Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort.

BACKGROUND: Comprehensive next-generation sequencing is widely used for precision oncology and precision prevention approaches. We aimed to determine the yield of actionable gene variants, the capacity to uncover hereditary predisposition and liquid biopsy appropriateness instead of, or in addition to, tumor tissue analysis, in a real-world cohort of cancer patients, who may benefit the most from comprehensive genomic profiling. METHODS: Seventy-eight matched germline/tumor tissue/liquid biopsy DNA and RNA samples were profiled using the Hereditary Cancer Panel (germline) and the TruSight Oncology 500 panel (tumor tissue/cfDNA) from 23 patients consecutively enrolled at our center according to at least one of the following criteria: no available therapeutic options; long responding patients potentially fit for other therapies; rare tumor; suspected hereditary cancer; primary cancer with high metastatic potential; tumor of unknown primary origin. Variants were annotated for OncoKB and AMP/ASCO/CAP classification. RESULTS: The overall yield of actionable somatic and germline variants was 57% (13/23 patients), and 43.5%, excluding variants previously identified by somatic or germline routine testing. The accuracy of tumor/cfDNA germline-focused analysis was demonstrated by overlapping results of germline testing. Five germline variants in BRCA1, VHL, CHEK1, ATM genes would have been missed without extended genomic profiling. A previously undetected BRAF p.V600E mutation was emblematic of the clinical utility of this approach in a patient with a liver undifferentiated embryonal sarcoma responsive to BRAF/MEK inhibition. CONCLUSIONS: Our study confirms the clinical relevance of performing extended parallel tumor DNA and cfDNA testing to broaden therapeutic options, to longitudinally monitor cfDNA during patient treatment, and to uncover possible hereditary predisposition following tumor sequencing in patient care.

Hellenic karst waters: geogenic and anthropogenic processes affecting their geochemistry and quality.

Karst hydrosystems represent one of the largest global drinking water resources, but they are extremely vulnerable to pollution. Climate change, high population density, intensive industrial, and agricultural activities are the principal causes of deterioration, both in terms of quality and quantity, of these resources. Samples from 172 natural karst springs were collected in the whole territory of Greece. To identify any geogenic contamination and/or anthropogenic pollution, analyses of their chemical compositions, in terms of major ions and trace elements, were performed and compared to the EU limits for drinking water. Based on chloride content, the collected karst springs were divided into two groups: low-chloride (< 100 mg L-1) and high-chloride content (> 100 mg L-1). An additional group of springs with calcium-sulfate composition was recognised. Nitrate concentrations were always below the EU limit (50 mg L-1), although some springs presented elevated concentrations. High contents in terms of trace elements, such as B, Sr, As, and Pb, sometimes exceeding the limits, were rarely found. The Greek karst waters can still be considered a good quality resource both for human consumption and for agriculture. The main issues derive from seawater intrusion in the aquifers along the coasts. Moreover, the main anthropogenic pollutant is nitrate, found in higher concentrations mostly in the same coastal areas where human activities are concentrated. Finally, high levels of potentially harmful trace elements (e.g. As, Se) are very limited and of natural origin (geothermal activity, ore deposits, etc.).

Lactoferrin concentration in breast milk of mothers of low-birth-weight newborns.

OBJECTIVES: Lactoferrin (LF) is a breast milk glycoprotein with protective effects against neonatal infections, mainly in premature and low-birth-weight (LBW) neonates. The aims of this study were to determine LF concentration in breast milk of mothers of LBW infants during the first 2 months postpartum, and to identify the factors associated with LF concentration. STUDY DESIGN: Prospective study conducted as a part of an ongoing clinical trial in three Neonatal Units in Peru. We included 346 mothers of neonates with a birth weight <2000 g. We measured LF concentration in four stages of lactation using a commercial enzyme-linked immunosorbent assay kit. Multivariate analysis was performed to assess the association between maternal and neonatal factors, and LF concentration. RESULTS: We collected 695 milk samples. LF mean concentration±standard deviation was 14.92±7.96 mg ml-1 in colostrum (n=277), 10.73±5.67 in transitional milk (n=55), 10.34±6.27 at 1 month (n=259) and 8.52±6.47 at 2 months (n=104). There was a significant difference in LF concentration between different stages of lactation (P<0.001). Mothers with higher LF concentration in colostrum had higher values in the following 2 months. High maternal income and multiple gestation were significantly associated with higher LF levels; in contrast, maternal peripartum infections and male neonatal gender were associated with lower LF levels. CONCLUSIONS: LF concentration in breast milk of mothers of LBW infants was high and remained elevated even at 1 and 2 months postpartum. LF concentration in colostrum was higher in mothers with higher income and multiple pregnancies, and lower in mothers with peripartum infections.

Characterization of the Etna volcanic emissions through an active biomonitoring technique (moss-bags): part 1--major and trace element composition.

Active biomonitoring using moss-bags was applied to an active volcanic environment for the first time. Bioaccumulation originating from atmospheric deposition was evaluated by exposing mixtures of washed and air-dried mosses (Sphagnum species) at 24 sites on Mt. Etna volcano (Italy). Concentrations of major and a large suite of trace elements were analysed by inductively coupled mass and optical spectrometry (ICP-MS and ICP-OES) after total acid digestion. Of the 49 elements analysed those which closely reflect summit volcanic emissions were S, Tl, Bi, Se, Cd, As, Cu, B, Na, Fe, Al. Enrichment factors and cluster analysis allowed clear distinction between volcanogenic, geogenic and anthropogenic inputs that affect the local atmospheric deposition. This study demonstrates that active biomonitoring with moss-bags is a suitable and robust technique for implementing inexpensive monitoring in scarcely accessible and harsh volcanic environments, giving time-averaged quantitative results of the local exposure to volcanic emissions. This task is especially important in the study area because the summit area of Mt. Etna is visited by nearly one hundred thousand tourists each year who are exposed to potentially harmful volcanic emissions.

Volcanogenic fluorine in rainwater around active degassing volcanoes: Mt. Etna and Stromboli Island, Italy.

Many studies have assessed the strong influence of volcanic activity on the surrounding environment. This is particularly true for strong gas emitters such as Mt. Etna and Stromboli volcanoes. Among volcanic gases, fluorine compounds are potentially very harmful. Fluorine cycling through rainwater in the above volcanic areas was studied analysing more than 400 monthly bulk samples. Data indicate that only approximately 1% of fluorine emission through the plume is deposited on the two volcanic areas by meteoric precipitations. Although measured bulk rainwater fluorine fluxes are comparable to and sometimes higher than in heavily polluted areas, their influence on the surrounding vegetation is limited. Only annual crops, in fact, show some damage that could be an effect of fluorine deposition, indicating that long-living endemic plant species or varieties have developed some kind of resistance.

Storage temperature effects on blood orange fruit quality.

Orange fruits of two blood varieties (Tarocco and Moro) were stored at 8 degrees C and 22 degrees C for 85 and 106 days, respectively, and analyzed periodically for standard quality parameters (total soluble solids, total acidity, ascorbic acid, juice yield, and rind color) and sensory influencing parameters (anthocyanins, and total and free hydroxycinnamic acids). A decrease in total acidity (TA) and juice yield during storage was observed for both cultivars; total soluble solids (TSS) increased only in the Tarocco oranges stored at 8 degrees C. The increase in TSS observed for Tarocco and the simultaneous decrease in TA in both varieties resulted in a higher maturity index (TSS/TA) for the two cultivars. No loss of vitamin C was noted in Tarocco orange at either temperature, whereas a sharp reduction in vitamin C occurred in the first 50 days of storage for Moro. A significant increase in anthocyanin content was observed in Tarocco and Moro stored at 8 degrees C. Overlong storage induces extensive hydrolysis of hydroxycinnamic derivatives to free acids in Moro orange and these, in turn, could develop the malodorous vinylphenols.

Hospital Reengineering Project at the "Policlinico A. Gemelli".

The "Policlinico A. Gemelli" in the context of ongoing change in the Italian Health Care Service, has developed a Strategic Plan for 1996-2000. In this context a major role is played by the reengineering project, divided into there sequential phases of implementation. The natural evolution of this project results in a department-oriented organization in order to complete and implement change.

Phase 2. Testing of solutions.

Phase 2 of reengineering project, the testing of solutions, was based on the definition of a Prototype, and the implementation of the Pilot phase. This gradual process has facilitated the organizational change and laid the foundations of subsequent extension phase. Ongoing initiatives concern the introduction of two new centers (wards and outpatient service) and the reorganization of ward and operating room activities.

Excellence in diagnostic imaging service management.

The identification of promoting factors of excellence improvement in radiology service management means to clearly assess how the different aspects of the service are managed. The key elements for intervention are sharply differentiated according to the service managerial level. The approach to continuous improvement should be a useful tool of assessment even when all its potentialities have been exhausted and new promoting factors are necessary to move to the subsequent stage.

Planning and scheduling radiologic exams.

Planning and scheduling of radiologic exams represent one of the crucial aspects in the performance of Diagnostic Imaging service, whose optimal management should lead to optimal efficiency and exploitation of technological and professional resources. A Diagnostic Imaging service with agreed and scheduled exams for customers achieves a more adequate, precise planning of the activity with optimum productivity of radiology rooms and anticipated workload assessment.

Radiology room productivity.

Radiology has a significant impact on all health care processes at the "Policlinico A. Gemelli". The performance of Radiology rooms was thus analyzed within the overall performance of health care processes (e.g. medical wards, emergency service, day hospital). In this context, in the assessment phase of the reengineering project the Radiology room productivity has been analyzed. From outcomes of this analysis it appears that there is a high potential for increasing the Radiology room productivity (except for TC and MRI rooms). It has been observed that a better ward/service communication, together with a better use and planning of Radiology rooms and resources would allow a more efficient performance of the service. The reengineering project has led to a reorganization of the communication between Radiology rooms and wards/day hospital, a better inpatient transfer system from wards to Radiology rooms and the planning of the requests for exams. At present, a team is working in order to introduce a medium term budget of exams for all the wards associated to the provision of care for those diseases for which patient admission can be planned based on available Radiology rooms.

Simulation of a cold-stressed finger including the effects of wind, gloves, and cold-induced vasodilatation.

The thermal response of fingers exposed to cold weather conditions has been simulated. Energy balance equations were formulated, in a former study, for the tissue layers and the arterial, venous, and capillary blood vessels. The equations were solved by a finite difference scheme using the Thomas algorithm and the method of alternating directions. At this stage of development the model does not include any autonomic control functions. Model simulations assumed an electrical heating element to be embedded in the glove layers applied on the finger. A 1.3 W power input was calculated for maintaining finger temperatures at their pre-cold exposure level in a 0 degree C environment. Alternate assumptions of nutritional (low) and basal (high) blood flows in the finger demonstrated the dominance of this factor in maintaining finger temperatures at comfortable levels. Simulated exposures to still and windy air, at 4.17 m/s (15 km/h), indicated the profound chilling effects of wind on fingers in cold environments. Finally, the effects of variable blood flow in the finger, known as "cold-induced vasodilatation," were also investigated. Blood flow variations were assumed to be represented by periodic, symmetric triangular waves allowing for gradual opening-closing cycles of blood supply to the tip of the finger. Results of this part of the simulation were compared with measured records of bare finger temperatures. Good conformity was obtained for a plausible pattern of change in blood flow, which was assumed to be provided in its entirety to the tip of the finger alone.

Immunologic parameters 2 years after high-titer measles immunization in Peruvian children.

Immunization with high-titer measles vaccines has been associated with excess mortality in children 2-4 years after vaccination. In this study, immunologic parameters in 64 Peruvian children who had been immunized an average of 27 months earlier with high-titer vaccines were compared with parameters in 76 recipients of low-titer vaccines. Delayed-type hypersensitivity, lymphocyte phenotype distributions by flow cytometry, and lymphoproliferation after phytohemagglutinin (PHA) stimulation were assessed. High-titer recipients had smaller indurations to tetanus, diphtheria, and Proteus (P < .05) antigens, decreased PHA stimulation (P = .04), and a lower percentage of CD4+ lymphocytes (P = .04) than low-titer recipients. After adjustment for sex, concurrent illnesses, and other variables in regression analyses, high-titer recipients had a lower percentage of CD4+ lymphocytes (P = .025) and decreased lymphocyte proliferation to PHA (P = .058). These results may provide a clue to the pathogenesis of delayed excess mortality after high-titer measles vaccination in some developing countries.

Encephalomyocarditis virus induced diabetes mellitus in mice: long-term changes in the structure and function of islets of Langerhans.

Adult male mice infected with the M variant of encephalomyocarditis virus develop hyperglycaemia acutely as a consequence of B cell injury. The severity of the metabolic disease is variable and many animals become normoglycaemic during convalescence. The islets of Langerhans of these mice exhibit minor structural changes, but there are no significant abnormalities of insulin and glucagon secretion. In contrast, animals with persistent hyperglycaemia exhibit striking morphological alterations in the islets. The A cell mass is prominent, whereas B cells are reduced in number and exhibit striking cytological features. These changes are associated with both hypoinsulinaemia and hyperglucagonaemia.

Effect of interferon on encephalomyocarditis virus infection of cultured mouse pancreatic B cells.

The M variant of encephalomyocarditis virus (EMC) produces a disease similar to human insulin-dependent diabetes mellitus in some but not all strains of mice. This diabetogenic M variant was found to induce fivefold more interferon than non-diabetogenic strains of EMC in cultures of mouse L 929 fibroblasts. When interferon induced by the M variant was added to monolayers of B cells from both diabetes-'susceptible' CD-1 mice and 'resistant' C57 bl/6 mice before EMC infection, B cell damage and virus replication were delayed. In addition, viral production in B cell cultures from C57 bl/6 mice was reduced five- to tenfold. A similar effect was not found when cultures from CD-1 mice were treated with interferon. Thus, interferon might play an important role in modulating the severity of the initial infection of B cells.

Description and surgical removal of the cranial cervical ganglia in 3- to 5-day-old chicks.

The cranial cervical sympathetic ganglion (CCG) provides the primary innervation of the pineal gland in several gallinaceous species. The CCG is located at the base of the skull near the exoccipital bone, dorsal to the level of the vagus and glossopharyngeal nerves. It occupies a much larger volume and appears pinkish-gray, instead of white, when compared to the petrosal ganglion. To surgically remove the CCG, chicks were anesthetized with halothane vapor. Following a small skin incision, blunt dissection was used to expose the CCG lying adjacent to the internal carotid. The ganglion was grasped with small forceps and pinched free of its fine neural connections to adjacent nerves. The success of the surgery was confirmed visually and by complete adrenergic dennervation of the pineal gland. The entire surgical procedure required approximately 20 min per bird. Mortality was less than 20% overall.

Land use and transportation issues in environmental control.

Analyses have been made of the effects of environmental controls and planning at regional, subarea, and project levels. The results obtained at the regional level are reviewed for a proposed highway development around Baltimore, Md. The findings for both short-term and long-term effects of alternative transport policies are summarized in respect of population and employment, economic indicators, traffic and travel, air quality, water and solid waste, noise, and environmentally sensitive areas. Problems at subarea and project levels are briefly considered.