MOViDA: multiomics visible drug activity prediction with a biologically informed neural network model.

MOTIVATION: The process of drug development is inherently complex, marked by extended intervals from the inception of a pharmaceutical agent to its eventual launch in the market. Additionally, each phase in this process is associated with a significant failure rate, amplifying the inherent challenges of this task. Computational virtual screening powered by machine learning algorithms has emerged as a promising approach for predicting therapeutic efficacy. However, the complex relationships between the features learned by these algorithms can be challenging to decipher. RESULTS: We have engineered an artificial neural network model designed specifically for predicting drug sensitivity. This model utilizes a biologically informed visible neural network, thereby enhancing its interpretability. The trained model allows for an in-depth exploration of the biological pathways integral to prediction and the chemical attributes of drugs that impact sensitivity. Our model harnesses multiomics data derived from a different tumor tissue sources, as well as molecular descriptors that encapsulate the properties of drugs. We extended the model to predict drug synergy, resulting in favorable outcomes while retaining interpretability. Given the imbalanced nature of publicly available drug screening datasets, our model demonstrated superior performance to state-of-the-art visible machine learning algorithms. AVAILABILITY AND IMPLEMENTATION: MOViDA is implemented in Python using PyTorch library and freely available for download at https://github.com/Luigi-Ferraro/MOViDA. Training data, RIS score and drug features are archived on Zenodo https://doi.org/10.5281/zenodo.8180380.

An integrated tumor, immune and microbiome atlas of colon cancer.

The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus bromii, associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches.

Clinical and electroencephalographic features of epilepsy in patients with triple X syndrome: A case series.

PURPOSE: Triple X syndrome, is an often undiagnosed chromosomal abnormality with an incidence of 1/1000 females. Main associated disorders are urogenital malformations, premature ovarian failure or primary amenorrhea, gastrointestinal problems, psychiatric disorders and epilepsy. To date, triple X is not related to a specific epileptic syndrome. Therefore, the purpose of this clinical series is to analyze seizure semiology, electroencephalogram features and the long-term outcome of 13 patients with epilepsy and triple X syndrome. METHODS: We retrospectively evaluated the long-term seizure outcome in patients with triple X syndrome who had been referred to 11 Epilepsy Centers in Italy. A close electroclinical follow-up was made for at least 2 years and outcomes were reported. RESULTS: Our case series confirms that epilepsy is not an occasional finding but part of the phenotypic spectrum of this syndrome. The seizure semiology shows an higher prevalence of focal seizures in 62% of patients. EEG findings of focal epileptic activity were reported in 85% of patients. Anti-seizure medications were successful in all our patients whom in most cases were responsive to monotherapy. CONCLUSION: According to our case series most successful drugs were VPA and LEV. Long term prognosis of epilepsy in our case series was good. Our experience suggests that all triple X patients achieve good seizure control and in 69% of cases normalization of the EEG.

Case Report: Remdesivir and Convalescent Plasma in a Newly Acute B Lymphoblastic Leukemia Diagnosis With Concomitant Sars-CoV-2 Infection.

Introduction: The spread of Covid-19 has worsened the prognosis of oncology patients, interrupting or delaying life-saving therapies and contextually increasing the risk of severe SARS-CoV-2 infections. Acute lymphoblastic leukemia (ALL) is the most frequent cancer in pediatric age and the management of this disease with concomitant SARS-COV-2 infection represents a challenging situation. Case presentation: We present the case of a 6-year-old female newly diagnosed with ALL during a documented SARS-CoV-2 infection. Our patient was admitted 20 days after SARS-CoV-2 detection for evening-rise fever. Laboratory testing showed severe neutropenia while chest x-ray detected moderate pulmonary involvement. Acute lymphoblastic leukemia diagnosis was made through morphological and molecular analysis on bone marrow aspirate. Given the stability of the blood count and clinical conditions, antiviral therapy with Remdesivir and Convalescent Plasma was started before antileukemic treatment, obtaining a rapid resolution of the infection. Conclusion: In our experience, the treatment with Remdesivir and Convalescent Plasma led to a rapid resolution of Sars-Cov-2 infection. Our case did not present any adverse event to the therapy. Thus, this treatment could be considered in patients with malignancies, in order to accelerate the resolution of the infection and begin immunosuppressive treatment safely. Further studies are required to confirm this hypothesis.

Three-Dimensional Sonographic Evaluation of the Position of the Fetal Conus Medullaris at First Trimester.

OBJECTIVE: The objective of this study was to assess the position of the conus medullaris (CM) at the first trimester 3D ultrasound in a cohort of structurally normal fetuses. METHODS: This was a multicenter prospective study involving a consecutive series of structurally normal fetuses between 11 and 13 weeks of gestation (CRL between 45 and 84 mm). All fetuses were submitted to 3D transvaginal ultrasound using a sagittal view of the spine as the starting plane of acquisition. At offline analysis, the position of the CM was evaluated by 2 independent operators with a quantitative and a qualitative method: (1) the distance between the most caudal part of the CM and the distal end of the coccyx (CMCd) was measured; (2) a line perpendicular to the fetal spine joining the tip of the CM to the anterior abdominal wall was traced to determine the level of this line in relation to the umbilical cord insertion (conus to abdomen line, CAL). Interobserver agreement for the CCMd was evaluated. Linear regression analysis was used to determine the association between the CMCd and CRL, and a normal range was computed based on the best-fit model. The absence of congenital anomalies was confirmed in all cases after birth. RESULTS: In the study period between December 2019 and March 2020, 143 fetuses were recruited. In 130 fetuses (90.9%), the visualization of the CM was feasible. The mean value of the CMCd was 1.09 ± 0.16 cm. The 95% limits of agreement for the interobserver variability in measurement of the CMCd were 0.24 and 0.26 cm. The interobserver variability based on the intra-class correlation coefficient (ICC) for the CCMd was good (ICC = 0.81). We found a positive linear relationship between the CCMd and CRL. In all these fetuses, the CAL encountered the abdominal wall at or above the level of the cord insertion. CONCLUSION: In normal fetuses, the assessment of the CM position is feasible at the first trimester 3D ultrasound with a good interobserver agreement. The CM level was never found below the fetal umbilical cord insertion, while the CMCd was noted to increase according to the gestational age, confirming the "ascension" of the CM during fetal life.

Iodine deficiency among Italian children and adolescents assessed through 24-hour urinary iodine excretion.

BACKGROUND: Iodine is an essential micronutrient for intellectual development in children. Information on iodine intakes based on 24-h urinary iodine excretion (UIE) is scant, because iodine status is only assessed by the measurement of urinary iodine concentration (UIC) in spot urine samples. OBJECTIVES: The aim of our study was to evaluate the iodine intake of school-age children and adolescents, using UIE measurement in 24-h urine collections. METHODS: The study population included 1270 healthy subjects (677 boys, 593 girls) aged 6-18 y (mean age ± SD: 10.3 ± 2.9) from 10 Italian regions. Daily iodine intake was estimated as UIE/0.92, based on the notion that $\sim$92% of the dietary iodine intake is absorbed. The adequacy of intakes was assessed according to the Dietary Reference Values for iodine of the European Food Safety Authority (EFSA). Body mass index (BMI) and UIC were also measured for each subject. RESULTS: Based on the scientific opinion of EFSA, 600 of 1270 subjects (47.2%) had a lower than adequate iodine intake, with a higher prevalence among girls (54.6%) compared with boys (40.2%) (P < 0.001). Although UIE and 24-h urinary volumes increased with age (P < 0.001), a progressive decrease in the percentage of subjects with iodine excretion <100 µg/24 h (P < 0.001) was observed, without any significant difference in the percentage of subjects with UIC <100 µg/L. No significant association was detected between BMI z-score and UIE (P = 0.603) or UIC (P = 0.869). CONCLUSIONS: A sizable proportion of our population, especially girls, appeared to be at risk of iodine inadequacy. The simple measurement of UIC could lead to underestimation of the occurrence of iodine deficiency in younger children, because of the age-related smaller urine volumes producing spuriously higher iodine concentrations.

Aspergillus myofasciitis in a chronic granulomatous disease patient: first case report.

Aspergillus myofasciitis is a rare infection of the muscles and their fascial sheaths that has been reported in patients with immune deficiencies of various kinds but, until now, not with chronic granulomatous disease (CGD). Patients affected by CGD are at high risk of invasive aspergillus infections. The case described involves a 14-year-old boy with a severe autosomal recessive CGD who was admitted to hospital with an Aspergillus myofasciitis of the left forearm. He was treated with liposomal amphotericin for 14 days and then with oral voriconazole for three months with an excellent clinical outcome. He did not evidence any recurrence in the following 30 months using itraconazole prophylaxis.

High sodium and low potassium intake among Italian children: relationship with age, body mass and blood pressure.

BACKGROUND: Hypertension is the leading cause of death in developed countries and reduction of salt intake is recommended as a key preventive measure. OBJECTIVE: To assess the dietary sodium and potassium intakes in a national sample of Italian children and adolescents and to examine their relationships with BMI and blood pressure (BP) in the framework of the MINISAL survey, a program supported by the Italian Ministry of Health. POPULATION AND METHODS: The study population included 1424 healthy subjects (766 boys, 658 girls) aged 6-18 years (mean age: 10.1±2.9) who were consecutively recruited in participating National Health Service centers in 10 Italian regions. Electrolyte intake was estimated from 24 hour urine collections tested for completeness by the concomitant measurement of creatinine content. Anthropometric indices and BP were measured with standardized procedures. RESULTS: The average estimated sodium intake was 129 mmol (7.4 g of salt) per day among boys and 117 mmol (6.7 g of salt) among girls. Ninety-three percent of the boys and 89% of the girls had a consumption higher than the recommended age-specific standard dietary target. The estimated average daily potassium intakes were 39 mmol (1.53 g) and 36 mmol (1.40 g), respectively, over 96% of the boys and 98% of the girls having a potassium intake lower than the recommended adequate intake. The mean sodium/potassium ratio was similar among boys and girls (3.5 and 3.4, respectively) and over 3-fold greater than the desirable level. Sodium intake was directly related to age, body mass and BP in the whole population. CONCLUSIONS: The Italian pediatric population is characterized by excessive sodium and deficient potassium intake. These data suggest that future campaigns should focus on children and adolescents as a major target in the framework of a population strategy of cardiovascular prevention.

Preliminary results on clinical effects of probiotic Lactobacillus salivarius LS01 in children affected by atopic dermatitis.

GOALS: The goal of this study was to evaluate the clinical efficacy of an intake of Lactobacillus salivarius LS01 (DSM 22775) for the treatment of atopic dermatitis (AD) in children. BACKGROUND: AD is an inflammatory and pruritic chronic relapsing skin disorder with multifactorial etiopathology. Some evidence suggests that probiotics may improve AD by modulating the immune system and the composition of intestinal microbiota. STUDY: A total of 43 patients aged from 0 to 11 years were enrolled in the study (M/F ratio=1:1) and treated with the probiotic strain L. salivarius LS01. Clinical efficacy of probiotic treatment was assessed from baseline by changes in itch index and in the objective SCORAD/SCORAD index. RESULTS: Patients being given probiotic treatment showed a significant improvement in clinical parameters (SCORAD and itch values) from baseline. The reduction in SCORAD and itch index observed after 4 weeks of treatment also persisted after the cessation of probiotic supplementation. CONCLUSIONS: L. salivarius LS01 seems to be able to improve the quality of life of children affected by AD and, as a consequence, it may have promising clinical and research implications.