison of off-pump coronary artery bypass grafting alone or combined with mitral valve plasty for coronary heart disease with moderate ischemic mitral insufficiency]

Objective: To compare the efficacy of off-pump coronary artery bypass grafting (CABG) or CABG plus mitral valve plasty (MVP) in patients with coronary heart disease complicated with moderate ischemic mitral insufficiency. Methods: The clinical data of 1 050 patients with coronary heart disease complicated with moderate ischemic mitral insufficiency who underwent surgical procedures from January 2009 to December 2020 were analyzed retrospectively. There were 733 males and 317 females, aging (63.3±9.0) years (range: 31 to 83 years). Patients were divided into CABG+MVP group and CABG group according to surgical methods, and the two groups of patients were matched for 1∶4 by the propensity score matching method. There were 107 patients in the CABG+MVP group and 406 patients in the CABG group after matching. The t test, Mann-Whitney U test, χ2 test, Fisher's exact probability method and repeated measures anova were used to compare the surgical outcomes and overall survival in the two groups. Results: There were no significant differences in perioperative death and postoperative complications between the two groups (all P>0.05). Compared with CABG group, CABG+MVP group had longer operation time ((5.6±1.2) hours vs. (4.2±1.0) hours, t=11.528, P<0.01), ICU stay(M(IQR))(43.0(47.3) hours vs. 25.0(33.6) hours, Z=2.483, P=0.013), and postoperative hospital stay (8(4) days vs. 7(5) days, Z=2.143, P=0.032). The amount of erythrocyte and platelet used in CABG+MVP group was significantly increased (2.0(6.5) U vs. 0(2.0) U, Z=7.084, P<0.01; 0(0.5) U vs. 0(0) U, Z=5.210, P<0.01). A total of 463 cases (93.9%) were followed up. Median follow-up was 32(31) months (range: 3 to 105 months). There was no significant difference in overall survival and no major adverse cardic and cerebrovascular events survival between CABG group and CABG+MVP group (P=0.196,P=0.305). Echocardiography showed that there was no significant difference in ejection fraction left ventricular end-diastolic diameter between the two groups (F=0.322, P=0.571; F=0.681, P=0.410). However, CABG+MVP improved mitral regurgitation better than CABG (F=160.222, P<0.01). Conclusions: For patients with coronary heart disease with moderate ischemic mitral insufficiency, the rates of all-cause mortality and major adverse cardiac and cerebrovascular events are similar between the two surgeries. Although CABG+MVP improves mitral regurgitation better than CABG, it increases the duration of surgery, ICU stay, postoperative hospital stay, and blood transfusion requirement.

Abstract 5268: The spectrum of FGFR mutations in pediatric and young adult solid tumor

Fibroblast growth factor receptors (FGFRs) are a family of receptor tyrosine kinases expressed on the cell membrane that play crucial roles in cellular lineage commitment, differentiation, proliferation, and apoptosis. Deregulated FGFR signaling is observed in a subset of tumors across various histologies, making FGFRs ideal therapeutic targets. We sought to determine the genetic landscape of FGFR-family variations in a cohort of pediatric and young adult patients with solid tumors. The CHOP Comprehensive Solid Tumor Panel was performed on 1,420 patients. The panel covers 238 cancer genes and screens for single nucleotide variants (SNVs), indels, copy number alterations, and 117 fusion gene partners interrogating over 700 exons for known and novel fusions. Identified variants were categorized and reported according to the AMP/ASCO/CAP guidelines. Fifty-six patients (4.1%), including 47 children and 9 young adults, were found to carry at least one FGFR alteration in their tumors. CNS tumors accounted for most of the cases (51 total, 87.9%), with pilomyxoid astrocytoma/pilocytic astrocytoma and dysembryoplastic neuroepithelial tumor the most common (13 and 12 patients, respectively). Non-CNS solid tumors included rhabdomyosarcoma (4 patients), neuroblastoma/ganglioneuroblastoma (2), and follicular thyroid carcinoma (1). FGFR somatic alterations were found in 56 tumors including 41 SNVs and small indels, 6 internal tandem duplications (ITDs), and 15 fusions genes. The most common SNVs observed were hotspot mutations p.K656E and p.N546K of FGFR1. Sequence alterations in FGFR1 contained 35 SNVs and small indels, mostly gain of function mutations located in the kinase domain, and 6 kinase domain ITDs. One SNV was identified in FGFR2 in the immunoglobulin domain. Two SNVs were reported in FGFR3, both of which were in the fibroblast growth factor receptor family domain, and 3 SNVs were identified in FGFR4, all occurring at the p.V550 codon located on the kinase domain. Companion mutations in non-FGFR genes were detected in 27 tumors, predominantly involving RAS signaling pathway genes including NF1 (14 variants), PIK3CA (8), PTPN11 (6) and PIK3R1 (4). Among fusion variants, FGFR1-TACC1 fusions were found in 5 patients, mostly in pediatric patients. One FGFR3-TACC3 fusion was identified in one young adult patient. Seven pediatric patients tested positive for FGFR2 fusions; all with different 3’ partners. The detection of an FGFR alteration defined or changed the histologic diagnosis for 22 patients. Our results reveal that FGFR alterations account for 4.1% (56/1420) of the patients with solid tumors tested in our laboratory. The majority of the FGFR-positive tumors are low-grade CNS tumors. Further, the identification of FGFR alterations can significantly improve the tumor diagnosis and provide genomic evidence for potential targeted treatment with FGFR inhibitors.

Citation Format: Jinhua Wu, Jeffrey Schubert, Feng Xu, Ariel Long, Maha Patel, Netta Golenberg, Weixuan Fu, Kajia Cao, Jiani Chen, Elizabeth H. Denenberg, Elizabeth A. Fanning, Rochelle Bagatell, Theodore W. Laetsch, Adam Resnick, Mariarita Santi, Phillip Jay B. Storm, Minjie Luo, Lea F. Surrey, Yiming Zhong, Marilyn M. Li. The spectrum of FGFR mutations in pediatric and young adult solid tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5268.

Genetic Analysis of Coronary Artery Disease Using Tree-Based Automated Machine Learning Informed By Biology-Based Feature Selection

Machine Learning (ML) approaches are increasingly being used in biomedical applications. Important challenges of ML include choosing the right algorithm and tuning the parameters for optimal performance. Automated ML (AutoML) methods, such as Tree-based Pipeline Optimization Tool (TPOT), have been developed to take some of the guesswork out of ML thus making this technology available to users from more diverse backgrounds. The goals of this study were to assess applicability of TPOT to genomics and to identify combinations of single nucleotide polymorphisms (SNPs) associated with coronary artery disease (CAD), with a focus on genes with high likelihood of being good CAD drug targets. We leveraged public functional genomic resources to group SNPs into biologically meaningful sets to be selected by TPOT. We applied this strategy to data from the U.K. Biobank, detecting a strikingly recurrent signal stemming from a group of 28 SNPs. Importance analysis of these SNPs uncovered functional relevance of the top SNPs to genes whose association with CAD is supported in the literature and other resources. Furthermore, we employed game-theory based metrics to study SNP contributions to individual-level TPOT predictions and discover distinct clusters of well-predicted CAD cases. The latter indicates a promising approach towards precision medicine.

[Clinical research progress in non-invasive positive pressure ventilation from 2020 to 2021]

Non-invasive positive pressure ventilation (NPPV), an essential respiratory support method, is widely used in acute/chronic respiratory failure and assisting rehabilitation in patients with chronic obstructive pulmonary disease (COPD). We searched the relevant research articles about NPPV published from 1^st October 2020 to 30^th September 2021 through Medline. Researches focusing on the clinical application and viral transmission protection during high-flow nasal cannula oxygen and NPPV in COVID-19, were mainly retrospective and of small sample size. It demonstrated that high-flow nasal cannula oxygen and NPPV might reduce intubation rates when treating patients with mild-to-moderate respiratory failure, but the risk of delayed intubation should draw particular precaution. When using NPPV in non-COVID-19-related de novo acute respiratory failure, diaphragm thickening fraction and tidal change of esophageal pressure were validated to predict the treatment outcome. In addition, some studies explored the compliance and related influencing factors associated with the treatment effects of early NPPV initiation on amyotrophic lateral sclerosis patients and the effects of NPPV on dynamic hyperinflation during exercise in COPD patients. Furthermore, the effectiveness of neurally adjusted ventilatory assist ventilation and a novel communication device optimizing the use of NPPV were also investigated and outlined.

PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods

MOTIVATION

Novel machine learning and statistical modeling studies rely on standardized comparisons to existing methods using well-studied benchmark datasets. Few tools exist that provide rapid access to many of these datasets through a standardized, user-friendly interface that integrates well with popular data science workflows.

RESULTS

This release of PMLB (Penn Machine Learning Benchmarks) provides the largest collection of diverse, public benchmark datasets for evaluating new machine learning and data science methods aggregated in one location. v1.0 introduces a number of critical improvements developed following discussions with the open-source community.

AVAILABILITY AND IMPLEMENTATION

PMLB is available at https://github.com/EpistasisLab/pmlb. Python and R interfaces for PMLB can be installed through the Python Package Index and Comprehensive R Archive Network, respectively.

Scale Drop Disease Virus Associated Yellowfin Seabream (Acanthopagrus latus) Ascites Diseases, Zhuhai, Guangdong, Southern China: The First Description

Scale drop disease virus (SDDV), an emerging piscine iridovirus prevalent in farmed Asian seabass Lates calcarifer in Southeast Asia, was firstly scientifically descripted in Singapore in 2015. Here, an SDDV isolate ZH-06/20 was isolated by inoculating filtered ascites from diseased juvenile yellowfin seabream into MFF-1 cell. Advanced cytopathic effects were observed 6 days post-inoculation. A transmission electron microscopy examination confirmed that numerous virion particles, about 140 nm in diameter, were observed in infected MFF-1 cell. ZH-06/20 was further purified and both whole genome and virion proteome were determined. The results showed that ZH-06/20 was composed of 131,122 bp with 135 putative viral proteins and 113 of them were further detected by virion proteome. Western blot analysis showed that no (or weak) cross-reaction was observed among several major viral proteins between ZH-06/20 and ISKNV-like megalocytivirus. An artificial challenge showed that ZH-06/20 could cause 100% death to juvenile yellowfin seabream. A typical sign was characterized by severe ascites, but not scale drop, which was considerably different from SDD syndrome in Asian seabass. Collectively, SDDV was confirmed, for the first time, as the causative agent of ascites diseases in farmed yellowfin seabream. Our study offers useful information to better understanding SDDV-associated diseases in farmed fish.

CCAT2 contributes to progression and treatment resistance of thyroid carcinoma

OBJECTIVE

The aim of this study is to uncover the correlations of the expression of colon cancer associated transcript 2 (CCAT2) in the clinical papillary thyroid carcinoma (PTC) and anaplastic thyroid carcinoma (ATC) specimens with the prognosis and chemoresistance of patients.

PATIENTS AND METHODS

The expression level of CCAT2 in the PTC and ATC specimens was determined using Real-Time quantitative Polymerase Chain Reaction (RT-qPCR), and the correlations of CCAT2 expression with the clinical features of patients were detected via χ2 test. Besides, survival analysis was conducted to verify the relation between CCAT2 expression and patients' survival. After knockdown or overexpression of CCAT2, the changes in the proliferation ability of human thyroid carcinoma cells were examined via Cell Counting kit-8 (CCK-8) assay, and the half maximal inhibitory concentration (IC50) values of doxorubicin and cisplatin were measured by methyl thiazolyl tetrazolium (MTT) assay.

RESULTS

According to the χ2-test results, the expression of CCAT2 was notably correlated with the capsular invasion and lymph node metastasis of PTC, and the capsular invasion, tumor size, and lymph node metastasis of ATC. It was discovered through the survival analysis that the expression of CCAT2 was notably associated with the poor prognosis of ATC patients. After knockdown of CCAT2, both the proliferation ability and the IC50 values of doxorubicin and cisplatin substantially declined in human thyroid carcinoma cells. The opposite conditions were found after CCAT2 was overexpressed in human thyroid carcinoma cells.

CONCLUSIONS

CCAT2 potentiates the proliferation ability and chemoresistance of cells, promotes the progression of thyroid carcinoma, and hinders the prognosis of ATC.

[Development and functional validation of a nano-delivery system of miR-16/polypeptide targeting ovarian cancer cells]

OBJECTIVE

To develop a nano-delivery system for targeted delivery of miR-16/polypeptide for enhancing cisplatin sensitivity of ovarian cancer.

OBJECTIVE

R9-SS-R9 and cRGD-R9-SS-R9 peptides were synthesized and self-assembled with miR-16 molecules to form a nano-delivery system. The stability, particle size, potential and morphology of the nanoparticles were determined by agarose gel electrophoresis, particle size potentiometer and transmission electron microscopy. CCK-8 assay was used to assess the toxicity of the polypeptides in ovarian cancer cells. Stem loop qRT-PCR and living cell imaging were used to verify the uptake efficiency and intracellular distribution of the nanoparticles. Flow cytometry and Western blotting were performed to verify the effect of the nanoparticles for enhancing cisplatin sensitivity of ovarian cancer cells and explore the possible mechanism.

OBJECTIVE

R9-SS-R9/miR-16 and cRGD-R9-SS-R9/miR-16 nanoparticles were successfully prepared. The nanoparticles, with a particle size below 150 nm, a dispersity index less than 0.1 and a potential of about 40 mV, showed a good serum stability. The polypeptide material had no obvious cytotoxicity. The miR-16/polypeptide nanoparticles could be efficiently absorbed by human ovarian cancer cells and were distributed in the cytoplasm. The nanoparticles significantly increased the intracellular expression level of miR-16 (P < 0.001) and decreased the expression of Bcl-2 and Chk-1 proteins in ovarian cancer cells, thus enabling miR-16 to promote apoptosis and enhance cisplatin sensitivity of the cells.

OBJECTIVE

We successfully prepared a miR-16/polypeptide nano-delivery system for targeted delivery of miR-16 to ovarian cancer cells for enhancing cisplatin sensitivity of the cancer cells.

PFOA Exposure Prior to Hepatocyte Differentiation Leads to Gene Expression Changes Implicated in Non-Alcoholic Fatty Liver Disease

Background: Perfluorooctanoic acid (PFOA), is a persistent fluorinated compound with oil and water repelling properties found in cookware, food packaging and municipal water systems. Adult animals exposed to PFOA develop hepatomegaly, fatty liver, peroxisome proliferation, and immunotoxicity. Rodents exposed to PFCs in utero have altered hepatic lipid metabolism, increased hepatic de novo lipogenesis and susceptibility to non-alcoholic fatty liver disease (NAFLD), but underlying molecular mechanisms remain unknown. With increasing rates of obesity, diabetes, and NAFLD it is critical to examine the mechanisms by which in utero exposure to PFOA contributes to the development of metabolic syndrome in offspring. Objective: To determine mechanism by which PFOA alters gene expression in undifferentiated hepatic progenitor cells. Design/methods: HepaRG cells, a human derived hepatocyte progenitor cell line, was treated with 0.5uM PFOA or vehicle for 48 hours followed by differentiation into hepatocytes. Total RNA was extracted using the RNeasy (Qiagen) [total RNA A260/280>2 and RNA integrity number >7 (Agilent Bioanalyzer)] to generate libraries with the Illumina TruSeq stranded total RNA kit. RNA-Seq was performed using 85 bp single-end read sequencing to generate >20 million reads per sample. RNAseq data was aligned to hg38 using STAR v2.6.1a and then quantified with featureCounts v1.6.2. DESeq2 identified differentially expressed genes via FDR (false discovery rate) after Bonferroni correction. Differentially expressed gene lists were used for Ingenuity Pathway Analysis (IPA) to identify pathways of biological significance.

Results: PFOA treatment resulted in increased expression of transcription factors EGR1 (early growth response protein 1), NR4A1 (nuclear receptor Nur77), EGR2 (early growth response protein 2), KLF10 (Krueppel-like factor 10) and FOSL1 (Fos-related antigen 1), key genes linked to impaired hepatic insulin signaling, hepatic lipid metabolism, steatosis and fibrosis (fold change > 1.5; q <0.05). IPA identified enrichment of canonical pathways with biological relevance including hepatic fibrosis signaling, stellate cell activation, VDR/RXR/TR activation, and Type 2 diabetes mellitus signaling (p<0.01). Conclusion: Hepatocyte progenitor cells exposed to low dose PFOA for 48 hours prior to differentiation results in changes in expression of key metabolic genes linked to the development of NAFLD and enrichment of biologically relevant pathways associated with hepatic fibrosis and hepatocellular carcinoma. These results suggest that PFOA exposure in utero may have lasting effects on hepatic glucose and lipid metabolism after differentiation. Further studies are needed to characterize the longstanding metabolic effects of in utero PFOA exposure in offspring and the mechanisms driving the persistence of these changes.

A Novel Graph Based Semi-Supervised Learning Approach to Identify Pathways Contributing to the Development of Diabetes and Obesity

Background: Gestational diabetes (GDM) has profound effects on the intrauterine metabolic milieu, induces marked abnormalities in fetal glucose and insulin secretion and is linked to obesity and diabetes in the offspring, but the mechanisms remain largely unknown. Epigenetic modifications in stems cells may be one mechanism by which an in utero exposure can lead to the development of diabetes and obesity later in life.

Objective: To identify novel pathways contributing to the development of diabetes and obesity in offspring exposed to GDM in utero by integrating data generated from transcriptome and methylome analysis from second trimester human amniocytes exposed to GDM in utero.

Methods: We analyzed RNAseq and genome wide DNA methylation data (ERRBS) generated from second trimester amniocytes obtained from women with GDM (n=14). Amniocytes have stem cells-like characteristics and are derived from the fetus. Expression data of 22,271 genes were retrieved from RNAseq data. CpGs with significant changes in DNA methylation were mapped into 20,028 genes by collapsing methylation probes into promoter and gene regions. To better understand the associations among diverse gene sets or among gene sets and GDM,we first constructed two weighted co-expression networks from RNAseq and DNA methylation data, respectively. Then, two co-expression networks were integrated using a linear combination. With the integrated co-expression network, graph-based label propagation algorithm was employed to prioritize GDM-associated genes.

Results: From the differential expression analysis between GDM and control, the top 20 query genes, including 11 genes and 9 methylated genes, were selected for label propagation. Finally, the top 100 genes were picked up for the pathway enrichment testusing an over-representation analysis approach. Significantly enriched pathways included: Interferon Signaling, N-glycan Antennae Elongation, Sphingolipid Pathway and Metabolism, Classical Complement Pathway, Complement and Coagulation Cascades, Tryptophan Metabolism, Peroxisomal Protein Import, Unsaturated Fatty Acid Metabolism, Complement Activation, Human Innate Immune Response, Ceramide Metabolism, Fertilization Pathway, Keratan Sulfate Biosynthesis Pathway, Transport to the Golgi and Modification Pathway (FDR q&lt;0.05 for all pathways).

Conclusion: Using a novel bioinformatic approach to synthesize transcriptome and methylome data derived from human amniocytes exposed to GDM in utero, we identified potential pathways involved in programming of diabetes and obesity in offspring including pathways involving the immune response, complex lipid metabolism, the complement pathway, and protein transport and processing. Further investigation of these pathways may yield new mechanisms contributing to diabetes and obesity.

Evaluating recommender systems for AI-driven biomedical informatics

Motivation

Many researchers with domain expertise are unable to easily apply machine learning (ML) to their bioinformatics data due to a lack of ML and/or coding expertise. Methods that have been proposed thus far to automate ML mostly require programming experience as well as expert knowledge to tune and apply the algorithms correctly. Here, we study a method of automating biomedical data science using a web-based AI platform to recommend model choices and conduct experiments. We have two goals in mind: first, to make it easy to construct sophisticated models of biomedical processes; and second, to provide a fully automated AI agent that can choose and conduct promising experiments for the user, based on the user’s experiments as well as prior knowledge. To validate this framework, we conduct an experiment on 165 classification problems, comparing to state-of-the-art, automated approaches. Finally, we use this tool to develop predictive models of septic shock in critical care patients.

Results

We find that matrix factorization-based recommendation systems outperform metalearning methods for automating ML. This result mirrors the results of earlier recommender systems research in other domains. The proposed AI is competitive with state-of-the-art automated ML methods in terms of choosing optimal algorithm configurations for datasets. In our application to prediction of septic shock, the AI-driven analysis produces a competent ML model (AUROC 0.85±0.02) that performs on par with state-of-the-art deep learning results for this task, with much less computational effort.

Availability and implementation

PennAI is available free of charge and open-source. It is distributed under the GNU public license (GPL) version 3.

Supplementary information

Supplementary data are available at Bioinformatics online.

[Absence of arterial duct in fetus: an autopsy analysis]

Objective: To analyze the absence of congenital arterial duct in fetus and to improve the diagnostic accuracy. Methods: Four hundred cases of congenital heart disease diagnosed by echocardiography during pregnancy were examined the fetal cardiovascular malformation and visceral malformation, and the absence of arterial duct was analyzed. Results: There were 24(6%)cases of absence of arterial duct, including 19 cases of left aortic arch and five cases of right aortic arch. There were 21 cases with main pulmonary arteries and 3 cases without main pulmonary arteries and branches. There were 15 cases of pulmonary artery stenosis with absence of arterial duct and the major cardiovascular malformations included six cases of single ventricle, six cases of atrial septal defect, four cases of single atrium, four cases of right atrium isomerism, four cases of double outlet right ventricle, four cases of anomalous pulmonary venous drainage, three cases of tetralogy of Fallot, and three cases of persistent left superior vena cava. There were seven cases of pulmonary atresia with absence of arterial duct and with systemic-pulmonary collateral circulation. There was one case of tetralogy of Fallot with absent pulmonary valve and absent arterial duct and the pulmonary artery was dilated. There was one case of aortopulmonary septal defect with absent arterial duct, with normal pulmonary artery. There were also seven cases of asplenia, seven cases of pulmonary abnormality and seven cases of visceral inversion. Conclusions: The absence of arterial duct is often associated with congenital heart disease. Pulmonary atresia is often associated with systemic-pulmonary collateral circulation. The visceral malformations are related to the accompanying congenital cardiovascular malformations.

Financial toxicity in lung cancer: an assessment of magnitude, perception, and impact on quality of life

BACKGROUND

Advances in lung cancer therapy have resulted in improved clinical outcomes. Unfortunately, advances can come at a financial cost to patients and their families that poses a significant risk to overall quality of life (QoL). Financial distress has been shown to be associated with increased symptom burden and decreased treatment compliance but the magnitude of financial distress is not well characterized in lung cancer populations.

PATIENTS AND METHODS

Patients with stage II-IV newly diagnosed lung cancer and starting first-line therapy were recruited at a tertiary academic institution between July 2018 and April 2019. The comprehensive score for financial toxicity (COST) was used to assess financial toxicity and the Functional Assessment of Cancer Therapy-Lung (FACT-L) was used to assess QoL. Associations between financial toxicity and baseline variables were assessed using multivariable linear regression and correlations were assessed using the Pearson correlation.

RESULTS

In this study, 143 consecutive patients were approached and 91.6% agreed to participate (N = 131). The median age was 65 years (35-90); 52.7% were male (n = 69), and 75.6% were white (n = 99). The inability to afford basic necessities and having <1 month of savings was associated with increased financial toxicity (P < 0.001) after adjusting for other factors such as age, race, insurance, and income. There was also a trend toward increased financial toxicity among those who were employed but on sick leave (P = 0.06). Increased financial toxicity was correlated with a decrease in QoL (correlation coefficient 0.41, P < 0.001). Patients' anticipated out-of-pocket (OOP) expenses for the upcoming 6 months ranged from $0 to $50 000 (median $2150). However, there was no correlation between anticipated OOP expenses and either financial toxicity or QoL.

CONCLUSIONS

These data identify key factors for identifying at-risk patients and builds a framework for exploring the benefit of financial counseling interventions, which may improve QoL and oncologic outcomes.

FAIMS-MS might contribute to phosphopeptides identification in plasma

FAIMS interface is gaining popularity because of the impressive 100-fold signal to noise enhancement in addition to the recent coupling to the Orbitrap technology, the most important analyzer developed in the last 20 years. The selection of group of ions and effective removal of single-charged ones at particular compensation voltages increases around 50% the proteome coverage at expenses of lower peptides coverage. However, specific setting for phosphoproteome analysis is yet poorly described. Here we have found the maximum transmission for several tryptic phosphopeptides isolated from a single complex mixture and we have set an experimental method based on five compensation voltages partially different to the ones described previously, demonstrating the relevance of voltages higher than 47 V, with an increase of around 20% of unique phosphopeptides. Using this experimental setup two complex phosphoproteomes isolates (SH-SY5Y cell line and plasma) were analyzed and found increments of 50% on phosphopeptides identification with the proposed method with respect to a previous one, for the cell line extract. Meanwhile for plasma 109 of the detected phosphopeptides are found for first time in this body fluid, presumably due to the release of intracellular proteins. With this FAIMS setup, 60% of the proteins identified are classified as very low abundant proteins.

The use of laser in dentistry: a narrative review

Implant dentistry has emerged as a first line of treatment to replace missing teeth for both the edentulous and partially dentate patients. Implant dentistry is accompanied by the onset of peri-implantitis (PIM). PIM is characterized by the inflammatory destruction of the implant-supporting tissues, because of biofilm formation on the implant surface. A history of periodontitis, poor oral hygiene, and smoking are considered as risk factors for PIM. Occasionally PIM is associated with iatrogenic factors, that, only recently, have been acknowledged as direct cause of PIM, i.e.: non-parallel adjacent implants or the presence of a gap, between fixture and prosthetic components. The use both of traditional protocols of nonsurgical periodontal therapy and the laser seems to be an effective alternative treatment modality for PMI. By the application of laser-assisted non-surgical peri-implant therapy the periodontal pocket depth was reduced. The present article illustrates the nonsurgical management of one case, where failure to remove residual cement, from an implant-supported dental prosthesis, seemed to cause PMI.

Embedding covariate adjustments in tree-based automated machine learning for biomedical big data analyses

Background

A typical task in bioinformatics consists of identifying which features are associated with a target outcome of interest and building a predictive model. Automated machine learning (AutoML) systems such as the Tree-based Pipeline Optimization Tool (TPOT) constitute an appealing approach to this end. However, in biomedical data, there are often baseline characteristics of the subjects in a study or batch effects that need to be adjusted for in order to better isolate the effects of the features of interest on the target. Thus, the ability to perform covariate adjustments becomes particularly important for applications of AutoML to biomedical big data analysis.

Results

We developed an approach to adjust for covariates affecting features and/or target in TPOT. Our approach is based on regressing out the covariates in a manner that avoids ‘leakage’ during the cross-validation training procedure. We describe applications of this approach to toxicogenomics and schizophrenia gene expression data sets. The TPOT extensions discussed in this work are available at https://github.com/EpistasisLab/tpot/tree/v0.11.1-resAdj.

Conclusions

In this work, we address an important need in the context of AutoML, which is particularly crucial for applications to bioinformatics and medical informatics, namely covariate adjustments. To this end we present a substantial extension of TPOT, a genetic programming based AutoML approach. We show the utility of this extension by applications to large toxicogenomics and differential gene expression data. The method is generally applicable in many other scenarios from the biomedical field.

Scaling tree-based automated machine learning to biomedical big data with a feature set selector

Motivation

Automated machine learning (AutoML) systems are helpful data science assistants designed to scan data for novel features, select appropriate supervised learning models and optimize their parameters. For this purpose, Tree-based Pipeline Optimization Tool (TPOT) was developed using strongly typed genetic programing (GP) to recommend an optimized analysis pipeline for the data scientist’s prediction problem. However, like other AutoML systems, TPOT may reach computational resource limits when working on big data such as whole-genome expression data.

Results

We introduce two new features implemented in TPOT that helps increase the system’s scalability: Feature Set Selector (FSS) and Template. FSS provides the option to specify subsets of the features as separate datasets, assuming the signals come from one or more of these specific data subsets. FSS increases TPOT’s efficiency in application on big data by slicing the entire dataset into smaller sets of features and allowing GP to select the best subset in the final pipeline. Template enforces type constraints with strongly typed GP and enables the incorporation of FSS at the beginning of each pipeline. Consequently, FSS and Template help reduce TPOT computation time and may provide more interpretable results. Our simulations show TPOT-FSS significantly outperforms a tuned XGBoost model and standard TPOT implementation. We apply TPOT-FSS to real RNA-Seq data from a study of major depressive disorder. Independent of the previous study that identified significant association with depression severity of two modules, TPOT-FSS corroborates that one of the modules is largely predictive of the clinical diagnosis of each individual.

Availability and implementation

Detailed simulation and analysis code needed to reproduce the results in this study is available at https://github.com/lelaboratoire/tpot-fss. Implementation of the new TPOT operators is available at https://github.com/EpistasisLab/tpot.

Supplementary information

Supplementary data are available at Bioinformatics online.

Transcriptomic changes in the nasal epithelium associated with diesel engine exhaust exposure

BACKGROUND

Diesel engine exhaust (DEE) exposure causes lung cancer, but the molecular mechanisms by which this occurs are not well understood.

OBJECTIVES

To assess transcriptomic alterations in nasal epithelium of DEE-exposed factory workers to better understand the cellular and molecular effects of DEE.

METHODS

Nasal epithelial brushings were obtained from 41 diesel engine factory workers exposed to relatively high levels of DEE (17.2-105.4 μg/m3), and 38 unexposed workers from factories without DEE exposure. mRNA was profiled for gene expression using Affymetrix microarrays. Linear modeling was used to identify differentially expressed genes associated with DEE exposure and interaction effects with current smoking status. Pathway enrichment among differentially expressed genes was assessed using EnrichR. Gene Set Enrichment Analysis (GSEA) was used to compare gene expression patterns between datasets.

RESULTS

225 genes had expression associated with DEE exposure after adjusting for smoking status (FDR q < 0.25) and were enriched for genes in pathways related to oxidative stress response, cell cycle pathways such as MAPK/ERK, protein modification, and transmembrane transport. Genes up-regulated in DEE-exposed individuals were enriched among the genes most up-regulated by cigarette smoking in a previously reported bronchial airway smoking dataset. We also found that the DEE signature was enriched among the genes most altered in two previous studies of the effects of acute DEE on PBMC gene expression. An exposure-response relationship was demonstrated between air levels of elemental carbon and the first principal component of the DEE signature.

CONCLUSIONS

A gene expression signature was identified for workers occupationally exposed to DEE that was altered in an exposure-dependent manner and had some overlap with the effects of smoking and the effects of acute DEE exposure. This is the first study of gene expression in nasal epithelial cells of workers heavily exposed to DEE and provides new insights into the molecular alterations that occur with DEE exposure.

Comparison of protective efficacy between two DNA vaccines encoding DnaK and GroEL against fish nocardiosis

Fish nocardiosis is a chronic granulomatous bacterial disease mainly caused by three pathogenic bacteria, including Nocardia seriolae, N. asteroids and N. salmonicida. Molecular chaperone DnaK and GroEL were identified to be the common antigens of the three pathogenic Nocardia species in our previous studies. To evaluate the immune protective effect of two DNA vaccines encoding DnaK or GroEL against fish nocardiosis, hybrid snakehead were vaccinated and the immune responses induced by these two vaccines were comparatively analyzed. The results suggested it needed at least 7 d to transport DnaK or GroEL gene from injected muscle to head kidney, spleen and liver and stimulate host's immune system for later protection after immunization by DNA vaccines. Additionally, non-specific immunity parameters (serum lysozyme (LYZ), peroxidase (POD), acid phosphatase (ACP), alkaline phosphatase (AKP) and superoxide dismutase (SOD) activities), specific antibody (IgM) production and immune-related genes (MHCIα, MHCIIα, CD4, CD8α, IL-1β and TNFα) were used to evaluate the immune responses induced in vaccinated hybrid snakehead. It proved that all the above-mentioned immune activities were significantly enhanced after immunization with these two DNA vaccines. The protective efficacy of pcDNA-DnaK and pcDNA-GroEL DNA vaccines, in terms of relative percentage survival (RPS), were 53.01% and 80.71% respectively. It demonstrated that these two DNA vaccines could increase the survival rate of hybrid snakehead against fish nocardiosis, albeit with variations in immunoprotective effects. Taken together, these results indicated that both pcDNA-DnaK and pcDNA-GroEL DNA vaccines could boost the innate, humoral and cellular immune response in hybrid snakehead and show highly protective efficacy against fish nocardiosis, suggesting that DnaK and GroEL were promising vaccine candidates. These findings will promote the development of DNA vaccines against fish nocardiosis in aquaculture.

[Short-term outcomes of sequential radial artery grafting in patients with coronary artery disease]

Objective: To explore the short-term outcomes of patients with coronary artery disease (CAD) who underwent coronary artery bypass graft (CABG) with sequential radial artery graft. Methods: Clinical data of patients with CAD who underwent CABG with sequential radial artery graft from August to December 2018 in Beijing Anzhen Hospital was retrospectively analyzed. Computer tomography angiography was employed to evaluate the patency of grafts and the incidence of adverse cardiovascular events was followed up 3 months after surgery. Results: A total of thirty patients were included, with an average age of (60.2±7.3) years old, among whom 83.3% were male, and 93.3% had three-vessel disease detected by coronary angiography. All patients had left internal mammary artery (LIMA) anastomosed to the left anterior descending (LAD) and sequential radial artery graft. Among sequential radial artery grafts, the most frequent anastomosis of sequential radial artery graft was aortic artery (AO)-first diagonal branch (D1)-first obtuse marginal branch (OM1) (13 patients, 43.3%), followed by AO-OM1-second obtuse marginal branch (OM2) (9 patients, 30.0%), and 18 patients also underwent saphenous vein graft. None of 30 patients experienced adverse cardiovascular events during postoperative period in hospital. Three-months follow-up outcomes showed that LIMA-LAD in 1 patient (3.3%) occluded, 3 patients had occluded anastomosis of sequential radial artery graft, 1 patient (3.3%) had heart failure, and 1 patient (3.3%) had recurrent angina. Conclusion: The radial artery could be used as the second arterial graft for CAD patients undergoing CABG with a sequential anastomosis technique, and these patients need regular anti-arterial spasm drug treatment after CABG.

Author Correction: ATF4 couples MYC-dependent translational activity to bioenergetic demands during tumour progression

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

ATF4 couples MYC-dependent translational activity to bioenergetic demands during tumour progression

The c-Myc oncogene (MYC) drives malignant progression, but also induces robust anabolic and proliferative programs leading to intrinsic stress. The mechanisms enabling adaptation to MYC-induced stress are not fully understood. We have uncovered an essential role for the transcription factor ATF4 in survival following MYC activation. MYC upregulates ATF4 by activating GCN2 kinase through uncharged tRNAs. Subsequently, ATF4 co-occupies promoter regions of over 30 MYC target genes, primarily those regulating amino acid and protein synthesis, including 4E-BP1, a negative regulator of translation. 4E-BP1 is essential to balance protein synthesis, relieving MYC-induced proteotoxic stress. 4E-BP1 activity is negatively regulated by mTORC1-dependent phosphorylation and inhibition of mTORC1 signaling rescues ATF4 deficient cells from MYC-induced ER stress. Acute deletion of ATF4 significantly delays MYC-driven tumor progression and increases survival in mouse models. Our results establish ATF4 as a cellular rheostat of MYC-activity, ensuring enhanced translation rates are compatible with survival and tumor progression.

Properties Investigation of GO/HA/Pt Composite Thin Film

Hydroxyapatite/graphene oxide/platinum (HA/GO/Pt) nanocomposite was synthesized and electrodeposited on a pure zirconium substrate. The coated zirconium was annealed at 200, 300, 400, and 600°C in vacuum furnace in presence of argon gas. The structure and morphology of the coated samples were characterized. Biocompatibility and wear and corrosion resistances of specimens were examined. The result of corrosion tests shows that the graphene into HA/Pt composites significantly improves their corrosion resistance. The wear tests results of uncoated and coated samples before and after annealing show that coated samples annealed at 300°C had better wear resistance compared with uncoated and coated samples at other temperatures. Furthermore, the biocompatibility test shows that the coatings improved the cell attachment and proliferation compared to the pure zirconium substrate.