RNA-seq validation: software for selection of reference and variable candidate genes for RT-qPCR.

BACKGROUND: Real-time quantitative PCR (RT-qPCR) is one of the most widely used gene expression analyses for validating RNA-seq data. This technique requires reference genes that are stable and highly expressed, at least across the different biological conditions present in the transcriptome. Reference and variable candidate gene selection is often neglected, leading to misinterpretation of the results. RESULTS: We developed a software named "Gene Selector for Validation" (GSV), which identifies the best reference and variable candidate genes for validation within a quantitative transcriptome. This tool also filters the candidate genes concerning the RT-qPCR assay detection limit. GSV was compared with other software using synthetic datasets and performed better, removing stable low-expression genes from the reference candidate list and creating the variable-expression validation list. GSV software was used on a real case, an Aedes aegypti transcriptome. The top GSV reference candidate genes were selected for RT-qPCR analysis, confirming that eiF1A and eiF3j were the most stable genes tested. The tool also confirmed that traditional mosquito reference genes were less stable in the analyzed samples, highlighting the possibility of inappropriate choices. A meta-transcriptome dataset with more than ninety thousand genes was also processed successfully. CONCLUSION: The GSV tool is a time and cost-effective tool that can be used to select reference and validation candidate genes from the biological conditions present in transcriptomic data.

Minor Salivary Gland Polymorphous Adenocarcinoma With Local Recurrence After Seven Years: A Case Report.

Polymorphous adenocarcinoma is a rare neoplasm of the minor salivary glands with an indolent behavior. Here, we report and describe the computed tomography (CT) and magnetic resonance imaging (MRI) of polymorphic adenocarcinoma in a 69-year-old patient who presented with local recurrence seven years after the initial treatment. On contrast CT, the primary lesion appeared heterogeneous and invaded the pterygopalatine fossa and the sphenopalatine foramen. The recurrent lesion on MRI showed a hypointense signal on the T1-weighted sequence, a hyperintense signal on the T2-weighted sequence, and heterogeneous enhancement with contrast. The patient underwent a new surgery for lesion resection and is currently under clinical and radiological follow-up. It is recommended to follow patients for at least 15 years after diagnosis, as local recurrences can occur up to 10 years after the initial treatment.

Evaluation of ventricular systolic function by speckle tracking technique in patients with biliary atresia before and after liver transplantation.

To evaluate the ventricular function of patients with biliary atresia (BA) before and after liver transplantation using two-dimensional speckle tracking. Observational, analytical study with healthy control group, volunteers. We recruited patients from 0 to 18 years old who were candidates for liver transplantation and patients after six months of liver transplantation performed for BA from January 1997 to August 2015 at Children's Institute of São Paulo University Medical School. The patients were submitted to a complete conventional echocardiographic study. After that, the images were captured for global longitudinal strain (GLS). A blood sample was collected for brain natriuretic peptide (BNP) level. Ejection fraction obtained by Simpson's method was significantly higher in the hepatic pre-transplantation group (p < 0.001), as well as left atrial size (p < 0.001) and left ventricle size (p = 0.039). The left ventricular mass index was significantly higher in pre-transplantation group (p < 0.001). The left atrium volume (p = 0.008) and the left ventricular mass index (p t = 0.035) were higher in the post-transplant group. It was observed that the lower the BNP, the lower/more negative the GLS in the post-transplant group (p = 0.038 and r = 0.427). Significant reduction in the overall longitudinal strain of the left ventricle was detected before (p = 0.01) and after liver transplantation (p = 0.019). A subclinical left ventricular systolic dysfunction was evidenced by two-dimensional speckle tracking technique before and after liver transplantation, even when compared to normal values of the last pediatric meta-analysis.

Outcomes of liver transplantation in pediatric recipients with cardiovascular disease.

LT exerts considerable stress on the heart perioperatively. Limited data exist on impact of cardiovascular diseases on LT children. This study evaluated the outcomes of children with CVD who underwent LT and compared with pretransplant findings. From 518 LT recipients, 82 (15.8%) had CVD. Sixty patients were classified as low-risk adjustment for congenital heart surgery 1 (RACHS 1 and 2). Five patients were classified as RACHS ≥3. The most common echocardiographic finding in the CVD patients (25/82) was ASD. CVD patients had more abnormal EKG (32.4% vs 14.5%, P < .001), abnormal chest X-ray (11.8% vs 1.4%, P < .001), and altered echocardiography (89.7% vs 15.4%, P < .001) findings compared with the No-CVD group pretransplant. Post-transplant, significant differences between groups were observed related to abnormal EKG (14.7% vs 7.0%, P = .03) and echocardiography (48.5% vs 3.2%, P < .01) findings. Pretransplant ASD spontaneously closed in 22 patients. At 1 and 5 years post-transplant, there was no difference in the survival rate between groups (P = .96). The prevalence of CVD in recipients of LT was high, and its presence was associated with significantly higher cardiac decompensation before and after LT. Minor and moderate cardiovascular disease did not impact the long-term survival.

Painful ulcers in a 5-year-old girl.

A 5-year-old girl was admitted to our clinic with several painful ulcers spreading from the right elbow to the armpit. The right axillary lymph node was palpable. She was previously treated in another service with oral amoxicillin for 10 days due to a diagnosis of impetigo. There was no resolution of the lesion after the treatment, so she looked for another doctor.