Artificial intelligence in chronic kidney diseases: methodology and potential applications.

Chronic kidney disease (CKD) represents a significant global health challenge, characterized by kidney damage and decreased function. Its prevalence has steadily increased, necessitating a comprehensive understanding of its epidemiology, risk factors, and management strategies. While traditional prognostic markers such as estimated glomerular filtration rate (eGFR) and albuminuria provide valuable insights, they may not fully capture the complexity of CKD progression and associated cardiovascular (CV) risks.This paper reviews the current state of renal and CV risk prediction in CKD, highlighting the limitations of traditional models and the potential for integrating artificial intelligence (AI) techniques. AI, particularly machine learning (ML) and deep learning (DL), offers a promising avenue for enhancing risk prediction by analyzing vast and diverse patient data, including genetic markers, biomarkers, and imaging. By identifying intricate patterns and relationships within datasets, AI algorithms can generate more comprehensive risk profiles, enabling personalized and nuanced risk assessments.Despite its potential, the integration of AI into clinical practice faces challenges such as the opacity of some algorithms and concerns regarding data quality, privacy, and bias. Efforts towards explainable AI (XAI) and rigorous data governance are essential to ensure transparency, interpretability, and trustworthiness in AI-driven predictions.

GLSTM: On Using LSTM for Glucose Level Prediction.

The Prediabetes impacts one in every three individuals, with a 10% annual probability of transitioning to type 2 diabetes without lifestyle changes or medical interventions. It's crucial to manage glycemic health to deter the progression to type 2 diabetes. In the United States, 13% of individuals (18 years of age and older) have diabetes, while 34.5% meet the criteria for prediabetes. Diabetes mellitus and prediabetes are more common in older persons. Currently, nevertheless, there aren't many noninvasive, commercially accessible methods for tracking glycemic status to help with prediabetes self-management. This study tackles the task of forecasting glucose levels using personalized prediabetes data through the utilization of the Long Short-Term Memory (LSTM) model. Continuous monitoring of interstitial glucose levels, heart rate measurements, and dietary records spanning a week were collected for analysis. The efficacy of the proposed model has been assessed using evaluation metrics including Root Mean Square Error (RMSE), Mean Squared Error (MSE), Mean Absolute Error (MAE), and the coefficient of determination (R2).

How Patients Feel with Telemedicine Devices as an Enabling Factor for Personalised Medicine: A Preliminary Study.

Telemonitoring tools have become essential in today's healthcare, representing fundamental resources for chronic disease home management supporting early detection of clinical worsening with great reduction of hospitalization costs. Therefore the investigation of the patient compliance is a key enabling point. We aim to assess how patients with chronic coronary syndromes evaluate a telemonitoring device meant for ongoing health monitoring. Twenty-six patients used the device for a week and subsequently filled out a well-designed questionnaire. The survey questions were about the device's ease of use, satisfaction levels, perceived effectiveness, and its influence on the patients' healthcare experiences. This study emphasizes the significance of focusing on patient needs in telemedicine and the importance of addressing these concerns to improve telehealth interventions.

Education in Health Informatics: Perspectives from the Italian Society for Biomedical Informatics (SIBIM).

The evolution of socio-technological habits together with the widespread demand of post-acute and chronic treatments outside hospital boundaries drove the increased demand of medical informatics experts to develop tools for and support healthcare professionals. The recent COVID-19 pandemic further highlighted the need of physicians able to manage diseases virtually and remotely. Moreover, healthcare professionals need to access to innovative techniques and procedures to manage biomedical data, cloud-based communication, and data sharing procedures, often connected to innovative devices to support an effective precision in the health treatments. In this paper we report the experiences of the Italian Biomedical Informatics Society (SIBIM), in the definition and promotion of eHealth educational topics in medical and health professions teaching programs, as well as in bioengineering schools, showing how SIBIM members' efforts have been applied towards increasing the level of eHealth contents in medical schools.

Leveraging graph neural networks for supporting automatic triage of patients.

Patient triage is crucial in emergency departments, ensuring timely and appropriate care based on correctly evaluating the emergency grade of patient conditions. Triage methods are generally performed by human operator based on her own experience and information that are gathered from the patient management process. Thus, it is a process that can generate errors in emergency-level associations. Recently, Traditional triage methods heavily rely on human decisions, which can be subjective and prone to errors. A growing interest has recently been focused on leveraging artificial intelligence (AI) to develop algorithms to maximize information gathering and minimize errors in patient triage processing. We define and implement an AI-based module to manage patients' emergency code assignments in emergency departments. It uses historical data from the emergency department to train the medical decision-making process. Data containing relevant patient information, such as vital signs, symptoms, and medical history, accurately classify patients into triage categories. Experimental results demonstrate that the proposed algorithm achieved high accuracy outperforming traditional triage methods. By using the proposed method, we claim that healthcare professionals can predict severity index to guide patient management processing and resource allocation.

MAATrica: a measure for assessing consistency and methods in medicinal and nutraceutical chemistry papers.

The growing number of scientific papers and document sources underscores the need for methods capable of evaluating the quality of publications. Researchers who are looking for relevant papers for their studies need ways to assess the scientific value of these documents. One approach involves using semantic search engines that can automatically extract important knowledge from the growing body of text. In this study, we introduce a new metric called "MAATrica," which serves as the foundation for an innovative method designed to evaluate research papers. MAATrica offers a new way to analyze and categorize text, focusing on the consistency of research documents in the life sciences, particularly in the fields of medicinal and nutraceutical chemistry. This method utilizes semantic descriptions to cover in silico experiments, as well as in vitro and in vivo essays. Created to aid in evaluation processes like peer review, MAATrica uses toolkits and semantic applications to build the proposed measure, identify scientific entities, and gather information. We have applied MAATrica to roughly 90,000 papers and present our findings here.

Sex-specific differences in myocardial glucose metabolic rate in non-diabetic, pre-diabetic and type 2 diabetic subjects.

BACKGROUND: Evidence has shown that women with type 2 diabetes (T2DM) have a higher excess risk for cardiovascular disease (CVD) than men with T2DM. Subjects with either T2DM or prediabetes exhibit myocardial insulin resistance, but it is still unsettled whether sex-related differences in myocardial insulin resistance occur in diabetic and prediabetic subjects. METHODS: We aimed to evaluate sex-related differences in myocardial glucose metabolic rate (MRGlu), assessed using dynamic PET with 18F-FDG combined with euglycemic-hyperinsulinemic clamp, in subjects with normal glucose tolerance (NGT; n = 20), prediabetes (n = 11), and T2DM (n = 26). RESULTS: Women with prediabetes or T2DM exhibited greater relative differences in myocardial MRGlu than men with prediabetes or T2DM when compared with their NGT counterparts. As compared with women with NGT, those with prediabetes exhibited an age-adjusted 35% lower myocardial MRGlu value (P = 0.04) and women with T2DM a 74% lower value (P = 0.006), respectively. Conversely, as compared with men with NGT, men with T2DM exhibited a 40% lower myocardial MRGlu value (P = 0.004), while no significant difference was observed between men with NGT and prediabetes. The statistical test for interaction between sex and glucose tolerance on myocardial MRGlu (P < 0.0001) was significant suggesting a sex-specific association. CONCLUSIONS: Our data suggest that deterioration of glucose homeostasis in women is associated with a greater impairment in myocardial glucose metabolism as compared with men. The sex-specific myocardial insulin resistance could be an important factor responsible for the greater effect of T2DM on the excess risk of cardiovascular disease in women than in men.

Machine learning pipeline to analyze clinical and proteomics data: experiences on a prostate cancer case.

Proteomic-based analysis is used to identify biomarkers in blood samples and tissues. Data produced by devices such as mass spectrometry requires platforms to identify and quantify proteins (or peptides). Clinical information can be related to mass spectrometry data to identify diseases at an early stage. Machine learning techniques can be used to support physicians and biologists in studying and classifying pathologies. We present the application of machine learning techniques to define a pipeline aimed at studying and classifying proteomics data enriched using clinical information. The pipeline allows users to relate established blood biomarkers with clinical parameters and proteomics data. The proposed pipeline entails three main phases: (i) feature selection, (ii) models training, and (iii) models ensembling. We report the experience of applying such a pipeline to prostate-related diseases. Models have been trained on several biological datasets. We report experimental results about two datasets that result from the integration of clinical and mass spectrometry-based data in the contexts of serum and urine analysis. The pipeline receives input data from blood analytes, tissue samples, proteomic analysis, and urine biomarkers. It then trains different models for feature selection, classification and voting. The presented pipeline has been applied on two datasets obtained in a 2 years research project which aimed to extract hidden information from mass spectrometry, serum, and urine samples from hundreds of patients. We report results on analyzing prostate datasets serum with 143 samples, including 79 PCa and 84 BPH patients, and an urine dataset with 121 samples, including 67 PCa and 54 BPH patients. As results pipeline allowed to identify interesting peptides in the two datasets, 6 for the first one and 2 for the second one. The best model for both serum (AUC=0.87, Accuracy=0.83, F1=0.81, Sensitivity=0.84, Specificity=0.81) and urine (AUC=0.88, Accuracy=0.83, F1=0.83, Sensitivity=0.85, Specificity=0.80) datasets showed good predictive performances. We made the pipeline code available on GitHub and we are confident that it will be successfully adopted in similar clinical setups.

Quantitative analysis of visually normal EEG reveals spectral power abnormalities in temporal lobe epilepsy.

OBJECTIVE: To compare quantitative spectral parameters of visually-normal EEG between Mesial Temporal Lobe Epilepsy (MTLE) patients and healthy controls (HC). METHOD: We enrolled 26 MTLE patients and 26 HC. From each recording we calculated total power of all frequency bands and determined alpha-theta (ATR) and alpha-delta (ADR) power ratios in different brain regions. Group-wise differences between spectral parameters were investigated (p < 0.05). To test for associations between spectral-power and cognitive status, we evaluated correlations between neuropsychological tests and quantitative EEG (qEEG) metrics. RESULTS: In all comparisons, ATR and ADR were significantly decreased in MTLE patients compared to HC, particularly over the hemisphere ipsilateral to epileptic activity. A positive correlation was seen in MTLE patients between ATR in ipsilateral temporal lobe, and results of neuropsychological tests of auditory verbal learning (RAVLT and RAVLT-D), short term verbal memory (Digit span backwards), and executive function (Weigl's sorting test). ADR values in the contralateral posterior region correlated positively with RAVLT-D and Digit span backwards tests. DISCUSSION: Results confirmed that the power spectrum of qEEG is shifted towards lower frequencies in MTLE patients compared to HC. CONCLUSION: Of note, our results were found in visually-normal recordings, providing further evidence of the value of qEEG for longitudinal monitoring of MTLE patients over time. Exploratory analysis of associations between qEEG and neuropsychological data suggest this could be useful for investigating effects of antiseizure medications on cognitive integrity in patients.

The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics.

The SARS-CoV-2 virus, which is a major threat to human health, has undergone many mutations during the replication process due to errors in the replication steps and modifications in the structure of viral proteins. The XBB variant was identified for the first time in Singapore in the fall of 2022. It was then detected in other countries, including the United States, Canada, and the United Kingdom. We study the impact of sequence changes on spike protein structure on the subvariants of XBB, with particular attention to the velocity of variant diffusion and virus activity with respect to its diffusion. We examine the structural and functional distinctions of the variants in three different conformations: (i) spike glycoprotein in complex with ACE2 (1-up state), (ii) spike glycoprotein (closed-1 state), and (iii) S protein (open-1 state). We also estimate the affinity binding between the spike protein and ACE2. The market binding affinity observed in specific variants raises questions about the efficacy of current vaccines in preparing the immune system for virus variant recognition. This work may be useful in devising strategies to manage the ongoing COVID-19 pandemic. To stay ahead of the virus evolution, further research and surveillance should be carried out to adjust public health measures accordingly.

Genome mining conformance to metabolite profile of Bacillus strains to control potato pathogens.

Biocontrol agents are safe and effective methods for controlling plant disease pathogens, such as Fusarium solani, which causes dry wilt, and Pectobacterium spp., responsible for potato soft rot disease. Discovering agents that can effectively control both fungal and bacterial pathogens in potatoes has always presented a challenge. Biological controls were investigated using 500 bacterial strains isolated from rhizospheric microbial communities, along with two promising biocontrol strains: Pseudomonas (T17-4 and VUPf5). Bacillus velezensis (Q12 and US1) and Pseudomonas chlororaphis VUPf5 exhibited the highest inhibition of fungal growth and pathogenicity in both laboratory (48%, 48%, 38%) and greenhouse (100%, 85%, 90%) settings. Q12 demonstrated better control against bacterial pathogens in vivo (approximately 50%). Whole-genome sequencing of Q12 and US1 revealed a genome size of approximately 4.1 Mb. Q12 had 4413 gene IDs and 4300 coding sequences, while US1 had 4369 gene IDs and 4255 coding sequences. Q12 exhibited a higher number of genes classified under functional subcategories related to stress response, cell wall, capsule, levansucrase synthesis, and polysaccharide metabolism. Both Q12 and US1 contained eleven secondary metabolite gene clusters as identified by the antiSMASH and RAST servers. Notably, Q12 possessed the antibacterial locillomycin and iturin A gene clusters, which were absent in US1. This genetic information suggests that Q12 may have a more pronounced control over bacterial pathogens compared to US1. Metabolic profiling of the superior strains, as determined by LC/MS/MS, validated our genetic findings. The investigated strains produced compounds such as iturin A, bacillomycin D, surfactin, fengycin, phenazine derivatives, etc. These compounds reduced spore production and caused deformation of the hyphae in F. solani. In contrast, B. velezensis UR1, which lacked the production of surfactin, fengycin, and iturin, did not affect these structures and failed to inhibit the growth of any pathogens. Our findings suggest that locillomycin and iturin A may contribute to the enhanced control of bacterial pectolytic rot by Q12.

Development of a predictive model to distinguish prostate cancer from benign prostatic hyperplasia by integrating serum glycoproteomics and clinical variables.

BACKGROUND: Prostate Cancer (PCa) represents the second leading cause of cancer-related death in men. Prostate-specific antigen (PSA) serum testing, currently used for PCa screening, lacks the necessary sensitivity and specificity. New non-invasive diagnostic tools able to discriminate tumoral from benign conditions and aggressive (AG-PCa) from indolent forms of PCa (NAG-PCa) are required to avoid unnecessary biopsies. METHODS: In this work, 32 formerly N-glycosylated peptides were quantified by PRM (parallel reaction monitoring) in 163 serum samples (79 from PCa patients and 84 from individuals affected by benign prostatic hyperplasia (BPH)) in two technical replicates. These potential biomarker candidates were prioritized through a multi-stage biomarker discovery pipeline articulated in: discovery, LC-PRM assay development and verification phases. Because of the well-established involvement of glycoproteins in cancer development and progression, the proteomic analysis was focused on glycoproteins enriched by TiO2 (titanium dioxide) strategy. RESULTS: Machine learning algorithms have been applied to the combined matrix comprising proteomic and clinical variables, resulting in a predictive model based on six proteomic variables (RNASE1, LAMP2, LUM, MASP1, NCAM1, GPLD1) and five clinical variables (prostate dimension, proPSA, free-PSA, total-PSA, free/total-PSA) able to distinguish PCa from BPH with an area under the Receiver Operating Characteristic (ROC) curve of 0.93. This model outperformed PSA alone which, on the same sample set, was able to discriminate PCa from BPH with an AUC of 0.79. To improve the clinical managing of PCa patients, an explorative small-scale analysis (79 samples) aimed at distinguishing AG-PCa from NAG-PCa was conducted. A predictor of PCa aggressiveness based on the combination of 7 proteomic variables (FCN3, LGALS3BP, AZU1, C6, LAMB1, CHL1, POSTN) and proPSA was developed (AUC of 0.69). CONCLUSIONS: To address the impelling need of more sensitive and specific serum diagnostic tests, a predictive model combining proteomic and clinical variables was developed. A preliminary evaluation to build a new tool able to discriminate aggressive presentations of PCa from tumors with benign behavior was exploited. This predictor displayed moderate performances, but no conclusions can be drawn due to the limited number of the sample cohort. Data are available via ProteomeXchange with identifier PXD035935.

Strategies and Trends in COVID-19 Vaccination Delivery: What We Learn and What We May Use for the Future.

Vaccination has been the most effective way to control the outbreak of the COVID-19 pandemic. The numbers and types of vaccines have reached considerable proportions, even if the question of vaccine procedures and frequency still needs to be resolved. We have come to learn the necessity of defining vaccination distribution strategies with regard to COVID-19 that could be used for any future pandemics of similar gravity. In fact, vaccine monitoring implies the existence of a strategy that should be measurable in terms of input and output, based on a mathematical model, including death rates, the spread of infections, symptoms, hospitalization, and so on. This paper addresses the issue of vaccine diffusion and strategies for monitoring the pandemic. It provides a description of the importance and take up of vaccines and the links between procedures and the containment of COVID-19 variants, as well as the long-term effects. Finally, the paper focuses on the global scenario in a world undergoing profound social and political change, with particular attention on current and future health provision. This contribution would represent an example of vaccination experiences, which can be useful in other pandemic or epidemiological contexts.

SARS-CoV-2 protein structure and sequence mutations: Evolutionary analysis and effects on virus variants.

The structure and sequence of proteins strongly influence their biological functions. New models and algorithms can help researchers in understanding how the evolution of sequences and structures is related to changes in functions. Recently, studies of SARS-CoV-2 Spike (S) protein structures have been performed to predict binding receptors and infection activity in COVID-19, hence the scientific interest in the effects of virus mutations due to sequence, structure and vaccination arises. However, there is the need for models and tools to study the links between the evolution of S protein sequence, structure and functions, and virus transmissibility and the effects of vaccination. As studies on S protein have been generated a large amount of relevant information, we propose in this work to use Protein Contact Networks (PCNs) to relate protein structures with biological properties by means of network topology properties. Topological properties are used to compare the structural changes with sequence changes. We find that both node centrality and community extraction analysis can be used to relate protein stability and functionality with sequence mutations. Starting from this we compare structural evolution to sequence changes and study mutations from a temporal perspective focusing on virus variants. Finally by applying our model to the Omicron variant we report a timeline correlation between Omicron and the vaccination campaign.

Analysis of age-dependent gene-expression in human tissues for studying diabetes comorbidities.

The study of the relationship between type 2 diabetes mellitus (T2DM) disease and other pathologies (comorbidities), together with patient age variation, poses a challenge for medical research. There is evidence that patients affected by T2DM are more likely to develop comorbidities as they grow older. Variation of gene expression can be correlated to changes in T2DM comorbidities insurgence and progression. Understanding gene expression changes requires the analysis of large heterogeneous data at different scales as well as the integration of different data sources into network medicine models. Hence, we designed a framework to shed light on uncertainties related to age effects and comorbidity by integrating existing data sources with novel algorithms. The framework is based on integrating and analysing existing data sources under the hypothesis that changes in the basal expression of genes may be responsible for the higher prevalence of comorbidities in older patients. Using the proposed framework, we selected genes related to comorbidities from existing databases, and then analysed their expression with age at the tissues level. We found a set of genes that changes significantly in certain specific tissues over time. We also reconstructed the associated protein interaction networks and the related pathways for each tissue. Using this mechanistic framework, we detected interesting pathways related to T2DM whose genes change their expression with age. We also found many pathways related to insulin regulation and brain activities, which can be used to develop specific therapies. To the best of our knowledge, this is the first study that analyses such genes at the tissue level together with age variations.

The IHI Rochester Report 2022 on Healthcare Informatics Research: Resuming After the CoViD-19.

In 2020, the CoViD-19 pandemic spread worldwide in an unexpected way and suddenly modified many life issues, including social habits, social relationships, teaching modalities, and more. Such changes were also observable in many different healthcare and medical contexts. Moreover, the CoViD-19 pandemic acted as a stress test for many research endeavors, and revealed some limitations, especially in contexts where research results had an immediate impact on the social and healthcare habits of millions of people. As a result, the research community is called to perform a deep analysis of the steps already taken, and to re-think steps for the near and far future to capitalize on the lessons learned due to the pandemic. In this direction, on June 09th-11th, 2022, a group of twelve healthcare informatics researchers met in Rochester, MN, USA. This meeting was initiated by the Institute for Healthcare Informatics-IHI, and hosted by the Mayo Clinic. The goal of the meeting was to discuss and propose a research agenda for biomedical and health informatics for the next decade, in light of the changes and the lessons learned from the CoViD-19 pandemic. This article reports the main topics discussed and the conclusions reached. The intended readers of this paper, besides the biomedical and health informatics research community, are all those stakeholders in academia, industry, and government, who could benefit from the new research findings in biomedical and health informatics research. Indeed, research directions and social and policy implications are the main focus of the research agenda we propose, according to three levels: the care of individuals, the healthcare system view, and the population view.

GTExVisualizer: a web platform for supporting ageing studies.

MOTIVATION: Studying ageing effects on molecules is an important new topic for life science. To perform such studies, the need for data, models, algorithms, and tools arises to elucidate molecular mechanisms. GTEx (standing for Genotype-Tissue Expression) portal is a web-based data source allowing to retrieve patients' transcriptomics data annotated with tissues, gender, and age information. It represents the more complete data sources for ageing effects studies. Nevertheless, it lacks functionalities to query data at the sex/age level, as well as tools for protein interaction studies, thereby limiting ageing studies. As a result, users need to download query results to proceed to further analysis, such as retrieving the expression of a given gene on different age (or sex) classes in many tissues. RESULTS: We present the GTExVisualizer, a platform to query and analyse GTEx data. This tool contains a web interface able to: (i) graphically represent and study query results; (ii) analyse genes using sex/age expression patterns, also integrated with network-based modules; and (iii) report results as plot-based representation as well as (gene) networks. Finally, it allows the user to obtain basic statistics which evidence differences in gene expression among sex/age groups. CONCLUSION: The GTExVisualizer novelty consists in providing a tool for studying ageing/sex-related effects on molecular processes. AVAILABILITY AND IMPLEMENTATION: GTExVisualizer is available at: http://gtexvisualizer.herokuapp.com. The source code and data are available at: https://github.com/UgoLomoio/gtex_visualizer.

Data-Independent Acquisition Mass Spectrometry of EPS-Urine Coupled to Machine Learning: A Predictive Model for Prostate Cancer.

Prostate cancer (PCa) is annually the most frequently diagnosed cancer in the male population. To date, the diagnostic path for PCa detection includes the dosage of serum prostate-specific antigen (PSA) and the digital rectal exam (DRE). However, PSA-based screening has insufficient specificity and sensitivity; besides, it cannot discriminate between the aggressive and indolent types of PCa. For this reason, the improvement of new clinical approaches and the discovery of new biomarkers are necessary. In this work, expressed prostatic secretion (EPS)-urine samples from PCa patients and benign prostatic hyperplasia (BPH) patients were analyzed with the aim of detecting differentially expressed proteins between the two analyzed groups. To map the urinary proteome, EPS-urine samples were analyzed by data-independent acquisition (DIA), a high-sensitivity method particularly suitable for detecting proteins at low abundance. Overall, in our analysis, 2615 proteins were identified in 133 EPS-urine specimens obtaining the highest proteomic coverage for this type of sample; of these 2615 proteins, 1670 were consistently identified across the entire data set. The matrix containing the quantified proteins in each patient was integrated with clinical parameters such as the PSA level and gland size, and the complete matrix was analyzed by machine learning algorithms (by exploiting 90% of samples for training/testing using a 10-fold cross-validation approach, and 10% of samples for validation). The best predictive model was based on the following components: semaphorin-7A (sema7A), secreted protein acidic and rich in cysteine (SPARC), FT ratio, and prostate gland size. The classifier could predict disease conditions (BPH, PCa) correctly in 83% of samples in the validation set. Data are available via ProteomeXchange with the identifier PXD035942.

Bioengineering and medical informatics education in MD programs: perspectives from three Italian experiences.

BACKGROUND: Given the impact of bioengineering and medical informatics technologies in health care, the design and implementation of education programs able to combine medical curricula with a proper teaching on engineering and informatics is now of paramount importance. In Italy, this goal has to fit in with the existing higher education system, which is structured into Bachelor programs and Master programs. Medicine and Surgery programs, instead, are designed as a six-year single-cycle Degree Program in Medicine and Surgery which comprises both class attendance and hospital internship and training. This program allows students to become Medical Doctors (MD). The different organization of this University program makes it not easy to introduce further contents, namely hard science courses, in the educational program. Notwithstanding this, we present here some recent innovative programs aimed at widening MD curriculum by including biomedical engineering and informatics subjects. In particular, we will introduce three of them. Two are joint-degree programs, the first between Humanitas University and Politecnico di Milano (MEDTEC School), and the second between University of Calabria and University Magna Graecia of Catanzaro (Medicina e Chirurgia TD). The Third one is a Professional Master coupled with an MD degree, based on a joint program among Pavia University, Pisa University, the Institute of Advanced studies in Pavia and the Scuola Superiore S. Anna in Pisa (MEET). CONTRIBUTION: The paper provides a description of the fundamental design principles of the three above mentioned programs, and explores some aspects of the teaching modules, highlighting their positive aspects. In particular, we show how the three different programs allow students to enrich their knowledge by studying engineering subjects and innovative methods and technologies, as well as their applications to patient care. CONCLUSIONS: The MEDTEC program is the first degree program at Italian and international scale which integrates medical and engineering subjects. In the following years, other programs were issued in Italy, defining similar education programs to couple a degree in medicine education with bioengineering and medical informatics, among which Medicina e Chirurgia TD and MEET. We believe the experiences described here in this paper represent the possibility of bridging the gap between medical and technological competencies.

Computational analysis of the sequence-structure relation in SARS-CoV-2 spike protein using protein contact networks.

The structure of proteins impacts directly on the function they perform. Mutations in the primary sequence can provoke structural changes with consequent modification of functional properties. SARS-CoV-2 proteins have been extensively studied during the pandemic. This wide dataset, related to sequence and structure, has enabled joint sequence-structure analysis. In this work, we focus on the SARS-CoV-2 S (Spike) protein and the relations between sequence mutations and structure variations, in order to shed light on the structural changes stemming from the position of mutated amino acid residues in three different SARS-CoV-2 strains. We propose the use of protein contact network (PCN) formalism to: (i) obtain a global metric space and compare various molecular entities, (ii) give a structural explanation of the observed phenotype, and (iii) provide context dependent descriptors of single mutations. PCNs have been used to compare sequence and structure of the Alpha, Delta, and Omicron SARS-CoV-2 variants, and we found that omicron has a unique mutational pattern leading to different structural consequences from mutations of other strains. The non-random distribution of changes in network centrality along the chain has allowed to shed light on the structural (and functional) consequences of mutations.