Applications of compressive sensing in spatial frequency domain imaging.

SIGNIFICANCE: Spatial frequency domain imaging (SFDI) is an imaging modality that projects spatially modulated light patterns to determine optical property maps for absorption and reduced scattering of biological tissue via a pixel-by-pixel data acquisition and analysis procedure. Compressive sensing (CS) is a signal processing methodology which aims to reproduce the original signal with a reduced number of measurements, addressing the pixel-wise nature of SFDI. These methodologies have been combined for complex heterogenous data in both the image detection and data analysis stage in a compressive sensing SFDI (cs-SFDI) approach, showing reduction in both the data acquisition and overall computational time. AIM: Application of CS in SFDI data acquisition and image reconstruction significantly improves data collection and image recovery time without loss of quantitative accuracy. APPROACH: cs-SFDI has been applied to an increased heterogenic sample from the AppSFDI data set (back of the hand), highlighting the increased number of CS measurements required as compared to simple phantoms to accurately obtain optical property maps. A novel application of CS to the parameter recovery stage of image analysis has also been developed and validated. RESULTS: Dimensionality reduction has been demonstrated using the increased heterogenic sample at both the acquisition and analysis stages. A data reduction of 30% for the cs-SFDI and up to 80% for the parameter recover was achieved as compared to traditional SFDI, while maintaining an error of <10 % for the recovered optical property maps. CONCLUSION: The application of data reduction through CS demonstrates additional capabilities for multi- and hyperspectral SFDI, providing advanced optical and physiological property maps.

Machine learning utilising spectral derivative data improves cellular health classification through hyperspectral infra-red spectroscopy.

The objective differentiation of facets of cellular metabolism is important for several clinical applications, including accurate definition of tumour boundaries and targeted wound debridement. To this end, spectral biomarkers to differentiate live and necrotic/apoptotic cells have been defined using in vitro methods. The delineation of different cellular states using spectroscopic methods is difficult due to the complex nature of these biological processes. Sophisticated, objective classification methods will therefore be important for such differentiation. In this study, spectral data from healthy/traumatised cell samples using hyperspectral imaging between 2500-3500 nm were collected using a portable prototype device. Machine learning algorithms, in the form of clustering, have been performed on a variety of pre-processing data types including 'raw' unprocessed, smoothed resampling, background subtracted and spectral derivative. The resulting clusters were utilised as a diagnostic tool for the assessment of cellular health and quantified using both sensitivity and specificity to compare the different analysis methods. The raw data exhibited differences for one of the three different trauma types applied, although unable to accurately cluster all the traumatised samples due to signal contamination from the chemical insult. The background subtracted and smoothed data sets reduced the accuracy further, due to the apparent removal of key spectral features which exhibit cellular health. However, the spectral derivative data-types significantly improved the accuracy of clustering compared to other data types, with both sensitivity and specificity for the background subtracted data set being >94% highlighting its utility to account for unknown signal contamination while maintaining important cellular spectral features.

Flow Cytometric Analysis of Hematopoietic Populations in Rat Bone Marrow. Impact of Trauma and Hemorrhagic Shock.

Severe injury and hemorrhagic shock (HS) result in multiple changes to hematopoietic differentiation, which contribute to the development of immunosuppression and multiple organ failure (MOF). Understanding the changes that take place during the acute injury phase may help predict which patients will develop MOF and provide potential targets for therapy. Obtaining bone marrow from humans during the acute injury phase is difficult so published data are largely derived from peripheral blood samples, which infer bone marrow changes that reflect the sustained inflammatory response. This preliminary and opportunistic study investigated leucopoietic changes in rat bone marrow 6 h following traumatic injury and HS. Terminally anesthetized male Porton Wistar rats were allocated randomly to receive a sham operation (cannulation with no injury) or femoral fracture and HS. Bone marrow cells were flushed from rat femurs and immunophenotypically stained with specific antibody panels for lymphoid (CD45R, CD127, CD90, and IgM) or myeloid (CD11b, CD45, and RP-1) lineages. Subsequently, cell populations were fluorescence-activated cell sorted for morphological assessment. Stage-specific cell populations were identified using a limited number of antibodies, and leucopoietic changes were determined 6 h following trauma and HS. Myeloid subpopulations could be identified by varying levels CD11b expression, CD45, and RP-1. Trauma and HS resulted in a significant reduction in total CD11b + myeloid cells including both immature (RP-1(-)) and mature (RP-1+) granulocytes. Multiple B-cell lymphoid subsets were identified. The total percentage of CD90+ subsets remained unchanged following trauma and HS, but there was a reduction in the numbers of maturing CD90(-) cells suggesting movement into the periphery. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.

Regenerative medicine and war: a front-line focus for UK defence.

The recent prolonged conflicts in Iraq and Afghanistan saw the advancement of deployed trauma care to a point never before seen in war. The rapid translation of lessons from combat casualty care research, facilitated by an appetite for risk, contributed to year-on-year improvements in care of the injured. These paradigms, however, can only ever halt the progression of damage. Regenerative medicine approaches, in contrast, hold a truly disruptive potential to go beyond the cessation of damage from blast or ballistic trauma, to stimulate its reversal, and to do so from a very early point following injury. The internationally distributed and, in parts austere environments in which operational medical care is delivered provide an almost unique challenge to the development and translation of regenerative medicine technologies. In parallel, however, an inherent appetite for risk means that Defence will always be an early adopter. In focusing our operational priorities for regenerative medicine, the authors conducted a review of the current research landscape in the UK and abroad and sought wide clinical opinion. Our priorities are all applicable very far forward in the patient care pathway, and are focused on three broad and currently under-researched areas, namely: (a) blood, as an engineered tissue; (b) the mechanobiology of deep tissue loss and mechanobiological approaches to regeneration, and; (c) modification of the endogenous response. In focusing on these areas, we hope to engender the development of regenerative solutions for improved functional recovery from injuries sustained in conflict.

Bacillus anthracis TIR Domain-Containing Protein Localises to Cellular Microtubule Structures and Induces Autophagy.

Toll-like receptors (TLRs) recognise invading pathogens and mediate downstream immune signalling via Toll/IL-1 receptor (TIR) domains. TIR domain proteins (Tdps) have been identified in multiple pathogenic bacteria and have recently been implicated as negative regulators of host innate immune activation. A Tdp has been identified in Bacillus anthracis, the causative agent of anthrax. Here we present the first study of this protein, designated BaTdp. Recombinantly expressed and purified BaTdp TIR domain interacted with several human TIR domains, including that of the key TLR adaptor MyD88, although BaTdp expression in cultured HEK293 cells had no effect on TLR4- or TLR2- mediated immune activation. During expression in mammalian cells, BaTdp localised to microtubular networks and caused an increase in lipidated cytosolic microtubule-associated protein 1A/1B-light chain 3 (LC3), indicative of autophagosome formation. In vivo intra-nasal infection experiments in mice showed that a BaTdp knockout strain colonised host tissue faster with higher bacterial load within 4 days post-infection compared to the wild type B. anthracis. Taken together, these findings indicate that BaTdp does not play an immune suppressive role, but rather, its absence increases virulence. BaTdp present in wild type B. anthracis plausibly interact with the infected host cell, which undergoes autophagy in self-defence.

Blast Wave Exposure to the Extremities Causes Endothelial Activation and Damage.

Extremity injury is a significant burden to those injured in explosive incidents and local ischaemia can result in poor functionality in salvaged limbs. This study examined whether blast injury to a limb resulted in a change in endothelial phenotype leading to changes to the surrounding tissue.The hind limbs of terminally anaesthetized rabbits were subjected to one of four blast exposures (high, medium, low, or no blast). Blood samples were analyzed for circulating endothelial cells pre-injury and at 1, 6, and 11 h postinjury as well as analysis for endothelial activation pre-injury and at 1, 6, and 12  h postinjury. Post-mortem tissue (12  h post-injury) was analysed for both protein and mRNA expression and also for histopathology. The high blast group had significantly elevated levels of circulating endothelial cells 6  h postinjury. This group also had significantly elevated tissue mRNA expression of IL-6, E-selection, TNF-α, HIF-1, thrombomodulin, and PDGF. There was a significant correlation between blast dose and the degree of tissue pathology (hemorrhage, neutrophil infiltrate, and oedema) with the worst scores in the high blast group. This study has demonstrated that blast injury can activate the endothelium and in some cases cause damage that in turn leads to pathological changes in the surrounding tissue. For the casualty injured by an explosion the damaging effects of hemorrhage and shock could be exacerbated by blast injury and vice versa so that even low levels of blast become damaging, all of which could affect tissue functionality and long-term outcomes.

A pre-clinical evaluation of silver, iodine and Manuka honey based dressings in a model of traumatic extremity wounds contaminated with Staphylococcus aureus.

Prevention of extremity war wound infection remains a clinical challenge. Staphylococcus aureus is the most common pathogen in delayed infection. We hypothesised that choice of wound dressings may affect bacterial burden over 7 days reflecting the current practice of delayed primary closure of wounds within this timeframe. A randomised controlled trial of 3 commercially available dressings (Inadine(®) (Johnson & Johnson, NJ, USA), Acticoat(®) (Smith & Nephew, Hull, UK), Activon Tulle (Advancis Medical, Nottingham, UK)) was conducted in a rabbit model of contaminated forelimb muscle injury. A positive control group treated with antibiotics was included. Groups were compared to a saline soaked gauze control. The primary outcome was a statistically significant reduction (p < 0.05) in tissue S. aureus at 7 days post-injury. Secondary outcome measurements included bacteraemias, observational data, whole blood determination, ELISA for plasma biomarkers, PCR array analysis of wound healing gene expression and muscle/lymph node histopathology. Antibiotic, Inadine and Acticoat groups had statistically significant lower bacterial counts (mean 7.13 [95% CI 0.00-96.31]×10(2); 1.66 [0.94-2.58]×10(5); 8.86 [0.00-53.35]×10(4)cfu/g, respectively) and Activon Tulle group had significantly higher counts (2.82 [0.98-5.61]×10(6)cfu/g) than saline soaked gauze control (7.58 [1.65-17.83]×10(5)cfu/g). There were no bacteraemias or significant differences in observational data or whole blood determination. There were no significant differences in muscle/loss or pathology and lymph node cross-sectional area or morphology. There were some significant differences between treatment groups in the plasma cytokines IL-4, TNFα and MCP-1 in comparison to the control. PCR array data demonstrated more general changes in gene expression in the muscle tissue from the Activon Tulle group than the Inadine or Acticoat dressings with a limited number of genes showing significantly altered expression compared to control. This study has demonstrated that both Acticoat(®) and Inadine(®) dressings can reduce the bacteria burden in a heavily contaminated soft tissue wound and so they may offer utility in the clinical setting particularly where surgical treatment is delayed.

Bacterial TIR-containing proteins and host innate immune system evasion.

The innate immune system provides the first line of host defence against invading pathogens. Key to upregulation of the innate immune response are Toll-like receptors (TLRs), which recognize pathogen-associated molecular patterns (PAMPs) and trigger a signaling pathway culminating in the production of inflammatory mediators. Central to this TLR signaling pathway are heterotypic protein-protein interactions mediated through Toll/interleukin-1 receptor (TIR) domains found in both the cytoplasmic regions of TLRs and adaptor proteins. Pathogenic bacteria have developed a range of ingenuous strategies to evade the host immune mechanisms. Recent work has identified a potentially novel evasion mechanism involving bacterial TIR domain proteins. Such domains have been identified in a wide range of pathogenic bacteria, and there is evidence to suggest that they interfere directly with the TLR signaling pathway and thus inhibit the activation of NF-κB. The individual TIR domains from the pathogenic bacteria Salmonella enterica serovar Enteritidis, Brucella sp, uropathogenic E. coli and Yersinia pestis have been analyzed in detail. The individual bacterial TIR domains from these pathogenic bacteria seem to differ in their modes of action and their roles in virulence. Here, we review the current state of knowledge on the possible roles and mechanisms of action of the bacterial TIR domains.

A Toll/interleukin (IL)-1 receptor domain protein from Yersinia pestis interacts with mammalian IL-1/Toll-like receptor pathways but does not play a central role in the virulence of Y. pestis in a mouse model of bubonic plague.

The Toll/interleukin (IL)-1 receptor (TIR) domain is an essential component of eukaryotic innate immune signalling pathways. Interaction between TIR domains present in Toll-like receptors and associated adaptors initiates and propagates an immune signalling cascade. Proteins containing TIR domains have also been discovered in bacteria. Studies have subsequently shown that these proteins are able to modulate mammalian immune signalling pathways dependent on TIR interactions and that this may represent an evasion strategy for bacterial pathogens. Here, we investigate a TIR domain protein from the highly virulent bacterium Yersinia pestis, the causative agent of plague. When overexpressed in vitro this protein is able to downregulate IL-1ß- and LPS-dependent signalling to NFκB and to interact with the TIR adaptor protein MyD88. This interaction is dependent on a single proline residue. However, a Y. pestis knockout mutant lacking the TIR domain protein was not attenuated in virulence in a mouse model of bubonic plague. Minor alterations in the host cytokine response to the mutant were indicated, suggesting a potential subtle role in pathogenesis. The Y. pestis mutant also showed increased auto-aggregation and reduced survival in high-salinity conditions, phenotypes which may contribute to pathogenesis or survival.

Yersinia pestis TIR-domain protein forms dimers that interact with the human adaptor protein MyD88.

Recent research has highlighted the presence of Toll/Interleukin 1 receptor (TIR)-domain proteins (Tdps) in a range of bacteria, suggested to form interactions with the human adaptor protein MyD88 and inhibit intracellular signaling from Toll-like receptors (TLRs). A Tdp has been identified in Yersinia pestis (YpTdp), a highly pathogenic bacterium responsible for plague. Expression of a number of YpTIR constructs of differing lengths (YpTIR1, S130-A285; YpTIR2, I137-I273; YpTIR3, I137-246; YpTIR4, D107-S281) as fusions with an N-terminal GB1 tag (the B1 immunoglobulin domain of Streptococcal protein G) yielded high levels of soluble protein. Subsequent purification yielded 4-6 mg/L pure, folded protein. Thrombin cleavage allowed separation of the GB1 tag from YpTIR4 resulting in folded protein after cleavage. Nuclear magnetic resonance spectroscopy, size exclusion chromatography, SDS-PAGE analysis and static light scattering all indicate that the YpTIR forms dimers. Generation of a double Cys-less mutant resulted in an unstable protein containing mainly monomers indicating the importance of disulphide bonds in dimer formation. In addition, the YpTIR constructs have been shown to interact with the human adaptor protein MyD88 using 2D NMR and GST pull down. YpTIR is an excellent candidate for further study of the mechanism of action of pathogenic bacterial Tdps.

Microbial TIR domains: not necessarily agents of subversion?

The Toll/interleukin-1 receptor (TIR) domain plays a crucial role in the mammalian innate immune response. Recently, proteins containing TIR domains have been described in bacteria and it has been suggested that these bacterial proteins are involved in subversion of the vertebrate immune system. Here we describe the distribution of TIR-domain proteins among bacteria, fungi, archaea and viruses and evaluate the subversion hypothesis in the light of our findings. We suggest that most TIR domains in bacteria have nothing to do with subverting eukaryotic cells; instead, TIR domains function simply as general purpose protein-protein interaction domains put to diverse uses.

Enhanced vaccine antigen delivery by Salmonella using antibiotic-free operator-repressor titration-based plasmid stabilisation compared to chromosomal integration.

Live attenuated bacteria provide the potential to replace traditional needle-based vaccination with an orally administered vaccine. The heterologous antigen gene is usually transformed as a multi-copy plasmid into the bacterial cell, but plasmids in live bacterial vaccine strains are often unstable, so an alternative approach is to integrate the single-copy antigen gene into the bacterial chromosome. We report a comparison between the chromosomally integrated and the plasmid-borne Bacillus anthracis protective antigen gene in live Salmonella enterica serovar Typhimurium, using the Operator-Repressor Titration (ORT) system to ensure stable plasmid maintenance. These studies demonstrate that the stabilised plasmid approach of gene expression produced greater amounts of antigenic protein, which in turn resulted in higher antibody responses and levels of protection in mice.