Comparison of manual and semi-automatic registration in augmented reality image-guided liver surgery: a clinical feasibility study.

BACKGROUND: The laparoscopic approach to liver resection may reduce morbidity and hospital stay. However, uptake has been slow due to concerns about patient safety and oncological radicality. Image guidance systems may improve patient safety by enabling 3D visualisation of critical intra- and extrahepatic structures. Current systems suffer from non-intuitive visualisation and a complicated setup process. A novel image guidance system (SmartLiver), offering augmented reality visualisation and semi-automatic registration has been developed to address these issues. A clinical feasibility study evaluated the performance and usability of SmartLiver with either manual or semi-automatic registration. METHODS: Intraoperative image guidance data were recorded and analysed in patients undergoing laparoscopic liver resection or cancer staging. Stereoscopic surface reconstruction and iterative closest point matching facilitated semi-automatic registration. The primary endpoint was defined as successful registration as determined by the operating surgeon. Secondary endpoints were system usability as assessed by a surgeon questionnaire and comparison of manual vs. semi-automatic registration accuracy. Since SmartLiver is still in development no attempt was made to evaluate its impact on perioperative outcomes. RESULTS: The primary endpoint was achieved in 16 out of 18 patients. Initially semi-automatic registration failed because the IGS could not distinguish the liver surface from surrounding structures. Implementation of a deep learning algorithm enabled the IGS to overcome this issue and facilitate semi-automatic registration. Mean registration accuracy was 10.9 ± 4.2 mm (manual) vs. 13.9 ± 4.4 mm (semi-automatic) (Mean difference - 3 mm; p = 0.158). Surgeon feedback was positive about IGS handling and improved intraoperative orientation but also highlighted the need for a simpler setup process and better integration with laparoscopic ultrasound. CONCLUSION: The technical feasibility of using SmartLiver intraoperatively has been demonstrated. With further improvements semi-automatic registration may enhance user friendliness and workflow of SmartLiver. Manual and semi-automatic registration accuracy were comparable but evaluation on a larger patient cohort is required to confirm these findings.

A directional fibre optic ultrasound transmitter based on a reduced graphene oxide and polydimethylsiloxane composite.

Strongly directional ultrasound sources are desirable for many minimally invasive applications, as they enable high-quality imaging in the presence of positioning uncertainty. All-optical ultrasound is an emerging paradigm that exhibits high frequencies, large bandwidths, and a strong miniaturisation potential. Here, we report the design, modelling, and fabrication of a highly directional fibre-optic ultrasound transmitter that uses a composite of reduced graphene oxide and polydimethylsiloxane as the optical ultrasound generator. The ultrasound transmitter, which had an outer diameter of just 630 µm, generated ultrasound with a pressure exceeding 0.4 MPa for axial distances up to 16 mm, at a large bandwidth of 24.3 MHz. The ultrasound beam exhibited low divergence, with a beam diameter ranging between 0.6 and 2.1 mm for distances between 0 and 16 mm. The presented directional optical ultrasound source is hence well-suited to high-resolution interventional imaging.

Dynamic physiological temperature and pressure sensing with phase-resolved low-coherence interferometry.

We report the development and characterisation of highly miniaturised fibre-optic sensors for simultaneous pressure and temperature measurement, and a compact interrogation system with a high sampling rate. The sensors, which have a maximum diameter of 250 µm, are based on multiple low-finesse optical cavities formed from polydimethylsiloxane (PDMS), positioned at the distal ends of optical fibres, and interrogated using phase-resolved low-coherence interferometry. At acquisition rates of 250 Hz, temperature and pressure changes of 0.0021 °C and 0.22 mmHg are detectable. An in vivo experiment demonstrated that the sensors had sufficient speed and sensitivity for monitoring dynamic physiological pressure waveforms. These sensors are ideally suited to various applications in minimally invasive surgery, where diminutive lateral dimensions, high sensitivity and low manufacturing complexities are particularly valuable.

Versatile and scalable fabrication method for laser-generated focused ultrasound transducers.

A versatile and scalable fabrication method for laser-generated focused ultrasound transducers is proposed. The method is based on stamping a coated negative mold onto polydimethylsiloxane, and it can be adapted to include different optical absorbers that are directly transferred or synthesized in situ. Transducers with a range of sizes down to 3 mm in diameter are presented, incorporating two carbonaceous (multiwalled carbon nanoparticles and candle soot nanoparticles) and one plasmonic (gold nanoparticles) optically absorbing component. The fabricated transducers operate at central frequencies in the vicinity of 10 MHz with bandwidths in the range of 15-20 MHz. A transducer with a diameter of 5 mm was found to generate a positive peak pressure greater than 35 MPa in the focal zone with a tight focal spot of 150 µm in lateral width. Ultrasound cavitation on the tip of an optical fiber was demonstrated in water for a transducer with a diameter as small as 3 mm.

Music-of-light stethoscope: a demonstration of the photoacoustic effect.

In this paper we present a system aimed at demonstrating the photoacoustic (PA) effect for educational purposes. PA imaging is a hybrid imaging modality that requires no contrast agent and has a great potential for spine and brain lesion characterisation, breast cancer and blood flow monitoring notably in the context of fetal surgery. It relies on combining light excitation with ultrasound reception. Our brief was to present and explain PA imaging in a public-friendly way suitable for a variety of ages and backgrounds. We developed a simple, accessible demonstration unit using readily available materials. We used a modulated light emitting diode (LED) torch and an electronic stethoscope. The output of a music player was used for light modulation and the chest piece of the stethoscope covered by a black tape was used as an absorbing target and an enclosed chamber. This demonstration unit was presented to the public at the Bloomsbury Festival On Light in October 2015. Our stall was visited by over 100 people of varying ages. Twenty families returned in-depth evaluation questionnaires, which show that our explanations of the photoacoustic effect were well understood. Their interest in biomedical engineering was increased.

Epidural catheter with integrated light guides for spectroscopic tissue characterization.

Epidural catheters are used to deliver anesthetics and opioids for managing pain in many clinical scenarios. Currently, epidural catheter insertion is performed without information about the tissues that are directly ahead of the catheter. As a result, the catheter can be incorrectly positioned within a blood vessel, which can cause toxicity. Recent studies have shown that optical reflectance spectroscopy could be beneficial for guiding needles that are used to insert catheters. In this study, we investigate the whether this technique could benefit the placement of catheters within the epidural space. We present a novel optical epidural catheter with integrated polymer light guides that allows for optical spectra to be acquired from tissues at the distal tip. To obtain an initial indication of the information that could be obtained, reflectance values and photon penetration depth were estimated using Monte Carlo simulations, and optical reflectance spectra were acquired during a laminectomy of a swine ex vivo. Large differences between the spectra acquired from epidural adipose tissue and from venous blood were observed. The optical catheter has the potential to provide real-time detection of intravascular catheter placement that could reduce the risk of complications.

Analysis of fumonisin contamination and the presence of Fusarium in wheat with kernel black point disease in the United States.

The ability of the fungus Fusarium proliferatum to cause kernel black point disease in wheat was previously established, but natural contamination of black point wheat with both F. proliferatum and fumonisin mycotoxins has not been studied in the United States. Low levels of fumonisins were detected in nine of 43 wheat samples with kernel black point disease that were obtained from across the United States. A subset of samples was contaminated with F. proliferatum as well as with F. fujikuroi, F. nygamai, F. thapsinum and F. verticillioides, species closely related to F. proliferatum and morphologically similar to it in that they produce chains of asexual spores, or conidia. Nevertheless, of conidial chain-forming fusaria isolated from symptomatic wheat, F. proliferatum dominated. In greenhouse tests, isolates of F. proliferatum and the other species recovered from wheat samples were able to cause symptoms of kernel black point and, in some cases, low levels of fumonisin contamination of wheat. These data add to the understanding of the risk of fumonisin contamination of wheat and the potential for Fusarium species to cause kernel black point disease and fumonisin contamination of wheat. Further, the results of this study indicate that while US-grown wheat can sporadically be contaminated by fumonisins, the natural contamination levels seem to be low. The observations made provide evidence that fumonisins are not likely to be a factor contributing to the ability of Fusarium to cause kernel black point disease.

Preliminary evaluation of noninvasive microscopic imaging techniques for the study of vocal fold development.

Understanding pediatric voice development and laryngeal pathology is predicated on a detailed knowledge of the microanatomy of the layered structure of the vocal fold. Our current knowledge of this microanatomy and its temporal evolution is limited by the lack of pediatric specimen availability. By providing the capability to image pediatric vocal folds in vivo, a noninvasive microscopy technique could greatly expand the existing database of pediatric laryngeal microanatomy and could furthermore make longitudinal studies possible. A variety of natural-contrast optical imaging technologies, including optical frequency domain imaging (OFDI), full-field optical coherence microscopy (FF-OCM), and spectrally encoded confocal microscopy (SECM) have been recently developed for noninvasive diagnosis in adult patients. In this paper, we demonstrate the potential of these three techniques for laryngeal investigation by obtaining images of excised porcine vocal fold samples. In our study, OFDI allowed visualization of the vocal fold architecture deep within the tissue, from the superficial mucosa to the vocalis muscle. The micron-level resolution of SECM allowed investigation of cells and extracellular matrix fibrils from the superficial mucosa to the intermediate layer of the lamina propria (LP) (350 microm penetration depth). The large field of view (up to 700 microm), penetration depth (up to 500 microm), and resolution (2x2x1microm [XxYxZ]) of FF-OCM enabled comprehensive three-dimensional evaluation of the layered structure of the LP. Our results suggest that these techniques provide important and complementary cellular and structural information, which may be useful for investigating pediatric vocal fold maturation in vivo.

High-speed polarization sensitive optical frequency domain imaging with frequency multiplexing.

Polarization sensitive optical coherence tomography (PS-OCT) provides a cross-sectional image of birefringence in biological samples that is complementary in many applications to the standard reflectance-based image. Recent ex vivo studies have demonstrated that birefringence mapping enables the characterization of collagen and smooth muscle concentration and distribution in vascular tissues. Instruments capable of applying these measurements percutaneously in vivo may provide new insights into coronary atherosclerosis and acute myocardial infarction. We have developed a polarization sensitive optical frequency domain imaging (PS-OFDI) system that enables high-speed intravascular birefringence imaging through a fiber-optic catheter. The novel design of this system utilizes frequency multiplexing to simultaneously measure reflectance of two incident polarization states, overcoming concerns regarding temporal variations of the catheter fiber birefringence and spatial variations in the birefringence of the sample. We demonstrate circular cross-sectional birefringence imaging of a human coronary artery ex vivo through a flexible fiber-optic catheter with an A-line rate of 62 kHz and a ranging depth of 6.2 mm.

Increased ranging depth in optical frequency domain imaging by frequency encoding.

A technique for increasing the ranging depth in optical frequency domain imaging utilizing frequency encoding is presented. Ranging depth is enhanced by using two interferometer reference arms with different path lengths and independent modulation frequencies (25 and 50 MHz). With this configuration, the sensitivity decreases by 6 dB over a depth range of 7 mm, approximately a threefold improvement over the conventional optical frequency domain imaging technique. We demonstrate that the reference arm frequency separation, tuning speed, center wavelength, and instantaneous coherence length determine the signal-to-cross-talk ratio.

Wheat kernel black point and fumonisin contamination by Fusarium proliferatum.

Fusarium proliferatum is a major cause of maize ear rot and fumonisin contamination and also can cause wheat kernel black point disease. The primary objective of this study was to determine whether nine F. proliferatum strains from wheat from Nepal can cause black point and fumonisin contamination in wheat kernels. For comparison, the study included three Fusarium strains from US maize. In test 1, all the strains but one produced significant symptoms of kernel black point; two strains decreased kernel yield; and four strains contaminated kernels with fumonisins B(1), B(2) and B(3) as determined by liquid chromatography-mass spectroscopy. Strain Ggm202 from Nepal, which produced the highest levels of fumonisins (mean = 49 microg g(-1)) on five wheat cultivars in test 1, was confirmed to produce fumonisins (mean = 38 microg g(-1)) on two cultivars in test 2. The data indicate a potential for fumonisin contamination of wheat infected with F. proliferatum.

Molecular biology of Fusarium mycotoxins.

As the 20th century ended, Fusarium mycotoxicology entered the age of genomics. With complete genomes of Fusarium graminearum and F. verticillioides and several Fusarium gene expression sequence databases on hand, researchers worldwide are working at a rapid pace to identify mycotoxin biosynthetic and regulatory genes. Seven classes of mycotoxin biosynthetic genes or gene clusters have been identified in Fusarium to date; four are polyketide synthase gene clusters for equisetin, fumonisins, fusarins, and zearalenones. Other Fusarium mycotoxin biosynthetic genes include a terpene cyclase gene cluster for trichothecenes, a cyclic peptide synthetase for enniatins, and a cytochrome P450 for butenolide. From the perspective of the United States Department of Agriculture, the ultimate goal of research on Fusarium molecular biology is to reduce mycotoxins in cereal grains. With this goal in mind, efforts have focused on identifying aspects of mycotoxin biosynthesis and regulation that can be exploited for mycotoxin control. New information on fungal and plant genomes and gene expression will continue to provide information on genes important for fungal-plant interactions and to facilitate the development of targeted approaches for breeding and engineering crops for resistance to Fusarium infection and mycotoxin contamination.

Estimation of the scattering coefficients of turbid media using angle-resolved optical frequency-domain imaging.

Noninvasive measurements of the scattering coefficients of optically turbid media using angle-resolved optical frequency-domain imaging (OFDI) are demonstrated. It is shown that, by incoherently averaging OFDI reflectance signals acquired at different backscattering angles, speckle noise is reduced, allowing scattering coefficients to be extracted from a single A-line with much higher accuracy than with measurements from conventional OFDI and optical coherence tomography systems. Modeling speckle as a random phasor sum, the relationship between the measurement accuracy and the number of compounded angles is derived. The sensitivity analysis is validated with measurements from a tissue phantom.

Complete genetic linkage maps from an interspecific cross between Fusarium circinatum and Fusarium subglutinans.

The Gibberella fujikuroi complex includes many plant pathogens of agricultural crops and trees, all of which have anamorphs assigned to the genus Fusarium. In this study, an interspecific hybrid cross between Gibberella circinata and Gibberella subglutinans was used to compile a genetic linkage map. A framework map was constructed using a total of 578 AFLP markers together with the mating type (MAT-1 and MAT-2) genes and the histone (H3) gene. Twelve major linkage groups were identified (n=12). Fifty percent of the markers showed significant deviation from the expected 1:1 transmission ratio in a haploid F(1) cross (P <0.05). The transmission of the markers on the linkage map was biased towards alleles of the G. subglutinans parent, with an estimated 60% of the genome of F(1) individuals contributed by this parent. This map will serve as a powerful tool to study the genetic architecture of interspecific differentiation and pathogenicity in the two parental genomes.

A novel gene cluster in Fusarium graminearum contains a gene that contributes to butenolide synthesis.

The development of expressed sequence tag (EST) databases, directed transformation and a sequenced genome has facilitated the functional analysis of Fusarium graminearum genes. Extensive analysis of 10,397 ESTs, derived from thirteen cDNA libraries of F. graminearum grown under diverse conditions, identified a novel cluster of eight genes (gene loci fg08077-fg08084) located within a 17kb region of genomic sequence contig 1.324. The expression of these genes is concomitantly up-regulated under growth conditions that promote mycotoxin production. Gene disruption and add-back experiments followed by metabolite analysis of the transformants indicated that one of the genes, fg08079, is involved in butenolide synthesis. The mycotoxin butenolide is produced by several Fusarium species and has been suggested, but not proven, to be associated with tall fescue toxicoses in grazing cattle. This is the first report of the identification of a gene involved in the biosynthetic pathway of butenolide.

Angle-resolved optical coherence tomography with sequential angular selectivity for speckle reduction.

We present a novel method for rapidly acquiring optical coherence tomography (OCT) images at multiple backscattering angles. By angularly compounding these images, high levels of speckle reduction were achieved. Signal-to-noise ratio (SNR) improvements of 3.4 dB were obtained from a homogeneous tissue phantom, which was in good agreement with the predictions of a statistical model of speckle that incorporated the optical parameters of the imaging system. In addition, the fast acquisition rate of the system (10 kHz A-line repetition rate) allowed angular compounding to be performed in vivo without significant motion artifacts. Speckle-reduced OCT images of human dermis show greatly improved delineation of tissue microstructure.

Biosynthesis ofFusarium mycotoxins and genomics ofFusarium verticillioides.

Analyses of mycotoxin biosynthetic genes inFusarium indicate that interspecies variation in trichothecene structure can result from differences in gene function and interspecies variation in fumonisin production/non-production can result from differences in the presence/absence of genes. Such variation is not always correlated with phylogenetic relationships of species as determined by sequencing primary metabolic genes; distantly related species can share the same mycotoxin biosynthetic genotype and resulting phenotype, while more closely related species can differ. These findings provide further evidence that the evolution of mycotoxin biosynthesis inFusarium has not always been congruent with the evolution of species.

Mycotoxins in developing countries: A case study of maize in Nepal.

Maize (Zea mays) is an important food crop in the foothills of the Nepal Himalaya Mountains. Surveys have found that maize in Nepal is contaminated withFusarium species, mainlyF. verticillioides andF. proliferatum, which produce fumonisins, andF. graminearum, which produces trichothecenes, mainly nivalenol and 4-deoxynivalenol. Maize from smallholder farms and markets is often contaminated with fumonisins and trichothecenes above 1000 ng/g, a level of concern for human health. These mycotoxins were not eliminated by traditional fermentation for producing maize beer, but Nepalese women were able to detoxify contaminated maize by hand-sorting visibly disease kernels. An integrated approach to reduce mycotoxins risks in maize in Nepal and other developing countries should include plant breeding to produce ear rot resistant cultivars, along with education in mycotoxins risks and in agricultural and grain storage practices to reduce mycotoxin contamination.

Speckle Reduction in OCT using Massively-Parallel Detection and Frequency-Domain Ranging.

Speckle noise significantly limits the information content provided by coherent optical imaging methods such as optical coherence tomography and its recent derivative, optical frequency-domain imaging (OFDI). In this paper, we demonstrate a novel OFDI system that simultaneously acquires hundreds of angularly resolved images, which can be compounded to reduce speckle noise. The system comprises an InGaAs line-scan camera and an interferometer, configured so that the elements of the detector array simultaneously capture light spanning a backscattering angular range of 32 degrees. On successive read-outs of the array, the wavelength of the laser source was stepped through a range of 130 nm centered at 1295 nm to concurrently generate 400 angle-resolved OFDI images. A theory of angle-resolved OFDI and the design equations of the system are presented. Incoherent averaging of the angle-resolved data is shown to yield substantial speckle reduction (as high as an 8 dB SNR improvement) in images of a tissue phantom and esophageal tissue ex vivo.

Tri1 in Fusarium graminearum encodes a P450 oxygenase.

Gibberella zeae (asexual state Fusarium graminearum) is a major causal agent of wheat head blight and maize ear rot in North America and is responsible for contamination of grain with deoxynivalenol and related trichothecene mycotoxins. To identify additional trichothecene biosynthetic genes, cDNA libraries were prepared from fungal cultures under trichothecene-inducing conditions in culture and in planta. A gene designated LH1 that was highly expressed under these conditions exhibited only moderate (59%) similarity to known trichothecene biosynthetic cytochrome P450s. To determine the function of LH1, gene disruptants were produced and assessed for trichothecene production. Gene disruptants no longer produced 15-acetyldeoxynivalenol, which is oxygenated at carbon 7 (C-7) and C-8, but rather accumulated calonectrin and 3-deacetylcalonectrin, which are not oxygenated at either C-7 or C-8. These results indicate that gene LH1 encodes a cytochrome P450 responsible for oxygenation at one or both of these positions. Despite the relatively low level of DNA and amino acid sequence similarity between the two genes, LH1 from G. zeae is the probable homologue of Tri1, which encodes a cytochrome P450 required for C-8 oxygenation in F. sporotrichioides.