Consensus clustering methodology to improve molecular stratification of non-small cell lung cancer.

Recent advances in machine learning research, combined with the reduced sequencing costs enabled by modern next-generation sequencing, paved the way to the implementation of precision medicine through routine multi-omics molecular profiling of tumours. Thus, there is an emerging need of reliable models exploiting such data to retrieve clinically useful information. Here, we introduce an original consensus clustering approach, overcoming the intrinsic instability of common clustering methods based on molecular data. This approach is applied to the case of non-small cell lung cancer (NSCLC), integrating data of an ongoing clinical study (PROMOLE) with those made available by The Cancer Genome Atlas, to define a molecular-based stratification of the patients beyond, but still preserving, histological subtyping. The resulting subgroups are biologically characterized by well-defined mutational and gene-expression profiles and are significantly related to disease-free survival (DFS). Interestingly, it was observed that (1) cluster B, characterized by a short DFS, is enriched in KEAP1 and SKP2 mutations, that makes it an ideal candidate for further studies with inhibitors, and (2) over- and under-representation of inflammation and immune systems pathways in squamous-cell carcinomas subgroups could be potentially exploited to stratify patients treated with immunotherapy.

Data on soil physicochemical properties and chemical composition of rainfall and of throughfall and stemflow generated by Turkey oak trees (Quercus cerris L.) in acid and sub-alkaline soils.

We report data on the physicochemical properties of soils collected in two adjacent areas, one acid and one sub-alkaline, both developed on sequential beds of Plio-pleistocene marine sediments, and on the chemical composition of ecological solutions (rainfall, throughfall and stemflow) separately collected in the two areas. Throughfall and stemflow were generated by Turkey oak trees (Quercus cerris L.), which was the dominant tree species in both study areas. These data are related to the original article "Soil affects throughfall and stemflow under Turkey oak (Quercus cerris L.)" (Corti et al., 2019) [1].

ReDecay: a novel approach to speed up the simulation at LHCb.

With the steady increase in the precision of flavour physics measurements collected during LHC Run 2, the LHCb experiment requires simulated data samples of larger and larger sizes to study the detector response in detail. The simulation of the detector response is the main contribution to the time needed to simulate full events. This time scales linearly with the particle multiplicity. Of the dozens of particles present in the simulation only the few participating in the signal decay under study are of interest, while all remaining particles mainly affect the resolutions and efficiencies of the detector. This paper presents a novel development for the LHCb simulation software which re-uses the rest of the event from previously simulated events. This approach achieves an order of magnitude increase in speed and the same quality compared to the nominal simulation.

Tracking a CAD-ALK gene rearrangement in urine and blood of a colorectal cancer patient treated with an ALK inhibitor.

BACKGROUND: Monitoring response and resistance to kinase inhibitors is essential to precision cancer medicine, and is usually investigated by molecular profiling of a tissue biopsy obtained at progression. However, tumor heterogeneity and tissue sampling bias limit the effectiveness of this strategy. In addition, tissue biopsies are not always feasible and are associated with risks due to the invasiveness of the procedure. To overcome these limitations, blood-based liquid biopsy analysis has proven effective to non-invasively follow tumor clonal evolution. PATIENTS AND METHODS: We exploited urine cell-free, trans-renal DNA (tr-DNA) and matched plasma circulating tumor DNA (ctDNA) to monitor a metastatic colorectal cancer patient carrying a CAD-ALK translocation during treatment with an ALK inhibitor. RESULTS: Using a custom next generation sequencing panel we identified the genomic CAD-ALK rearrangement and a TP53 mutation in plasma ctDNA. Sensitive assays were developed to detect both alterations in urine tr-DNA. The dynamics of the CAD-ALK rearrangement in plasma and urine were concordant and paralleled the patient's clinical course. Detection of the CAD-ALK gene fusion in urine tr-DNA anticipated radiological confirmation of disease progression. Analysis of plasma ctDNA identified ALK kinase mutations that emerged during treatment with the ALK inhibitor entrectinib. CONCLUSION: We find that urine-based genetic testing allows tracing of tumor-specific oncogenic rearrangements. This strategy could be effectively applied to non-invasively monitor tumor evolution during therapy. The same approach could be exploited to monitor minimal residual disease after surgery with curative intent in patients whose tumors carry gene fusions. The latter could be implemented without the need of patient hospitalization since urine tr-DNA can be self-collected, is stable over time and can be shipped at specified time-points to central labs for testing.

Differences in the availability of diagnostics and treatment modalities for chronic hepatitis B across Europe.

The prevalence and management of chronic hepatitis B virus (HBV) infection differ among European countries. The availability and reimbursement of diagnostics and drugs may also vary, determining distinct treatment outcomes. Herein, we analyse differences in medical facilities for the care of patients with chronic HBV infection across Europe. A survey was sent to the members of the ESCMID Study Group for Viral Hepatitis, all of whom are experts in chronic HBV infection management. The comprehensive survey asked questions regarding hepatitis B surface antigen (HBsAg) prevalence, the availability of diagnostics and drugs marketed, and distinct clinical practice behaviours in the management of chronic HBV infection. World Bank data were used to assess the economic status of the countries. With 16 expert physicians responding (69%), the HBsAg prevalence rates were <1% in France, Hungary, Italy, The Netherlands, Portugal, Spain, and the UK, intermediate (1-5%) in Turkey, Romania, and Serbia, and high (>5%) in Albania and Iran. Regarding the availability and reimbursement of HBV diagnostics (HBV DNA and liver stiffness measurement), HBV drugs (interferon, lamivudine, tenofovir, and entecavir), HBV prophylaxis, and duration of HBeAg-positive and HBeAg-negative HBV infection, the majority of high-income and middle-income countries had no restrictions; Albania, Iran and Serbia had several restrictions in diagnostics and HBV drugs. The countries in the high-income group were also the ones with no restrictions in medical facilities, whereas the upper-middle-income countries had some restrictions. The prevalence of chronic HBV infection is much higher in southern and eastern than in western European countries. Despite the availability of European guidelines, policies for diagnostics and treatment vary significantly across European countries.

Draft Genome Sequence of the Host-Restricted Salmonella enterica Serovar Abortusovis Strain SS44.

Salmonella enterica serovar Abortusovis is a pathogen strictly adapted to ovines, in which it causes abortion. To enhance our understanding of this pathogen, we assembled the first draft sequence of an S. Abortusovis genome (strain SS44). The obtained genomic data might facilitate the study of S. enterica evolution and host adaptation.

From rainfall to throughfall in a maritime vineyard.

This study deals with the characteristics of throughfall produced by vine (Vitis vinifera L.) in one of the most common pedoclimatic conditions for grape production: a soil derived from marine sediments under a temperate Mediterranean climate, and located rather close to the seacoast. To distinguish the contribution of the plant from that of the atmospheric deposition, the throughfall was collected for more than one year under real and artificial (plastic) vines; for the same period, also the bulk precipitation was collected. The solution collected were analysed for pH, electrical conductivity, and concentration of cations and anions. For each event, the ionic fluxes of bulk precipitation and throughfall were calculated. Results indicated that the chemical composition of the bulk precipitation was strongly influenced by the proximity of the seashore and, to a lesser extent, by local anthropic activities and windblown material coming from distant areas. The chemical composition of the throughfall was affected by the same factors of bulk precipitation, but also by solubilisation of dry deposition trapped by the canopies, agronomic practices, plant, and living-on-the-leaves microorganisms. The comparison of the characteristics of the throughfall of the real with the artificial vines revealed that the vines are a source of Mg and K. During winter season, the reduction of Ca, NH(4) and PO(4) from bulk precipitation to throughfall was ascribed to the formation of biogenic minerals on the plant surface. The presence of these minerals was proved by X-ray diffraction on the powders collected during the winter season on the surface of cordons and fruiting canes. We conclude that an approach to the estimation of the nutritional potentiality of the soil that includes the contribution of the throughfall is functional to the management of the agro-ecosystem.

Etiopathology of Arnold-Chiari malformation: a fetal rat model of dysraphism.

OBJECTIVES: We report an experimental fetal rat model with the aim of comparing two surgical methods used to check Arnold-Chiari Malformation (ACM) by dysraphism. We also wanted to (1) determine which type(s) of ACM akin to human anatomical findings were generated with the model and (2) study whether a cerebrospinal fluid pressure gradient could be responsible for ACM's etiopathology. MATERIALS AND METHODS: At E20, a mean of two fetuses per pregnant rat underwent an incision at the 2-3 lumbar level, deep into the medulla oblongata central canal, by two different surgical methods. Cesarian section was performed at E22. Dysraphic fetuses were examined clinically. Those born alive and controls without lesions were anatomically and histologically studied. RESULTS: Method 2 was better than method 1 at reproducing the model. 100% of operated fetuses showed no spontaneous motility or sensibility to pressure on the posterior limbs in addition to anatomopathological evidence of type II ACM. CONCLUSIONS: A high rate of ACM could be checked by dysraphism with both methods. The opening of the central canal was demonstrated to generate a cerebrospinal fluid pressure gradient responsible for the herniation of encephalic structures comparable with human ACM. We believe this model may be useful for evaluating further strategies for prenatal treatment.

Transient elastography for the assessment of liver fibrosis in patients with chronic viral hepatitis: the missing tool?

The fibrogenic evolution of chronic viral hepatitis B and C towards cirrhosis represents a key issue in clinical Hepatology whose monitoring still relies on liver biopsy and consequent histopathological staging. In the last decade, non-invasive methodologies have been proposed to predict the presence of fibrosis in chronic liver disease. Most of these methods are based on algorithms, including biochemical parameters, which have demonstrated an acceptable diagnostic accuracy towards the two extremities of the fibrogenetic process. The introduction of transient elastography has represented a further advancement in clinical Hepatology and it seems that the combination of different non-invasive methodologies will provide an improvement in the clinical management of disease progression in viral chronic hepatitis. Studies, conducted especially in chronic viral hepatitis C, suggest that transient elastography is a useful technique for the detection of severe fibrosis-cirrhosis and for the exclusion of significant fibrosis (>or=F2), that could be employed as "diagnostic discriminator" for establishing clinical priorities and reducing the number of liver biopsies. This review article will focus on the clinical utility of this novel methodology for the assessment of liver fibrosis in chronic viral hepatitis and will highlight potential further advantages.

Reliability of transient elastography for the diagnosis of advanced fibrosis in chronic hepatitis C.

BACKGROUND: Transient elastography (TE) has received increasing attention as a means to evaluate disease progression in patients with chronic liver disease. AIM: To assess the value of TE for predicting the stage of fibrosis. METHODS: Liver biopsy and TE were performed in 150 consecutive patients with chronic hepatitis C-related hepatitis (92 men and 58 women, age 50.6 (SD 12.5) years on the same day. Necro-inflammatory activity and the degree of steatosis at biopsy were also evaluated. RESULTS: The areas under the curve for the prediction of significant fibrosis (> or = F2), advanced fibrosis (> or = F3) or cirrhosis were 0.91, 0.99 and 0.98, respectively. Calculation of multilevel likelihood ratios showed that values of TE < 6 or > or = 12, < 9 or > or = 12, and < 12 or > or = 18, clearly indicated the absence or presence of significant fibrosis, advanced fibrosis, and cirrhosis, respectively. Intermediate values could not be reliably associated with the absence or presence of the target condition. The presence of inflammation significantly affected TE measurements in patients who did not have cirrhosis (p<0.0001), even after adjusting for the stage of fibrosis. Importantly, TE measurements were not influenced by the degree of steatosis. CONCLUSIONS: TE is more suitable for the identification of patients with advanced fibrosis than of those with cirrhosis or significant fibrosis. In patients in whom likelihood ratios are not optimal and do not provide a reliable indication of the disease stage, liver biopsy should be considered when clinically indicated. Necro-inflammatory activity, but not steatosis, strongly and independently influences TE measurement in patients who do not have cirrhosis.

Postsurgical osteomyelitis caused by Enterobacter sakazakii in a healthy young man.

Enterobacter sakazakii, a Gram-negative rod-shaped bacterium, is a rare cause of invasive infections (meningitis, sepsis, necrotizing enterocolitis) with high death rates (40-80%), primarily in newborns. In contrast to the high number of cases in newborns, infants and children, there are only a few reported cases of E. sakazakii infections in adults, generally in subjects with pre-existing conditions such as neoplasms, and just one osteomyelitis of the foot. We report a confirmed case of postsurgical osteomyelitis of the femur caused by E. sakazakii in a young otherwise healthy man.

Measurement of the K0 charge radius and a CP-violating asymmetry and a search for CP-violating E1 direct photon emission in the rare decay KL--> pi+ pi- e+ e-.

Using the complete KTeV data set of 5,241 candidate K(L)--> pi(+) pi(-) e(+) e(-) decays (including an estimated background of 204 +/- 14 events), we have measured the coupling g(CR)= 0.163 +/- 0.0149(stat) +/- 0.023(syst) of the CP conserving charge radius process and from it determined a K(0) charge radius of = [-0.077 +/- 0.007(stat) +/- 0.011(syst)]fm(2). We have determined a first experimental upper limit of 0.04 (90% C.L.) /g(e1)/ / /g(M1)/ of the couplings for the E1 and M1 direct photon emission processes. We also report the measurement of /g(M1)/ including a vector form factor /g(M1)/(1 + (a(1)/a(2))/((M(2)(p)-(M(2)(k))= 2M(K)E(gamma*)), where vector /g(M1)/= 1.11+/- 0.12(stat) +/- 0.08(syst) and a(1)/a(2) = [-0.744 +/- 0.027(stat) +/- 0.032(syst)] GeV(2)/c(2). Finally, a CP-violating asymmetry of [13.6 +/- 1.4(stat) +/- 1.5(syst)]% in the CP and T odd angle phi between the decay planes of the e(+) e(-) and pi(+) pi(-) pairs in the K(L) center of mass is reported.

Simultaneous effect of cyclodextrin complexation, pH, and hydrophilic polymers on naproxen solubilization.

The effect of pH variation on complexation and solubilization of naproxen (pK(a) 4.2) with natural betaCyclodextrin (betaCyD) and various neutral, cationic and anionic betaCyD-derivatives has been investigated. The combined effect of pH variation and hydrophilic polymer addition on CyD solubilizing and complexing efficiency has also been determined. Phase-solubility analysis in buffered aqueous solutions (pH from 1.1 to 6.5) was used to study the interaction of the drug with each CyD, in the presence or not of the water-soluble polymer. A clear influence of the substituent type was observed, the methylderivative being the most efficient agent; on the contrary, unexpectedly, no influence of the CyD charge in the interaction with the ionizable drug was detected. As expected, total drug solubility increased with increasing pH; however, the solubility increment with respect to drug alone obtained by CyD complexation progressively decreased, with a parallel reduction of the complex stability, attributed to the reduced affinity of charged drug for the hydrophobic CyD cavity. The addition of the polymer in part counterbalanced the destabilizing effect obtained with increasing pH, by improving the CyD complexation power towards naproxen. In particular, the presence of PVP allowed an increase of the complex stability constant with hydroxypropyl betaCyD up to 60% with respect to the corresponding drug-CyD binary system. Therefore, the combined strategy of pH control and polymer addition to the CyD complexing medium can be successfully exploited to improve naproxen solubilization and reduce the amount of CyD needed. The construction of theoretical drug solubility curves as a function of pH for any given CyD and polymer concentration enables selection of the best experimental conditions for obtaining the desired drug solubility value.

Influence of cyclodextrins and chitosan, separately or in combination, on glyburide solubility and permeability.

The effect of chitosan and of different concentrations of beta- or hydroxypropyl-beta-cyclodextrins, separately or in various (w/w) combinations, on the dissolution characteristics of glyburide (an oral hypoglycemic agent subject to incomplete and variable bioavailability) and on its permeability through Caco-2 cells has been investigated. Cyclodextrins (and particularly the hydroxypropyl-derivative, in virtue of its higher water solubility) were clearly more effective than chitosan in enhancing the drug dissolution properties: the aqueous glyburide solubility was improved 40-fold in the presence of 25 mM hydroxypropyl-beta-cyclodextrin, 25-fold in the presence of 13 mM beta-cyclodextrin (saturation solubility) and only 3-fold in the presence of chitosan at its saturation concentration (0.5% w/v). When chitosan and cyclodextrin were simultaneously present, a strong reduction of the cyclodextrin solubilizing efficiency towards the drug was observed, and it was attributed to a possible competition effect of polymer and glyburide for the interaction with the macrocycle. By contrast, permeation studies revealed that chitosan was more powerful than cyclodextrins in enhancing the glyburide permeability through Caco-2 cells. This was probably in virtue of the polymer's favourable effect on the tight junctions opening, as demonstrated by the significant decrease in the transepithelial electrical resistance recorded in its presence. Moreover, interestingly, when using the carriers together, conversely from solubility studies, a significant (P < 0.05) synergistic effect in enhancing glyburide apparent permeability was revealed in permeation experiments.

Influence of formulation and process variables on in vitro release of theophylline from directly-compressed Eudragit matrix tablets.

Extended-release theophylline (TP) matrix tablets were prepared by direct compression of drug and different pH-dependent (Eudragit L100, S100 and L100-55) and pH-independent (Eudragit RLPO and RSPO) polymer combinations. The influence of varying the polymer/polymer (w/w) ratio and the drug incorporation method (simple blend or solid dispersion) was also evaluated. Drug release, monitored using the Through Flow Cell system, markedly depended on both the kind of Eudragit polymer combinations used and their relative content in the matrix. Maintaining a constant 1:1 (w/w) drug/polymers ratio, the selection of appropriate mixtures of pH-dependent and pH-independent polymers enabled achievement of a suitable control of TP release. In particular, matrices with a 0.7:0.3 w/w mixture of Eudragit L100-Eudragit RLPO showed highly reproducible drug release profiles, with an almost zero-order kinetic, and allowed 100% released drug after 360 min. As for the effect of the drug incorporation method, simple blending was better than the solid dispersion technique, which not only did not improve the release data reproducibility, but also caused, unexpectedly, a marked slowing down in drug release rate.

Interaction of naproxen with ionic cyclodextrins in aqueous solution and in the solid state.

The possible role of the cyclodextrin charge in the interaction with an acidic drug such as naproxen (pKa 4.8) has been evaluated. Sulfobutylether-beta-cyclodextrin (SBE-betaCyd) and trimethylammonium-beta-cyclodextrin (TMA-betaCyd) were selected as, respectively, anionically and cationically charged carriers and their performance was compared with that of the parent beta-cyclodextrin (betaCyd) and of its methyl-derivative (Me betaCyd) previously found as the best partner for the drug. Interactions in solution were investigated by phase-solubility, fluorescence and circular dichroism analyses. Equimolar drug-carrier products prepared by different techniques (blending, cogrinding, sealed-heating, colyophilization) were characterized by differential scanning calorimetry and X-ray powder diffractometry and tested for drug dissolution properties. Anionic charges of SBE-betaCyd did not negatively influence interactions in unbuffered aqueous solutions (pH approximately 5) with the acidic drug. In fact, it was a very effective carrier, exhibiting solubilizing and complexing properties considerably better than the parent betaCyd and comparable to those of Me betaCyd. On the contrary, the positive charges of TMA-betaCyd did not favour interactions with the counter-ionic drug (despite the presence of about 60% ionised drug) and it was less efficacious also than native betaCyd. Therefore, the role of the Cyd charge on the complexing and solubilizing properties towards naproxen was not important whereas other factors, such as steric hindrance effects and favourable hydrophobic interactions were significant in determining the drug affinity for the Cyd inclusion. Solid state studies evidenced similar amorphizing properties of both charged Cyds towards naproxen. On the other hand, dissolution tests, in agreement with solution studies, showed that all products with SBE-betaCyd exhibited significantly better dissolution properties than the corresponding ones with TMA-betaCyd. A clear influence of the preparation method of drug-Cyd solid systems on the performance of the end product was also observed. Colyophilization was the most effective technique, followed by the cogrinding one. Colyophilized product with SBE-betaCyd allowed a 10-times increase in drug dissolution efficiency (D.E.) (with respect to the five-times increase obtained with the corresponding coground product) and a reduction of t(50%) from about 60 min (for the coground product) to less than 2 min.

Rectal bleeding by Dieulafoy-like lesion: successful endoscopic treatment.

A 81-year old woman affected by chronic renal failure, non insulin-dependent diabetes mellitus (NIDM) and hypertension, had an severe anemia massive hematochezia. The colonoscopy could not localize the bleeding site except some blood spots in the rectum. The patient was readmitted after 1 month with hypovolemic shock by massive hematochezia and required several blood transfusions. The endoscopic examination showed an important arterial bleeding treated successfully with epinephrine and bipolar elettro-coagulation (BICAP). We suggested that the patient presented a Dieulafoy-like lesion; this is an uncommon gastrointestinal cause of bleeding due to a defect of a submucosal artery without evidence of atherosclerosis or vasculitis. Both chronic renal failure and age could be considered as predisponent factors in this patient. Hematochezia is the most important sign and is often complicated by haemorrhagic shock. The diagnosis was delayed due to the difficulty in localizing the bleeding site; moreover, the patient needed several blood transfusions. The arteriographic diagnosis associated to endoscopic treatment by epinephrine and BICAP enabled a successful therapy.