A mutation-based radiomics signature predicts response to imatinib in Gastrointestinal Stromal Tumors (GIST).

Objectives: To develop a mutation-based radiomics signature to predict response to imatinib in Gastrointestinal Stromal Tumors (GISTs). Methods: Eighty-two patients with GIST were enrolled in this retrospective study, including 52 patients from one center that were used to develop the model, and 30 patients from a second center to validate it. Reference standard was the mutational status of tyrosine-protein kinase (KIT) and platelet-derived growth factor α (PDGFRA). Patients were dichotomized in imatinib sensitive (group 0 - mutation in KIT or PDGFRA, different from exon 18-D842V), and imatinib non-responsive (group 1 - PDGFRA exon 18-D842V mutation or absence of mutation in KIT/PDGFRA). Initially, 107 texture features were extracted from the tumor masks of baseline computed tomography scans. Different machine learning methods were then implemented to select the best combination of features for the development of the radiomics signature. Results: The best performance was obtained with the 5 features selected by the ANOVA model and the Bayes classifier, using a threshold of 0.36. With this setting the radiomics signature had an accuracy and precision for sensitive patients of 82 % (95 % CI:60-95) and 90 % (95 % CI:73-97), respectively. Conversely, a precision of 80 % (95 % CI:34-97) was obtained in non-responsive patients using a threshold of 0.9. Indeed, with the latter setting 4 patients out of 5 were correctly predicted as non-responders. Conclusions: The results are a first step towards using radiomics to improve the management of patients with GIST, especially when tumor tissue is unavailable for molecular analysis or when molecular profiling is inconclusive.

The mechanism and energetics of a ligand-controlled hydrophobic gate in a mammalian two pore channel.

In the last decade two-pore intracellular channels (TPCs) attracted the interest of researchers, still some key questions remain open. Their importance for vacuolar (plants) and endo-lysosomal (animals) function highlights them as a very attractive system to study, both theoretically and experimentally. Indicated as key players in the trafficking of the cell, today they are considered a new potential target for avoiding virus infections, including those from coronaviruses. A particular boost for theoretical examinations has been made with recent high-resolution X-ray and cryo-EM structures. These findings have opened the way for efficient and precise computational studies at the atomistic level. Here we report a set of multiscale-calculations performed on the mTPC1, a ligand- and voltage-gated sodium selective channel. The molecular dynamics and enhanced molecular dynamics simulations were used for a thorough analysis of the mammalian TPC1 behaviour in the presence and absence of the ligand molecule, with a special accent on the supposed bottleneck, the hydrophobic gate. Moreover, from the reconstructed free energy obtained from enhanced simulations, we have calculated the macroscopic conductance of sodium ions through the mTPC1, which we compared with measured single-channel conductance values. The hydrophobic gate works as a steric barrier and the key parameters are its flexibility and the dimension of the sodium first hydration shell.

Electronic and Optical Properties of Small Metal Fluoride Clusters.

We report a systematic investigation on the electronic and optical properties of the smallest stable clusters of alkaline-earth metal fluorides, namely, MgF2, CaF2, SrF2, and BaF2. For these clusters, we perform density functional theory (DFT) and time-dependent DFT (TDDFT) calculations with a localized Gaussian basis set. For each molecule ((MF2) n , n = 1-3, M = Mg, Ca, Sr, Ba), we determine a series of molecular properties, namely, ground-state energies, fragmentation energies, electron affinities, ionization energies, fundamental energy gaps, optical absorption spectra, and exciton binding energies. We compare electronic and optical properties between clusters of different sizes with the same metal atom and between clusters of the same size with different metal atoms. From this analysis, it turns out that MgF2 clusters have distinguished ground-state and excited-state properties with respect to the other fluoride molecules. Sizeable reductions of the optical onset energies and a consistent increase of excitonic effects are observed for all clusters under study with respect to the corresponding bulk systems. Possible consequences of the present results are discussed with respect to applied and fundamental research.

Molecular basis for the different interactions of congeneric substrates with the polyspecific transporter AcrB.

The drug/proton antiporter AcrB, which is part of the major efflux pump AcrABZ-TolC in Escherichia coli, is the paradigm transporter of the resistance-nodulation-cell division (RND) superfamily. Despite the impressive ability of AcrB to transport many chemically unrelated compounds, only a few of these ligands have been co-crystallized with the protein. Therefore, the molecular features that distinguish good substrates of the pump from poor ones have remained poorly understood to date. In this work, a thorough in silico protocol was employed to study the interactions of a series of congeneric compounds with AcrB to examine how subtle chemical differences affect the recognition and transport of substrates by this protein. Our analysis allowed us to discriminate among different compounds, mainly in terms of specific interactions with diverse sub-sites within the large distal pocket of AcrB. Our findings could provide valuable information for the design of new antibiotics that can evade the antimicrobial resistance mediated by efflux pump machinery.

A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds.

We present an on-line database of all-atom force-field parameters and molecular properties of compounds with antimicrobial activity (mostly antibiotics and some beta-lactamase inhibitors). For each compound, we provide the General Amber Force Field parameters for the major species at physiological pH, together with an analysis of properties of interest as extracted from µs-long molecular dynamics simulations in explicit water solution. The properties include number and population of structural clusters, molecular flexibility, hydrophobic and hydrophilic molecular surfaces, the statistics of intraand inter-molecular H-bonds, as well as structural and dynamical properties of solvent molecules within first and second solvation shells. In addition, the database contains several key molecular parameters, such as energy of the frontier molecular orbitals, vibrational properties, rotational constants, atomic partial charges and electric dipole moment, computed by Density Functional Theory. The present database (to our knowledge the first extensive one including dynamical properties) is part of a wider project aiming to build-up a database containing structural, physico-chemical and dynamical properties of medicinal compounds using different force-field parameters with increasing level of complexity and reliability. The database is freely accessible at http://www.dsf.unica.it/translocation/db/.

Procalcitonin in detecting neonatal nosocomial sepsis.

OBJECTIVE: To investigate the accuracy of procalcitonin (PCT) as a diagnostic marker of nosocomial sepsis (NS) and define the most accurate cut-off to distinguish infected from uninfected neonates. SETTING: Six neonatal intensive care units (NICUs). PATIENTS: 762 neonates admitted to six NICUs during a 28-month observational study for whom at least one serum sample was taken on admission. MAIN OUTCOME MEASURES: Positive and negative predictive values at different PCT cut-off levels. RESULTS: The overall probability of an NS was doubled or more if PCT was >0.5 ng/ml. In very-low-birth-weight (VLBW) infants, a cut-off of >2.4 ng/ml gave a positive predictive value of NS near to 50% with a probability of a false-positive diagnosis of NS in about 10% of the patients. CONCLUSIONS: In VLBW neonates, a serum PCT value >2.4 ng/ml prompts early empirical antibiotic therapy, while in normal-birth-weight infants, a PCT value ≤2.4 ng/ml carries a low risk of missing an NS.

Effects of abscisic acid on ethylene biosynthesis and perception in Hibiscus rosa-sinensis L. flower development.

The effect of the complex relationship between ethylene and abscisic acid (ABA) on flower development and senescence in Hibiscus rosa-sinensis L. was investigated. Ethylene biosynthetic (HrsACS and HrsACO) and receptor (HrsETR and HrsERS) genes were isolated and their expression evaluated in three different floral tissues (petals, style-stigma plus stamens, and ovaries) of detached buds and open flowers. This was achieved through treatment with 0.1 mM 1-aminocyclopropane-1-carboxylic acid (ACC) solution, 500 nl l(-1) methylcyclopropene (1-MCP), and 0.1 mM ABA solution. Treatment with ACC and 1-MCP confirmed that flower senescence in hibiscus is ethylene dependent, and treatment with exogenous ABA suggested that ABA may play a role in this process. The 1-MCP impeded petal in-rolling and decreased ABA content in detached open flowers after 9 h. This was preceded by an earlier and sequential increase in ABA content in 1-MCP-treated petals and style-stigma plus stamens between 1 h and 6 h. ACC treatment markedly accelerated flower senescence and increased ethylene production after 6 h and 9 h, particularly in style-stigma plus stamens. Ethylene evolution was positively correlated in these floral tissues with the induction of the gene expression of ethylene biosynthetic and receptor genes. Finally, ABA negatively affected the ethylene biosynthetic pathway and tissue sensitivity in all flower tissues. Transcript abundance of HrsACS, HrsACO, HrsETR, and HrsERS was reduced by exogenous ABA treatment. This research underlines the regulatory effect of ABA on the ethylene biosynthetic and perception machinery at a physiological and molecular level when inhibitors or promoters of senescence are exogenously applied.

Reference values of blood cell counts in the first days of life.

The lack of updated neonatal reference values for hematological parameters impacts significantly with clinical management of both healthy and sick newborns. The present pilot study was thus aimed at assessing updated hematological Italian reference values in late preterm and term newborns. From January 2004 to December 2008 hematological laboratory tests were performed in 1175 newborns (820 healthy and 355 sick controls) between 33-41 weeks of gestation, during the first four days after birth. Hematological parameters were sorted for gender and gestational age and statistically analyzed. No gender-related differences were observed at different weeks of gestation and no significant differences were found when study population was sub-grouped for late preterm and term newborns. During the first 4 days of life erythrocytes and platelets remained stable whilst white blood cell counts and differentials were significantly modified. This study shares updated reference values for hematological parameters in the early phases after birth and offers additional support for improving the management of sick infants.

Determinants of nosocomial infection in 6 neonatal intensive care units: an Italian multicenter prospective cohort study.

BACKGROUND: Nosocomial infections are still a major cause of morbidity and mortality among neonates admitted to neonatal intensive care units (NICUs). OBJECTIVE: To describe the epidemiology of nosocomial infections in NICUs and to assess the risk of nosocomial infection related to the therapeutic procedures performed and to the clinical characteristics of the neonates at birth and at admission to the NICU, taking into account the time between the exposure and the onset of infection. DESIGN: A multicenter, prospective cohort study. PATIENTS AND SETTING: A total of 1,692 neonates admitted to 6 NICUs in Italy were observed and monitored for the development of nosocomial infection during their hospital stay. METHODS: Data were collected on the clinical characteristics of the neonates admitted to the NICUs, their therapeutic interventions and treatments, their infections, and their mortality rate. The cumulative probability of having at least 1 infection and the cumulative probability of having at least 1 infection or dying were estimated. The hazard ratio (HR) for the first infection and the HR for the first infection or death were also estimated. RESULTS: A total of 255 episodes of nosocomial infection were diagnosed in 217 neonates, yielding an incidence density of 6.9 episodes per 1,000 patient-days. The risk factors related to nosocomial infection in very-low-birth-weight neonates were receipt of continuous positive airway pressure (HR, 3.8 [95% confidence interval {CI}, 1.7-8.1]), a Clinical Risk Index for Babies score of 4 or greater (HR, 2.2 [95% CI, 1.4-3.4]), and a gestational age of less than 28 weeks (HR, 2.1 [95% CI, 1.2-3.8]). Among heavier neonates, the risk factors for nosocomial infection were receipt of parenteral nutrition (HR, 8.1 [95% CI, 3.2-20.5]) and presence of malformations (HR, 2.3 [95% CI, 1.5-3.5]). CONCLUSIONS: Patterns of risk factors for nosocomial infection differ between very-low-birth-weight neonates and heavier neonates. Therapeutic procedures appear to be strong determinants of nosocomial infection in both groups of neonates, after controlling for clinical characteristics.

Solar UV-B radiation influences carotenoid accumulation of tomato fruit through both ethylene-dependent and -independent mechanisms.

The effect of UV-B shielding on ethylene production in ripening tomato fruits and the contribution of ethylene and UV-B radiation on carotenoid accumulation and profile during ripening were assessed to get more insight about the interplay between these two regulatory factors. To this aim, rin and nor tomato mutants, unable to produce ripening ethylene, and cv Ailsa Craig were cultivated under control or UV-B depleted conditions until full fruit ripening. The significantly decreased ethylene evolution following UV-B depletion, evident only in Ailsa Craig, suggested the requirement of functional rin and nor genes for UVB-mediated ethylene production. Carotenoid content and profile were found to be controlled by both ethylene and UV-B radiation. This latter influenced carotenoid metabolism either in an ethylene-dependent or -independent way, as indicated by UVB-induced changes also in nor and rin carotenoid content and confirmed by correlation plots between ethylene evolution and carotenoid accumulation performed separately for control and UV-B shielded fruits. In conclusion, natural UV-B radiation influences carotenoid metabolism in a rather complex way, involving ethylene-dependent and -independent mechanisms, which seem to act in an antagonistic way.

Cost analysis of an Italian neonatal hearing screening programme.

AIM: The objective of this study was to estimate the cost of a Universal Neonatal Hearing Screening (UNHS) programme in an Italian region. METHODS: A cost analysis of a regional UNHS programme was carried out on 32,502 newborns. 31,992 (98.4%) were no audiological risk (NAR) subjects and 510 were babies with audiological risk (WAR) (1.6%). UNHS was performed on two levels. The first level involved otoacustic emission (OAE) testing on NAR subjects, while the second level involved auditory brainstem response (ABR) testing of WAR and of NAR with 2nd OAE Refer tests. RESULTS: The cost of screening was 13.32 euro per screened NAR infant. The total cost (OAE+ABR) was 16.58 euro, spreading the cost over the whole NAR population. The total cost per screened infant in the WAR population was 415.9 euro. The average cost per detected case in the NAR population was 32,951 euro, while in the WAR population it was 11,303 euro. CONCLUSIONS: The cost of UNHS in our region is comparable to the cost per diagnosed case of other neonatal screening programmes, and it is justified when it allows us to intervene at an early stage. On the basis of both the cost of our regional screening programme and the incidence of hearing impairment, we can conclude that the cost-effectiveness of our programme has been demonstrated.

Diagnostic accuracy of S100B urinary testing at birth in full-term asphyxiated newborns to predict neonatal death.

BACKGROUND: Neonatal death in full-term infants who suffer from perinatal asphyxia (PA) is a major subject of investigation, since few tools exist to predict patients at risk of ominous outcome. We studied the possibility that urine S100B measurement may identify which PA-affected infants are at risk of early postnatal death. METHODOLOGY/PRINCIPAL FINDINGS: In a cross-sectional study between January 1, 2001 and December 1, 2006 we measured S100B protein in urine collected from term infants (n = 132), 60 of whom suffered PA. According to their outcome at 7 days, infants with PA were subsequently classified either as asphyxiated infants complicated by hypoxic ischemic encephalopathy with no ominous outcome (HIE Group; n = 48), or as newborns who died within the first post-natal week (Ominous Outcome Group; n = 12). Routine laboratory variables, cerebral ultrasound, neurological patterns and urine concentrations of S100B protein were determined at first urination and after 24, 48 and 96 hours. The severity of illness in the first 24 hours after birth was measured using the Score for Neonatal Acute Physiology-Perinatal Extension (SNAP-PE). Urine S100B levels were higher from the first urination in the ominous outcome group than in healthy or HIE Groups (p<0.001 for all), and progressively increased. Multiple logistic regression analysis showed a significant correlation between S100B concentrations and the occurrence of neonatal death. At a cut-off >1.0 microg/L S100B had a sensitivity/specificity of 100% for predicting neonatal death. CONCLUSIONS/SIGNIFICANCE: Increased S100B protein urine levels in term newborns suffering PA seem to suggest a higher risk of neonatal death for these infants.

Plasma concentrations of carbohydrates and sugar alcohols in term newborns after milk feeding.

Nonglucose carbohydrates such as galactose, mannose, and inositol play a clinically important role in fetal and neonatal nutrition, though little is known about their metabolism in the neonate. The aim of this study was to determine whether postprandial changes in plasma carbohydrate and sugar alcohol concentrations are affected by clinical variables such as postnatal age (PNA), milk type, feeding volume, or feeding duration in term newborns. Neonates (n = 26) taking intermittent enteral feedings were enrolled. Blood samples were obtained at baseline (immediately before the start of a feeding) and at 2-3 subsequent time points up to 110 min. Postprandial rise was only observed for plasma glucose concentrations [Glu] and plasma galactose concentrations [Gal] and clinical variables did not predict this change. Despite equimolar delivery in milk, the median of [Glu] rise minus [Gal] rise from baseline to second postprandial plasma sample was 674 microM (-38, 3333 microM; p < 0.0001), reflecting efficient hepatic first-pass metabolism of galactose. A significant PNA effect on [Gal] was observed such that for each day PNA there was an 18% decrease in [Gal] (p = 0.03). [Gal] are a function of PNA, suggesting maintenance of a significant ductus venosus shunt in term infants.

Reliability assessment of glucose measurement by HemoCue analyser in a neonatal intensive care unit.

BACKGROUND: Rapid and reliable bed-side determination of blood glucose concentration is very important in the management of acutely ill infants and especially in premature newborns. HemoCue is an easy-to-use glucose analyser. The aim of the present study was to examine the usefulness of the HemoCue glucose analyser compared to a reference plasma glucose method (SYS, BM/Hitachi 747/737) in a neonatal intensive care unit (NICU). METHODS: Seventy-eight consecutive neonates admitted to our NICU were enrolled in the study. At the time of the study all patients were grouped according to nutritional management (parenteral or enteral nutrition), haematocrit values and birth weight. The effects of feeding management, haematocrit values, and birth weight on accuracy and precision of the device were evaluated. RESULTS: Overall data linear regression analysis yielded an r-value of 0.905 and the Bland-Altman method demonstrated that HemoCue overestimates plasma glucose by 0.932 mmol/L. Evaluation of our data by receiver operating characteristic curve demonstrated 100% sensitivity cutoff at 4.1 mmol/L. CONCLUSIONS: HemoCue cannot be used satisfactorily in the management of glycaemia in the NICU. In the preterm population, birth weight had a dramatic influence on HemoCue accuracy. Low haematocrit and parenteral feeding further contributed to a decrease in the accuracy of this device.

Urinary S100B protein concentrations are increased in intrauterine growth-retarded newborns.

BACKGROUND: Intrauterine growth retardation is one of the major causes of perinatal mortality and morbidity. To date, there are no reliable methods to detect brain damage in these patients. METHODS: We conducted a case-control study in tertiary NICUs from December 2001 to December 2003 with 42 intrauterine growth retardation infants and 84 controls. Routine laboratory variables, neurologic outcome at 7-day follow-up, ultrasound imaging, and urine concentrations of S100B protein were determined at 5 time points. Urine S100B levels were measured by an immunoluminometric assay at first urination, 24, 48, and 72 hours, and 7 days after birth. Routine laboratory parameters and neurologic patterns were assessed at the same time as urine sampling. RESULTS: S100B protein was significantly higher at all of the monitoring time points in urine taken from intrauterine growth retardation newborns than in control infants. When intrauterine growth retardation infants were corrected for the presence of abnormal (group A) or normal (group B) neurologic examination 7 days after birth, S100B was significantly higher at all of the predetermined monitoring time points in group A infants than in group B or controls. At a cutoff of 7.37 multiples of median at first urination, S100B achieved a sensitivity of 95% and a specificity of 99.1% as a single marker for predicting an adverse neurologic outcome. Twenty of 126 patients had neurologic abnormalities, making an overall prevalence of the disease in our population of 15.9% (pretest probability). With respect to the performance of S100B in predicting brain damage, its positive and negative predictive values were 91.0% and 99.0%, respectively. CONCLUSIONS: Increased urine S100B protein levels in intrauterine growth retardation newborns in the first week after birth suggest the presence of brain damage reasonably because of intrauterine hypoxia. Longitudinal S100B protein measurements soon after birth are a useful tool to identify which intrauterine growth retardation infants are at risk of possible neurologic sequelae.

Lack of effect of dietary nucleotide supplementation on erythrocyte 2,3-diphosphoglycerate concentration. A study on preterm neonates.

BACKGROUND: Recently we demonstrated an increased 2,3-diphosphoglycerate (2,3-DPG) erythrocyte concentration in rat pups subjected to nucleotide-enriched artificial feeding. DESIGN: The present study was carried out to test the hypothesis that a possible increase in 2,3-DPG concentration can also be obtained in human neonates who are fed nucleotide-enriched formula. Preterm neonates born or referred to the neonatal intensive care unit of the G. Gaslini Hospital, Genoa University, with a gestational age >30 weeks and <37 weeks were enrolled in our randomized trial. Recruitment took place within 48-72 hours from birth. Only newborns of mothers deciding not to breast-feed were eligible to be randomized for the supplemented group (FN) or non-supplemented group (RF). Breast-fed newborns were considered the control group (C). The study window (for supplementation and blood samples) was restricted to the first two weeks following birth (from the 2nd (t1) to the 16th (t2) day of life). At the end of our study, only 21 neonates were eligible for statistical analysis. RESULTS: The stimulating action of dietary nucleotides on 2,3-DPG concentration failed to be demonstrated; increases in 2,3-DPG concentration that were observed in newborns fed with nucleotide supplemented formula (FN) were comparable to those observed in newborns fed with regular formula (RF) and breast-fed newborns. CONCLUSIONS: The EC recommendation for the amount of nucleotides allowed in formula milk does not seem to be high enough to have positive effects on 2,3-DPG synthesis. Whether this possible 'pharmacological' effect can be achieved by a higher intake of ingested nucleotides and/or a change in the proportions of single nucleotides contained in milk formulas remain interesting end points to be elucidated.

Pulmonary hypertension following L-lysine ibuprofen therapy in a preterm infant with patent ductus arteriosus.

Patent ductus arteriosus is one of the most common congenital abnormalities found in premature infants. Ibuprofen, a nonsteroidal drug that is commonly used as an antipyretic, analgesic and anti-inflammatory agent, is also used to induce closure of symptomatic patent ductus arteriosus in preterm infants. Recently, we gave L-lysine ibuprofen to a preterm infant with respiratory distress to induce closure of a patent ductus arteriosus, and the infant experienced pulmonary hypertension. Only 3 cases of pulmonary hypertension following early administration of an ibuprofen solution buffered with tromethamine have previously been reported. However, this severe side effect has never been observed in multicentre, randomized, double-blind controlled trials, nor in recent reviews or meta-analyses of L-lysine ibuprofen use.

Congenital fibrous hamartoma of the knee.

A full-term male infant presented at birth with a hard swelling of the left knee. The lemon-sized lesion was fixed to the underlying knee muscles, while the overlying skin was stretched and shiny; there was no bruit. Radiography, sonography and MRI suggested a soft-tissue tumour. After surgical excision, histology showed the presence of fibrous and mesenchymal tissue, with mature adipose tissue. Fibrous hamartoma of infancy was diagnosed. Among soft-tissue tumours, fibrous hamartoma of infancy is a rare and benign lesion, occurring in the first 2 years of life. The tumour mainly affects the trunk, axilla, and upper extremities. This infant had unique involvement of the knee. The treatment of choice is local excision.

Nonimmune idiopathic hydrops fetalis and congenital lymphatic dysplasia.

Six newborns that presented at birth with nonimmune hydrops fetalis and for whom no cause could be found were investigated for the presence of lymphatic dysplasia. Careful analysis led to findings of some degree of lymphatic dysplasia in all patients. This suggests that lymphatic dysplasia may represent at least part of the causes that are responsible for the "idiopathic" form of nonimmune hydrops fetalis. Carefully searching for lymphatic dysplasia in these patients, and if indicated in their relatives, as well as establishing the exact nature of the lymphatic dysplasia must be carried out so as to provide proper genetic counseling to families with nonimmune hydrops.