Assessment of CBCT-based synthetic CT generation accuracy for adaptive radiotherapy planning.

PURPOSE: Cone-beam CT (CBCT)-based synthetic CT (sCT) dose calculation has the potential to make the adaptive radiotherapy (ART) pathway more efficient while removing subjectivity. This study assessed four sCT generation methods using 15 head-and-neck rescanned ART patients. Each patient's planning CT (pCT), rescan CT (rCT), and CBCT post-rCT was acquired with the CBCT deformably registered to the rCT (dCBCT). METHODS: The four methods investigated were as follows: method 1-deformably registering the pCT to the dCBCT. Method 2-assigning six mass density values to the dCBCT. Method 3-iteratively removing artifacts and correcting the dCBCT Hounsfield units (HU). Method 4-using a cycle general adversarial network machine learning model (trained with 45 paired pCT and CBCT). Treatment plans were created on the rCT and recalculated on each sCT. Planning target volume (PTV) and organ-at-risk (OAR) structures were contoured by clinicians on the rCT (high-dose PTV, low-dose PTV, spinal canal, larynx, brainstem, and parotids) to allow the assessment of dose-volume histogram statistics at clinically relevant points. RESULTS: The HU mean absolute error (MAE) and minimum dose gamma index pass rate (2%/2 mm) were calculated, and the generation time was measured for 15 patients using the rCT as the comparator. For methods 1-4 the MAE, gamma index analysis, and generation time were as follows: 59.7 HU, 100.0%, and 143 s; 164.2 HU, 95.2%, and 232 s; 75.7 HU, 99.9%, and 153 s; and 79.4 HU, 99.8%, and 112 s, respectively. Dose differences for PTVs and OARs were all <0.3 Gy except for method 2 (<0.5 Gy). CONCLUSION: All methods were considered clinically viable. The machine learning method was found to be most suitable for clinical implementation due to its high dosimetric accuracy and short generation time. Further investigation is required for larger anatomical changes between the CBCT and pCT and for other anatomical sites.

Outcomes following common bile duct exploration versus endoscopic stone extraction before, during and after laparoscopic cholecystectomy for patients with common bile duct stones.

BACKGROUND: Laparoscopic common bile duct exploration (LCBDE) and endoscopic retrograde cholangiopancreatography (ERCP) are two methods of retrieving common bile duct (CBD) stones. The best method for CBD stone removal is debatable. The aim of this study was to compare outcomes following LCBDE and/or ERCP, including laparoscopic cholecystectomy. METHODS: Data were collected retrospectively for patients undergoing LCBDE and/or ERCP at a single centre from 2008 to 2018. Patients were grouped by intention-to-treat (single-stage LCBDE, pre-operative-, intra-operative-, or post-operative ERCP) and eventual plan (surgical or endoscopic). Outcomes included complication rates (minor Clavien-Dindo 1/2, major Clavien-Dindo 3/4, non-biliary complications) and mortality. RESULTS: Of 671 patients, 578 patients received LCBDE and 93 patients received ERCP as primary care. Endoscopic clearance had significantly higher complications and mortality compared to surgical clearance. On an intention-to-treat basis LCBDE had the lowest minor-, major- and non-biliary complications, and mortality (5.2%, 6.1%, 2.9% and 0.5%, respectively), whilst pre-operative ERCP the worst (39.6%, 27.1%, 29.2% and 8.3%, respectively) (p=<0.001). LCBDE and postERCP had similar major complications and mortality. CONCLUSION: Surgical clearance of CBD stones was potentially safer than endoscopic clearance. Pre-operative ERCP had the worst outcomes. LCBDE and postERCP are likely to have similar short-term patient outcomes.

Confinement loss of anti-resonant capillaries with curved boundaries.

A systematic analysis of the dependence of the confinement loss of an anti-resonant capillary on the curvature of the core surround is presented. The core boundary is described by circular arcs and the construction allows for a wide range of core shapes to be considered. It is found that both negative and positive curvatures substantially reduce the confinement loss relative to that of a circular anti-resonant capillary and that this effect is insensitive to the size of the core relative to the wavelength and to the properties of the glass capillary wall. In contrast, for a solid core surround there is a small increase in the confinement loss with curvature. Results of scalar and vector calculations are shown to be similar. A qualitative explanation of the results is proposed based on azimuthal confinement of the wave fields generated by the curved boundaries.

The benefit of MR-only radiotherapy treatment planning for anal and rectal cancers: A planning study.

INTRODUCTION: Limited evidence exists showing the benefit of magnetic resonance (MR)-only radiotherapy treatment planning for anal and rectal cancers. This study aims to assess the impact of MR-only planning on target volumes (TVs) and treatment plan doses to organs at risks (OARs) for anal and rectal cancers versus a computed tomography (CT)-only pathway. MATERIALS AND METHODS: Forty-six patients (29 rectum and 17 anus) undergoing preoperative or radical external beam radiotherapy received CT and T2 MR simulation. TV and OARs were delineated on CT and MR, and volumetric arc therapy treatment plans were optimized independently (53.2 Gy/28 fractions for anus, 45 Gy/25 fractions for rectum). Further treatment plans assessed gross tumor volume (GTV) dose escalation. Differences in TV volumes and OAR doses, in terms of Vx Gy (organ volume (%) receiving x dose (Gy)), were assessed. RESULTS: MR GTV and primary planning TV (PTV) volumes systematically reduced by 13 cc and 98 cc (anus) and 44 cc and 109 cc (rectum) respectively compared to CT volumes. Statistically significant OAR dose reductions versus CT were found for bladder and uterus (rectum) and bladder, penile bulb, and genitalia (anus). With GTV boosting, statistically significant dose reductions were found for sigmoid, small bowel, vagina, and penile bulb (rectum) and vagina (anus). CONCLUSION: Our findings provide evidence that the introduction of MR (whether through MR-only or CT-MR pathways) to radiotherapy treatment planning for anal and rectal cancers has the potential to improve treatments. MR-related OAR dose reductions may translate into less treatment-related toxicity for patients or greater ability to dose escalate.

Quantitative analysis of anti-resonance in single-ring, hollow-core fibres.

The dependence of the confinement loss of unjacketed and jacketed single-ring fibres on structural parameters and the wavelength is analysed with reference to an anti-resonant model for which an analytic expression for the loss is available. Provided leakage through the gaps between the cladding capillaries is suppressed, the loss of unjacketed structures follows the prediction of the analytic model closely in terms of the scaling with respect to the radius and glass thickness of the capillaries, and the ratio of the wavelength to the core radius. The absolute value of the confinement loss and its dependence on the dielectric constant differ significantly from the analytic model; these differences are discussed in terms of the negative curvature of the core-cladding boundary. The loss of jacketed structures does not follow the anti-resonant model as closely, but there is sufficient similarity to conclude that anti-resonance in the glass and air regions of the cladding is key to understanding the guidance mechanism.

Correction to: An Acute General Surgical Unit (AGSU) Negates the Impact of the Tokyo Guidelines 2018 (TG18) Diagnostic Criteria for the Treatment of Acute Cholecystitis.

The original article can be found online.

An Acute General Surgical Unit (AGSU) Negates the Impact of the Tokyo Guidelines 2018 (TG18) Diagnostic Criteria for the Treatment of Acute Cholecystitis.

PURPOSE: The Tokyo Guidelines 2018 (TG18) were developed to aid diagnosis and treatment for acute cholecystitis. The benefits of being treated in an acute general surgical unit (AGSU) include earlier diagnosis and treatment. This study aims to define the usefulness of TG18 before and after the introduction of AGSU. METHODOLOGY: Patients who underwent cholecystectomy at Northern Health were audited retrospectively and assessed for TG18 diagnostic criteria and outcomes between 1 February 2012 and 1 February 2014 (one-year pre- and post-AGSU). RESULTS: Five hundred and eighty-seven patients underwent emergency cholecystectomy with 203 (34.6%) patients having a suspected diagnosis, and 234 (39.9%) patients with a definitive diagnosis of acute cholecystitis using TG18 diagnostic criteria. After the introduction of AGSU, time from imaging to operation improved from 2.5 to 1.7 days (p = 0.012). There were more operations occurring during in-hours following AGSU implementation (75.8% vs. 62.7%, p < 0.001). Maximum pre-operative CRP of >26.6 mg/L had a higher likelihood of Clavien-Dindo complication grade 3 or 4 (OR 3.86, 95%CI 1.18-12.63, p = 0.027) compared with TG18 definitive diagnosis criteria (OR 1.50, 95%CI 0.46-4.91, p = 0.501). Surprisingly, there was a trend towards higher complications and readmissions for patients operated within 24 h, although this trend was not significant. CONCLUSION: Patients with suspected acute cholecystitis should be stratified clinically and with CRP in an AGSU with TG18 adding little value in a busy metropolitan unit.

Aspects of in vivo endotracheal tube intracuff pressure in cats.

OBJECTIVES: To determine the endotracheal tube cuff pressure produced with two inflation techniques, in two brands of endotracheal tube in cats. To determine the inspiratory pressure which produces an audible leak when the intracuff pressure is 30 cmH2O. STUDY DESIGN: Prospective, clinical, randomized study. ANIMALS: A total of 40 client-owned healthy adult cats. METHODS: Following induction of anaesthesia, endotracheal intubation was performed with a Parker Flex-Tip PFLP (Parker; n = 20) or Flexicare VentiSeal (Flexicare; n = 20) endotracheal tube. For each cat, the endotracheal tube cuff was inflated using two methods, minimum occlusive volume (MOV) and pilot balloon palpation (PBP). Intracuff pressure was recorded. Cuff pressure was then set at 30 cmH2O and the pressure within the breathing system when a manual breath first caused an audible leak was measured. RESULTS: PBP pressure was lower for Parker (36 ± 13 cmH2O) compared with Flexicare (45 ± 13 cmH2O, p = 0.048). MOV pressure was not different between tube types (56 ± 28 versus 66 ± 25 cmH2O for Parker and Flexicare, respectively, p = 0.247). MOV produced a higher pressure than PBP for Parker (56 ± 28 versus 36 ± 13 cmH2O, p = 0.001) and Flexicare (66 ± 25 versus 45 ± 13 cmH2O, p = 0.007). When intracuff pressure was set at 30 cmH2O, 95% of cats did not develop an audible leak until the inspiratory pressure was greater than 10 and 12 cmH2O for Parker and Flexicare tubes, respectively. CONCLUSIONS: PBP produced lower cuff pressures than MOV, although both techniques produced a cuff pressure above that at which mucosal blood flow is believed to be restricted. A cuff pressure of 30 cmH2O may be sufficient to prevent audible leak in most cats if respiratory pressures are kept at 10-12 cmH2O or below. CLINICAL RELEVANCE: To ensure a safe endotracheal tube cuff pressure, use of a specifically designed pressure gauge is recommended.

Defining the Diverse Cell Populations Contributing to Lignification in Arabidopsis Stems.

Many land plants evolved tall and sturdy growth habits due to specialized cells with thick lignified cell walls: tracheary elements that function in water transport and fibers that function in structural support. The objective of this study was to define how and when diverse cell populations contribute lignin precursors, monolignols, to secondary cell walls during lignification of the Arabidopsis (Arabidopsis thaliana) inflorescence stem. Previous work demonstrated that, when lignin biosynthesis is suppressed in fiber and tracheary element cells with thickened walls, fibers become lignin-depleted while vascular bundles still lignify, suggesting that nonlignifying neighboring xylem cells are contributing to lignification. In this work, we dissect the contributions of different cell types, specifically xylary parenchyma and fiber cells, to lignification of the stem using cell-type-specific promoters to either knock down an essential monolignol biosynthetic gene or to introduce novel monolignol conjugates. Analysis of either reductions in lignin in knockdown lines, or the addition of novel monolignol conjugates, directly identifies the xylary parenchyma and fiber cell populations that contribute to the stem lignification and the developmental timing at which each contribution is most important.

Identification of Cytauxzoon felis antigens via protein microarray and assessment of expression library immunization against cytauxzoonosis.

BACKGROUND: Cytauxzoonosis is a disease of felids in North America caused by the tick-transmitted apicomplexan parasite Cytauxzoon felis. Cytauxzoonosis is particularly virulent for domestic cats, but no vaccine currently exists. The parasite cannot be cultivated in vitro, presenting a significant limitation for vaccine development. METHODS: Recent sequencing of the C. felis genome has identified over 4300 putative protein-encoding genes. From this pool we constructed a protein microarray containing 673 putative C. felis proteins. This microarray was probed with sera from C. felis-infected and naïve cats to identify differentially reactive antigens which were incorporated into two expression library vaccines, one polyvalent and one monovalent. We assessed the efficacy of these vaccines to prevent of infection and/or disease in a tick-challenge model. RESULTS: Probing of the protein microarray resulted in identification of 30 differentially reactive C. felis antigens that were incorporated into the two expression library vaccines. However, expression library immunization failed to prevent infection or disease in cats challenged with C. felis. CONCLUSIONS: Protein microarray facilitated high-throughput identification of novel antigens, substantially increasing the pool of characterized C. felis antigens. These antigens should be considered for development of C. felis vaccines, diagnostics, and therapeutics.

Mode symmetry in microstructured fibres revisited.

Motivated by the recent development of hollow-core, microstructured optical fibres without a translationally-periodic cladding structure, an analysis of the symmetry-induced properties of the modes of a uniform fibre with CMv point group symmetry is presented. Modes are classified according to the irreducible representations of the longitudinal components of the electric and magnetic fields; the radial component of the electric field and azimuthal component of the magnetic field share the symmetry of the longitudinal component of the electric field, while the radial component of the magnetic field and the azimuthal component of the electric field have the same symmetry as the longitudinal magnetic field. The symmetry class of the lowest order modes in fibres with point group CMv with M from 1 to 10 is given. The work is closely related to previous analyses, but clarifies the symmetry relationship between the two orthogonal modes in a degenerate pair and how the different symmetries of the longitudinal electric and magnetic field components emerge from the governing equations.

The composition of surface wax on trichomes of Arabidopsis thaliana differs from wax on other epidermal cells.

To protect plants against biotic and abiotic stress, the waxy cuticle must coat all epidermis cells. Here, two independent approaches addressed whether cell-type-specific differences exist between wax compositions on trichomes and other epidermal cells of Arabidopsis thaliana, possibly with different protection roles. First, the total waxes from a mutant lacking trichomes (gl1) were compared to waxes from wild type and a trichome-rich mutant (cpc tcl1 etc1 etc3). In the stem wax, compounds with aliphatic chains longer than 31 carbons (derived from C32 precursors) increased in relative abundance in cpc tcl1 etc1 etc3 over gl1. Similarly, the leaf wax from the trichome-rich mutant contained higher amounts of C32+ compounds as compared to gl1. Second, leaf trichomes were isolated, and their waxes were analyzed. The wax mixtures of the trichome-rich mutant and the wild type were similar, comprising alkanes and alkenes as well as branched and unbranched primary alcohols. The direct analyses of trichome waxes confirmed that they contained relatively high concentrations of C32+ compounds, compared with the pavement cell wax inferred from analysis of gl1 leaves. Finally, the cell-type-specific wax compositions were put into perspective with expression patterns of wax biosynthesis genes in trichomes and pavement cells. Analyses of published transcriptome data (Marks et al., ) revealed that core enzymes involved in elongation of wax precursors to various carbon chain lengths are expressed differentially between epidermis cell types. By combining the chemical and gene expression data, we identified promising gene candidates involved in the formation of C32+ aliphatic chains.

Arabidopsis ketoacyl-CoA synthase 16 (KCS16) forms C36 /C38 acyl precursors for leaf trichome and pavement surface wax.

The aliphatic waxes sealing plant surfaces against environmental stress are generated by fatty acid elongase complexes, each containing a ß-ketoacyl-CoA synthase (KCS) enzyme that catalyses a crucial condensation forming a new C─C bond to extend the carbon backbone. The relatively high abundance of C35 and C37 alkanes derived from C36 and C38 acyl-CoAs in Arabidopsis leaf trichomes (relative to other epidermis cells) suggests differences in the elongation machineries of different epidermis cell types, possibly involving KCS16, a condensing enzyme expressed preferentially in trichomes. Here, KCS16 was found expressed primarily in Arabidopsis rosette leaves, flowers and siliques, and the corresponding protein was localized to the endoplasmic reticulum. The cuticular waxes on young leaves and isolated leaf trichomes of ksc16 loss-of-function mutants were depleted of C35 and C37 alkanes and alkenes, whereas expression of Arabidopsis KCS16 in yeast and ectopic overexpression in Arabidopsis resulted in accumulation of C36 and C38 fatty acid products. Taken together, our results show that KCS16 is the sole enzyme catalysing the elongation of C34 to C38 acyl-CoAs in Arabidopsis leaf trichomes and that it contributes to the formation of extra-long compounds in adjacent pavement cells.

Attenuation of model hollow-core, anti-resonant fibres.

An analytic expression is obtained for the confinement loss of model anti-resonant fibres consisting of concentric regions of air and glass. Hankel functions in the regions surrounding the air core are approximated by their asymptotic form; apart from this, results are correct to leading order in the small parameter 1/(k0rc), where rc is the core radius and k0 the free space wavenumber. The results extend and generalise previous solutions for propagation in a hollow glass tube and a thin-walled capillary. Comparison with exact numerical calculations shows that the analytic expression provides an accurate description of the loss, including its dependence on the mode, the core radius and the widths of the surrounding glass and air regions. The relevance of the results to the recent generation of hollow-core, anti-resonant photonic crystal fibres is discussed.

Spatiotemporal patterns and relationships among the diet, biochemistry, and exposure to flame retardants in an apex avian predator, the peregrine falcon.

Flame retardants (FR) are industrial chemicals and some are proven environmental contaminants that accumulate in predatory birds. Few studies have examined the influence of diet on FR profiles in nestling raptors and the possible physiological implications of such FR exposure. The objectives of this research were (1) to determine spatial patterns of ≤ 48 polybrominated diphenyl ether (PBDE) congeners and ≤ 26 non-PBDE FRs, including organophosphate esters (OPEs), in nestling peregrine falcons (Falco peregrinus) across the Canadian Great Lakes-St. Lawrence River Basin (GL-SLR; 2010) and in the eastern Canadian Arctic (2007); (2) to identify temporal changes in FR concentrations from the mid-2000s to 2010 in GL-SLR peregrine nestlings; (3) to investigate the role of diet using stable isotopes on exposure patterns of quantifiable FRs; and (4) to assess possible associations between circulating FRs and total (T) thyroxine (TT4) and triiodothyronine (TT3), tocopherol, retinol and oxidative status (isoprostanes). The summed concentrations of the top 5 PBDEs (Σ5) (BDE-47, -99, -100, -154, -153) were significantly higher in rural nestlings than urban nestlings in the GL-SLR, followed by the eastern Arctic nestlings. The PBDE congener profile of rural nestlings was dominated by BDE-99 (34‰), whereas BDE-209 (31‰) became dominant in the 2010 urban PBDE profile marking a shift since the mid-2000s. Low (ppb) concentrations of 25 novel non-PBDE FRs (e.g., 1,2-bis-(2,4,6-tribromophenoxy)ethane (BTBPE), decabromodiphenylethane (DBDPE)) were measured in the nestlings in at least one region, with the first report in peregrines of 15 novel non-PBDE FRs (e.g., 2-ethyl-1-hyxyl 2,3,4,5-tetrabromobenzoate (EHTBB), pentabromo allyl ether (PBPAE), tetrabromoethylcyclohexane (α-, ß-DBE-DBCH)) as well as of tris (2-butoxyethyl) phosphate (TBOEP) (0-7.5ng/g ww) > tris(2-chloroisopropyl) phosphate (TCIPP) (0.1-5.5ng/g ww) > tris(2-chloroethyl) phosphate (TCEP) (0.02-2.0ng/g ww) > tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) (0-1.0ng/g ww). Within the GL-SLR, the urban nestlings' diet had significantly more terrestrial sources (greater δ13C values) than the broader, more aquatic-based diet of rural peregrines. Dietary source (δ13C) was significantly associated with concentrations of Σ5PBDE, BDE-209, EHTBB, and 2,2-4,4',5,5'-hexabromobiphenyl (BB-153), with trophic level (δ15N) also positively associated with BDE-209 levels. Compared to urban nestlings, the rural nestlings had significantly lower circulating concentrations of thyroxine (TT4), triiodothyronine (TT3), a greater proportion of TT3 relative to TT4 (TT3:TT4), tocopherol and oxidative status (isoprostanes), but higher retinol levels; the most recalcitrant PBDE congener, BDE-153, in combination with low concentrations of some novel FRs, particularly octabromotrimethylphenyllindane (OBIND), may influence circulating thyroid hormones, especially TT4, and retinol levels of peregrine falcon nestlings. These associations of FR-endocrine-biochemical measures suggest possible exposure-related changes in these birds and further study is warranted.

Evaluation of High Dosages of Oral Meloxicam in American Kestrels ( Falco sparverius ).

To evaluate the toxicity of short-term high doses of meloxicam in American kestrels ( Falco sparverius ), 32 male captive-born, 1- to 4-year-old American kestrels were randomly assigned to 4 groups: 3 groups treated with meloxicam (n = 9 per group) and a control group (n = 5). Meloxicam was administered orally via feeding tube in the proventriculus at 2, 10, and 20 mg/kg every 12 hours for 7 days for the treatment groups, while the control group received saline solution. The birds were evaluated for the presence of clinical signs, abnormalities in the complete blood cell count and in the plasma biochemical panel for the 20-mg/kg group, and gross and histopathologic lesions. No clinical signs or mortality were observed in any group. No significant differences of clinical relevance were found in results of the packed cell volume, total solids, and biochemical panel, and no evidence of renal toxicity was found in the treatment or control groups. A significant correlation was found between hepatic lipidosis and meloxicam dose (P = .02). Two of 9 birds in the 20-mg/kg group developed gastric ulcers, although this result was not significant. None of the birds in the 2- and 10-mg/kg groups had similar lesions. Finally, meloxicam dosages up to 20 mg/kg did not result in nephrotoxicity in American kestrels. Further toxicologic studies to evaluate hepatotoxicity and gastrotoxicity of meloxicam in avian species are needed.

Fine structure of the Arabidopsis stem cuticle: effects of fixation and changes over development.

MAIN CONCLUSION: The Arabidopsis cuticle, as observed by electron microscopy, consists primarily of the cutin/cutan matrix. The cuticle possesses a complex substructure, which is correlated with the presence of intracuticular waxes. The plant cuticle is composed of an insoluble polyester, cutin, and organic solvent soluble cuticular waxes, which are embedded within and coat the surface of the cutin matrix. How these components are arranged in the cuticle is not well understood. The Arabidopsis cuticle is commonly understood as 'amorphous,' lacking in ultrastructural features, and is often observed as a thin (~80-100 nm) electron-dense layer on the surface of the cell wall. To examine this cuticle in more detail, we examined cuticles from both rapidly elongating and mature sections of the stem and compared the preservation of the cuticles using conventional chemical fixation methods and high-pressure freezing/freeze-substitution (HPF/FS). We found that HPF/FS preparation revealed a complex cuticle substructure, which was more evident in older stems. We also found that the cuticle increases in thickness with development, indicating an accretion of polymeric material, likely in the form of the non-hydrolyzable polymer, cutan. When wax was extracted by chloroform immersion prior to sample preparation, the contribution of waxes to cuticle morphology was revealed. Overall, the electron-dense cuticle layer was still visible but there was loss of the cuticle substructure. Furthermore, the cuticle of cer6, a wax-deficient mutant, also lacked this substructure, suggesting that these fine striations were dependent on the presence of cuticular waxes. Our findings show that HPF/FS preparation can better preserve plant cuticles, but also provide new insights into the fine structure of the Arabidopsis cuticle.

Linking carbon stock change from land-use change to consumption of agricultural products: Alternative perspectives.

Agricultural expansion driven by growing demand has been a key driver for carbon stock change as a consequence of land-use change (CSC-LUC). However, its relative role compared to non-agricultural and non-productive drivers, as well as propagating effects were not clearly addressed. This study contributed to this subject by providing alternative perspectives in addressing these missing links. A method was developed to allocate historical CSC-LUC to agricultural expansions by land classes (products), trade, and end use. The analysis for 1995-2010 leads to three key trends: (i) agricultural land degradation and abandonment is found to be a major (albeit indirect) driver for CSC-LUC, (ii) CSC-LUC is spurred by the growth of cross-border trade, (iii) non-food use (excluding liquid biofuels) has emerged as a significant contributor of CSC-LUC in the 2000's. In addition, the study demonstrated that exact values of CSC-LUC at a single spatio-temporal point may change significantly with different methodological settings. For example, CSC-LUC allocated to 'permanent oil crops' changed from 0.53 Pg C (billion tonne C) of carbon stock gain to 0.11 Pg C of carbon stock loss when spatial boundaries were changed from global to regional. Instead of comparing exact values for accounting purpose, key messages for policymaking were drawn from the main trends. Firstly, climate change mitigation efforts pursued through a territorial perspective may ignore indirect effects elsewhere triggered through trade linkages. Policies targeting specific commodities or types of consumption are also unable to quantitatively address indirect CSC-LUC effects because the quantification changes with different arbitrary methodological settings. Instead, it is recommended that mobilising non-productive or under-utilised lands for productive use should be targeted as a key solution to avoid direct and indirect CSC-LUC.

Multimodality imaging with CT, MR and FDG-PET for radiotherapy target volume delineation in oropharyngeal squamous cell carcinoma.

BACKGROUND: This study aimed to quantify the variation in oropharyngeal squamous cell carcinoma gross tumour volume (GTV) delineation between CT, MR and FDG PET-CT imaging. METHODS: A prospective, single centre, pilot study was undertaken where 11 patients with locally advanced oropharyngeal cancers (2 tonsil, 9 base of tongue primaries) underwent pre-treatment, contrast enhanced, FDG PET-CT and MR imaging, all performed in a radiotherapy treatment mask. CT, MR and CT-MR GTVs were contoured by 5 clinicians (2 radiologists and 3 radiation oncologists). A semi-automated segmentation algorithm was used to contour PET GTVs. Volume and positional analyses were undertaken, accounting for inter-observer variation, using linear mixed effects models and contour comparison metrics respectively. RESULTS: Significant differences in mean GTV volume were found between CT (11.9 cm(3)) and CT-MR (14.1 cm(3)), p < 0.006, CT-MR and PET (9.5 cm(3)), p < 0.0009, and MR (12.7 cm(3)) and PET, p < 0.016. Substantial differences in GTV position were found between all modalities with the exception of CT-MR and MR GTVs. A mean of 64 %, 74 % and 77 % of the PET GTVs were included within the CT, MR and CT-MR GTVs respectively. A mean of 57 % of the MR GTVs were included within the CT GTV; conversely a mean of 63 % of the CT GTVs were included within the MR GTV. CT inter-observer variability was found to be significantly higher in terms of position and/or volume than both MR and CT-MR (p < 0.05). Significant differences in GTV volume were found between GTV volumes delineated by radiologists (9.7 cm(3)) and oncologists (14.6 cm(3)) for all modalities (p = 0.001). CONCLUSIONS: The use of different imaging modalities produced significantly different GTVs, with no single imaging technique encompassing all potential GTV regions. The use of MR reduced inter-observer variability. These data suggest delineation based on multimodality imaging has the potential to improve accuracy of GTV definition. TRIAL REGISTRATION: ISRCTN Registry: ISRCTN34165059 . Registered 2nd February 2015.

Signatures of adaptation to plant parasitism in nematode genomes.

Plant-parasitic nematodes cause considerable damage to global agriculture. The ability to parasitize plants is a derived character that appears to have independently emerged several times in the phylum Nematoda. Morphological convergence to feeding style has been observed, but whether this is emergent from molecular convergence is less obvious. To address this, we assess whether genomic signatures can be associated with plant parasitism by nematodes. In this review, we report genomic features and characteristics that appear to be common in plant-parasitic nematodes while absent or rare in animal parasites, predators or free-living species. Candidate horizontal acquisitions of parasitism genes have systematically been found in all plant-parasitic species investigated at the sequence level. Presence of peptides that mimic plant hormones also appears to be a trait of plant-parasitic species. Annotations of the few genomes of plant-parasitic nematodes available to date have revealed a set of apparently species-specific genes on every occasion. Effector genes, important for parasitism are frequently found among those species-specific genes, indicating poor overlap. Overall, nematodes appear to have developed convergent genomic solutions to adapt to plant parasitism.