An artificial neural network stratifies the risks of reintervention and mortality after endovascular aneurysm repair:a retrospective observational study

Background Lifelong surveillance after endovascular repair (EVAR) of abdominal aortic aneurysms (AAA) is considered mandatory to detect potentially life-threatening endograft complications. A minority of patients require reintervention but cannot be predictively identified by existing methods. This study aimed to improve the prediction of endograft complications and mortality, through the application of machine-learning techniques. Methods Patients undergoing EVAR at 2 centres were studied from 2004-2010. Pre-operative aneurysm morphology was quantified and endograft complications were recorded up to 5 years following surgery. An artificial neural networks (ANN) approach was used to predict whether patients would be at low- or high-risk of endograft complications (aortic/limb) or mortality. Centre 1 data were used for training and centre 2 data for validation. ANN performance was assessed by Kaplan-Meier analysis to compare the incidence of aortic complications, limb complications, and mortality; in patients predicted to be low-risk, versus those predicted to be high-risk. Results 761 patients aged 75 +/- 7 years underwent EVAR. Mean follow-up was 36+/- 20 months. An ANN was created from morphological features including angulation/length/areas/diameters/ volume/tortuosity of the aneurysm neck/sac/iliac segments. ANN models predicted endograft complications and mortality with excellent discrimination between a low-risk and high-risk group. In external validation, the 5-year rates of freedom from aortic complications, limb complications and mortality were 95.9% vs 67.9%; 99.3% vs 92.0%; and 87.9% vs 79.3% respectively (p0.001) Conclusion This study presents ANN models that stratify the 5-year risk of endograft complications or mortality using routinely available pre-operative data

Endovascular strategy or open repair for ruptured abdominal aortic aneurysm: one-year outcomes from the IMPROVE randomized trial.

AIMS: To report the longer term outcomes following either a strategy of endovascular repair first or open repair of ruptured abdominal aortic aneurysm, which are necessary for both patient and clinical decision-making. METHODS AND RESULTS: This pragmatic multicentre (29 UK and 1 Canada) trial randomized 613 patients with a clinical diagnosis of ruptured aneurysm; 316 to an endovascular first strategy (if aortic morphology is suitable, open repair if not) and 297 to open repair. The principal 1-year outcome was mortality; secondary outcomes were re-interventions, hospital discharge, health-related quality-of-life (QoL) (EQ-5D), costs, Quality-Adjusted-Life-Years (QALYs), and cost-effectiveness [incremental net benefit (INB)]. At 1 year, all-cause mortality was 41.1% for the endovascular strategy group and 45.1% for the open repair group, odds ratio 0.85 [95% confidence interval (CI) 0.62, 1.17], P = 0.325, with similar re-intervention rates in each group. The endovascular strategy group and open repair groups had average total hospital stays of 17 and 26 days, respectively, P < 0.001. Patients surviving rupture had higher average EQ-5D utility scores in the endovascular strategy vs. open repair groups, mean differences 0.087 (95% CI 0.017, 0.158), 0.068 (95% CI -0.004, 0.140) at 3 and 12 months, respectively. There were indications that QALYs were higher and costs lower for the endovascular first strategy, combining to give an INB of £3877 (95% CI £253, £7408) or €4356 (95% CI €284, €8323). CONCLUSION: An endovascular first strategy for management of ruptured aneurysms does not offer a survival benefit over 1 year but offers patients faster discharge with better QoL and is cost-effective. CLINICAL TRIAL REGISTRATION: ISRCTN 48334791

Regulation of Coronafacoyl Phytotoxin Production by the PAS-LuxR Family Regulator CfaR in the Common Scab Pathogen Streptomyces scabies

Potato common scab is an economically important crop disease that is characterized by the formation of superficial, raised or pitted lesions on the potato tuber surface. The most widely distributed causative agent of the disease is Streptomyces scabies, which produces the phytotoxic secondary metabolite thaxtomin A that serves as a key virulence factor for the organism. Recently, it was demonstrated that S. scabies can also produce the phytotoxic secondary metabolite coronafacoyl-L-isoleucine (CFA-L-Ile) as well as other related metabolites in minor amounts. The expression of the biosynthetic genes for CFA-L-Ile production is dependent on a PAS-LuxR family transcriptional regulator, CfaR, which is encoded within the phytotoxin biosynthetic gene cluster in S. scabies. In this study, we show that CfaR activates coronafacoyl phytotoxin production by binding to a single site located immediately upstream of the putative -35 hexanucleotide box within the promoter region for the biosynthetic genes. The binding activity of CfaR was shown to require both the LuxR and PAS domains, the latter of which is involved in protein homodimer formation. We also show that CFA-L-Ile production is greatly enhanced in S. scabies by overexpression of both cfaR and a downstream co-transcribed gene, orf1. Our results provide important insight into the regulation of coronafacoyl phytotoxin production, which is thought to contribute to the virulence phenotype of S. scabies. Furthermore, we provide evidence that CfaR is a novel member of the PAS-LuxR family of regulators, members of which are widely distributed among actinomycete bacteria

The coronafacoyl phytotoxins: structure, biosynthesis, regulation and biological activities

Phytotoxins are secondary metabolitesthat contribute to the development and/or severity ofdiseases caused by various plant pathogenic microorganisms.The coronafacoyl phytotoxins are an importantfamily of plant toxins that are known or suspectedto be produced by several phylogenetically distinctplant pathogenic bacteria, including the gammaproteobacteriumPseudomonas syringae and the actinobacteriumStreptomyces scabies. At least sevendifferent family members have been identified, ofwhich coronatine was the first to be described and isthe best-characterized. Though nonessential for diseasedevelopment, coronafacoyl phytotoxins appear toenhance the severity of disease symptoms induced bypathogenic microbes during host infection. In addition,the identification of coronafacoyl phytotoxinbiosynthetic genes in organisms not known to be plantpathogens suggests that these metabolites may haveadditional roles other than as virulence factors. Thisreview focuses on our current understanding of thestructures, biosynthesis, regulation, biological activitiesand evolution of coronafacoyl phytotoxins as wellas the different methods that are used to detect thesemetabolites and the organisms that produce them.Keywords Phytotoxins Secondary metabolites Coronatine N-Coronafacoyl-L-isoleucine Pseudomonas Streptomyce

Phylogenetic analysis of PAS-LuxR family proteins from <i>Streptomyces</i> and other actinomycetes.

<p>The phylogenetic trees were constructed based on the amino acid sequences of the PAS domain (A) and the LuxR DNA binding domain (B). The trees were constructed using the maximum likelihood algorithm, and bootstrap values ≥50% for 1000 repetitions are shown. The scale bar indicates the number of amino acid substitutions per site. Family members that have been shown experimentally to be functionally interchangeable are indicated with *.</p

Bacterial strains and plasmids used in this study.

<p>^† Apra^R, Thio^R, Kan^R and Cml^R = apramycin, thiostrepton, kanamycin and chloramphenicol resistance, respectively.</p><p>n/a = not applicable.</p><p>Bacterial strains and plasmids used in this study.</p

Sequence logo of PAS-LuxR protein binding sites.

<p>The logo was constructed using WebLogo [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122450#pone.0122450.ref035" target="_blank">35</a>] with the PimM and CfaR binding sites shown below. The overall height of the stack reflects the sequence conservation at that position, and the height of the letters within the stack designates the relative frequency of the corresponding base at that position [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122450#pone.0122450.ref038" target="_blank">38</a>].</p

The CfaR PAS domain is required for DNA binding and protein dimerization.

<p>(A) EMSA results using CfaR^full-HIS₆, CfaR^ΔLuxR-HIS₆ and CfaR^ΔPAS-HIS₆ with DNA fragment <i>a</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122450#pone.0122450.g002" target="_blank">Fig 2A</a>). A control reaction (-) in which no protein was added was also included. The DNA-protein complex observed is indicated with *. (B) Analysis of protein dimerization using chemical crosslinking and SDS-PAGE. CfaR^full-HIS₆, CfaR^ΔLuxR-HIS₆ and CfaR^ΔPAS-HIS₆ were either treated with glutaraldehyde (+) or with solvent alone (-), after which the proteins were separated by SDS-PAGE and were visualized by staining with Coomassie brilliant blue. Protein monomers are indicated with black arrows and dimers with *. The sizes (in kDa) of the protein molecular weight marker (M) bands used for size estimation are also shown.</p

CfaR^full-HIS₆ binds to a single site within the <i>cfaR—cfa1</i> intergenic region.

<p>(A) Map of the <i>cfaR—cfa1</i> intergenic region showing the location of the DNA fragments (indicated by the black bars and labeled <i>a—f</i>) used for EMSAs. The position of the 16 bp palindrome identified upstream of <i>cfa1</i> is indicated with the white triangle. (B) EMSA s for CfaR^full—HIS₆ with the DNA fragments <i>a—f</i>. Reactions contained 50 ng of DNA with (result+) and without (-) CfaR^full—HIS₆ protein (3.7 pmol). DNA-protein complexes observed are indicated with *. (C) Sequence of the 40 bp oligonucleotide P1 probe used for EMSAs. The 16 bp palindromic sequence identified upstream of <i>cfa1</i> is shown in bold. (D) EMSA results for CfaR^full—HIS₆ with the P1 oligonucleotide probe. Reactions contained 0.1 pmol of biotin-labeled probe with (+) and without (-) CfaR^full—HIS₆ protein (2 pmol). Negative control reactions contained the 40 bp biotin-labeled oligonucleotide P2 probe in place of P1. In addition, competition assays were performed in which an excess (10×) of unlabelled (cold) probe (P1 or P2) was included in the reaction. DNA-protein complexes observed are indicated with *.</p