Spontaneous movements in the newborns: a tool of quantitative video analysis of preterm babies.

BACKGROUND AND OBJECTIVES: The number of preterm babies is steadily growing world-wide and these neonates are at risk of neuro-motor-cognitive deficits. The observation of spontaneous movements in the first three months of age is known to predict such risk. However, the analysis by specifically trained physiotherapists is not suited for the clinical routine, motivating the development of simple computerized video analysis systems, integrated with a well-structured Biobank to make available for preterm babies a growing service with diagnostic, prognostic and epidemiological purposes. METHODS: MIMAS (Markerless Infant Movement Analysis System) is a simple, low-cost system of video analysis of spontaneous movements of newborns in their natural environment, based on a single standard RGB camera, without markers attached to the body. The original videos are transformed into binarized sequences highlighting the silhouette of the baby, in order to minimize the illumination effects and increase the robustness of the analysis; such sequences are then coded by a large set of parameters (39) related to the spatial and spectral changes of the silhouette. The parameter vectors of each baby were stored in the Biobank together with related clinical information. RESULTS: The preliminary test of the system was carried out at the Gaslini Pediatric Hospital in Genoa, where 46 preterm (PT) and 21 full-term (FT) babies (as controls) were recorded at birth (T0) and 8-12 weeks thereafter (T1). A simple statistical analysis of the data showed that the coded parameters are sensitive to the degree of maturation of the newborns (comparing T0 with T1, for both PT and FT babies), and to the conditions at birth (PT vs. FT at T0), whereas this difference tends to vanish at T1. Moreover, the coding method seems also able to detect the few 'abnormal' preterm babies in the PT populations that were analyzed as specific case studies. CONCLUSIONS: Preliminary results motivate the adoption of this tool in clinical practice allowing for a systematic accumulation of cases in the Biobank, thus for improving the accuracy of data analysis performed by MIMAS and ultimately allowing the adoption of data mining techniques.

Hypoxia Predicts Poor Prognosis in Neuroblastoma Patients and Associates with Biological Mechanisms Involved in Telomerase Activation and Tumor Microenvironment Reprogramming.

The biological and clinical heterogeneity of neuroblastoma (NB) demands novel biomarkers and therapeutic targets in order to drive the most appropriate treatment for each patient. Hypoxia is a condition of low-oxygen tension occurring in poorly vascularized tumor tissues. In this study, we aimed to assess the role of hypoxia in the pathogenesis of NB and at developing a new clinically relevant hypoxia-based predictor of outcome. We analyzed the gene expression profiles of 1882 untreated NB primary tumors collected at diagnosis and belonging to four existing data sets. Analyses took advantage of machine learning methods. We identified NB-hop, a seven-gene hypoxia biomarker, as a predictor of NB patient prognosis, which is able to discriminate between two populations of patients with unfavorable or favorable outcome on a molecular basis. NB-hop retained its prognostic value in a multivariate model adjusted for established risk factors and was able to additionally stratify clinically relevant groups of patients. Tumors with an unfavorable NB-hop expression showed a significant association with telomerase activation and a hypoxic, immunosuppressive, poorly differentiated, and apoptosis-resistant tumor microenvironment. NB-hop defines a new population of NB patients with hypoxic tumors and unfavorable prognosis and it represents a critical factor for the stratification and treatment of NB patients.

PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data.

Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an accurate and fast method to measure gene expression. Reproducibility of the analyses is the main limitation of RT-qPCR experiments. Galaxy is an open, web-based, genomic workbench for a reproducible, transparent, and accessible science. Our aim was developing a new Galaxy tool for the analysis of RT-qPCR expression data. Our tool was developed using Galaxy workbench version 19.01 and functions implemented in several R packages. We developed PIPE-T, a new Galaxy tool implementing a workflow, which offers several options for parsing, filtering, normalizing, imputing, and analyzing RT-qPCR data. PIPE-T requires two input files and returns seven output files. We tested the ability of PIPE-T to analyze RT-qPCR data on two example datasets available in the gene expression omnibus repository. In both cases, our tool successfully completed execution returning expected results. PIPE-T can be easily installed from the Galaxy main tool shed or from Docker. Source code, step-by-step instructions, and example files are available on GitHub to assist new users to install, execute, and test PIPE-T. PIPE-T is a new tool suitable for the reproducible, transparent, and accessible analysis of RT-qPCR expression data.