Ensemble neural network model for detecting thyroid eye disease using external photographs

PURPOSE

To describe an artificial intelligence platform that detects thyroid eye disease (TED).

DESIGN

Development of a deep learning model.

METHODS

1944 photographs from a clinical database were used to train a deep learning model. 344 additional images ('test set') were used to calculate performance metrics. Receiver operating characteristic, precision-recall curves and heatmaps were generated. From the test set, 50 images were randomly selected ('survey set') and used to compare model performance with ophthalmologist performance. 222 images obtained from a separate clinical database were used to assess model recall and to quantitate model performance with respect to disease stage and grade.

RESULTS

The model achieved test set accuracy of 89.2%, specificity 86.9%, recall 93.4%, precision 79.7% and an F1 score of 86.0%. Heatmaps demonstrated that the model identified pixels corresponding to clinical features of TED. On the survey set, the ensemble model achieved accuracy, specificity, recall, precision and F1 score of 86%, 84%, 89%, 77% and 82%, respectively. 27 ophthalmologists achieved mean performance of 75%, 82%, 63%, 72% and 66%, respectively. On the second test set, the model achieved recall of 91.9%, with higher recall for moderate to severe (98.2%, n=55) and active disease (98.3%, n=60), as compared with mild (86.8%, n=68) or stable disease (85.7%, n=63).

CONCLUSIONS

The deep learning classifier is a novel approach to identify TED and is a first step in the development of tools to improve diagnostic accuracy and lower barriers to specialist evaluation.

Research on the diagnostic effect of PCT level in serum on patients with sepsis due to different pathogenic causes

OBJECTIVE

To investigate the diagnostic effect of procalcitonin level in serum for patients with sepsis due to different pathogenic causes.

PATIENTS AND METHODS

The clinical data of 132 sepsis patients were analyzed. Those patients were admitted to the Affiliated Hospital of Medical School of Ningbo University from January 2014 to January 2017. According to the blood culture results before antimicrobial therapy, patients were divided into two groups: Gram-negative bacteria group (G- group) and Gram-positive bacteria group (G+ group). The indexes, such as SOFA score, APACHE II score, length of stay in hospital and mortality rate, were used to evaluate disease severity of the two groups. The procalcitonin, WBC, hs-CRP and NEU% were detected and compared between the two groups of patients.

RESULTS

A total of 132 pathogenic bacteria were detected in 132 patients, of which 44 patients were infected with G- bacteria and 88 patients were infected with G+ bacteria. Patients in G- group were mainly infected with Escherichia coli, Acinetobacter baumannii, and Klebsiella pneumoniae, while patients in G+ group were mainly infected with Staphylococcus epidermidis and Staphylococcus aureus. The SOFA score, APACHE II score and mortality rate in G- group were higher than those in G+ group. The PCT levels in G- group and G+ group were (54.89±21.64) ng/mL and (21.13±1.30) ng/mL, respectively. The PCT level in G- group was higher than that in G+ group, and the difference was statistically significant between them (p<0.05). There was no statistically significant difference in length of stay in hospital between the two groups (p>0.05). There were no statistically significant differences in WBC, hs-CRP and NEU% between the two groups (p>0.05).

CONCLUSIONS

The procalcitonin level in serum of sepsis patients at early stage of bloodstream infection is significantly elevated and has diagnostic value for different pathogenic bacteria groups. It can also reflect the disease severity and predict the prognosis of sepsis patients.

Finding associated variants in genome-wide association studies on multiple traits

Motivation

Many variants identified by genome-wide association studies (GWAS) have been found to affect multiple traits, either directly or through shared pathways. There is currently a wealth of GWAS data collected in numerous phenotypes, and analyzing multiple traits at once can increase power to detect shared variant effects. However, traditional meta-analysis methods are not suitable for combining studies on different traits. When applied to dissimilar studies, these meta-analysis methods can be underpowered compared to univariate analysis. The degree to which traits share variant effects is often not known, and the vast majority of GWAS meta-analysis only consider one trait at a time.

Results

Here, we present a flexible method for finding associated variants from GWAS summary statistics for multiple traits. Our method estimates the degree of shared effects between traits from the data. Using simulations, we show that our method properly controls the false positive rate and increases power when an effect is present in a subset of traits. We then apply our method to the North Finland Birth Cohort and UK Biobank datasets using a variety of metabolic traits and discover novel loci.

Availability and implementation

Our source code is available at https://github.com/lgai/CONFIT.

Supplementary information

Supplementary data are available at Bioinformatics online.

Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes

Motivation

There is recent interest in using gene expression data to contextualize findings from traditional genome-wide association studies (GWAS). Conditioned on a tissue, expression quantitative trait loci (eQTLs) are genetic variants associated with gene expression, and eGenes are genes whose expression levels are associated with genetic variants. eQTLs and eGenes provide great supporting evidence for GWAS hits and important insights into the regulatory pathways involved in many diseases. When a significant variant or a candidate gene identified by GWAS is also an eQTL or eGene, there is strong evidence to further study this variant or gene. Multi-tissue gene expression datasets like the Gene Tissue Expression (GTEx) data are used to find eQTLs and eGenes. Unfortunately, these datasets often have small sample sizes in some tissues. For this reason, there have been many meta-analysis methods designed to combine gene expression data across many tissues to increase power for finding eQTLs and eGenes. However, these existing techniques are not scalable to datasets containing many tissues, like the GTEx data. Furthermore, these methods ignore a biological insight that the same variant may be associated with the same gene across similar tissues.

Results

We introduce a meta-analysis model that addresses these problems in existing methods. We focus on the problem of finding eGenes in gene expression data from many tissues, and show that our model is better than other types of meta-analyses.

Availability and Implementation

Source code is at https://github.com/datduong/RECOV.

Supplementary information

Supplementary data are available at Bioinformatics online.

Effect of fixation time on breast biomarker expression: a controlled study using cell line-derived xenografted (CDX) tumours

AIMS

Altering the length of time specimens are placed in fixative without compromising analytical testing accuracy is a continuous challenge in the anatomical pathology lab. The aim of this study was to determine under controlled conditions the effects of variable fixation time on breast biomarker expression in human breast cancer cell line-derived xenografted (CDX) tumours.

METHODS

CDX tumours using strong oestrogen receptor (ER)-positive, Her2-negative (MCF7) and weak ER-positive, Her2 equivocal (T47D) breast cancer cell lines were fixed for various times ranging from 1 to 336 hours in 10% neutral buffered formalin. CDX tumours were processed according to routine biomarker testing protocols and stained for ER and Her2 immunohistochemistry (IHC) and processed for HER2 fluorescence in situ hybridisation (FISH). The tumours were evaluated using Allred scoring for ER and current ASCO/CAP guidelines for Her2, and by objective cell counting methodology.

RESULTS

No differences were found in expression of ER in either MCF7 or T47D CDX tumours under variable fixation. T47D tumours displayed equivocal Her2 staining when fixed for 24 hours, but fixation for ≤8 hours resulted in consistently negative staining while tumours fixed for >72 hours demonstrated consistent equivocal staining (p<0.01). Cell counting assays revealed only a significant increase in sensitivity in tumours fixed for >72 hours (p<0.01). As expected, FISH results were unaffected by variable fixation.

CONCLUSIONS

Neither shortened nor prolonged fixation affects ER expression, consistent with previous findings. In equivocal Her2-expressing tumours, however, increasing fixation increased the sensitivity of Her2 IHC reporting while not affecting FISH.

[Expression and significance of FoxM1 in esophageal squamous cell carcinoma cells in vitro and in vivo]

OBJECTIVE

To investigate the expression and significance of FoxM1 in esophageal squamous cell carcinoma (ESCC) cell lines and tissues.

METHODS

Western blot assay was used to detect the expression of FoxM1 in human esophageal epithelial cells and esophageal squamous cell cancer cell lines TE1, TE10, TE11 and Eca109 cells. To determine whether down-regulation of FoxM1 expression could inhibit the aggressive phenotype of ESCC cells, we knocked down the expression of FoxM1 by using FoxM1-shRNA in TE1 cells. Then we detected the cell proliferation, migration and invasion of TE1 cells by MTT assay, scratch assay and transwell assay. Furthermore, the effect of FoxM1 knockdown on tumorigenicity in nude mice was evaluated. Finally, immunohistochemical staining was used to detect the expression of FoxM1 in 99 cases of ESCC tissues and adjacent normal esophageal tissues. χ(2) test was used to analyze the correlations between the expression of FoxM1 and clinicopathologic characteristics and prognosis of ESCC patients.

RESULTS

Western blot data showed that FoxM1 expression was lower in normal esophageal epithelial cells and highly expressed in four esophageal cancer cell lines, especially in TE1 cells. Knockdown of FoxM1 inhibited the growth, invasion and migration of TE1 cells and reduced their tumorigenicity in nude mice.The positive expression rate of FoxM1 in ESCC was 61.6% (61/99), significantly higher than that in the paired adjacent normal tissues (24.2%, 24/99) (P<0.05). The positive expression rate of FoxM1 in ESCC tissues was 61.6% (61/99), significantly higher than that in the paired adjacent normal tissues (24.2%, 24/99) (P<0.05). FoxM1 expression was significantly and positively correlated with lymph node metastasis, clinical stage and invasive depth (P<0.05). The median survival time was 42.3 months in 38 cases of patients with negative FoxM1 expression, and 33.0 months in 61 cases of positive FoxM1 expression, and the difference was statistically significant (P=0.036).

CONCLUSIONS

FoxM1 is highly expressed in ESCC, and significantly correlated with the initiation, development and prognosis of esophageal cancer. FOXM1 might be an indicator to predict the prognosis and serve as a potential target for therapy in esophageal cancer.

[Endovascular stent-grafting of descending thoracic aortic lesions]

OBJECTIVE

To discuss the feasibility of endoluminal stent-grafting for descending thoracic aortic lesions.

METHODS

12 patients underwent stent-grafting of the thoracic aorta with Talent (11 patients) and Vanguard (1) device. Endovascular technique was used in 12 patients with descending thoracic aortic aneurysms (5 patients), Stanford B dissections (6), and pseudoaneurysm (1). 13 straight stent-grafts were inserted through 18-24 F theaths via a femoral arteriotomy under local (2 patients) or general (10) anesthesia.

RESULTS

The procedure was technically successful in all patients without aneurysm rupture, paraplegia, and organs or limbs ischemia. There were 3 early endoleaks. Follow-up showed that 4 of 5 aortic aneurysms were excluded completely and one endoleak was changed into persistent. Four entries of 6 patients with stanford B dissection were excluded and 2 early endoleaks were sealed during one month after operation. Four false lumen were filled completely and 2 false lumen were filled partly by thrombosis.

CONCLUSION

Descending thoracic aortic stent-grafting is a safe, highly successful and feasible alternative to conventional surgery. The long-term result remains unclear, especially that of the endovascular repair of Stanford B dissection.

[Studies on the chemical constituents of Evodia rutaecarpa (Juss.) Benth. var. officinalis (Dode) Huang]

AIM

To study the chemical constituents of the unriped fruits from Evodia rutaecarpa (Juss.) Benth. var. officinalis (Dode) Huang.

METHODS

Various chromatographic techniques were used to separate and purify the constituents. Their structures were elucidated on the physico-chemical properties and spectral data.

RESULTS

A lot of compounds were isolated of the unriped fruits from Evodia rutaecarpa (Juss.) Benth. var. officinalis (Dode) Huang. This paper reports mainly compounds identified as shihulimonin A, emodin, physcion, chrysophanol and limonin.

CONCLUSION

Shihulimonin A is a new compound. Emodin, physcion and chrysophanol were isolated from the Evodia for the first time.

Transcatheter closure of secundum atrial septal defects using Amplatzer device

OBJECTIVE

To evaluate the feasibility and short term results of transcatheter closure of secundum atrial septal defects (TCSASDs) using Amplatzer occluder device. A new self-centering device, the Amplatzer atrial septal occluder, has recently been evaluated in an animal model with excellent results. This paper reports our clinical research with this device.

METHODS

30 patients underwent an attempt at TCSASDs at an average age of 35.6 +/- 15.9 y (range, 5-62 y) and average weight of 63.6 +/- 14.5 kg (range, 17-78 kg) using the Amplatzer atrial septal occluder. The average ASD diameter measured by transesophageal echocardiography (TEE) was 23.6 +/- 4.0 mm (range, 16-31 mm), and the average atrial septal defects (ASD) balloon stretched diameter was 25.2 +/- 5.8 mm (range, 9-34 mm). All patients had right atrial and ventricular volume overload with a Qp/Qs of 3.4 +/- 1.2 (1.4-5.2). A F8-12 catheter was used for delivery of the device in all patients.

RESULTS

The device was placed correctly in all patients. There was immediate and complete closure in 30 patients. The average device waist size used to close the defect was 25.6 +/- 5.9 mm (range, 9-34 mm). There was no episode of device embolization or any other complication. Follow-up was performed using transthoracic echocardiography (TTE) 1 day, 1 month, 3 months, 6 months and 1 year after the procedure. The first day after operation; there was complete closure of the ASD in all patients; there have been no episodes of endocarditis, thromboembolism, or wire fracture.

CONCLUSION

TCSASDs using the Amplatzer occluder device was an efficient nonsurgical method which had a very high technical success rate and satisfactory short term and follow-up results.

[Major dissection after PTCA is a strong independent predictor of early luminal deterioration]

OBJECTIVE

To investigate the early natural course of dissection after PTCA and its relation to early luminal deterioration.

METHODS

One hundred and five patients who underwent relook coronary arteriography within 24 hours of PTCA were retrospectively analyzed. The patients were subdivided into no dissection and type A, B, C, D, and E dissection. Minimal luminal diameter (MLD) was measured immediately after PTCA and at relook coronary arteriography. The changes were correlated with the severity of the dissections.

RESULTS

Immediately after PTCA, the MLD in all 6 groups was > 2.0 mm. Except for type A dissection, the MLD, however, was deteriorated significantly at the relook coronary arteriography next day. The factors contributing to the deterioration were analyzed by covariance analysis, which showed a significant linear relation with the MLD immediately after PTCA and the type of dissection. Multivariate stepwise regression analysis was used to investigate if the patients' demographic factors and coronary lesion characteristics were also related to the MLD deterioration. The results showed that multivessel disease and the type of dissection were two independent risk factors of the MLD deterioration.

CONCLUSION

Even if the results immediately after PTCA were acceptable, MLD will deteriorate over time. The degree of the deterioration was not only related to elastic recoil, but also to the type of dissection. Type C, D and E dissections were unstable, causing much more damage to the MLD than type A and B dissections, which mandated immediate stent implantation to prevent early luminal deterioration and late restenosis. Stent implantation was usually unnecessary in type A and B dissections. Multivessel disease was also involved in the process of the MLD deterioration. The mechanism is unclear, but might be related to coronary lesion characteristics.

[Abdominal aortic aneurysm treated by endovascular stent-graft and conventional surgical repair: a comparison]

OBJECTIVE

To evaluate the feasibility of abdominal aortic aneurysm (AAA) treated by endovascular stent-graft.

METHODS

The clinical data of 52 patients with AAA treated by endovascular stent-graft (n = 20) and conventional surgical repair (n = 32) were analysed retrospectively. Patients conditions, operative hours, blood loss, function recovery and complications were compared.

RESULTS

No significant difference was observed in sex, age, other disease, anesthesia risk category, aneurysm type, aneurysm diameter, technical success rate, and mortality rate between the groups (P > 0.05). The patients who underwent intraluminal treatment had significant reductions in operative time, blood loss, intensive care unit and hospitalization. But there was a high complication rate in the endovascular stent-graft group. All complications were connected with the interventional technique; endo-leak was the chief complication after operation.

CONCLUSIONS

Endovascular treatment has marked merits such as reduced trauma, short hospitalization stays, and early functional recovery. It is suitable for the patients who can't undergo open surgical repair. But the complications caused by this technique needs further study.

Relationship between expression of type III collagen and phenotype of vascular smooth muscle cells in neointimal of stented coronary artery

OBJECTIVE

To investigate the secretive features of type III collagen in restenosis of the stented coronary artery and the relationship between the expression of type III. collagen and vascular smooth muscle cells (VSMCs).

METHODS

An animal model of restenosis was established by implanting oversized tantalum stents into the coronary arteries in 26 dogs. At the 7th, 14th and 28th days after implantation, the stented coronaries were harvested. Transmission electronic microscopy and immunohistochemistry were employed to investigate the features of type III collagen secretion and VSMCs' phenotype. The expression of type III collagen was quantified and compared for the three stages.

RESULTS

Migration and proliferation of VSMCs were the main features at the 7th day after injury. At the 14th day, proliferation of VSMCs reached the peak while much more secretion of collagen was noticeable. VSMCs began to transform from the synthetic phenotype to the contractile phenotype at the 28th day, when a great quantity of collagen was also secreted. The quantity of secreted type III collagen was greater at the 14th and 28th day than that at the 7th day (P < 0.05). The stain density of type III collagen was positively correlated to neointimal thickness at both of 14th and 28th day.

CONCLUSION

The pathological bases of restenosis are variant in different period of restenosis formation. Type III collagen may play an important role in the late stage of restenosis after coronary stenting.

[Endoluminal stent-graft repair of aortic aneurysms]

OBJECTIVE

To study the clinical value of the treatment of aortic aneurysms with endovascular stent-graft prosthesis.

METHODS

After a unilateral surgical arteriotomy, Talent, Vanguard and Chinese stent-graft were advanced through the femoral arteries and placed in the proper position of the aneurysm sac under X-ray fluoroscopic guidance.

RESULTS

Four patients with descending aneurysm, 1 patient with abdominal aortic aneurysm (AAA) involving the renal artery, superior mesenteric artery and celiac artery, and 1 patient with right common iliac artery aneurysm received straight stent-grafts. Five patients with infrarenal AAA received bifurcated stent-grafts. CT and MRA were performed during a follow-up of 3 - 19 months. Aortic aneurysms were completely excluded from the circulation. Five patients prolonged fever was noted and 1 patient was found to have a leakage 3 months later, and hemiplegia in 1 after procedure.

CONCLUSIONS

Endovascular treatment of aortic aneurysm is technically feasible and can effectively exclude aortic aneurysms from the circulation. Endoluminal repair may serve as an interventional strategy to treat aneurysm, especially in patients at high surgical risk, but long term effect needs further study.

[Expression of epidermal growth factor receptor in human endometrium, decidua and trophoblast cells]

OBJECTIVE

To study the expression of epidermal growth factor receptor (EGFR) expression in human normal endometrium, decidua and trophoblast cells of early pregnancy, and to explore the effect of EGFR on cell proliferation and development.

METHODS

To localize the EGFR expression in glandular and stromal cells of normal endometrium, decidua with immunohistochemical method (ABC), and to analyse the related quantity of EGFR mRNA by RT-PCR method.

RESULTS

There were EGFR expression in both normal endometrium and decidua. EGFR protein located on cell membrane, nuclear membrane and in the cytoplasm as well, and located in the neuclear of glandular and stromal cells in decidua. The expression of EGFR in glandular cells was significantly stronger than that in the stroma (P < 0.05), while there was no difference of EGFR expression in the glands during the menstrual cycle (P > 0.05). However, the expression of EGFR in the glands of decidua was significantly higher than that in the proliferative and secretory endometrium (P < 0.05). The intensity of staining in stromal cells listed in order from the strongest was early decidua > secretory endometrium > proliferative endometrium, the differences were significant (P < 0.05). The related quantity of EGFR mRNA expression in proliferative, secretory endometrium, decidua and trophoblasts were: 0.531 +/- 0.061, 0.594 +/- 0.121, 0.732 +/- 0.032, 0.828 +/- 0.034, respectively. There was no difference during the menstrual cycle, but that in the decidua and trophoblasts were significantly higher than that in the proliferative and secretory endometrium (P < 0.05), and that in the trophoblasts was the highest.

CONCLUSION

EGFR expression was present in the proliferative and secretory endometrium, decidua and trophoblasts of early pregnancy, and it was significantly higher in the decidua and trophoblasts than that during the menstrual cycle.

Angioplasty through a stent side door

Angioplasty was performed by entering a Gianturco-Roubin stent from the side through the coils of a previously-implanted hanging stent in an ostial lesion in a saphenous vein graft. No complications and no visible damage occurred to the stent. Although this method carries a possible risk of entrapment or damage to the stent, it is feasible when other options have failed.