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On February 23, 2018, PubMed Central Canada (PMC Canada) will be taken offline permanently. No author manuscripts will be deleted, and the approximately 2,900 manuscripts authored by Canadian Institutes of Health Research (CIHR)-funded researchers currently in the archive will be copied to the National Research Council’s (NRC) Digital Repository over the coming months. These manuscripts along with all other content will also remain publicly searchable on PubMed Central (US) and Europe PubMed Central, meaning such manuscripts will continue to be compliant with the Tri-Agency Open Access Policy on Publications.

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1.  Diagnostic accuracy of high-resolution MRI as a method to predict potentially safe endoscopic and surgical planes in patients with early rectal cancer 
BMJ Open Gastroenterology  2017;4(1):e000151.
Introduction
Early rectal cancer (ERC) assessment should include prediction of the potential excision plane to safely remove lesions with clear deep margins and feasibility of organ preservation.
Method
MRI accuracy for differentiating ≤T1sm2 (partially preserved submucosa) or ≤T2 (partially preserved muscularis) versus >T2 tumours was compared with the gold standard of pT stage T1sm1/2 versus ≤pT2 versus >pT2. N stage was also compared. The MRI protocol employed a standard surface phased array coil with a high resolution (0.6×0.6×3 mm resolution). The staging data were analysed from a prospectively recorded database of all ERC (≤mrT3b) treated by primary surgery.
Results
Of 65 0.7 suggesting good agreement. 44 out of 65 patients underwent radical surgery and 22 out of 44 were ≤mrT2. MRI accuracy to predict lymph node status was 84% (95% CI 70% to 92%), PPV 71% and NPV 90%. Among the 21 out of 65 (32%) patients undergoing local excision or TEM, 20 out of 21 were staged as MR≤T2 and confirmed as such by pathology. On follow-up, none had relapse. If the decision had been made to offer local excision on MRI TN staging rather than clinical assessment, a significant increase in organ preservation surgery from 32% to 60% would have been observed (difference 23%, 95% CI 9% to 35%).
Conclusions
MRI is a useful tool for multidisciplinary teams (MDTs) wishing to optimise treatment options for ERC; these study findings will be validated in a prospective multicentre trial.
doi:10.1136/bmjgast-2017-000151
PMCID: PMC5730880
COLORECTAL CANCER; STAGING; ENDOSCOPIC POLYPECTOMY; ABDOMINAL MRI
2.  Hepatoid adenocarcinoma of the lung metastasizing to the tonsil 
Molecular and Clinical Oncology  2017;6(5):705-707.
Hepatoid adenocarcinoma (HAC) is a rare tumor that typically originates in gastrointestinal tissue, such as the stomach, but can also occasionally originate in the lung. The majority of HACs express α-fetoprotein (AFP) on tumor cells, and serum AFP can be used as a marker of response to treatment or disease progression. HAC has a poor prognosis, although early diagnosis and aggressive treatment can result in long-term survival. To the best of our knowledge, this is the first reported case of HAC metastasizing to the tonsil. Irradiation using intensity-modulated radiation therapy (IMRT) to 30 Gray (Gy) achieved a significant, and durable tumor response. IMRT can be considered for local control of HAC at other metastatic sites of disease.
doi:10.3892/mco.2017.1215
PMCID: PMC5431682
α-fetoprotein; tonsillar metastasis; intensity-modulated radiation therapy; palliation of symptoms; survival
3.  Ecological immunization: in situ training of free-ranging predatory lizards reduces their vulnerability to invasive toxic prey 
Biology Letters  2016;12(1):20150863.
In Australia, large native predators are fatally poisoned when they ingest invasive cane toads (Rhinella marina). As a result, the spread of cane toads has caused catastrophic population declines in these predators. Immediately prior to the arrival of toads at a floodplain in the Kimberley region, we induced conditioned taste aversion in free-ranging varanid lizards (Varanus panoptes), by offering them small cane toads. By the end of the 18-month study, only one of 31 untrained lizards had survived longer than 110 days, compared to more than half (nine of 16) of trained lizards; the maximum known survival of a trained lizard in the presence of toads was 482 days. In situ aversion training (releasing small toads in advance of the main invasion front) offers a logistically simple and feasible way to buffer the impact of invasive toads on apex predators.
doi:10.1098/rsbl.2015.0863
PMCID: PMC4785923  PMID: 26740565
invasive species; Bufo marinus; taste aversion; conditioned taste aversion; ecological impact; varanid
4.  Evaluation of Android Smartphones for Telepathology 
Background:
In the year 2014, Android smartphones accounted for one-third of mobile connections globally but are predicted to increase to two-thirds by 2020. In developing countries, where teleconsultations can benefit health-care providers most, the ratio is even higher. This study compared the use of two Android phones, an 8 megapixel (MP) and a 16 MP phone, for capturing microscopic images.
Method:
The Android phones were used to capture images and videos of a gastrointestinal biopsy teaching set of referred cases from the Armed Forces Institute of Pathology (AFIP). The acquired images and videos were reviewed online by two pathologists for image quality, adequacy for diagnosis, usefulness of video overviews, and confidence in diagnosis, on a 5-point Likert scale.
Results:
The results show higher means in a 5-point Likert scale for the 8 MP versus the 16 MP phone that were statistically significant in adequacy of images (4.0 vs. 3.75) for rendering diagnosis and for agreement with the reference diagnosis (2.33 vs. 2.07). Although the quality of images was found higher in the 16 MP phone (3.8 vs. 3.65), these were not statistically significant. Adding video images of the entire specimen was found to be useful for evaluating the slides (combined mean, 4.0).
Conclusion:
For telepathology and other image dependent practices in developing countries, Android phones could be a useful tool for capturing images.
doi:10.4103/jpi.jpi_93_16
PMCID: PMC5404633
Android; developing countries; Likert scale; telepathology
5.  The things they carried: The pathogenic effects of old and new parasites following the intercontinental invasion of the Australian cane toad (Rhinella marina) 
Brought to Australia in 1935 to control agricultural pests (from French Guiana, via Martinique, Barbados, Jamaica, Puerto Rico and Hawai'i), repeated stepwise translocations of small numbers of founders enabled the cane toad (Rhinella marina) to escape many parasites and pathogens from its native range. However, the infective organisms that survived the journey continue to affect the dynamics of the toad in its new environment. In Australia, the native-range lungworm Rhabdias pseudosphaerocephala decreases its host's cardiac capacity, as well as growth and survival, but not rate of dispersal. The lungworm is most prevalent in long-colonised areas within the toads' Australian range, and absent from the invasion front. Several parasites and pathogens of Australian taxa have host-shifted to cane toads in Australia; for example, invasion-front toads are susceptible to spinal arthritis caused by the soil bacterium, Ochrobactrum anthropi. The pentastome Raillietiella frenata has host-shifted to toads and may thereby expand its Australian range due to the continued range expansion of the invasive toads. Spill-over and spill-back of parasites may be detrimental to other host species; however, toads may also reduce parasite loads in native taxa by acting as terminal hosts. We review the impact of the toad's parasites and pathogens on the invasive anuran's biology in Australia, as well as collateral effects of toad-borne parasites and pathogens on other host species in Australia. Both novel and co-evolved pathogens and parasites may have played significant roles in shaping the rapid evolution of immune system responses in cane toads within their invaded range.
Graphical abstract
Image 1
Highlights
•Invasive cane toads have lost many parasites due to serial translocations.•One native lungworm (Rhabdias pseudosphaerocephala) has been retained.•Toads have also acquired novel parasites and pathogens from Australian hosts.•Toads either amplify parasite numbers or act as a parasite sink.•Differences in immune function exist between toad populations within Australia.
doi:10.1016/j.ijppaw.2016.12.001
PMCID: PMC5715224
Rhabdias pseudosphaerocephala; Ecoimmunology; Invasion; Enemy release hypothesis; Immune function; Bufo; Pathogen-mediated selection 1
6.  A new technique for the radiolabelling of mixed leukocytes with zirconium‐89 for inflammation imaging with positron emission tomography 
Mixed leukocyte (white blood cells [WBCs]) trafficking using positron emission tomography (PET) is receiving growing interest to diagnose and monitor inflammatory conditions. PET, a high sensitivity molecular imaging technique, allows precise quantification of the signal produced from radiolabelled moieties. We have evaluated a new method for radiolabelling WBCs with either zirconium‐89 (89Zr) or copper‐64 (64Cu) for PET imaging. Chitosan nanoparticles (CNs) were produced by a process of ionotropic gelation and used to deliver radiometals into WBCs. Experiments were carried out using mixed WBCs freshly isolated from whole human blood. WBCs radiolabelling efficiency was higher with [89Zr]‐loaded CN (76.8 ± 9.6% (n = 12)) than with [64Cu]‐loaded CN (26.3 ± 7.0 % (n = 7)). [89Zr]‐WBCs showed an initial loss of 28.4 ± 5.8% (n = 2) of the radioactivity after 2 h. This loss was then followed by a plateau as 89Zr remains stable in the cells. [64Cu]‐WBCs showed a loss of 85 ± 6% (n = 3) of the radioactivity after 1 h, which increased to 96 ± 6% (n = 3) loss after 3 h. WBC labelling with [89Zr]‐loaded CN showed a fast kinetic of leukocyte association, high labelling efficiency and a relatively good retention of the radioactivity. This method using 89Zr has a potential application for PET imaging of inflammation.
doi:10.1002/jlcr.3392
PMCID: PMC5074313  PMID: 27061114
PET; Zr‐89; Cu‐64; inflammation imaging; white blood cell trafficking; chitosan nanoparticles
7.  Use of programme budgeting and marginal analysis as a framework for resource reallocation in respiratory care in North Wales, UK 
Background
Since the global financial crisis, UK NHS spending has reduced considerably. Respiratory care is a large cost driver for Betsi Cadwaladr University Health Board, the largest health board in Wales. Under the remit of ‘prudent healthcare’ championed by the Welsh Health Minister, a Programme Budgeting Marginal Analysis (PBMA) of the North Wales respiratory care pathway was conducted.
Methods
A PBMA panel of directors of medicines management, therapies finance, planning, public health and healthcare professionals used electronic voting to establish criteria for decision-making and vote on candidate interventions in which to disinvest and invest.
Results
A sum of £86.9 million was spent on respiratory care in 2012–13. Following extensive discussion of 13 proposed candidate interventions facilitated by a chairperson, 4 candidates received recommendations to disinvest, 7 to invest and 2 to maintain current activity. Marginal analysis prioritized mucolytics and high antibiotic prescribing as areas for disinvestment, and medicines waste management and pulmonary rehabilitation for investment.
Conclusions
This exercise demonstrates the potential for health boards to use evidence-based approaches to reach potentially controversial disinvestment and investment decisions. Initial progress has begun with communication from the Medical Director in relation to the disinvestment in mucolytics prescribing and possible redirection of funding options being explored.
doi:10.1093/pubmed/fdv128
PMCID: PMC5072164  PMID: 26377991
disinvestment; health economics; healthcare resources; investment; marginal analysis; programme budgeting; public health; resource reallocation
8.  Antiviral gene expression in psoriasis 
Background
Psoriasis patients have relatively infrequent cutaneous viral infections compared to atopic dermatitis patients. Increased expression of four antiviral proteins (MX1, BST2, ISG15, and OAS2) has been reported in psoriatic skin and genetic studies of psoriasis have identified susceptibility genes in antiviral pathways.
Objective
To determine if psoriasis is associated with pervasive expression of antiviral genes in skin and blood.
Methods
We performed RNA-sequencing on skin samples of 18 subjects with chronic plaque psoriasis and 16 healthy controls. We examined the expression of a pre-defined set of 42 antiviral genes, each of which has been shown in previous studies to inhibit viral replication. In parallel, we examined antiviral gene expression in atopic dermatitis, non-lesional psoriatic skin, and psoriatic blood. We performed HIV-1 infectivity assays in CD4+ peripheral blood T cells from psoriatic and healthy individuals.
Results
We observed significant overexpression of 16 antiviral genes in lesional psoriatic skin, with a greater than two-fold increase in ISG15, RSAD2, IRF7, MX2, and TRIM22 (p<1E-07). None of these genes was overexpressed in atopic dermatitis skin (p<0.0001) or non-lesional psoriatic skin. In contrast to the skin compartment, no differences in antiviral gene expression were detected in the peripheral blood of psoriasis cases compared to healthy controls. CD4+ T cells from both psoriatic and healthy patients supported HIV-1 infection at a similar rate.
Conclusion
Our findings highlight psoriasis as an inflammatory disease with cutaneous but not systemic immune activation against viral pathogens.
doi:10.1111/jdv.13091
PMCID: PMC4580491  PMID: 25809693
9.  Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome 
Environmental Science & Technology  2016;50(18):9807-9815.
Antibiotic resistance is increasingly widespread, largely due to human influence. Here, we explore the relationship between antibiotic resistance genes and the antimicrobial chemicals triclosan, triclocarban, and methyl-, ethyl-, propyl-, and butylparaben in the dust microbiome. Dust samples from a mixed-use athletic and educational facility were subjected to microbial and chemical analyses using a combination of 16S rRNA amplicon sequencing, shotgun metagenome sequencing, and liquid chromatography tandem mass spectrometry. The dust resistome was characterized by identifying antibiotic resistance genes annotated in the Comprehensive Antibiotic Resistance Database (CARD) from the metagenomes of each sample using the Short, Better Representative Extract Data set (ShortBRED). The three most highly abundant antibiotic resistance genes were tet(W), blaSRT-1, and erm(B). The complete dust resistome was then compared against the measured concentrations of antimicrobial chemicals, which for triclosan ranged from 0.5 to 1970 ng/g dust. We observed six significant positive associations between the concentration of an antimicrobial chemical and the relative abundance of an antibiotic resistance gene, including one between the ubiquitous antimicrobial triclosan and erm(X), a 23S rRNA methyltransferase implicated in resistance to several antibiotics. This study is the first to look for an association between antibiotic resistance genes and antimicrobial chemicals in dust.
doi:10.1021/acs.est.6b00262
PMCID: PMC5032049  PMID: 27599587
11.  Measurement of the centrality dependence of the charged-particle pseudorapidity distribution in proton–lead collisions at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s_{_\text {NN}}} = 5.02$$\end{document}sNN=5.02 TeV with the ATLAS detector 
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The centrality dependence of the mean charged-particle multiplicity as a function of pseudorapidity is measured in approximately 1 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\upmu $$\end{document}μb\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{-1}$$\end{document}-1 of proton–lead collisions at a nucleon–nucleon centre-of-mass energy of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s_{_\text {NN}}} = 5.02$$\end{document}sNN=5.02 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {TeV}$$\end{document}TeV using the ATLAS detector at the Large Hadron Collider. Charged particles with absolute pseudorapidity less than 2.7 are reconstructed using the ATLAS pixel detector. The collision centrality is characterised by the total transverse energy measured in the Pb-going direction of the forward calorimeter. The charged-particle pseudorapidity distributions are found to vary strongly with centrality, with an increasing asymmetry between the proton-going and Pb-going directions as the collisions become more central. Three different estimations of the number of nucleons participating in the collision have been carried out using the Glauber model as well as two Glauber–Gribov inspired extensions to the Glauber model. Charged-particle multiplicities per participant pair are found to vary differently for these three models, highlighting the importance of including colour fluctuations in nucleon–nucleon collisions in the modelling of the initial state of collisions.
doi:10.1140/epjc/s10052-016-4002-3
PMCID: PMC5312138
12.  CD4+ T-cell survival in the GI tract requires dectin-1 during fungal infection 
Mucosal Immunology  2015;9(2):492-502.
Dectin-1 is an innate antifungal C-type lectin receptor necessary for protective antifungal immunity. We recently discovered that Dectin-1 is involved in controlling fungal infections of the gastrointestinal (GI) tract, but how this C-type lectin receptor mediates these activities is unknown. Here, we show that Dectin-1 is essential for driving fungal-specific CD4+ T-cell responses in the GI tract. Loss of Dectin-1 resulted in abrogated dendritic cell responses in the mesenteric lymph nodes (mLNs) and defective T-cell co-stimulation, causing substantial increases in CD4+ T-cell apoptosis and reductions in the cellularity of GI-associated lymphoid tissues. CD8+ T-cell responses were unaffected by Dectin-1 deficiency. These functions of Dectin-1 have significant implications for our understanding of intestinal immunity and susceptibility to fungal infections.
doi:10.1038/mi.2015.79
PMCID: PMC4677461  PMID: 26349660
13.  Making microbiology of the built environment relevant to design 
Microbiome  2016;4:6.
Architects are enthusiastic about “bioinformed design” as occupant well-being is a primary measure of architectural success. However, architects are also under mounting pressure to create more sustainable buildings. Scientists have a critical opportunity to make the emerging field of microbiology of the built environment more relevant and applicable to real-world design problems by addressing health and sustainability in tandem. Practice-based research, which complements evidence-based design, represents a promising approach to advancing knowledge of the indoor microbiome and translating it to architectural practice.
doi:10.1186/s40168-016-0152-7
PMCID: PMC4754988  PMID: 26880354
Architecture; Buildings; Microbiome; Microbial ecology; Bioinformed design; Sustainability
14.  Advancing infection control in dental care settings 
Background and Overview
The authors set out to identify factors associated with implementation by U.S. dentists of four practices first recommended in the Centers for Disease Control and Prevention’s Guidelines for Infection Control in Dental Health-Care Settings—2003.
Methods
In 2008, the authors surveyed a stratified random sample of 6,825 U.S. dentists. The response rate was 49 percent. The authors gathered data regarding dentists’ demographic and practice characteristics, attitudes toward infection control, sources of instruction regarding the guidelines and knowledge about the need to use sterile water for surgical procedures. Then they assessed the impact of those factors on the implementation of four recommendations: having an infection control coordinator, maintaining dental unit water quality, documenting percutaneous injuries and using safer medical devices, such as safer syringes and scalpels. The authors conducted bivariate analyses and proportional odds modeling.
Results
Responding dentists in 34 percent of practices had implemented none or one of the four recommendations, 40 percent had implemented two of the recommendations and 26 percent had implemented three or four of the recommendations. The likelihood of implementation was higher among dentists who acknowledged the importance of infection control, had practiced dentistry for less than 30 years, had received more continuing dental education credits in infection control, correctly identified more surgical procedures that require the use of sterile water, worked in larger practices and had at least three sources of instruction regarding the guidelines. Dentists with practices in the South Atlantic, Middle Atlantic or East South Central U.S. Census divisions were less likely to have complied.
Conclusions
Implementation of the four recommendations varied among U.S. dentists. Strategies targeted at raising awareness of the importance of infection control, increasing continuing education requirements and developing multiple modes of instruction may increase implementation of current and future Centers for Disease Control and Prevention guidelines.
PMCID: PMC4624311  PMID: 23024311
Dentistry; infection control; guidelines
15.  Alumni-based evaluation of a novel veterinary curriculum: are Nottingham graduates prepared for clinical practice? 
Veterinary Record Open  2015;2(2):e000116.
Introduction
Outcomes-based education has been the core of the curriculum strategy of the Nottingham School of Veterinary Medicine and Science (SVMS) since its inception in 2006. As part of the ongoing curriculum evaluation, the first two graduating cohorts were invited to provide an appraisal of their preparation by the SVMS curriculum for their role in clinical practice. This paper provides brief accounts of the SVMS curriculum model, the development of the evaluation instrument and the findings of the alumni survey.
Materials and Methods
The evaluation instrument contained 25 attributes expected of SVMS graduates. Alumni rated their preparation for practice in relation to each attribute.
Results
The four highest rated characteristics were compassion for animals and the application of ethics to animal welfare; communication skills; recognising own limitations and seeking help and advice where needed and clinical examination skills. The four lowest rated were clinical case management and therapeutic strategies; dealing with veterinary public health and zoonotic issues; knowledge of current veterinary legislation and dealing with emergency and critical care cases. Free text responses were in line with these quantitative findings.
Conclusion
The results indicate that this sample of SVMS graduates were satisfied with their undergraduate education and felt well prepared for their role in clinical practice.
doi:10.1136/vetreco-2015-000116
PMCID: PMC4567166  PMID: 26392910
Pets; Clinical; Economics; Health; Large animals
16.  Prognostic role of the LCS6 KRAS variant in locally advanced rectal cancer: results of the EXPERT-C trial 
Annals of Oncology  2015;26(9):1936-1941.
KRAS mutation has been reported as a marker of radio-resistance in rectal cancer and unfavourable outcome in both colon and rectal cancer. This study suggests that a single-nucleotide polymorphism of the KRAS gene (LCS-6 variant) may predict response to neoadjuvant treatment and mitigate the poor prognosis associated with KRAS mutation in locally advanced rectal cancer.
Background
Lethal-7 (let-7) is a tumour suppressor miRNA which acts by down-regulating several oncogenes including KRAS. A single-nucleotide polymorphism (rs61764370, T > G base substitution) in the let-7 complementary site 6 (LCS-6) of KRAS mRNA has been shown to predict prognosis in early-stage colorectal cancer (CRC) and benefit from anti-epidermal growth factor receptor monoclonal antibodies in metastatic CRC.
Patients and methods
We analysed rs61764370 in EXPERT-C, a randomised phase II trial of neoadjuvant CAPOX followed by chemoradiotherapy, surgery and adjuvant CAPOX plus or minus cetuximab in locally advanced rectal cancer. DNA was isolated from formalin-fixed paraffin-embedded tumour tissue and genotyped using a PCR-based commercially available assay. Kaplan–Meier method and Cox regression analysis were used to calculate survival estimates and compare treatment arms.
Results
A total of 155/164 (94.5%) patients were successfully analysed, of whom 123 (79.4%) and 32 (20.6%) had the LCS-6 TT and LCS-6 TG genotype, respectively. Carriers of the G allele were found to have a statistically significantly higher rate of complete response (CR) after neoadjuvant therapy (28.1% versus 10.6%; P = 0.020) and a trend for better 5-year progression-free survival (PFS) [77.4% versus 64.5%: hazard ratio (HR) 0.56; P = 0.152] and overall survival (OS) rates (80.3% versus 71.9%: HR 0.59; P = 0.234). Both CR and survival outcomes were independent of the use of cetuximab. The negative prognostic effect associated with KRAS mutation appeared to be stronger in patients with the LCS-6 TT genotype (HR PFS 1.70, P = 0.078; HR OS 1.79, P = 0.082) compared with those with the LCS-6 TG genotype (HR PFS 1.33, P = 0.713; HR OS 1.01, P = 0.995).
Conclusion
This analysis suggests that rs61764370 may be a biomarker of response to neoadjuvant treatment and an indicator of favourable outcome in locally advanced rectal cancer possibly by mitigating the poor prognosis of KRAS mutation. In this setting, however, this polymorphism does not appear to predict cetuximab benefit.
doi:10.1093/annonc/mdv285
PMCID: PMC4551162  PMID: 26162609
LCS-6 KRAS variant; single-nucleotide polymorphism; let-7; KRAS; cetuximab; rectal cancer
17.  Jet energy measurement and its systematic uncertainty in proton–proton collisions at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s}=7$$\end{document}s=7 TeV with the ATLAS detector 
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The jet energy scale (JES) and its systematic uncertainty are determined for jets measured with the ATLAS detector using proton–proton collision data with a centre-of-mass energy of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s}=7$$\end{document}s=7 TeV corresponding to an integrated luminosity of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$4.7$$\end{document}4.7\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\,\,\text{ fb }^{-1}$$\end{document}fb-1. Jets are reconstructed from energy deposits forming topological clusters of calorimeter cells using the anti-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$k_{t}$$\end{document}kt algorithm with distance parameters \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R=0.4$$\end{document}R=0.4 or \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R=0.6$$\end{document}R=0.6, and are calibrated using MC simulations. A residual JES correction is applied to account for differences between data and MC simulations. This correction and its systematic uncertainty are estimated using a combination of in situ techniques exploiting the transverse momentum balance between a jet and a reference object such as a photon or a \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$Z$$\end{document}Z boson, for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${20} \le p_{\mathrm {T}}^\mathrm {jet}<{1000}\, ~\mathrm{GeV }$$\end{document}20≤pTjet<1000GeV and pseudorapidities \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$|\eta |<{4.5}$$\end{document}|η|<4.5. The effect of multiple proton–proton interactions is corrected for, and an uncertainty is evaluated using in situ techniques. The smallest JES uncertainty of less than 1 % is found in the central calorimeter region (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$|\eta |<{1.2}$$\end{document}|η|<1.2) for jets with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${55} \le p_{\mathrm {T}}^\mathrm {jet}<{500}\, ~\mathrm{GeV }$$\end{document}55≤pTjet<500GeV. For central jets at lower \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p_{\mathrm {T}}$$\end{document}pT, the uncertainty is about 3 %. A consistent JES estimate is found using measurements of the calorimeter response of single hadrons in proton–proton collisions and test-beam data, which also provide the estimate for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p_{\mathrm {T}}^\mathrm {jet}> 1$$\end{document}pTjet>1 TeV. The calibration of forward jets is derived from dijet \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p_{\mathrm {T}}$$\end{document}pT balance measurements. The resulting uncertainty reaches its largest value of 6 % for low-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p_{\mathrm {T}}$$\end{document}pT jets at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$|\eta |=4.5$$\end{document}|η|=4.5. Additional JES uncertainties due to specific event topologies, such as close-by jets or selections of event samples with an enhanced content of jets originating from light quarks or gluons, are also discussed. The magnitude of these uncertainties depends on the event sample used in a given physics analysis, but typically amounts to 0.5–3 %.
doi:10.1140/epjc/s10052-014-3190-y
PMCID: PMC4684939  PMID: 26709345
18.  Extramural venous invasion is a potential imaging predictive biomarker of neoadjuvant treatment in rectal cancer 
British Journal of Cancer  2013;110(1):19-25.
Background:
Extramural venous invasion (EMVI) is a poor prognostic factor in rectal cancer and identified on magnetic resonance imaging (MRI) (mrEMVI). The clinical relevance of improvement in mrEMVI following neoadjuvant therapy is unknown. This study aimed to demonstrate that regression of mrEMVI following neoadjuvant chemoradiotherapy (CRT) results in improved outcomes and mrEMVI can be used as an imaging biomarker
Methods:
Retrospective analysis of prospectively collected data was conducted examining the staging and post-treatment MRIs of patients who had presented with EMVI-positive rectal cancer. All patients had undergone neoadjuvant CRT and curative surgery. Changes in mrEMVI were graded with a new MRI-based TRG scale–mr-vTRG; and related to disease-free survival (DFS). The study fulfilled Reporting Recommendations for Tumour Marker Prognostic Studies criteria for biomarkers.
Results:
Sixty-two patients were included. Thirty-five patients showed more than 50% fibrosis of mrEMVI (mr-vTRG 1-3); 3-year DFS 87.8% and 9% recurrence. Twenty-seven patients showed less than 50% fibrosis (mr-vTRG 4-5); 3-year DFS 45.8% with 44% recurrence – P<0.0001. On multivariate Cox-regression, only mr-vTRG 4-5 increased risk of disease recurrence – HR=5.748.
Conclusion:
Patients in whom there has been a significant response of EMVI to CRT show improved DFS. Those patients with poor response should be considered for intensive treatment. As an imaging biomarker in rectal cancer, mrEMVI can be used.
doi:10.1038/bjc.2013.603
PMCID: PMC3887281  PMID: 24300971
rectal cancer; venous invasion; EMVI; neoadjuvant chemoradiotherapy; follow-up; recurrence
19.  Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source 
Indoor Air  2013;24(1):41-48.
Architects and engineers are beginning to consider a new dimension of indoor air: the structure and composition of airborne microbial communities. A first step in this emerging field is to understand the forces that shape the diversity of bioaerosols across space and time within the built environment. In an effort to elucidate the relative influences of three likely drivers of indoor bioaerosol diversity – variation in outdoor bioaerosols, ventilation strategy, and occupancy load – we conducted an intensive temporal study of indoor airborne bacterial communities in a high-traffic university building with a hybrid HVAC (mechanically and naturally ventilated) system. Indoor air communities closely tracked outdoor air communities, but human-associated bacterial genera were more than twice as abundant in indoor air compared with outdoor air. Ventilation had a demonstrated effect on indoor airborne bacterial community composition; changes in outdoor air communities were detected inside following a time lag associated with differing ventilation strategies relevant to modern building design. Our results indicate that both occupancy patterns and ventilation strategies are important for understanding airborne microbial community dynamics in the built environment.
doi:10.1111/ina.12047
PMCID: PMC4285785  PMID: 23621155
Bioaerosol; Airborne bacterial community; Natural ventilation; Built environment; Indoor microbial ecology
20.  Lipopolysaccharide stimulates platelets through an IL-1β autocrine loop 
Journal of immunology (Baltimore, Md. : 1950)  2013;191(10):10.4049/jimmunol.1300354.
Lipopolysaccharide (LPS) activates platelets through TLR4, aiding productive sepsis, with stimulated splicing and translation of stored heteronuclear pro-Interleukin-1β (IL-1β)RNA. Although the IL1R1 receptor for IL1 shares downstream components with the TLR4 receptor, platelets are not known to express IL1R1, nor are they known to respond to this cytokine. We show by flow cytometry and western blotting that platelets express IL1R1, and that IL-1β and IL-1α stimulate heteronuclear I-1β splicing and translation of the newly made mRNA in platelets. Platelets also respond to the IL-1β they make, which is exclusively associated with shed microparticles. Specific blockade of IL1R1 with IL1 receptor antagonist (IL1Ra) suppressed platelet stimulation by IL1, so IL-1β stimulates its own synthesis in an autocrine signaling loop. Strikingly, IL1Ra inhibition, pharmacologic or genetic suppression of pro-IL-1β processing to active cytokine by caspase-1, or blockade of de novo protein synthesis also blocked LPS-induced IL-1β mRNA production. Robust stimulation of platelets by LPS therefore also required IL-1β amplification. Activated platelets made IL-1β in vivo as IL-1β rapidly accumulated in occluded murine carotid arteries by post-transcriptional RNA splicing unique to platelets. We conclude IL-1β is a platelet agonist, that IL-1β acts through an autocrine stimulatory loop, that an IL-1β autocrine loop is required to amplify platelet activation by LPS, and that platelets immobilized in occlusive thrombi are activated over time to produce IL-1β. IL1 is a new platelet agonist that promotes its own synthesis, connecting thrombosis with immunity.
doi:10.4049/jimmunol.1300354
PMCID: PMC3818355  PMID: 24081990
21.  The role of pre-treatment diffusion-weighted MRI in predicting long-term outcome of colorectal liver metastasis 
The British Journal of Radiology  2013;86(1030):20130281.
Objective:
To determine the prognostic value of pre-treatment apparent diffusion coefficient (ADC) of colorectal liver metastases in predicting disease response, progression-free survival (PFS) and overall survival (OS).
Methods:
We retrospectively reviewed 102 patients who underwent pre-treatment diffusion-weighted MRI using a breath-hold (b=0, 150, 500) or a free-breathing (b=0, 50, 100, 250, 500, 750) technique. The mean ADC (b=0–500) and mean flow-insensitive ADC (ADChigh) values (breath-hold: b=150 and 500; free-breathing: b=100 and 500) of up to three hepatic lesions were evaluated in each patient. Clinical and laboratory parameters were recorded. Tumour response was assessed by Response Evaluation Criteria in Solid Tumors (RECIST) criteria at 12 weeks after treatment. Associations between tumour response, ADC values and clinical/laboratory parameters were examined by one-way analysis of variance. The relationship of ADC with PFS and OS was determined by Kaplan–Meier analysis.
Results:
62 patients responded to chemotherapy at 12 weeks. The pre-treatment mean ADC and mean ADChigh were higher in the non-responding group than in the responding group (1.55 vs 1.36, p=0.033; 1.40 vs 1.16, p=0.024). However, the PFS and OS of the two groups of patients stratified by the median of mean ADC values or threshold derived by receiver operating characteristic analysis were not statistically significant. By multivariate Cox regression analysis, patients with ≤2 metastases and response to chemotherapy showed better PFS; white cell count ≤10 and surgical treatment were associated with better OS.
Conclusion:
Colorectal liver metastasis with higher pre-treatment mean ADC and mean ADChigh was associated with poorer response to chemotherapy. However, ADC and ADChigh values did not predict the patient outcome in this study cohort.
Advances in knowledge:
High mean ADC values of colorectal liver metastases on pre-treatment diffusion-weighted MRI is associated with poorer response to chemotherapy.
doi:10.1259/bjr.20130281
PMCID: PMC3798332  PMID: 23995873
22.  Adjuvant therapy decisions based on magnetic resonance imaging of extramural venous invasion and other prognostic factors in colorectal cancer 
Introduction
There remains a lack of high quality randomised trial evidence for the use of adjuvant chemotherapy in stage II rectal cancer, particularly in the presence of high risk features such as extramural venous invasion (EMVI). The aim of this study was to explore this issue through a survey of colorectal surgeons and gastrointestinal oncologists.
Methods
An electronic survey was sent to a group of colorectal surgeons who were members of the Association of Coloproctology of Great Britain and Ireland. The survey was also sent to a group of gastrointestinal oncologists through the Pelican Cancer Foundation. Reminder emails were sent at 4 and 12 weeks.
Results
A total of 142 surgeons (54% response rate) and 99 oncologists (68% response rate) responded to the survey. The majority in both groups of clinicians thought EMVI was an important consideration in adjuvant treatment decision making and commented routinely on this in their multidisciplinary team meeting. Although both would consider treating patients on the basis of EMVI detected by magnetic resonance imaging, oncologists were more selective. Both surgeons and oncologists were prepared to offer patients with EMVI adjuvant chemotherapy but there was lack of consensus on the benefit.
Conclusions
This survey reinforces the evolution in thinking with regard to adjuvant therapy in stage II disease. Factors such as EMVI should be given due consideration and the prognostic information we offer patients must be more accurate. Historical data may not accurately reflect today’s practice and it may be time to consider an appropriately designed trial to address this contentious issue.
doi:10.1308/003588414X13814021678835
PMCID: PMC4473443  PMID: 25245736
Rectal cancer; Extramural venous invasion; Adjuvant chemotherapy
23.  Muon reconstruction efficiency and momentum resolution of the ATLAS experiment in proton–proton collisions at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s}=7$$\end{document}s=7 TeV in 2010 
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This paper presents a study of the performance of the muon reconstruction in the analysis of proton–proton collisions at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s}=7$$\end{document}s=7 TeV at the LHC, recorded by the ATLAS detector in 2010. This performance is described in terms of reconstruction and isolation efficiencies and momentum resolutions for different classes of reconstructed muons. The results are obtained from an analysis of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$J/\psi $$\end{document}J/ψ meson and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$Z$$\end{document}Z boson decays to dimuons, reconstructed from a data sample corresponding to an integrated luminosity of 40 pb\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{-1}$$\end{document}-1. The measured performance is compared to Monte Carlo predictions and deviations from the predicted performance are discussed.
doi:10.1140/epjc/s10052-014-3034-9
PMCID: PMC4371051  PMID: 25814911
24.  Light-quark and gluon jet discrimination in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$pp$$\end{document}pp collisions at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s}=7\mathrm {\ TeV}$$\end{document}s=7TeV with the ATLAS detector 
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A likelihood-based discriminant for the identification of quark- and gluon-initiated jets is built and validated using 4.7 fb\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{-1}$$\end{document}-1 of proton–proton collision data at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s}=7$$\end{document}s=7 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathrm {\ TeV}$$\end{document}TeV collected with the ATLAS detector at the LHC. Data samples with enriched quark or gluon content are used in the construction and validation of templates of jet properties that are the input to the likelihood-based discriminant. The discriminating power of the jet tagger is established in both data and Monte Carlo samples within a systematic uncertainty of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\approx $$\end{document}≈ 10–20 %. In data, light-quark jets can be tagged with an efficiency of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\approx 50\,\%$$\end{document}≈50% while achieving a gluon-jet mis-tag rate of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\approx 25\,\%$$\end{document}≈25% in a \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p_{\mathrm {T}}$$\end{document}pT range between \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$40\mathrm {\ GeV}$$\end{document}40GeV and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$360\mathrm {\ GeV}$$\end{document}360GeV for jets in the acceptance of the tracker. The rejection of gluon-jets found in the data is significantly below what is attainable using a Pythia 6 Monte Carlo simulation, where gluon-jet mis-tag rates of 10 % can be reached for a 50 % selection efficiency of light-quark jets using the same jet properties.
doi:10.1140/epjc/s10052-014-3023-z
PMCID: PMC4370928  PMID: 25814910