Translational challenges and opportunities in biofilm science: a BRIEF for the future.

Biofilms are increasingly recognised as a critical global issue in a multitude of industries impacting health, food and water security, marine sector, and industrial processes resulting in estimated economic cost of $5 trillion USD annually. A major barrier to the translation of biofilm science is the gap between industrial practices and academic research across the biofilms field. Therefore, there is an urgent need for biofilm research to notice and react to industrially relevant issues to achieve transferable outputs. Regulatory frameworks necessarily bridge gaps between different players, but require a clear, science-driven non-biased underpinning to successfully translate research. Here we introduce a 2-dimensional framework, termed the Biofilm Research-Industrial Engagement Framework (BRIEF) for classifying existing biofilm technologies according to their level of scientific insight, including the understanding of the underlying biofilm system, and their industrial utility accounting for current industrial practices. We evidence the BRIEF with three case studies of biofilm science across healthcare, food & agriculture, and wastewater sectors highlighting the multifaceted issues around the effective translation of biofilm research. Based on these studies, we introduce some advisory guidelines to enhance the translational impact of future research.

Wet-chemical etching of atom probe tips for artefact free analyses of nanoscaled semiconductor structures.

We introduce an innovative specimen preparation method employing the selectivity of a wet-chemical etching step to improve data quality and success rates in the atom probe analysis of contemporary semiconductor devices. Firstly, on the example of an SiGe fin embedded in SiO2 we demonstrate how the selective removal of SiO2 from the final APT specimen significantly improves accuracy and reliability of the reconstructed data. With the oxide removal, we eliminate the origin of shape artefacts, i.e. the formation of a non-hemispherical tip shape, that are typically observed in the reconstructed volume of complex systems. Secondly, using the same approach, we increase success rates to ∼90% for the damage-free, 3D site-specific localization of short (250 nm), vertical Si nanowires at the specimen apex. The impact of the abrupt emitter radius change that is introduced by this specimen preparation method is evaluated as being minor using field evaporation simulation and comparison of different reconstruction schemes. The Ge content within the SiGe fin as well as the 3D boron distribution in the Si NW as resolved by atom probe analysis are in good agreement with TEM/EDS and ToF-SIMS analysis, respectively.

Si1-x Ge x /Si Interface Profiles Measured to Sub-Nanometer Precision Using uleSIMS Energy Sequencing.

The utility of energy sequencing for extracting an accurate matrix level interface profile using ultra-low energy SIMS (uleSIMS) is reported. Normally incident O2 (+) over an energy range of 0.25-2.5 keV were used to probe the interface between Si0.73Ge0.27/Si, which was also studied using high angle annular dark field scanning transmission electron microscopy (HAADF-STEM). All the SIMS profiles were linearized by taking the well understood matrix effects on ion yield and erosion rate into account. A method based on simultaneous fitting of the SIMS profiles measured at different energies is presented, which allows the intrinsic sample profile to be determined to sub-nanometer precision. Excellent agreement was found between the directly imaged HAADF-STEM interface and that derived from SIMS. Graphical Abstract ᅟ.

The journey to femtosecond laser-assisted cataract surgery: new beginnings or a false dawn?

Femtosecond laser-assisted cataract surgery (FLACS) represents a potential paradigm shift in cataract surgery, but it is not without controversy. Advocates of the technology herald FLACS as a revolution that promises superior outcomes and an improved safety profile for patients. Conversely, detractors point to the large financial costs involved and claim that similar results are achievable with conventional small-incision phacoemulsification. This review provides a balanced and comprehensive account of the development of FLACS since its inception. It explains the physiology and mechanics underlying the technology, and critically reviews the outcomes and implications of initial studies. The benefits and limitations of using femtosecond laser accuracy to create corneal incisions, anterior capsulotomy, and lens fragmentation are explored, with reference to the main platforms, which currently offer FLACS. Economic considerations are discussed, in addition to the practicalities associated with the implementation of FLACS in a healthcare setting. The influence on surgical training and skills is considered and possible future applications of the technology introduced. While in its infancy, FLACS sets out the exciting possibility of a new level of precision in cataract surgery. However, further work in the form of large scale, phase 3 randomised controlled trials are required to demonstrate whether its theoretical benefits are significant in practice and worthy of the necessary huge financial investment and system overhaul. Whether it gains widespread acceptance is likely to be influenced by a complex interplay of scientific and socio-economic factors in years to come.

Giant reduction of InN surface electron accumulation: compensation of surface donors by Mg dopants.

Extreme electron accumulation with sheet density greater than 10(13) cm(-2) is almost universally present at the surface of indium nitride (InN). Here, x-ray photoemission spectroscopy and secondary ion mass spectrometry are used to show that the surface Fermi level decreases as the Mg concentration increases, with the sheet electron density falling to below 10(8) cm(-2). Surface space-charge calculations indicate that the lowering of the surface Fermi level increases the density of unoccupied donor-type surface states and that these are largely compensated by Mg acceptors in the near-surface hole depletion region rather than by accumulated electrons. This is a significant step towards the realization of InN-based optoelectronic devices.

Accurate ultra-low-energy secondary ion mass spectrometry analysis of wide bandgap GaN/In(x)Ga(1-x)N structures using optical conductivity enhancement.

Ultra-low-energy secondary ion mass spectrometry has been used to undertake a structural analysis of GaN-In(x)Ga(1-x)N (x approximately 0.25) quantum wells used in optoelectronic devices. The high resistivity of intrinsic GaN-In(x)Ga(1-x)N restricts the necessary electrical path between the analyzed area and the instrument ground potential resulting in surface charge accumulation. Consequently, unstable and unrepresentative depth profiles tend to be produced. A technique known as optical conductivity enhancement (OCE) has been used during depth profiling to reduce the material resistivity. This creates an electrical path between the sample and holder, eliminating charge build up and resulting in accurate depth profiles.

A validated model of calf compression and deep vessel collapse during external cuff inflation.

This paper presents a validated model of calf compression with an external pressure cuff as used for deep vein thrombosis. Magnetic resonance (MR) images of calf geometry were used to generate subject-specific finite-element (FE) models of the calf cross section. Ultrasound images of deep vessel collapse obtained through a water-filled cuff were used to validate model behavior. Calf/cuff pressure interface measurements were applied to the FE model and the resulting tissue deformation was compared with MR image in normal volunteers (three females, four males, age range 20-55) using two distinct cuffs. MR observations and the model results showed good qualitative agreement. A similar reduction in cross-sectional area of the posterior tibial veins was obtained under both symmetric compression (89%) and asymmetric compression (81%), but greater compression of the anterior tibial veins was achieved with symmetric compression. The need to account for the effective compressibility of the calf tissue suggests that external measurements of the calf tissue deformation will not accurately predict deep vessel collapse. These results have implications for the modification of venous haemodynamics by such systems and could help to improve cuff design.

Intermittent pneumatic compression - systems and applications.

PRIMARY OBJECTIVE: The purpose of this review is to survey the types of intermittent pneumatic compression systems that are currently used, and their medical applications. MAIN OUTCOMES AND RESULTS: Intermittent compression devices have taken many forms since their initial development, but medical justifications for particular properties of cuff design, compression timing and pressure are often weak. Intermittent compression is well established, and effective in the prevention of deep vein thrombosis (DVT) and reduction of lymphoedema. Other therapeutic applications, such as in chronic arterial and venous disease, are not yet as well accepted, but may become more popular as published evidence increases. CONCLUSIONS: The full potential of intermittent pneumatic compression has probably not yet been realized, and requires better quality research. System design must follow physiological evidence, and while complexity in that design may allow greater therapeutic flexibility, it may incur greater financial cost, difficulty in use, and in the prevention of DVT in particular may be unnecessary.

Stem cells in the hair follicle and interfollicular epidermis of mice following topical application of fluocinolone acetonide.

One of the major adverse reactions to chronic treatment with glucocorticoids is cutaneous atrophy followed by resistance to continued treatment. Chebotaev et al. report that keratinocytes from both the hair follicle bulge and interfollicular epidermis of mice express the glucocorticoid receptor. Unexpectedly, however, bulge keratinocytes appeared to develop resistance more slowly than interfollicular keratinocytes, and appeared not to contribute to the repair of the atrophic epithelium.

SPINE bioinformatics and data-management aspects of high-throughput structural biology.

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high-throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high-throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high-throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.

The effect of intermittent pneumatic compression on the bone uptake of (99m)Tc-labelled methylene diphosphonate in the lower limb.

INTRODUCTION: Venous compression of the lower limbs will obstruct outflow through the deep and superficial veins, yet inflow will continue, without continual swelling of the limb. It is hypothesised that venous channels in the long bones act as collateral channels to restore outflow, and therefore general blood flow through bone will increase. Such a hemodynamic change should affect the uptake of radiopharmaceuticals by the bone, though uptake changes in themselves would not definitely indicate flow changes. The purpose of this study, therefore, was to determine whether bone uptake in the lower limb is affected by intermittent venous compression, irrespective of the mechanism involved. MATERIALS AND METHODS: The effect of intermittent pneumatic compression of the thigh and calf on the uptake of (99m)Tc-methylene diphosphonate (MDP) was studied in 24 patients. All were undergoing routine bone imaging for medical conditions that were not focused on their lower limbs, and received 1 h of the therapy at 60 mmHg on one limb only, after injection of the radiopharmaceutical. Three hours after injection the relative difference in uptake (net counts per pixel) between the two limbs was calculated. The standard imaging protocol was otherwise unchanged. RESULTS: The median differences in uptake in the intermittently compressed limb compared with the contralateral limb were +7.6% (interquartile range +3.9% to +16.0%, p<0.0005 [Wilcoxon]) for the anterior aspect of the femur; +11.7% (interquartile range +4.3% to +22.2%, p<0.0005) posterior, femur; +10.5% (interquartile range +6.5% to +13.8%, p<0.0005) anterior, tibia; +10.6% (interquartile range +5.5% to +17.6%, p<0.0005) posterior, tibia. CONCLUSION: Intermittent pneumatic compression clearly and significantly increased the uptake of (99m)Tc-MDP in long bones. These data are consistent with increases in blood flow through bone, though a direct mechanical influence on the bone cannot be excluded. This effect should be given consideration during routine therapeutic and thromboprophylactic use of intermittent compression, and if the mechanism of the uptake changes can be established, their possible clinical uses should be investigated.

Systemic haemostasis after intermittent pneumatic compression. Clues for the investigation of DVT prophylaxis and travellers thrombosis.

Intermittent pneumatic compression (IPC) is known to provide effective prophylaxis against post-surgical deep-vein thrombosis (DVT), and other procedures based on reducing venous stasis have been promoted recently to minimize the risk of thromboembolism after long-haul travel ('travellers thrombosis'). This study sought to measure the effects of IPC on systemic haemostasis, which are currently disputed. IPC was applied for 120 min on 21 male, non-smoking volunteers ranging in age from 19 to 47 years. IPC promoted a significant increase in global fibrinolytic potential. Levels of urokinase plasminogen activator activity (uPA) measured using an amidolytic assay were raised after IPC. However, enzyme-linked immunosorbent assays (ELISA) of uPA antigen, and the activities of tissue plasminogen activator (tPA) and plasminogen activator inhibitor 1 (PAI-1) were not statistically different from those in control experiments. IPC led to highly significant falls in factor VIIa, associated with increased levels of tissue factor pathway inhibitor (TFPI). IPC enhances fibrinolysis and suppresses procoagulant activation. Measurements of specific fibrinolytic components do not reflect overall fibrinolytic activity and are highly dependent on the method of assay. The results provide important clues for detailed studies of the effects of haemodynamics on systemic haemostasis.

Genetic regulation of mouse stem cells: identification of two keratinocyte stem cell regulatory loci.

It is well documented that the bulge of hair follicle is a 'niche' for a significant population of mouse keratinocyte stem cells, and 95% of rodent clonogenic keratinocytes originate from the bulge region. The ability to form colonies in vitro is a well recognized test for keratinocyte stem cells. We analyzed the epidermis of seven mouse strains and their segregating crosses [(BALB/c x C57BL/6)F1; (BALB/c x CB6F1); (C57BL/ 6 x CB6F1); (CBF1 x CBF1)F2] for their clonogenic activity in vitro. We found that keratinocyte colony (KC) number is a new quantitative multigenic trait. The analysis of KC size in two parental strains (C57BL/6 and BALB/c), the F1 generation and the segregating crosses demonstrated that the size of KC is a quantitative complex trait also. We determined that mouse epidermis has at least two subpopulations of keratinocytes that gave small (< 2 mm2) and large (> 2 mm2) colonies. The differences in the number of small and large colonies between parental strains (C57BL/6, BALB/c) were significant (P < 0.01). A genome-wide scan of the intercross and the two backcrosses maps the number of small KC to the central region of mouse Chromosome 9 (genomewide P value = 0.01). We define this locus as Ksc1. The proximal region of chromosome 4 is associated with the high number of large KC. We defined this locus as Ksc2. We found that Ksc1 and minor loci on chromosomes 6 and 7 map close, if not equal to, loci associated with mouse skin carcinogenesis. We conclude that mouse epidermis has at least two subpopulations of clonogenic keratinocyte stem cells that are regulated by different genes. We suggest that keratinocyte stem cells responsible for small colonies may play a major role in the regulation of resistance or sensitivity to skin carcinogenesis. Investigation of the genes regulating the stem cell number should provide new insight into the mechanisms of skin carcinogenesis, and should help to develop new approaches for therapies not only against active proliferating tumor cells but also quiescent tumor stem cells.

Lymph node metastasis from a primary skin carcinoid tumour.

Carcinoid tumours are uncommon neuroendocrine neoplasms that may be found anywhere in the body but are most commonly seen in the gastro-intestinal and respiratory tracts. Metastasis to the skin occurs in a small proportion of these but primary cutaneous carcinoid tumours are exceedingly rare. There have been five previous cases of primary carcinoid tumours occurring in the skin. To our knowledge, this is the first report of metastasis from a primary cutaneous carcinoid tumour.

Selective expression of prion protein in peripheral tissues of the adult mouse.

The level of expression of normal cellular prion protein, PrP(c) (cellular prion protein), controls both the rate and the route of neuroinvasive infection, from peripheral entry portal to the CNS. Paradoxically, an overview of the distribution of PrP(c) within tissues outside the CNS is lacking. We have used novel antibodies that recognise cellular prion protein in glutaraldehyde-fixed tissue (in order to optimise immunohistochemical labelling of this conformationally labile protein), in combination with in situ hybridisation, to examine the expression of PrP(c) in peripheral tissues of the adult mouse. We found that although prion protein is expressed in many tissues, it is expressed at high levels only in discrete subpopulations of cells. Prominent amongst these are elements of the "hardwired neuroimmune network" that integrate the body's immune defence and neuroendocrine systems under CNS control. These prion protein-expressing elements include small diameter afferent nerves in the skin and the lamina propria of the aerodigestive tract, sympathetic ganglia and nerves, antigen presenting and processing cells (both follicular and non-follicular dendritic cells) and sub-populations of lymphocytes particularly in skin, gut- and bronchus-associated lymphoid tissues. Prion protein is also expressed in the parasympathetic and enteric nervous systems, in the dispersed neuroendocrine system, and in peripheral nervous system axons and their associated Schwann cells. This selective expression of cellular prion protein provides a variety of alternative routes for the propagation and transport of prion infection entering from peripheral sites, either naturally (via the aerodigestive tract or abraded skin) or experimentally (by intraperitoneal injection) to the brain. Key regulatory cells that express prion protein, and in particular enteroendocrine cells in the mucosal wall of the gut, and dendritic cells that convey pathogens from epithelial layers to secondary lymphoid organs, may be particularly important in the transmission of infection in the periphery.

A marked disparity between the expression of prion protein and its message by neurones of the CNS.

Expression of the normal cellular form of prion protein is both necessary and rate-limiting in the spread of prion disease, yet its cellular expression in vivo is poorly understood. To optimise immunohistochemical labelling of this protein in mouse brain, we have developed novel antibodies that recognise cellular prion protein in glutaraldehyde-fixed tissue. Expression was found to be predominantly neuronal, and to differ between different classes of neurone. Thus, neurones immunoreactive for GABA expressed very high levels of normal prion protein; most projection neurones expressed much lower levels, particularly on their axons in the major fibre tracts, and some neurones (e.g. those positive for dopamine) displayed no detectable prion protein. In marked contrast, all neurones, even those that were immunonegative, expressed high levels of message for prion protein, shown by non-radioactive in situ hybridisation. Glia expressed very low levels of message, and undetectable levels of prion protein. We conclude that the steady-state level of prion protein, which differs so markedly between different neuronal types, is primarily controlled post-transcriptionally, possibly by differences in protein trafficking or degradation. These marked differences in the way different neurones produce and/or degrade their normal cellular prion protein may influence the selective spread and neurotoxic targeting of prion diseases within the CNS.

A job well done.

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