Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM? Platform

Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™. The robust bioinformatic pipeline allowed us to correctly call both Single Nucleotide Variants (SNVs) and indels with a detection limit of 5%, achieving 100% specificity and 96% sensitivity. This workflow was also validated in 13 FFPE NSCLC biopsies. Furthermore, a specific protocol for low input gDNA capable of producing good sequencing data with high coverage, high uniformity, and a low error rate was also optimized. In conclusion, we demonstrate the feasibility of obtaining gDNA from FFPE samples suitable for NGS by performing appropriate quality controls. The optimized workflow, capable of screening low input gDNA, highlights NGS as a potential tool in the detection, disease monitoring, and treatment of NSCLC.     

13.3% efficient solution deposited Cu(In,Ga)Se2 solar cells processed with different sodium salt sources

In this work, we obtain the highest reported power conversion efficiency (13.3%) for sulfur‐free CIGSe solar cells by solution processing. Intentional sodium incorporation is achieved directly by dissolving sodium salts in the ink. The effect on solar cell properties of three sodium sources is investigated: NaCl, NaHCO₂, and NaSCN. A comparison is made with absorbers grown on soda‐lime glass substrates and in the absence of sodium sources. The incorporation via sodium salts yields significantly better results, which is attributed to enhanced‐sodium availability. A comparison with identically annealed sputtered metal precursor layers capable of delivering 15.1% module efficiency suggests that the cell results are limited by the selenization procedure. Copyright © 2015 John Wiley & Sons, Ltd.     

Toxic metals in the atmosphere in Lahore, Pakistan

Aerosol mass (PM₁₀ and PM_2.5) and detailed elemental composition were measured in monthly composites during the calendar year of 2007 at a site in Lahore, Pakistan. Elemental analysis revealed extremely high concentrations of Pb (4.4 μg m^− 3), Zn (12 μg m^− 3), Cd (0.077 μg m^− 3), and several other toxic metals. A significant fraction of the concentration of Pb (84%), Zn (98%), and Cd (90%) was contained in the fine particulate fraction (PM_2.5 and smaller); in addition, Zn and Cd were largely (≥ 60%) water soluble. The 2007 annual average PM₁₀ mass concentration was 340 μg m^− 3, which is well above the WHO guideline of 20 μg m^− 3. Dust sources were found to contribute on average (maximum) 41% (70%) of PM₁₀ mass and 14% (29%) of PM_2.5 mass on a monthly basis. Seasonally, concentrations were found to be lowest during the monsoon season (July-September). Principle component analysis identified seven factors, which combined explained 91% of the variance of the measured components of PM₁₀. These factors included three industrial sources, re-suspended soil, mobile sources, and two regional secondary aerosol sources likely from coal and/or biomass burning. The majority of the Pb was found to be associated with one industrial source, along with a number of other toxic metals including As and Cr. Cadmium, another toxic metal, was found at concentrations 16 times higher than the maximum exposure level recommended by the World Health Organization, and was concentrated in one industrial source that was also associated with Zn. These results highlight the importance of focusing control strategies not only on reducing PM mass concentration, but also on the reduction of toxic components of the PM as well, to most effectively protect human health and the environment.     

Electrospinning: A Novel Method to Incorporate POSS Into a Polymer Matrix

The effectiveness of electrospinning as a simple approach to disperse POSS into a polymer matrix at a nm‐level has been assessed. Electrospun and cast films were prepared by dissolving CA and epoxycyclohexylisobutyl POSS in the solvent mixture acetone/DMAc. The membranes were characterized by SEM, TEM and WAXD. Whereas films produced by casting showed µm‐sized POSS crystals, thus suggesting a small affinity between the polymer matrix and the POSS molecules, those prepared by electrospinning were characterized by a nanometric POSS distribution. This is explained by considering the peculiar solvent evaporation mechanism, occurring during the electrospinning process, which allows to produce nanofibers characterized by a silsesquioxane dispersion similar to that present in solution.

     

Studies on the effects of phosphine on Salmonella enterica serotype Enteritidis in culture medium and in black pepper (Piper nigrum)

The effect of phosphine on Salmonella enterica serotype Enteritidis inoculated in culture medium and in black pepper grains (Piper nigrum), as well as on the reduction of the microbial load of the dried and moisturized product, was verified. The postfumigation effect was verified in inoculated samples with 0.92 and 0.97 water activity (a(w)) exposed to 6 g/m(3) phosphine for 72 h, dried to 0.67 a(w), and stored for 24, 48, and 72 h. No decreases were observed in Salmonella Enteritidis populations in culture medium when fumigant concentrations up to 6 g/m(3) were applied for 48 h at 35°C. However, the colonies showed reductions in size and atypical coloration as the phosphine concentration increased. No reduction in Salmonella counts occurred on the inoculated dried samples after fumigation. On the other hand, when phosphine at concentrations of 6 g/m(3) was applied on moisturized black pepper for 72 h, decreases in Salmonella counts of around 80% were observed. The counts of total aerobic mesophilic bacterium populations of the dried and moisturized black pepper were not affected by the fumigant treatment. The results of the postfumigation studies indicated that Salmonella Enteritidis was absent in the fumigated grains after drying and storage for 72 h, indicating a promising application for this technique. It was concluded that for Salmonella Enteritidis control, phosphine fumigation could be applied to black pepper grains before drying and the producers should rigidly follow good agricultural practices, mainly during the drying process, in order to avoid product recontamination. Additional work is needed to confirm the findings with more Salmonella serotypes and strains.     

Sustainability and property valuation: a risk-based approach

The proportion of sustainable property in the total building stock remains small. One reason is that the financial added value resulting from sustainability is not sufficiently taken into account in property valuation due to the tendency of valuations to lag behind market trends. Quantitative information is provided to integrate those aspects of sustainability relating to value into valuations and thereby contribute to the reduction of valuation lag. The Centre for Corporate Responsibility and Sustainability (CCRS) Economic Sustainability Indicator (ESI) measures the risk of property to lose value and the opportunity to gain value due to future developments (e.g. climate change or rising energy prices). Five groups of value-related sustainability features were identified: flexibility and polyvalence; energy and water dependency; accessibility and mobility; security; and health and comfort. By minimizing the risk of loss in value through future developments, those sustainability features contribute to the property value. Their effects on property value were quantified by risk modelling. As an indicator for future-oriented property risk, the ESI is integrated into the discount rate of discounted cash flow valuations. The approach was tested for plausibility and practicability on more than 200 properties.

La proportion de biens immobiliers durables dans le parc immobilier total demeure faible. L'explication tient pour une part au fait que la valeur ajoutée financière résultant de la durabilité n'est pas suffisamment prise en compte dans l'évaluation des biens immobiliers en raison du fait que les évaluations tendent à avoir du retard sur les tendances du marché. Des informations quantitatives sont fournies afin d'intégrer les aspects de la durabilité liés à la valeur dans les évaluations et de contribuer ainsi à la réduction du retard dans les évaluations. L'Indicateur de Durabilité Economique (ESI) du Centre pour la Responsabilité et la Durabilité en Entreprise (CCRS) mesure le risque de perte de valeur des biens immobiliers et la possibilité d'en accroître la valeur du fait des évolutions futures (par ex. changement climatique et hausse des prix énergétiques). Cinq groupes de fonctions de durabilité liées à la valeur ont été identifiés: flexibilité et polyvalence, dépendance vis-à-vis de l'énergie et de l'eau; accessibilité et mobilité; sécurité; santé et confort. En minimisant le risque d'une perte de valeur causée par les évolutions futures, ces fonctions de durabilité contribuent à la valeur des biens immobiliers. Leurs effets sur la valeur des biens immobiliers ont été quantifiés par une modélisation des risques. En tant qu'indicateur du risque prospectif pour les biens immobiliers, l'ESI est intégré au taux d'actualisation des flux de trésorerie actualisés. Cette approche a été testée quant à sa plausibilité et sa praticabilité sur plus de 200 biens immobiliers.

Mots clés: flux de trésorerie actualisés, indicateur de durabilité économique, évaluation des biens immobiliers, modèle de risque, fonctions de durabilité, durabilité, bâtiments durables     

Marriage as a risk factor for internalizing disorders: Clarifying scope and specificity.

Objective: Marital discord has been linked to both depression and anxiety; however, our understanding of how marriage contributes to the development of internalizing symptoms is limited in scope and lacking specificity. First, it is unclear whether the marital relationship contributes to the broad dimension of internalizing symptoms as opposed to specific diagnoses. Second, it is unclear how the marital relationship contributes to internalizing symptoms: through global marital dissatisfaction or through specific relationship processes (and which processes). The purpose of the present study was to address these 2 issues and, more generally, to develop a comprehensive and refined framework within which to understand the role of marriage in the developmental course of internalizing symptoms. Method: Questionnaire and interview data were collected from 102 husbands and wives 5 times over the first 7 years of marriage. Results: Results indicated that marital discord during the transition into marriage was associated with the broad dimension of internalizing symptoms for husbands but not for wives. Further, both global marital dissatisfaction and an imbalance of power and control put husbands at significant risk for symptoms over the first 7 years of marriage, whereas low levels of emotional intimacy put wives at significant risk. Conclusions: Results exemplify the need to routinely consider intimate relationship processes in etiological models of depression and anxiety and to identify specific clinical targets that can be prioritized in interventions aimed at preventing internalizing disorders. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

Immune-Pineal Axis: Nuclear Factor κB (NF-κB) Mediates the Shift in the Melatonin Source from Pinealocytes to Immune Competent Cells

Pineal gland melatonin is the darkness hormone, while extra-pineal melatonin produced by the gonads, gut, retina, and immune competent cells acts as a paracrine or autocrine mediator. The well-known immunomodulatory effect of melatonin is observed either as an endocrine, a paracrine or an autocrine response. In mammals, nuclear translocation of nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) blocks noradrenaline-induced melatonin synthesis in pinealocytes, which induces melatonin synthesis in macrophages. In addition, melatonin reduces NF-κB activation in pinealocytes and immune competent cells. Therefore, pathogen- or danger-associated molecular patterns transiently switch the synthesis of melatonin from pinealocytes to immune competent cells, and as the response progresses melatonin inhibition of NF-κB activity leads these cells to a more quiescent state. The opposite effect of NF-κB in pinealocytes and immune competent cells is due to different NF-κB dimers recruited in each phase of the defense response. This coordinated shift of the source of melatonin driven by NF-κB is called the immune-pineal axis. Finally, we discuss how this concept might be relevant to a better understanding of pathological conditions with impaired melatonin rhythms and hope it opens new horizons for the research of side effects of melatonin-based therapies.     

Acid-Base Interactions and Interphase Formation in Particulate-Filled Polymers

Particulate-filled composites were prepared from CaCO 3 and polymer matrices of various acid-base characters. Interfacial interaction of the components was characterized by the reversible work of adhesion, which was calculated either from dipole-dipole or acid-base interactions. The thickness of the spontaneously formed interlayer was derived from the tensile strength of the composites. The results proved that acid-base interactions play an important role in interphase formation. The strength of interfacial adhesion is determined by the joint effect of dispersion forces and acid-base interactions. Stronger interaction leads to a thicker interphase with decreased mobility. Treatment of CaCO 3 with an aliphatic fatty acid leads to a decrease in the strength of interaction, and to changes both in the thickness and properties of the interphase. In composites containing coated fillers, acid-base interactions influence composite properties less due to the neutral character of the surface.     

The mediating role of coping: A cross-sectional analysis of the relationship between coping self-efficacy and coping effectiveness among athletes.

This study examines the relationship among global coping self-efficacy, coping, and coping effectiveness within athletes. We hypothesized that there would be a positive association between coping self-efficacy and coping effectiveness, which would be mediated by coping. It was also predicted that coping strategies within the task-oriented coping dimension would be positively associated with coping effectiveness, whereas strategies from the disengagement- and distraction-oriented coping dimensions would be negatively associated with coping effectiveness. Participants were 353 athletes between the ages of 18 and 29 years, who completed a measure of coping self-efficacy the night before they competed, in addition to a measure of the athletes' use of coping strategies and their perceived coping effectiveness, which was completed immediately after the competitive event. Results revealed that higher global coping self-efficacy scores were significantly (r = .33, p