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.     

An effective multipurpose building block for 3D electropolymerisation: 2,2′-Bis(2,2′-bithiophene-5-yl)-3,3′-bithianaphthene

Novel thiophene-based oligomer, 2,2′-bis(2,2′-bithiophene-5-yl)-3,3′-bithianaphthene (TX), was designed and synthesized, and its electrochemical and spectral properties characterised. TX was readily polymerised electrochemically to form well organized conducting homopolymer films on various solid electrode substrates. Moreover, it was successfully used for deposition by electropolymerisation of electrochemically active thin films of co-polymers with three different monomers of functionalised bis(2,2′-bithienyl)methane derivatives. It appeared that TX was an effective crosslinker and 3D promoter in these electropolymerisations involving co-monomers intrinsically showing limited aptitude for the electropolymerisation or forming polymer films of low conductivity. This attractive TX ability stems from combination of its (i) high conjugation efficiency in each of the two planar moieties, (ii) intrinsic 3D structure on account of the presence of the central node, and (iii) intrinsic regioselectivity in electropolymerisation on account of the positions of the two available free α-thiophene sites.     

Coupling hydrothermal liquefaction and aqueous phase reforming for integrated production of biocrude and renewable H2

Lignin-rich stream from lignocellulosic ethanol production was converted into biocrude by continuous hydrothermal liquefaction (HTL) while hydrogen was produced by aqueous phase reforming (APR) of the HTL aqueous by-product. The effects of Na₂CO₃ and NaOH were investigated both in terms of processability of the feedstock as well as yield and composition of the obtained products. A maximum biocrude yield of 27 wt% was reached in the NaOH-catalyzed runs. A relevant amount of dissolved phenolics were detected in the co-produced aqueous phase (AP), and removed by liquid–liquid extraction using butyl acetate or diethyl ether, preserving the APR catalyst stability and reaching an hydrogen yield up to 146 mmol H₂ L⁻¹ AP. Preliminary mass balances integrating HTL and APR showed that the hydrogen provided by APR may account for up to 46% of the hydrogen amount theoretically required for upgrading the HTL biocrude, thus significantly improving the process performance and sustainability.     

The application of virtual reality technology in rehabilitation.

Virtual reality (VR) is an emerging technology with a variety of potential benefits for many aspects of rehabilitation assessment, treatment, and research. Through its capacity to allow the creation and control of dynamic 3-dimensional, ecologically valid stimulus environments within which behavioral responding can be recorded and measured, VR offers clinical assessment and rehabilitation options that are not available with traditional methods. Initial applications of VR in other aspects of medicine and psychology have yielded encouraging results, but continued research and understanding of this evolving technology will be crucial for its effective integration into rehabilitation. This article provides a brief introduction to VR technology, examines the specific benefits VR offers consumers and providers of rehabilitation services and discusses potential areas of application and important considerations in applying this technology. Finally, 2 examples of current Vr applications are presented. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Effect of electric and flow parameters on PEF treatment efficiency

The effects of both the electric and flow parameters on the lethality and energy efficiency of a pulsed electric fields (PEF) treatment were studied. An experimental plan was designed in order to study the microbial inactivation of Saccharomyces cerevisiae and Escherichia coli cells inoculated in a buffer solution. The following process parameters were taken into consideration: electric field strength (13-30 kV/cm), total specific energy input (20-110 J/mL), flow rate of the processed stream (1-4 L/h) and number of passes through the chamber (up to 5).The results showed that, at a fixed flow rate (2 L/h), microbial inactivation of both microbial strains increased with increasing field strength and applied energy input. The maximum inactivation level (5.9 Log-cycles for S. cerevisiae and 7.0 Log-cycles for E. coli) corresponded to the more intensive PEF treatment (30 kV/cm and 110 J/mL). However, for any given field strength applied, the inactivation rate decreased by increasing the energy input. This behavior was attributed to the presence of heterogeneous treatment conditions due, for example, to a different morphology (size and shape) or cell membrane (composition, structure), a local variation of the electric field strength in the treatment chamber, the tendency of microbial cells to form clusters, or a non-uniform distribution of the residence time of the product in the PEF chamber.A more effective stirring of the microbial suspensions which was achieved, at a fixed field strength (18 kV/cm), either by increasing the flow rate with a single pass operation through the PEF chamber, or by operating in re-circulating mode at a constant flow rate, provided a significant increase in the effectiveness and energy efficiency of the pulse treatment.A mathematical model based on the Weibull distribution adequately described the inactivation kinetics of both microbial strains under different flow dynamic conditions.