Complete populations of virtual patients for in silico clinical trials.

MOTIVATION: Model-based approaches to safety and efficacy assessment of pharmacological drugs, treatment strategies or medical devices (In Silico Clinical Trial, ISCT) aim to decrease time and cost for the needed experimentations, reduce animal and human testing, and enable precision medicine. Unfortunately, in presence of non-identifiable models (e.g. reaction networks), parameter estimation is not enough to generate complete populations of Virtual Patients (VPs), i.e. populations guaranteed to show the entire spectrum of model behaviours (phenotypes), thus ensuring representativeness of the trial. RESULTS: We present methods and software based on global search driven by statistical model checking that, starting from a (non-identifiable) quantitative model of the human physiology (plus drugs PK/PD) and suitable biological and medical knowledge elicited from experts, compute a population of VPs whose behaviours are representative of the whole spectrum of phenotypes entailed by the model (completeness) and pairwise distinguishable according to user-provided criteria. This enables full granularity control on the size of the population to employ in an ISCT, guaranteeing representativeness while avoiding over-representation of behaviours. We proved the effectiveness of our algorithm on a non-identifiable ODE-based model of the female Hypothalamic-Pituitary-Gonadal axis, by generating a population of 4 830 264 VPs stratified into 7 levels (at different granularity of behaviours), and assessed its representativeness against 86 retrospective health records from Pfizer, Hannover Medical School and University Hospital of Lausanne. The datasets are respectively covered by our VPs within Average Normalized Mean Absolute Error of 15%, 20% and 35% (90% of the latter dataset is covered within 20% error). Availability and implementation. Our open-source software is available at https://bitbucket.org/mclab/vipgenerator. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems.

MOTIVATION: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g. enable in silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models. Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems. RESULTS: In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2-compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialized SBML simulators. AVAILABILITY AND IMPLEMENTATION: SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica.

Clinical phenotype in genetically confirmed von Willebrand disease type 2N patients reflects a haemophilia A phenotype.

INTRODUCTION: Von Willebrand disease (VWD) type 2N is characterized by a defective binding of factor VIII (FVIII) to von Willebrand factor (VWF) resulting in diminished plasma FVIII levels and a clinical phenotype mimicking mild haemophilia A. Several mutations in the FVIII binding site of VWF have been reported. AIM: This study aims to examine the effect of genotype on clinical phenotype in a cohort of VWD 2N patients. METHODS: Patients with at least one genetically confirmed 2N mutation were selected retrospectively from a cohort of patients with suspected VWD. Clinical and laboratory phenotypes including bleeding scores (BS) were obtained and analysed. RESULTS: Forty-two VWD 2N patients with a mean age of 44 years were included. Eleven patients were homozygous or compound heterozygous (genetically confirmed group) and 31 patients were heterozygously affected (carriers group). Statistically significant differences between genetically confirmed VWD 2N patients and carriers were found in FVIII activity, VWF antigen levels, VWF-FVIII binding capacity, FVIII/VWF antigen ratio (all P<0.001), VWF-ristocetin activity (p=0.001) and VWF collagen binding (P = 0.002). Median BS was 6 in genetically confirmed VWD 2N patients compared with 3 in carriers (P = 0.047). Haemarthrosis, muscle haematomas and postpartum haemorrhage were only reported in genetically confirmed 2N patients. CONCLUSION: Phenotypic analysis showed that all laboratory parameters are lower in genetically confirmed VWD 2N patients compared with heterozygous 2N carriers. The clinical phenotype in genetically confirmed VWD 2N patients is comparable to mild haemophilia A patients and more severe than heterozygous 2N carriers.

Interstitial 4q Deletion and Isodicentric Y-Chromosome in a Patient with Dysmorphic Features.

We present a 2-year-old boy with a de novo 46,XY,idic(Y)(q11.221),del(4)(q26q31.1) karyotype. G-banding, FISH, MLPA, and SNP-array techniques were used to characterize the 24-Mb deletion in 4q and the breakpoint in the isodicentric Y-chromosome region between 15,982,252 and 15,989,842 bp. The patient presented with mild facial dysmorphism, hemangioma, mild frontal cerebral atrophy, and Dandy-Walker variant. Essentially, this case reveals that patients can present more complex genomic imbalances than initially suspected.

Different conformation of two supernumerary 18p isochromosomes, one with a concomitant partial 18q trisomy.

The presence of a supernumerary 18p isochromosome is a rare chromosomal abnormality that results in 18p tetrasomy. This is a report on the clinical, cytogenetic and molecular findings of 2 non-related patients with a supernumerary 18p isochromosome. Both patients present some features of the 18p tetrasomy syndrome (strabismus, low-set ears, long and narrow fingers and toes), but additional characteristics were also observed. Cytogenetic analysis, FISH, MLPA and SNP array techniques showed that one of the isochromosomes is symmetric and monocentric, while the other is asymmetric and dicentric, yet resulting in a similar tetrasomy of the 18pter-18p10 region, followed by a partial 18q11.2 trisomy, an unprecedented finding in the literature.

Advances in the epidemiology, pathogenesis, and management of Cushing's syndrome complications.

Cushing's syndrome (CS) is a clinical condition resulting from chronic exposure to glucocorticoid excess. As a consequence, hypercortisolism contributes significantly to the early development of systemic disorders by direct and/or indirect effects. Complications such as obesity, hypertension, diabetes, dyslipidemia, and hypercoagulability cause premature atherosclerosis and increase cardiovascular mortality. Impairment of the skeletal system is a relevant cause of morbidity and disability in these patients especially due to the high prevalence of vertebral fractures. In addition, muscle weakness, emotional lability, depression, and impairment of quality of life are very common. Clinical management of these patients is complex and should be particularly careful in identifying global cardiovascular risks and aim at controlling all complications. Although the primary goal in the prevention and treatment of complications is the correction of hypercortisolism, treatment does not completely eliminate these comorbidities. Given that cardiovascular risk and fracture risk can persist after cure, early detection of each morbidity could prevent the development of irreversible damage. In this review we present the various complications of CS and their pathogenetic mechanisms. We also suggest the clinical management of these patients based on our extensive clinical experience and on the available literature.

Fine-needle aspiration cytology of adrenal masses: a re-assessment with histological confirmation.

BACKGROUND: Fine-needle aspiration (FNA) of adrenal masses is a method currently indicated in lesions suspected of being extra-adrenal in origin; even though its diagnostic reliability has already been determined in many studies, few have used histological examination obtained after adrenalectomy for diagnostic confirmation. AIM: To analyze the diagnostic performance of adrenal FNA in subjects with an available histological confirmation. SUBJECTS AND METHODS: Fifty subjects (26 benign adrenal lesions, 9 primary malignant lesions, and 15 metastatic lesions) who had undergone ultrasound (US)-guided adrenal FNA and then adrenalectomy were re-analyzed retrospectively. RESULTS: FNA guaranteed a sensitivity of 85.7% and a specificity of 100% in all subjects; after having divided the subjects into oncologic and non-oncologic groups, the sensitivity of the test in oncologic patients (100%) increased significantly compared to non-oncologic (57.1%) with no difference in specificity (100% in both groups). Considering also non-diagnostic samples in our analysis (no.=11; 22% of all samples studied), FNA correctly diagnosed malignancy only in 75% of the cases and benignancy only in 66.6%; however, even after including non-diagnostic samples, the percentage of correct malignancy diagnosis remained significantly higher in oncologic (93.3%) than in non-oncologic patients (44.4%) without significant statistical difference between the 2 groups regarding the percentage of correct benignancy diagnosis (respectively 100% and 63.6%). CONCLUSIONS: Our study, based on histological confirmation, underlines the low discriminant value of US-guided adrenal FNA, though the method may have value in oncologic patients.

Assessment of the awareness and management of cardiovascular complications of acromegaly in Italy. The COM.E.T.A. (COMorbidities Evaluation and Treatment in Acromegaly) Study.

BACKGROUND: During the course of acromegaly, cardiovascular, respiratory, and metabolic co-morbidities contribute to enhanced mortality. In 2002, the Pituitary Society and the European Neuroendocrine Association sponsored a Consensus Workshop in Versailles during which guidelines for diagnosis and treatment of co-morbidities in acromegaly were defined. However, as for other guidelines previously issued in the field, no data are available on their clinical application. AIM: The aim of this work coordinated by the Italian Study group on co-morbidities evaluation and treatment in acromegaly (COM.E.T.A.) was to assess, on a national basis, the application in the clinical practice of the Versailles criteria for diagnosis and treatment of cardiovascular comorbities in acromegaly. MATERIALS AND METHODS: In January 2007 an ad hoc designed questionnaire was sent by mail to 130 endocrine Centers in Italy. RESULTS: The guidelines have been generally well perceived and translated in clinical practice. Specifically: 1) echocardiography is considered the mainstay for the diagnosis and follow-up; 2) ambulatory blood pressure monitoring and blood lipid assessment are performed in most hypertensive patients; 3) most endocrinologists directly manage hypertension and are aware of the uncertainty of the effect of the control of the disease on blood pressure levels; 4) ACE inhibitors and angiotensin receptors blockers are first-choice anti-hypertensive treatment; 5) approximately half of the centers consider somatostatin analogues of paramount relevance for biochemical control of disease; 6) awareness that left ventricular hypertrophy and heart failure are the most relevant cardiovascular complications is high although the impact of ischemic, arrhythmic, and valvular complications on prognosis is less well perceived. CONCLUSION: The results of the present survey suggest that previuosly issued guidelines are generally carefully followed in the clinical practice. On the other side, a certain lack of awareness of emerging aspects of the cardiovascular comorbities of acromegaly confirms the necessity of periodically updating the guidelines based on the availability of new clinical information.

Diagnosis and complications of Cushing's syndrome: a consensus statement.

In October 2002, a workshop was held in Ancona, Italy, to reach a Consensus on the management of Cushing's syndrome. The workshop was organized by the University of Ancona and sponsored by the Pituitary Society, the European Neuroendocrine Association, and the Italian Society of Endocrinology. Invited international participants included almost 50 leading endocrinologists with specific expertise in the management of Cushing's syndrome. The consensus statement on diagnostic criteria and the diagnosis and treatment of complications of this syndrome reached at the workshop is hereby summarized.

Cyclical Cushing's syndrome in a patient with a bronchial neuroendocrine tumor (typical carcinoid) expressing ghrelin and growth hormone secretagogue receptors.

A 56-yr-old woman was referred with a diagnosis of Cushing's disease. Hypertension and severe hypokalemia were present and high urinary free cortisol/cortisone ratio was detected, raising a suspicion of an ectopic ACTH syndrome. Inferior petrosal sinus sampling, thoracic computed tomography, and octreotide scans were negative. Remission and relapse periods lasting 3-4 months were observed during the 3.5 yr of follow-up. Finally a thoracic computed tomography scan showed a basal paracardic nodule in the left lung. After surgery, a well-differentiated neuroendocrine tumor (typical bronchial carcinoid) was diagnosed, staining positively for ACTH. RT-PCR revealed expression of proopiomelanocortin, CRH receptor, and V3 vasopressin receptor. Somatostatin receptor type 1, 2, 3, and 5 mRNA was detected only in tumoral tissue. Interestingly, we observed the simultaneous presence of ghrelin and both GH secretagogue (GHS) receptors (1a and 1b) mRNA in tumoral tissue but not in the normal lung. This finding correlates with the in vivo ACTH hyperresponsiveness to hexarelin (a GHS). This is the first report of a cyclical ectopic ACTH-secreting tumor with an in vivo ACTH response to hexarelin coupled with the tumoral expression of ghrelin and GHS receptors. This finding might imply an autocrine/paracrine modulatory effect of ghrelin in bronchial ACTH-secreting tumors.

Transforming growth factor beta1: implications in adrenocortical tumorigenesis.

TGFbeta1, a multifunctional growth modulator, inhibits the proliferation of epithelial cells. TGFbeta1 signaling is dependent on the heterodimerization of the TGFbeta1 receptor II (TGFbeta1RII) with the TGFbeta1 receptor I (TGFbeta1RI). The cytoplasmic proteins Smads are the mediators of the TGFbeta1 signal. TGFbeta1 regulates adult and fetal adrenal growth and function. Previously we have shown by Northern analysis that TGFbeta1mRNA was well expressed in normal adrenal and in adrenocortical adenomas but reduced in carcinomas. To investigate whether TGFbeta1 receptors may act as tumor suppressors of adrenal tumorigenesis, 16 adenomas and 12 carcinomas were studied. We have used SSCP analysis to scan for inactivating mutations in carcinomas. All tumor samples were negative for somatic alterations of both genes. A competitive RT-PCR system was developed to compare the levels of expression of TGFbeta1, TGFbeta1R-I and TGFbeta1R-II, Smad-2 and Smad-4 genes in all tumors. In our study, we confirmed the presence of reduced levels of TGFbeta1 in carcinomas. On the contrary, Smad-4 gene levels were elevated in carcinomas when compared to that of adenomas. No significant differences were observed in gene expression of TGFbeta1RI and Smad-2. Our results suggest that mutations of TGFbeta1 receptors appear not to be involved in adrenal tumorigenesis. Adrenal carcinomas showed a significant reduction of the TGFbeta1 mRNA levels but on the contrary Smad 4 mRNA levels were significantly increased.

The influence of life stress, personality, and learning history on illness behavior.

Previous research has suggested that prior learning experiences and current reinforcement contingencies account for a substantial portion of the variance in illness behaviors. The present study examined the role of other variables (e.g., stimulus and organismic variables). Two hundred and sixty four college students completed questionnaires that included the Life Events Survey, Hassles Scale, Hypochondriasis Scale (MMPI), Illness Attitude Scale, and a Medical Problems Survey. It emerged that social learning variables accounted for significant portions of variance in symptom reporting behavior even after other demographic, current stressor, and personality variables were accounted for. The advantages of using behavioral assessment models for conceptualizing influential variables is highlighted and directions for future research discussed.

Laser Doppler blood flow studies during open muscle biopsy in patients with neuromuscular diseases.

Laser Doppler measurements of skeletal muscle blood flow were performed in 12 patients with neuromuscular disorders and 6 controls. The mean resting blood flows and postocclusive reactive hyperemias were similar for the patients with neuropathic disorders and for controls. The patients with myopathic disorders had higher resting muscle blood flows and reactive hyperemias. Correlation of blood flow results and muscle biopsy characteristics suggested that muscle type grouping was not associated with a change in skeletal muscle blood flow, whereas muscle fiber degeneration was associated with an increased blood flow.