Estimation of predictive accuracy in survival analysis using R and S-PLUS

When the purpose of a survival regression model is to predict future outcomes, the predictive accuracy of the model needs to be evaluated before practical application. Various measures of predictive accuracy have been proposed for survival data, none of which has been adopted as a standard, and their inclusion in statistical software is disregarded. We developed the surev library for R and S-PLUS, which includes functions for evaluating the predictive accuracy measures proposed by Schemper and Henderson. The library evaluates the predictive accuracy of parametric regression models and of Cox models. The predictive accuracy of the Cox model can be obtained also when time-dependent covariates are included because of non-proportional hazards or when using Bayesian model averaging. The use of the library is illustrated with examples based on a real data set.     

Meta-modelling and graph grammars for multi-paradigm modelling in AToM<Superscript>3</Superscript>

This paper presents the combined use of meta-modelling and graph grammars for the generation of visual modelling tools for simulation formalisms. In meta-modelling, formalisms are described at a meta-level. This information is used by a meta-model processor to generate modelling tools for the described formalisms. We combine meta-modelling with graph grammars to extend the model manipulation capabilities of the generated modelling tools: edit, simulate, transform into another formalism, optimize and generate code. We store all (meta-)models as graphs, and thus, express model manipulations as graph grammars.We present the design and implementation of these concepts in AToM³ (A_To_ol for M_ulti-formalism, M_eta-M_odelling). AToM³ supports modelling of complex systems using different formalisms, all meta-modelled in their own right. Models in different formalisms may be transformed into a single common formalism for further processing. These transformations are specified by graph grammars. Mosterman and Vangheluwe [18] introduced the term multi-paradigm modelling to denote the combination of multiple formalisms, multiple abstraction levels, and meta-modelling. As an example of multi-paradigm modelling we present a meta-model for the Object-Oriented Continuous Simulation Language OOCSMP, in which we combine ideas from UML class diagrams (to express the OOCSMP model structure), Causal Block Diagrams (CBDs), and Statecharts (to specify the methods of the OOCSMP classes). A graph grammar is able to generate OOCSMP code, and then a compiler for this language (C-OOL) generates Java applets for the simulation execution.     

Quantitative Plasma Proteomics to Identify Candidate Biomarkers of Relapse in Pediatric/Adolescent Hodgkin Lymphoma

Classical pediatric Hodgkin Lymphoma (HL) is a rare malignancy. Therapeutic regimens for its management may be optimized by establishing treatment response early on. The aim of this study was to identify plasma protein biomarkers enabling the prediction of relapse in pediatric/adolescent HL patients treated under the pediatric EuroNet-PHL-C2 trial. We used untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics at the time of diagnosis—before any therapy—as semiquantitative method to profile plasma proteins specifically associated with relapse in 42 children with nodular sclerosing HL. In both the exploratory and the validation cohorts, six proteins (apolipoprotein E, C4b-binding protein α chain, clusterin, fibrinogen γ chain, prothrombin, and vitronectin) were more abundant in the plasma of patients whose HL relapsed (|fold change| ≥ 1.2, p < 0.05, Student’s t-test). Predicting protein function with the Gene Ontology classification model, the proteins were included in four biological processes (p < 0.01). Using immunoblotting and Luminex assays, we validated two of these candidate biomarkers—C4b-binding protein α chain and clusterin—linked to innate immune response function (GO:0045087). This study identified C4b-binding protein α chain and clusterin as candidate early plasma biomarkers of HL relapse, and important for the purpose of shedding light on the molecular scenario associated with immune response in patients treated under the EuroNet-PHL-C2 trial.     

Tumor-Stroma Ratio and Programmed Cell Death Ligand 1 Expression in Preoperative Biopsy and Matched Laryngeal Carcinoma Surgical Specimen

Programmed cell death ligand 1 (PD-L1) seems to rely on close relations between neoplastic and immune cells in the tumor microenvironment. Tumor to stroma ratio (TSR) has been associated with prognosis in different malignancies. The aims of this exploratory investigation were to analyze for the first time the: (i) association between TSR, PD-L1 expression and other clinical–pathological features in laryngeal squamous cell carcinoma (LSCC) biopsies and paired surgical specimens; (ii) prognostic and predictive role of TSR and PD-L1. TSR, PD-L1 expression (in terms of combined positive score [CPS]), and other clinical–pathological features were analyzed in biopsies and surgical specimens of 43 consecutive LSCC cases. A CPS < 1 evaluated on surgical specimens was associated with a low TSR (stroma rich) on both biopsies and surgical specimens (p = 0.0143 and p = 0.0063). Low TSR showed a significant negative prognostic value when evaluated on both biopsies and surgical specimens (HR = 8.808, p = 0.0003 and HR = 11.207, p = 0.0002). CPS ≥ 1 appeared to be a favorable prognostic factor (HR = 0.100, p = 0.0265). The association between bioptic and surgical specimen TSR and PD-L1 expression should be further investigated for a potential impact on targeted treatments, also with regard to immunotherapeutic protocols.     

Prediction of Drug Synergism between Peptides and Antineoplastic Drugs Paclitaxel, 5-Fluorouracil,and Doxorubicin Using In Silico Approaches

Chemotherapy is the main treatment for most early-stage cancers; nevertheless, its efficacy is usually limited by drug resistance, toxicity, and tumor heterogeneity. Cell-penetrating peptides (CPPs) are small peptide sequences that can be used to increase the delivery rate of chemotherapeutic drugs to the tumor site, therefore contributing to overcoming these problems and enhancing the efficacy of chemotherapy. The drug combination is another promising strategy to overcome the aforementioned problems since the combined drugs can synergize through interconnected biological processes and target different pathways simultaneously. Here, we hypothesized that different peptides (P1–P4) could be used to enhance the delivery of chemotherapeutic agents into three different cancer cells (HT-29, MCF-7, and PC-3). In silico studies were performed to simulate the pharmacokinetic (PK) parameters of each peptide and antineoplastic agent to help predict synergistic interactions in vitro. These simulations predicted peptides P2–P4 to have higher bioavailability and lower T_max, as well as the chemotherapeutic agent 5-fluorouracil (5-FU) to have enhanced permeability properties over other antineoplastic agents, with P3 having prominent accumulation in the colon. In vitro studies were then performed to evaluate the combination of each peptide with the chemotherapeutic agents as well as to assess the nature of drug interactions through the quantification of the Combination Index (CI). Our findings in MCF-7 and PC-3 cancer cells demonstrated that the combination of these peptides with paclitaxel (PTX) and doxorubicin (DOXO), respectively, is not advantageous over a single treatment with the chemotherapeutic agent. In the case of HT-29 colorectal cancer cells, the combination of P2–P4 with 5-FU resulted in synergistic cytotoxic effects, as predicted by the in silico simulations. Taken together, these findings demonstrate that these CPP6-conjugates can be used as adjuvant agents to increase the delivery of 5-FU into HT-29 colorectal cancer cells. Moreover, these results support the use of in silico approaches for the prediction of the interaction between drugs in combination therapy for cancer.     

Particle Size Modulates Silver Nanoparticle Toxicity during Embryogenesis of Urchins Arbacia lixula and Paracentrotus lividus

Silver nanoparticles represent a threat to biota and have been shown to cause harm through a number of mechanisms, using a wide range of bioassay endpoints. While nanoparticle concentration has been primarily considered, comparison of studies that have used differently sized nanoparticles indicate that nanoparticle diameter may be an important factor that impacts negative outcomes. In considering this, the aim of the present study was to determine if different sizes of silver nanoparticles (AgNPs; 10, 20, 40, 60 and 100 nm) give rise to similar effects during embryogenesis of Mediterranean sea urchins Arbacia lixula and Paracentrotus lividus, or if nanoparticle size is a parameter that can modulate embryotoxicity and spermiotoxicity in these species. Fertilised embryos were exposed to a range of AgNP concentrations (1–1000 µg L⁻¹) and after 48 h larvae were scored. Embryos exposed to 1 and 10 µg L⁻¹ AgNPs (for all tested sizes) showed no negative effect in both sea urchins. The smaller AgNPs (size 10 and 20 nm) caused a decrease in the percentage of normally developed A. lixula larvae at concentrations ≥50 µg L⁻¹ (EC₅₀: 49 and 75 μg L⁻¹, respectively) and at ≥100 µg L⁻¹ (EC₅₀: 67 and 91 μg L⁻¹, respectively) for P. lividus. AgNPs of 40 nm diameter was less harmful in both species ((EC₅₀: 322 and 486 μg L⁻¹, for P. lividus and A. lixula, respectively)). The largest AgNPs (60 and 100 nm) showed a dose-dependent response, with little effect at lower concentrations, while more than 50% of larvae were developmentally delayed at the highest tested concentrations of 500 and 1000 µg L⁻¹ (EC₅₀(100 nm); 662 and 529 μg L⁻¹, for P. lividus and A. lixula, respectively. While AgNPs showed no effect on the fertilisation success of treated sperm, an increase in offspring developmental defects and arrested development was observed in A. lixula larvae for 10 nm AgNPs at concentrations ≥50 μg L⁻¹, and for 20 and 40 nm AgNPs at concentrations >100 μg L⁻¹. Overall, toxicity was mostly ascribed to more rapid oxidative dissolution of smaller nanoparticles, although, in cases, Ag⁺ ion concentrations alone could not explain high toxicity, indicating a nanoparticle-size effect.     

Comment on Chen et al. "Fabrication and photovoltaic conversion enhancement of graphene/n-Si Schottky barrier solar cells by electrophoretic deposition", Electrochimica Acta, 2014

In a recent article, Chen et al. [Electrochimica Acta, 2014, 130: 279] presented their fabrication and characterization results on a graphene/n-Si solar cell where the Au nanoparticles were inserted in graphene to increase its optical and electrical properties. The higher efficiency of the device was attributed to increased conductivity of graphene after doping with Au nanoparticles. However, the knowledge in the field of Schottky diode solar cells relates this to increased band bending at the junction. Also, to explain the instability behaviour, they concluded that the growth of silicon oxide on the Si surface or oxygen adsorption on the window layer resulted in the device performance increasing initially and decreasing in the end. However, this instability seems to be due to variation in series resistance reduced at the beginning because of slightly lowered Fermi level and increased at the end by the self-compensation by deep in-diffusion of Au nanoparticles into n-Si layer. We also propose that inserting a very thin p-type layer at the junction will enhance the carrier collection and performance of this device.     

Strain-specific polyketide synthase genes of Aspergillus niger

In silico comparison of 34 putative pks genes in Aspergillus niger strain CBS 513.88 versus A. niger strain ATCC 1015 genome revealed significant nucleotide identity (>95% covering a minimum of 99% of the gene sequence) for 31 of these genes (approximately 91%). A. niger CBS 513.88 harbors three putative pks genes (An01g01130, An11g05940, and An15g07920), for which nucleotide identity was not found in A. niger ATCC 1015. To compare the results of the in silico analysis with the in vivo situation, experimental data were obtained for a large number of A. niger strains obtained from different substrates and geographical regions. Three putative pks genes that were found to be variable between the two A. niger strains using bioinformatics tools were in fact strain-specific genes based on experimental data. The PCR amplification signals for the An01g01130, An11g05940, and An15g07920 pks genes were detected in only 97%, 71%, and 26% of the strains, respectively. Southern blot analyses confirmed the PCR data. Because one of the strain-specific pks genes (An15g07920) is located in a putative ochratoxin cluster, we focused our investigation on that region. We assessed the ochratoxin production capability of the 119 A. niger strains and found a positive association between the presence of this pks gene and the capability of the respective strain to produce ochratoxin.     

Effect of ultraviolet processing on selected properties of egg white

The effect of ultraviolet processing (10.6 and 63.7 kJ m(-2)) on selected properties of egg white (absorbance, particle size, protein fractions, free sulfhydryl content, immunoreactivity, viscosity, gelling and foaming properties) was investigated. Ultraviolet exposure induced the development of browning, the formation of large protein aggregates by disulfide exchange, and protein backbone cleavage. However, egg white proteins were differently sensitive to UV radiation. No changes in immunoreactivity, gelling temperature and gel firmness were observed. Independently on the UV dose, light treated egg white produced foams with higher stability. This effect was attributed to protein aggregates jamming in the fluid interstices between bubbles and/or to the higher viscosity of the aqueous phase. The latter was also associated to higher foam volume.     

Superconducting Vortex Lattice Configurations on Periodic Potentials: Simulation and Experiment

Nb films have been fabricated on top of array of Ni nanodots. The array of periodic pinning potentials modifies the vortex lattice for specific values of the external applied magnetic field. By means of an implemented code developed from scratch, computer simulations based only on the vortex?Cvortex and the vortex?Cnanodot interactions provide the total interaction between vortices and pinning sites as well as the position of the vortices in the array unit cell. This simulation approach could be performed on square, rectangular or triangular arrays of nanodefects of different size.