ePlatypus: an ecosystem for computational analysis of immunogenomics data

MOTIVATION

The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner.

RESULTS

Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand-receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science.

AVAILABILITY AND IMPLEMENTATION

Platypus code used in this manuscript can be found at github.com/alexyermanos/Platypus.

Is it possible to predict the severity of acute appendicitis? Reliability of predictive models based on easily available blood variables

INTRODUCTION

Recent evidence confirms that the treatment of acute appendicitis is not necessarily surgical, and selected patients with uncomplicated appendicitis can benefit from a non-operative management. Unfortunately, no cost-effective test has been proven to be able to effectively predict the degree of appendicular inflammation as yet, therefore, patient selection is too often left to the personal choice of the emergency surgeon. Our paper aims to clarify if basic and readily available blood tests can give reliable prognostic information to build up predictive models to help the decision-making process.

METHODS

Clinical notes of 2275 patients who underwent an appendicectomy with a presumptive diagnosis of acute appendicitis were reviewed, taking into consideration basic preoperative blood tests and histology reports on the surgical specimens. Variables were compared with univariate and multivariate analysis, and predictive models were created.

RESULTS

18.2% of patients had a negative appendicectomy, 9.6% had mucosal only inflammation, 53% had transmural inflammation and 19.2% had gangrenous appendicitis. A strong correlation was found between degree of inflammation and lymphocytes count and CRP/Albumin ratio, both at univariate and multivariate analysis. A predictive model to identify cases of gangrenous appendicitis was developed.

CONCLUSION

Low lymphocyte count and high CRP/Albumin ratio combined into a predictive model may have a role in the selection of patients who deserve appendicectomy instead of non-operative management of acute appendicitis.

Translating from proteins to ribonucleic acids for ligand-binding site detection

Identifying druggable ligand-binding sites on the surface of the macromolecular targets is an important process in structure-based drug discovery. Deep-learning models have been shown to successfully predict ligand-binding sites of proteins. As a step toward predicting binding sites in RNA and RNA-protein complexes, we employ three-dimensional convolutional neural networks. We introduce a dataset splitting approach to minimize structure-related bias in training data, and investigate the influence of protein-based neural network pre-training before fine-tuning on RNA structures. Models that were pre-trained on proteins considerably outperformed the models that were trained exclusively on RNA structures. Overall, 71% of the known RNA binding sites were correctly located within 4 Å of their true centres with a structural overlap of at least 25%.

Interstitial lung diseases in a lung cancer screening trial

We assessed the prevalence of interstitial lung disease (ILD) in a cohort of smokers included in a lung cancer screening trial. Two observers independently reviewed, for the presence of findings consistent with ILD, the computed tomography (CT) examinations of 692 heavy smokers recruited by the Multicentric Italian Lung Detection (MILD) trial. Four CT patterns were considered: usual interstitial pneumonia (UIP), other chronic interstitial pneumonia (OCIP), respiratory bronchiolitis (RB) and indeterminate. Subsequently, the evolution of ILD in those subjects who had undergone a repeat CT examination after 3 yrs was assessed. The UIP pattern and the OCIP pattern were identified in two (0.3%) out of 692 and 26 (3.8%) out of 692 patients, respectively; 109 (15.7%) out of 692 patients showed CT abnormalities consistent with RB, while an indeterminate CT pattern was reported in 21 out of 692 (3%) patients. Age, male sex and current smoking status were factors associated with the presence of OCIP and UIP (combined) pattern, although the relationship did not attain statistical significance. A progression of the disease was observed in three (25%) out of 12 subjects with OCIP who underwent repeat CT after 3 yrs. Thin-section CT features of ILD, probably representing smoking-related ILD, are not uncommon in a lung cancer screening population and should not be overlooked.

Body and risk: cultural ambivalence towards radioactivity through the history of two protagonists

Two women with profoundly different backgrounds were brought together in a destiny that saw their paths cross and join in the discovery of radioactivity: Marie Curie and Blanche Wittman. The former was one of the greatest women scientists of all time, the only woman to have won the Nobel Prize for science. Noted for her extraordinary humanitarian spirit, and despite scandal over an affair that saw her hounded by journalists, she dedicated most of her life to scientific research. The latter passed into history as the "Queen of Hysterics" during her hospitalisation in the famous Parisian asylum Pitié Salpêtrière. After her recovery, she became a close assistant of Marie Curie in the extraction of radium from pitchblende, until her death sixteen years of toil later. The discovery of radioactivity was the common denominator underlying the vicissitudes of their lives, the same radioactivity that was so acclaimed and of such incredible diagnostic and therapeutic potential while at the same time so underrated in the everyday life of the time that disregarded, almost disparagingly, the deleterious biologic effects it was capable of provoking. At the beginning of the twentieth century, those effects were in fact often underestimated or scarcely considered, and it was only after World War II that there came an awareness of the ambiguous properties of ionising radiation. After numerous studies on radiation exposure, much of the current debate concerns the possible effects of exposure to small doses, such as those delivered in most radiological examinations. The theories proposed include the unorthodox theory of hormesis, which requires careful reevaluation. Much light has been shed on radiology since the time of Blanche and Marie, but there still remain many shadows to dispel, and this can only be done by serious and constant scientific commitment.