Where physics meets chemistry:thin film deposition from reactive plasmas

Functionalising surfaces using polymeric thin films is an industrially important field. One technique for achieving nanoscale, controlled surface functionalization is plasma deposition. Plasma deposition has advantages over other surface engineering processes, including that it is solvent free, substrate and geometry independent, and the surface properties of the film can be designed by judicious choice of precursor and plasma conditions. Despite the utility of this method, the mechanisms of plasma polymer growth are generally unknown, and are usually described by chemical (i.e., radical) pathways. In this review, we aim to show that plasma physics drives the chemistry of the plasma phase, and surface-plasma interactions. For example, we show that ionic species can react in the plasma to form larger ions, and also arrive at surfaces with energies greater than 1000 kJ∙mol–1 (>10 eV) and thus facilitate surface reactions that have not been taken into account previously. Thus, improving thin film deposition processes requires an understanding of both physical and chemical processes in plasma

Comparative study of natural terpenoid precursors in reactive plasmas for thin film deposition

If plasma polymer thin films are to be synthesised from sustainable and natural precursors of chemically heterogeneous composition, it is important to understand the extent to which this composition influences the mechanism of polymerisation. To this end, a well-studied monoterpene alcohol, terpinen-4-ol, has been targeted for a comparative study with the naturally occurring mix of terpenes (viz. Melaleuca alternifolia oil) from which it is commonly distilled. Positive ion mode mass spectra of both terpinen-4-ol and M. alternifolia oil showed a decrease in disparities between the type and abundance of cationic species formed in their respective plasma environments as applied plasma power was increased. Supplementary biological assay revealed the antibacterial action of both terpinen-4-ol and M. alternifolia derived coatings with respect to S. aureus bacteria, whilst cytocompatibility was demonstrated by comparable eukaryotic cell adhesion to both coatings. Elucidating the processes occurring within the reactive plasmas can enhance the economics of plasma polymer deposition by permitting use of the minimum power, time and precursor pre-processing required to control the extent of monomer fragmentation and fabricate a film of the desired thickness and functionality

Cell sheets in cell therapies

This review aims to provide a broad introduction to the use of cell sheets and the role of materials in the delivery of cell sheets to patients within a clinical setting. Traditionally, cells sheets have been, and currently are, fabricated using established and accepted cell culture methods within standard formats (e.g., petri dishes) utilizing biological substrates. Synthetic surfaces provide a far more versatile system for culturing and delivering cell sheets. This has the potential to positively affect quality, and efficient, localized cell delivery has a significant impact on patient outcome and on the overall cost of goods. We highlight current applications of these advanced carriers and future applications of these surfaces and cell sheets with an emphasis both on clinical use and regulatory requirements

An international working group consensus report for the prioritization of molecular biomarkers for Ewing sarcoma

The advent of dose intensified interval compressed therapy has improved event-free survival for patients with localized Ewing sarcoma (EwS) to 78% at 5 years. However, nearly a quarter of patients with localized tumors and 60-80% of patients with metastatic tumors suffer relapse and die of disease. In addition, those who survive are often left with debilitating late effects. Clinical features aside from stage have proven inadequate to meaningfully classify patients for risk-stratified therapy. Therefore, there is a critical need to develop approaches to risk stratify patients with EwS based on molecular features. Over the past decade, new technology has enabled the study of multiple molecular biomarkers in EwS. Preliminary evidence requiring validation supports copy number changes, and loss of function mutations in tumor suppressor genes as biomarkers of outcome in EwS. Initial studies of circulating tumor DNA demonstrated that diagnostic ctDNA burden and ctDNA clearance during induction are also associated with outcome. In addition, fusion partner should be a pre-requisite for enrollment on EwS clinical trials, and the fusion type and structure require further study to determine prognostic impact. These emerging biomarkers represent a new horizon in our understanding of disease risk and will enable future efforts to develop risk-adapted treatment

The Genomic Distribution and Function of Histone Variant HTZ-1 during C. elegans Embryogenesis

In all eukaryotes, histone variants are incorporated into a subset of nucleosomes to create functionally specialized regions of chromatin. One such variant, H2A.Z, replaces histone H2A and is required for development and viability in all animals tested to date. However, the function of H2A.Z in development remains unclear. Here, we use ChIP-chip, genetic mutation, RNAi, and immunofluorescence microscopy to interrogate the function of H2A.Z (HTZ-1) during embryogenesis in Caenorhabditis elegans, a key model of metazoan development. We find that HTZ-1 is expressed in every cell of the developing embryo and is essential for normal development. The sites of HTZ-1 incorporation during embryogenesis reveal a genome wrought by developmental processes. HTZ-1 is incorporated upstream of 23% of C. elegans genes. While these genes tend to be required for development and occupied by RNA polymerase II, HTZ-1 incorporation does not specify a stereotypic transcription program. The data also provide evidence for unexpectedly widespread independent regulation of genes within operons during development; in 37% of operons, HTZ-1 is incorporated upstream of internally encoded genes. Fewer sites of HTZ-1 incorporation occur on the X chromosome relative to autosomes, which our data suggest is due to a paucity of developmentally important genes on X, rather than a direct function for HTZ-1 in dosage compensation. Our experiments indicate that HTZ-1 functions in establishing or maintaining an essential chromatin state at promoters regulated dynamically during C. elegans embryogenesis

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

All-sky search for continuous gravitational waves from isolated neutron stars using Advanced LIGO O2 data

© 2019 American Physical Society. We present results of an all-sky search for continuous gravitational waves (CWs), which can be produced by fast spinning neutron stars with an asymmetry around their rotation axis, using data from the second observing run of the Advanced LIGO detectors. Three different semicoherent methods are used to search in a gravitational-wave frequency band from 20 to 1922 Hz and a first frequency derivative from -1×10-8 to 2×10-9 Hz/s. None of these searches has found clear evidence for a CW signal, so upper limits on the gravitational-wave strain amplitude are calculated, which for this broad range in parameter space are the most sensitive ever achieved

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

An experimental and analytical study of an asymmetric capacitively coupled plasma used for plasma polymerization

Plasma processing is widely used to provide novel surface modifications to materials for a variety of applications. Typically, the systems used to carry out these modifications are poorly characterised. Here we describe the basics of a global model for