Standardizing digital biobanks: integrating imaging, genomic, and clinical data for precision medicine.

Advancements in data acquisition and computational methods are generating a large amount of heterogeneous biomedical data from diagnostic domains such as clinical imaging, pathology, and next-generation sequencing (NGS), which help characterize individual differences in patients. However, this information needs to be available and suitable to promote and support scientific research and technological development, supporting the effective adoption of the precision medicine approach in clinical practice. Digital biobanks can catalyze this process, facilitating the sharing of curated and standardized imaging data, clinical, pathological and molecular data, crucial to enable the development of a comprehensive and personalized data-driven diagnostic approach in disease management and fostering the development of computational predictive models. This work aims to frame this perspective, first by evaluating the state of standardization of individual diagnostic domains and then by identifying challenges and proposing a possible solution towards an integrative approach that can guarantee the suitability of information that can be shared through a digital biobank. Our analysis of the state of the art shows the presence and use of reference standards in biobanks and, generally, digital repositories for each specific domain. Despite this, standardization to guarantee the integration and reproducibility of the numerical descriptors generated by each domain, e.g. radiomic, pathomic and -omic features, is still an open challenge. Based on specific use cases and scenarios, an integration model, based on the JSON format, is proposed that can help address this problem. Ultimately, this work shows how, with specific standardization and promotion efforts, the digital biobank model can become an enabling technology for the comprehensive study of diseases and the effective development of data-driven technologies at the service of precision medicine.

Addressing adverse synergies between chemical and biological pollutants at schools-The 'SynAir-G' hypothesis.

While the number and types of indoor air pollutants is rising, much is suspected but little is known about the impact of their potentially synergistic interactions, upon human health. Gases, particulate matter, organic compounds but also allergens and viruses, fall within the 'pollutant' definition. Distinct populations, such as children and allergy and asthma sufferers are highly susceptible, while a low socioeconomic background is a further susceptibility factor; however, no specific guidance is available. We spend most of our time indoors; for children, the school environment is of paramount importance and potentially amenable to intervention. The interactions between some pollutant classes have been studied. However, a lot is missing with respect to understanding interactions between specific pollutants of different classes in terms of concentrations, timing and sequence, to improve targeting and upgrade standards. SynAir-G is a European Commission-funded project aiming to reveal and quantify synergistic interactions between different pollutants affecting health, from mechanisms to real life, focusing on the school setting. It will develop a comprehensive and responsive multipollutant monitoring system, advance environmentally friendly interventions, and disseminate the generated knowledge to relevant stakeholders in accessible and actionable formats. The aim of this article it to put forward the SynAir-G hypothesis, and describe its background and objectives.

A Biobanking System for Diagnostic Images: Architecture Development, COVID-19-Related Use Cases, and Performance Evaluation.

BACKGROUND: Systems capable of automating and enhancing the management of research and clinical data represent a significant contribution of information and communication technologies to health care. A recent advancement is the development of imaging biobanks, which are now enabling the collection and storage of diagnostic images, clinical reports, and demographic data to allow researchers identify associations between lifestyle and genetic factors and imaging-derived phenotypes. OBJECTIVE: The aim of this study was to design and evaluate the system performance of a network for an operating biobank of diagnostic images, the Bio Check Up Srl (BCU) Imaging Biobank, based on the Extensible Neuroimaging Archive Toolkit open-source platform. METHODS: Three usage cases were designed focusing on evaluation of the memory and computing consumption during imaging collections upload and during interactions between two kinds of users (researchers and radiologists) who inspect chest computed tomography scans of a COVID-19 cohort. The experiments considered three network setups: (1) a local area network, (2) virtual private network, and (3) wide area network. The experimental setup recorded the activity of a human user interacting with the biobank system, which was continuously replayed multiple times. Several metrics were extracted from network traffic traces and server logs captured during the activity replay. RESULTS: Regarding the diagnostic data transfer, two types of containers were considered: the Web and the Database containers. The Web appeared to be the more memory-hungry container with a higher computational load (average 2.7 GB of RAM) compared to that of the database. With respect to user access, both users demonstrated the same network performance level, although higher resource consumption was registered for two different actions: DOWNLOAD & LOGOUT (100%) for the researcher and OPEN VIEWER (20%-50%) for the radiologist. CONCLUSIONS: This analysis shows that the current setup of BCU Imaging Biobank is well provisioned for satisfying the planned number of concurrent users. More importantly, this study further highlights and quantifies the resource demands of specific user actions, providing a guideline for planning, setting up, and using an image biobanking system.

Evaluation of AI-Based Segmentation Tools for COVID-19 Lung Lesions on Conventional and Ultra-low Dose CT Scans.

A reliable diagnosis and accurate monitoring are pivotal steps for treatment and prevention of COVID-19. Chest computed tomography (CT) has been considered a crucial diagnostic imaging technique for the injury assessment of the viral pneumonia. Furthermore, the automatization of the segmentation methods for lung alterations helps to speed up the diagnosis and lighten radiologists' workload. Considering the assiduous pathology monitoring, ultra-low dose (ULD) chest CT protocols have been implemented to drastically reduce the radiation burden. Unfortunately, the available AI technologies have not been trained on ULD-CT data and validated and their applicability deserves careful evaluation. Therefore, this work aims to compare the results of available AI tools (BCUnet, CORADS AI, NVIDIA CLARA Train SDK and CT Pneumonia Analysis) on a dataset of 73 CT examinations acquired both with conventional dose (CD) and ULD protocols. COVID-19 volume percentage, resulting from each tool, was statistically compared. This study demonstrated high comparability of the results on CD-CT and ULD-CT data among the four AI tools, with high correlation between the results obtained on both protocols (R > .68, P < .001, for all AI tools).

Bleeding epulis gravidarum: what to evaluate?

INTRODUCTION: Hormonal changes during pregnancy may induce modifications in oral mucosa. Epulis gravidarum (EG) is an oral disease arising during pregnancy, usually regressing after delivery. A case of EG managed at our department is described and those previously reported in literature are reviewed in order to define EG clinical features for stratifying the risk of complications and the need of surgery during pregnancy as well as which factors should be considered more relevant in EG management. EVIDENCE ACQUISITION: Electronic databases (Medline, Embase, Web of Sciences, Scopus and Cochrane Library) were searched from inception of each databases until May 2021 to identify clinical studies on management of EG diagnosed during pregnancy. The aim of this review was to identify factors influencing the need and timing of surgical management. EVIDENCE SYNTHESIS: A woman with a triplet pregnancy suffering from EG, complicated by profuse bleeding, required Caesarean section (CS) given the triplet pregnancy and the impending preterm labor. The surgical removal of EG was not performed because it spontaneously regressed without consequences 40 days after delivery. Review analysis indicated that EG clinical management is dependent on types of symptoms and their severity. Multilinear regression analysis showed that operative management strategy was associated with bone loss on X-ray (t=4.23, P=0.003), while EG surgical treatment during pregnancy was associated with pain (t=-2.91, P=0.03). No significant differences were found in management strategy, according to pain (P=0.12), interference with mastication (P=0.98) and speech (P=0.36). A poor oral hygiene was described in 71% of patients as hypothetical trigger. CONCLUSIONS: EG management strategy depends on bleeding, pain and bone loss on X-ray. A multidisciplinary approach is useful to perform a rapid and appropriate diagnosis and to better evaluate pros and cons of surgery during pregnancy and following management.

Association between lymphadenopathy after toxoplasmosis seroconversion in pregnancy and risk of congenital infection.

The aim of the study was to describe the pregnancy outcome of a large cohort of women with toxoplasmosis seroconversion in pregnancy and to investigate the relation between maternal lymphadenopathy and risk of congenital toxoplasmosis (CT). This was a retrospective study involving women with confirmed toxoplasmosis seroconversion in pregnancy between 2001 and 2017. Women were clinically evaluated for lymphadenopathy and classified as follows: lymphadenopathy absent (L-) or lymphadenopathy present (L+). The mothers were treated and followed-up according to local protocol, and neonates were monitored at least for 1 year in order to diagnose CT. A total of 218 women (one twin pregnancy) were included in the analysis. Pregnancy outcome was as follows: 149 (68%) of children not infected, 62 (28.3%) infected, 4 (1.8%) first trimester termination of pregnancy, 2 (0.9%) first trimester miscarriages, and 3 (1.4%) stillbirths (of which one already counted in the infected cohort). 13.8% of women were L+ , and they were nearly three times more likely to have a child with CT compared to L- women (aOR, 2.90; 95%CI, 1.28-6.58). Moreover, the result was still statistically significant when the analysis was restricted to 81 children whose mothers were clinically examined and received treatment within 5 weeks from estimated time of infection. In conclusion, there is a positive association between L+ status in pregnant women, and risk of CT also confirmed when restricting the analysis to women with early diagnosis of seroconversion and treatment. This data could be very useful in counselling pregnant women with toxoplasmosis seroconversion and lead to direct a more specific therapeutic and diagnostic protocol.

Computerized cardiotocography in singleton gestations with diabetes mellitus: a retrospective study.

BACKGROUND: The aim of this study was to evaluate the use of computerized cardiotocography (C-CTG) in women with diabetes mellitus. METHODS: This was a retrospective cohort study of women with diabetes mellitus referred to University of Naples Federico II from January 2018 to January 2020 for antenatal monitoring. Only women who underwent antenatal monitoring with C-CTG were included in the study. For the purpose of this study only the C-CTG recorded at the time of outpatient admission were analyzed. Women were divided into four groups: 1) women with diabetes mellitus type 1; 2) women with diabetes mellitus type 2; 3) women with gestational diabetes mellitus (GDM); 4) control group without diabetes mellitus. The primary outcome of the study was the C-CTG short term variability (STV). RESULTS: A total of 298 patients were included in the study, 89 with type 1 diabetes (group 1), 27 with type 2 diabetes (group 2), 77 with GDM (group 3) and 105 controls (group 4). Fetal heart rate was statistically higher in pregnant women with pre-pregnancy diabetes both Type 1 and 2 compared to gestational diabetes and physiological pregnancies. The parameters of STV, APRS and DPRS were statistically lower in the pregnant group with pre-pregnancy type 1 diabetes than in type 2 and compared to group 3 and 4. CONCLUSIONS: Fetal heart rate was statistically higher in pregnant women with pre-pregnancy diabetes, both Type 1 and 2, compared to gestational diabetes and controls. STV, APRS and DPRS were statistically lower in the pregnant group with pre-pregnancy type 1 diabetes than in type 2 and compared to group 3 and 4.

An integrated approach based on advanced CTG parameters and Doppler measurements for late growth restriction management.

BACKGROUND: The clinical diagnosis of late Fetal Growth Restriction (FGR) involves the integration of Doppler ultrasound data and Fetal Heart Rate (FHR) monitoring through computer assisted computerized cardiotocography (cCTG). The aim of the study was to evaluate the diagnostic power of combined Doppler and cCTG parameters by contrasting late FGR -and healthy controls. METHODS: The study was conducted from January 2018 to May 2020. Only pregnant women who had the last Doppler measurement obtained within 1 week before delivery and cCTG performed within 24 h before delivery were included in the study. Two hundred forty-nine pregnant women fulfilling the inclusion criteria were enrolled in the study; 95 were confirmed as late FGR and 154 were included in the control group. RESULTS: Among the extracted cCTG parameters, Delta Index, Short Term Variability (STV), Long Term Variability (LTV), Acceleration and Deceleration Phase Rectified Slope (APRS, DPRS) values were lower in the late FGR participants compared to the control group. In the FGR cohort, Delta, STV, APRS, and DPRS were found different when stratifying by MCA_PI (MCA_PI <5th centile or > 5th centile). STV and DPRS were the only parameters to be found different when stratifying by (UA_PI >95th centile or UA_PI <95th centile). Additionally, we measured the predictive power of cCTG parameters toward the identification of associated Doppler measures using figures of merit extracted from ROC curves. The AUC of ROC curves were accurate for STV (0,70), Delta (0,68), APRS (0,65) and DPRS (0,71) when UA_PI values were > 95th centile while, the accuracy attributable to the prediction of MCA_PI was 0.76, 0.77, 0.73, and 0.76 for STV, Delta, APRS, and DPRS, respectively. An association of UA_PI>95th centile and MCA_PI<5th centile with higher risk for NICU admission, was observed, while CPR < 5th centile resulted not associated with any perinatal outcome. Values of STV, Delta, APRS, DPRS were significantly lower for FGR neonates admitted to NICU, compared with the uncomplicated FGR cohort. CONCLUSIONS: The results of this study show the contribution of advanced cCTG parameters and fetal Doppler to the identification of late FGR and the association of those parameters with the risk for NICU admission. TRIAL REGISTRATION: Retrospectively registered.

Community-Based Rehabilitation Indicators: Validation and Preliminary Evidence for Disability in Italy.

Community-based rehabilitation (CBR) is a multi-sectorial community strategy for guaranteeing that people with disabilities enjoy the same rights and opportunities as all other community members. CBR is organized in a five-component matrix-namely, health, education, social, livelihood, and empowerment. To measure the effectiveness of CBR, the World Health Organization (WHO) has developed standardized indicators. The objective of the present study is to translate and validate the CBR indicators (CBR-Is), providing preliminary evidence of their use for disability in Italy. After obtaining permission from the WHO, the CBR-Is followed a process of translation and cross-cultural adaptation according to international guidelines. An examination of internal consistency and reliability was than performed. The intra-rater reliability was estimated using the Intraclass Correlation Coefficient with a 95% confidence interval. In order to measures the differences between people with and without disabilities, an independent sample t-test was used for quantitative indicators. The Italian version of the CBR-Is (IT-CBR-Is) was administered to 234 people. The internal consistency showed a good value, with a Cronbach's alpha coefficient of 0.862, and the intra-rater reliability analysis showed solid values for each domain (range: 0.723-0.882). Statistically significant differences between people with and without disabilities were found for each domain of the CBR matrix-namely, health, social, education, livelihood, and empowerment. The IT-CBR-Is are consistent and reliable measures when used to investigate disability in a community-based inclusive development perspective. National stakeholders can now have specific indicators to implement services and actions for people with disabilities.

How does DICOM support big data management? Investigating its use in medical imaging community.

The diagnostic imaging field is experiencing considerable growth, followed by increasing production of massive amounts of data. The lack of standardization and privacy concerns are considered the main barriers to big data capitalization. This work aims to verify whether the advanced features of the DICOM standard, beyond imaging data storage, are effectively used in research practice. This issue will be analyzed by investigating the publicly shared medical imaging databases and assessing how much the most common medical imaging software tools support DICOM in all its potential. Therefore, 100 public databases and ten medical imaging software tools were selected and examined using a systematic approach. In particular, the DICOM fields related to privacy, segmentation and reporting have been assessed in the selected database; software tools have been evaluated for reading and writing the same DICOM fields. From our analysis, less than a third of the databases examined use the DICOM format to record meaningful information to manage the images. Regarding software, the vast majority does not allow the management, reading and writing of some or all the DICOM fields. Surprisingly, if we observe chest computed tomography data sharing to address the COVID-19 emergency, there are only two datasets out of 12 released in DICOM format. Our work shows how the DICOM can potentially fully support big data management; however, further efforts are still needed from the scientific and technological community to promote the use of the existing standard, encouraging data sharing and interoperability for a concrete development of big data analytics.

A Machine Learning Approach to Monitor the Emergence of Late Intrauterine Growth Restriction.

Late intrauterine growth restriction (IUGR) is a fetal pathological condition characterized by chronic hypoxia secondary to placental insufficiency, resulting in an abnormal rate of fetal growth. This pathology has been associated with increased fetal and neonatal morbidity and mortality. In standard clinical practice, late IUGR diagnosis can only be suspected in the third trimester and ultimately confirmed at birth. This study presents a radial basis function support vector machine (RBF-SVM) classification based on quantitative features extracted from fetal heart rate (FHR) signals acquired using routine cardiotocography (CTG) in a population of 160 healthy and 102 late IUGR fetuses. First, the individual performance of each time, frequency, and nonlinear feature was tested. To improve the unsatisfactory results of univariate analysis we firstly adopted a Recursive Feature Elimination approach to select the best subset of FHR-based parameters contributing to the discrimination of healthy vs. late IUGR fetuses. A fine tuning of the RBF-SVM model parameters resulted in a satisfactory classification performance in the training set (accuracy 0.93, sensitivity 0.93, specificity 0.84). Comparable results were obtained when applying the model on a totally independent testing set. This investigation supports the use of a multivariate approach for the in utero identification of late IUGR condition based on quantitative FHR features encompassing different domains. The proposed model allows describing the relationships among features beyond the traditional linear approaches, thus improving the classification performance. This framework has the potential to be proposed as a screening tool for the identification of late IUGR fetuses.

miR-16-5p, miR-103-3p, and miR-27b-3p as Early Peripheral Biomarkers of Fetal Growth Restriction.

Current tests available to diagnose fetal hypoxia in-utero lack sensitivity thus failing to identify many fetuses at risk. Emerging evidence suggests that microRNAs derived from the placenta circulate in the maternal blood during pregnancy and may be used as non-invasive biomarkers for pregnancy complications. With the intent to identify putative markers of fetal growth restriction (FGR) and new therapeutic druggable targets, we examined, in maternal blood samples, the expression of a group of microRNAs, known to be regulated by hypoxia. The expression of microRNAs was evaluated in maternal plasma samples collected from (1) women carrying a preterm FGR fetus (FGR group) or (2) women with an appropriately grown fetus matched at the same gestational age (Control group). To discriminate between early- and late-onset FGR, the study population was divided into two subgroups according to the gestational age at delivery. Four microRNAs were identified as possible candidates for the diagnosis of FGR: miR-16-5p, miR-103-3p, miR-107-3p, and miR-27b-3p. All four selected miRNAs, measured by RT-PCR, resulted upregulated in FGR blood samples before the 32nd week of gestation. By contrast, miRNA103-3p and miRNA107-3p, analyzed between the 32nd and 37th week of gestation, showed lower expression in the FGR group compared to aged matched controls. Our results showed that measurement of miRNAs in maternal blood may form the basis for a future diagnostic test to determine the degree of fetal hypoxia in FGR, thus allowing the start of appropriate therapeutic interventions to alleviate the burden of this disease.

Antenatal cardiotocography with and without computer analysis in high-risk pregnancy: a randomized clinical trial.

BACKGROUND: Cardiotocography or nonstress test is a technical means of recording the fetal heartbeat and uterine contractions for antenatal monitoring. OBJECTIVE: This study aimed to evaluate whether antepartum cardiotocography with computer analysis (computerized cardiotocography) increases the incidence of cesarean delivery in women with high-risk pregnancies but without intrauterine growth restriction. STUDY DESIGN: This was a parallel group nonblinded randomized clinical trial of singletons with high-risk pregnancies admitted for inpatient monitoring between 24 0/7 and 37 6/7 weeks' gestation. Eligible participants were randomly allocated in a 1:1 ratio to antenatal monitoring with either standard cardiotocography or computerized cardiotocography. Women randomized to the computerized cardiotocography arm received cardiotocographic monitoring with computerized analysis in a central monitoring station. The primary outcome was the incidence of cesarean delivery. RESULTS: Overall, 28 women were enrolled in this trial. In addition, 14 women were randomized to the computerized cardiotocography group and 14 women to the control group. No woman was excluded after randomization or lost to follow-up. Cesarean delivery occurred in 9 women (64.3%) in the computerized cardiotocography group and 9 women (64.3%) in the control group (relative risk, 1.00; 95% confidence interval, 0.21-4.69).There was no significant between-group difference in preterm birth, gestational age at delivery, Apgar score, and birthweight. CONCLUSION: Among women with high-risk pregnancies, use of computerized cardiotocography for antenatal monitoring did not result in a significant increase in cesarean delivery compared with standard cardiotocography. The results of this single-center randomized trial require confirmation in multicenter studies.

First trimester ultrasound features of X-linked Opitz syndrome and early molecular diagnosis: case report and review of the literature.

X-linked Opitz G/BBB syndrome (XLOS) is a multiple congenital disorder inherited in an X-linked manner. XLOS may be suspected, in prenatal age, on the basis of sonographic findings in the second and/or third trimester of gestation. Pathogenetic variants in MID1 gene have been reported in individuals with XLOS. Prenatal genetic testing is offered for pregnancies at risk, in which the mutation in the family has been identified. To date no cases of prenatal diagnosis, based on first-trimester ultrasound data, have been reported. We present a case of a fetus at 12 gestational weeks with ultrasound multiple anomalies, including increased nuchal translucency, heart defects, cleft lip and palate, enlarged fourth ventricle absence of ductus venosus and family hystory of XLOS. The genetic prenatal test detected the c(0).1286-1G > T mutation of MID1 gene. Data about prenatal ultrasonographic findings consistent with XLOS are limited to second and third trimester. This is the first case reporting ultrasound detectable midline defects suggestive of XLOS as early as the first trimester of gestation. This case also suggests that when multiple anomalies are detected in a fetus with normal chromosomal structure, the possibility of a monogenic disorder must be considered.

Impact of nuchal cord on antenatal and intrapartum foetal heart rate surveillance and perinatal outcome.

Analysing antepartum and intrapartum computerised cardiotocographic (cCTG) parameters in physiological term pregnancies with nuchal (NC) or body cord (BC), in order to correlate them with labour events and neonatal outcome. We enrolled 808 pregnant women, composed of 264 with 'one NC', 121 with 'multiple NCs', 39 with BC and 384 with 'no NC', were monitored from the 37th week of gestation before labour, while 49 pregnant women with 'one or more NCs' and 47 with 'no NCs' were analysed during labour. No differences in maternal characteristics, foetal pH at birth and 5-min Apgar score were observed. The birth weight was significantly lower in the 'multiple NCs' group, while 1-minute Apgar score was lower in the BC group than the other groups, respectively. No relevant differences in cCTG parameters were observed, except for LTI, Delta and number of variable decelerations in antepartum period and only variable deceleration in intrapartum period.Impact statementWhat is already known on this subject? Ultrasound cannot predict which foetuses with NCs are likely to have problem during labour. The question arose if single or multiple NC could affects FHR monitoring prior and during labour.What do the results of this study add? Computerised cardiotocography (cCTG) is a standardised method developed to reduce inter- and intra-observer variability and the poor reproducibility of visual analysis. Few studies have investigated the influence of NCs on FHR variability and, to our knowledge, no one has evaluated its linear and nonlinear characteristics in antepartum and intrapartum period using a computerised analysis system. No differences in maternal characteristics, foetal pH at birth and 5-min Apgar score were observed. Birth weight was significantly lower in the 'multiple NCs' group, while 1-min Apgar score was lower in the BC group than the other groups, respectively. Foetuses with 'one or more NCs' evidenced a larger number of prolonged second stage and meconium-stained liquor cases, while the operative vaginal delivery and emergency caesarean section rates were unchanged. No relevant differences in cCTG parameters were observed, except for LTI, Delta and number of variable decelerations in antepartum period and only variable deceleration in intrapartum period.What are the implications of these findings for clinical practice and/or further research? cCTG monitoring results confirmed their usefulness for assessing the state of good oxygenation for all foetuses investigated.

Intrapartum cardiotocography with and without computer analysis: a systematic review and meta-analysis of randomized controlled trials.

Objective: To evaluate whether intrapartum cardiotocography with computer analysis decreases the incidence of newborn metabolic acidosis or obstetric intervention when compared with visual analysis through a systematic review with meta-analysis of randomized controlled trials.Methods: The research was conducted using Medline, Embase, Web of Science, Scopus, ClinicalTrial.gov, Ovid and Cochrane Library as electronic databases from the inception of each database to May 2018. Selection criteria included randomized trial evaluating women with cephalic presentation at term or late preterm term during labor who were randomized to electronic fetal heart rate monitoring with either computer analysis (i.e. intervention group) or standard visual analysis (i.e. control group). Trials evaluating antenatal fetal heart rate monitoring in women not in labor were excluded. The primary outcome was incidence of newborn metabolic acidosis, defined as pH less than 7.05 and base deficit greater than 12 mmol/L. Secondary outcomes were mode of delivery, admission to neonatal intensive care unit, hypoxic-ischemic encephalopathy, and perinatal death. The summary measures were reported as relative risk (RR) with 95% confidence interval (CI).Results: Three randomized controlled trials (RCTs), including 54,492 participants, which met inclusion criteria for this meta-analysis, were analyzed. All the included trials enrolled women with cephalic presentation at term or late preterm. Women were randomized in the active first stage of labor and all of them received continuous cardiotocography (CTG) from randomization until delivery. Women who received continuous CTG during labor with computerized analysis had similar risk of newborn metabolic acidosis. No between group differences were found in the secondary outcomes.Conclusions: Compared with visual analysis, use of computer analysis of fetal monitoring signals during labor did not significantly reduce the rate of metabolic acidosis or obstetric intervention.

Bringing radiomics into a multi-omics framework for a comprehensive genotype-phenotype characterization of oncological diseases.

Genomic and radiomic data integration, namely radiogenomics, can provide meaningful knowledge in cancer diagnosis, prognosis and treatment. Despite several data structures based on multi-layer architecture proposed to combine multi-omic biological information, none of these has been designed and assessed to include radiomic data as well. To meet this need, we propose to use the MultiAssayExperiment (MAE), an R package that provides data structures and methods for manipulating and integrating multi-assay experiments, as a suitable tool to manage radiogenomic experiment data. To this aim, we first examine the role of radiogenomics in cancer phenotype definition, then the current state of radiogenomics data integration in public repository and, finally, challenges and limitations of including radiomics in MAE, designing an extended framework and showing its application on a case study from the TCGA-TCIA archives. Radiomic and genomic data from 91 patients have been successfully integrated in a single MAE object, demonstrating the suitability of the MAE data structure as container of radiogenomic data.

Incidence of toxoplasmosis in pregnancy in Campania: A population-based study on screening, treatment, and outcome.

INTRODUCTION: The aim of this study was to evaluate the incidence of toxoplasmosis infection during pregnancy and to describe the characteristics of the serological status, management, follow-up and treatment. MATERIAL AND METHODS: This is a population-based cohort study of women referred for suspected toxoplasmosis during pregnancy from January, 2001 to December, 2012. Suspected toxoplasmosis was defined as positive IgM antibody during pregnancy. Women with suspected toxoplasmosis during pregnancy were classified into three groups: seroconversion, suspected infection, or no infection in pregnancy. Women in the first and second group were treated according to local protocol, and amniocentesis with toxoplasmosis PCR detection and serial detailed ultrasound scans were offered. Neonates were investigated for congenital toxoplasmosis at birth and were monitored for at least one year after birth. RESULTS: During the study period, there were 738,588 deliveries in Campania. Of them 1159 (0.2%) were referred to our Institution for suspected toxoplasmosis during pregnancy: 183 (15.8%) women were classified as seroconversion, 381 (32.9%) were suspected infection, and 595 (51.3%) were not infected in pregnancy. Neonatal outcome was available for 476 pregnancies, including 479 neonates (3 twins, 473 singletons), out of the 564 pregnancies with seroconversion or suspected infection. 384 (80.2%) babies were not infected at birth and at follow-up, 67 (14.0%) had congenital toxoplasmosis, 10 (2.1%) were voluntary induced termination of pregnancy, 15 (3.1%) were spontaneous miscarriage, and 4 (0.8%) were stillbirth (of which one counted already in the infected cohort). Considering cases of congenital toxoplasmosis, the transmission rate in women with seroconversion was 32.9% (52/158), and in women with suspected infection was 4.7% (15/321). CONCLUSIONS: Toxoplasmosis is uncommon in pregnancy with overall incidence of seroconversion and suspected infection in pregnancy of 0.8 per 1000 live births and incidence of congenital toxoplasmosis 0.1 per 1000 live births when applying a strict protocol of screening, follow-up, and treatment. 51.3% (595/1159) of women referred to our center for suspected infection were actually considered not infected.

Numerical simulation of novel concept 4D cardiac microtomography for small rodents based on all-optical Thomson scattering X-ray sources.

Accurate dynamic three-dimensional (4D) imaging of the heart of small rodents is required for the preclinical study of cardiac biomechanics and their modification under pathological conditions, but technological challenges are met in laboratory practice due to the very small size and high pulse rate of the heart of mice and rats as compared to humans. In 4D X-ray microtomography (4D µCT), the achievable spatio-temporal resolution is hampered by limitations in conventional X-ray sources and detectors. Here, we propose a proof-of-principle 4D µCT platform, exploiting the unique spatial and temporal features of novel concept, all-optical X-ray sources based on Thomson scattering (TS). The main spatial and spectral properties of the photon source are investigated using a TS simulation code. The entire data acquisition workflow has been also simulated, using a novel 4D numerical phantom of a mouse chest with realistic intra- and inter-cycle motion. The image quality of a typical single 3D time frame has been studied using Monte Carlo simulations, taking into account the effects of the typical structure of the TS X-ray beam. Finally, we discuss the perspectives and shortcomings of the proposed platform.

Expanded carrier screening: A current perspective.

Prenatal carrier screening has expanded to include a large number of genes offered to all couples considering pregnancy or with an ongoing pregnancy. Expanded carrier screening refers to identification of carriers of single-gene disorders outside of traditional screening guidelines. Expanded carrier screening panels include numerous autosomal recessive and X-linked genetic conditions, including those with a very low carrier frequency, as well as those with mild or incompletely penetrant phenotype. Therefore, the clinical utility of these panels is still subject of debate. Priority should be given to carrier screening panels that include a comprehensive set of severe childhood-onset disorders. Psychosocial support and genetic couseling should be available prior to screening and for the return of positive results. Systems are needed to reduce the risk of misinterpreting results. Finally, attention should be paid on the impact of expanded carrier screening on health care organizations and burden of cost.