Recommended reporting standards for test accuracy studies of infectious diseases of finfish, amphibians, molluscs and crustaceans: the STRADAS-aquatic checklist

Complete and transparent reporting of key elements of diagnostic accuracy studies for infectious diseases in cultured and wild aquatic animals benefits end-users of these tests, enabling the rational design of surveillance programs, the assessment of test results from clinical cases and comparisons of diagnostic test performance. Based on deficiencies in the Standards for Reporting of Diagnostic Accuracy (STARD) guidelines identified in a prior finfish study (Gardner et al. 2014), we adapted the Standards for Reporting of Animal Diagnostic Accuracy Studies—paratuberculosis (STRADAS-paraTB) checklist of 25 reporting items to increase their relevance to finfish, amphibians, molluscs, and crustaceans and provided examples and explanations for each item. The checklist, known as STRADAS-aquatic, was developed and refined by an expert group of 14 transdisciplinary scientists with experience in test evaluation studies using field and experimental samples, in operation of reference laboratories for aquatic animal pathogens, and in development of international aquatic animal health policy. The main changes to the STRADAS-paraTB checklist were to nomenclature related to the species, the addition of guidelines for experimental challenge studies, and the designation of some items as relevant only to experimental studies and ante-mortem tests. We believe that adoption of these guidelines will improve reporting of primary studies of test accuracy for aquatic animal diseases and facilitate assessment of their fitness-for-purpose. Given the importance of diagnostic tests to underpin the Sanitary and Phytosanitary agreement of the World Trade Organization, the principles outlined in this paper should be applied to other World Organisation for Animal Health (OIE)-relevant species.

Preoperative assessment of deep myometrial and cervical invasion in endometrial carcinoma: comparison of magnetic resonance imaging and histopathologic evaluation

This study aimed to evaluate the accuracy of magnetic resonance imaging (MRI) in the detection of deep myometrial invasion and cervical extension by endometrial carcinoma. This prospective study included 101 patients with histologically documented endometrial carcinoma, between July 1998 and April 2004. The findings of preoperative pelvic MRI were compared with histological diagnosis. From 101 cases studied by pelvic MRI, 43 were classified as deep myometrial invasion (50% of myometrium), where the pathological evaluation confirmed as having deep myometrial invasion. Cervical extension in the MRI study was found in 19 cases. Pathologic study found cervical extension and/or invasion in 31 cases including all cases identified by MRI. The accuracy, sensitivity and specificity of MRI were 95%, 89%, 100%, detecting deep myometrial invasion and 88%, 61%, 100%, detecting cervical invasion, respectively. The high accuracy achieved makes MRI an adequate method for determine the depth of myometrial and cervical invasion in endometrial carcinoma.

Head repositioning accuracy in patients with neck pain and asymptomatic subjects: concurrent validity, influence of motion speed, motion direction and target distance

Background: Cervicocephalic kinesthetic deficiencies have been demonstrated in patients with chronic neck pain (NP). On the other hand, authors emphasized the use of different motion speeds for assessing functional impairment of the cervical spine. Purpose: The objectives of this study were (1) to investigate the head repositioning accuracy in NP patients and control subjects and (2) to assess the influence of target distance, motion speed, motion direction and pain. Materials and methods: Seventy-one subjects (36 healthy subjects and 35 NP patients; age 30–55 years) performed the head repositioning test (HRT) at two different speeds for horizontal and vertical movements and at two different distances. For each condition, six consecutive trials were sampled. Results: The study showed the validity and reproducibility of the HRT, confirming a dysfunctional threshold of 4.5°. Normative values of head repositioning error up to 3.6° and 7.1° were identified for healthy and NP subjects, respectively. A distance of 180 cm from the target and a natural motion speed increased HRT accuracy. Repositioning after extension movement showed a significantly larger error in both groups. Intensity, duration of pain as well as pain level did not significantly alter head repositioning error. Conclusions: The assessment of proprioceptive performance in healthy and NP subjects allowed the validation of the HRT. The HRT is a simple, not expensive and fast test, easily implementable in daily practice to assess and monitor treatment and evolution of proprioceptive cervical deficits.

Roof region dependent wind potential assessment with different RANS turbulence models.

The analysis of the wind flow around buildings has a great interest from the point of view of the wind energy assessment, pollutant dispersion control, natural ventilation and pedestrians wind comfort and safety. Since LES turbulence models are computationally time consuming when applied to real geometries, RANS models are still widely used. However, RANS models are very sensitive to the chosen turbulence parametrisation and the results can vary according to the application. In this investigation, the simulation of the wind flow around an isolated building is performed using various types of RANS turbulence models in the open source code OpenFOAM, and the results are compared with benchmark experimental data. In order to confirm the numerical accuracy of the simulations, a grid dependency analysis is performed and the convergence index and rate are calculated. Hit rates are calculated for all the cases and the models that successfully pass a validation criterion are analysed at different regions of the building roof, and the most accurate RANS models for the modelling of the flow at each region are identified. The characteristics of the wind flow at each region are also analysed from the point of view of the wind energy generation, and the most adequate wind turbine model for the wind energy exploitation at each region of the building roof is chosen.

Application-Based Analysis of Register File Criticality for Reliability Assessment in Embedded Microprocessors

There is an increasing concern to reduce the cost and overheads during the development of reliable systems. Selective protection of most critical parts of the systems represents a viable solution to obtain a high level of reliability at a fraction of the cost. In particular to design a selective fault mitigation strategy for processor-based systems, it is mandatory to identify and prioritize the most vulnerable registers in the register file as best candidates to be protected (hardened). This paper presents an application-based metric to estimate the criticality of each register from the microprocessor register file in microprocessor-based systems. The proposed metric relies on the combination of three different criteria based on common features of executed applications. The applicability and accuracy of our proposal have been evaluated in a set of applications running in different microprocessors. Results show a significant improvement in accuracy compared to previous approaches and regardless of the underlying architecture.

IMPLEMENTATION OF PHOTOGRAMMETRY TO IMPROVE PROACTIVE ASSESSMENT OF RETAINING WALLS ALONG TRANSPORTATION CORRIDORS

Retaining walls are important assets in the transportation infrastructure and assessing their condition is important to prolong their performance and ultimately their design life. Retaining walls are often overlooked and only a few transportation asset management programs consider them in their inventory. Because these programs are few, the techniques used to assess their condition focus on a qualitative assessment as opposed to a quantitative approach. The work presented in this thesis focuses on using photogrammetry to quantitatively assess the condition of retaining walls. Multitemporal photogrammetry is used to develop 3D models of the retaining walls, from which offset displacements are measured to assess their condition. This study presents a case study from a site along M-10 highway in Detroit, MI were several sections of retaining walls have experienced horizontal displacement towards the highway. The results are validated by comparing with field observations and measurements. The limitations of photogrammetry were also studied by using a small scale model in the laboratory. The analysis found that the accuracy of the offset displacement measurements is dependent on the distance between the retaining wall and the sensor, location of the reference points in 3D space, and the focal length of the lenses used by the camera. These parameters were not ideal for the case study at the M-10 highway site, but the results provided consistent trends in the movement of the retaining wall that couldn’t be validated from offset measurements. The findings of this study confirm that photogrammetry shows promise in generating 3D models to provide a quantitative condition assessment for retaining walls within its limitations.

Assessment of the Occurrence and Potential Risks of Antibiotics and their Metabolites in South Florida Waters Using Liquid Chromatography Tandem Mass Spectrometry

An automated on-line SPE-LC-MS/MS method was developed for the quantitation of multiple classes of antibiotics in environmental waters. High sensitivity in the low ng/L range was accomplished by using large volume injections with 10-mL of sample. Positive confirmation of analytes was achieved using two selected reaction monitoring (SRM) transitions per antibiotic and quantitation was performed using an internal standard approach. Samples were extracted using online solid phase extraction, then using column switching technique; extracted samples were immediately passed through liquid chromatography and analyzed by tandem mass spectrometry. The total run time per each sample was 20 min. The statistically calculated method detection limits for various environmental samples were between 1.2 and 63 ng/L. Furthermore, the method was validated in terms of precision, accuracy and linearity. The developed analytical methodology was used to measure the occurrence of antibiotics in reclaimed waters (n=56), surface waters (n=53), ground waters (n=8) and drinking waters (n=54) collected from different parts of South Florida. In reclaimed waters, the most frequently detected antibiotics were nalidixic acid, erythromycin, clarithromycin, azithromycin trimethoprim, sulfamethoxazole and ofloxacin (19.3-604.9 ng/L). Detection of antibiotics in reclaimed waters indicates that they can’t be completely removed by conventional wastewater treatment process. Furthermore, the average mass loads of antibiotics released into the local environment through reclaimed water were estimated as 0.248 Kg/day. Among the surface waters samples, Miami River (reaching up to 580 ng/L) and Black Creek canal (up to 124 ng/L) showed highest concentrations of antibiotics. No traces of antibiotics were found in ground waters. On the other hand, erythromycin (monitored as anhydro erythromycin) was detected in 82% of the drinking water samples (n.d-66 ng/L). The developed approach is suitable for both research and monitoring applications. Major metabolites of antibiotics in reclaimed wates were identified and quantified using high resolution benchtop Q-Exactive orbitrap mass spectrometer. A phase I metabolite of erythromycin was tentatively identified in full scan based on accurate mass measurement. Using extracted ion chromatogram (XIC), high resolution data-dependent MS/MS spectra and metabolic profiling software the metabolite was identified as desmethyl anhydro erythromycin with molecular formula C36H63NO12 and m/z 702.4423. The molar concentration of the metabolite to erythromycin was in the order of 13 %. To my knowledge, this is the first known report on this metabolite in reclaimed water. Another compound acetyl-sulfamethoxazole, a phase II metabolite of sulfamethoxazole was also identified in reclaimed water and mole fraction of the metabolite represent 36 %, of the cumulative sulfamethoxazole concentration. The results were illustrating the importance to include metabolites also in the routine analysis to obtain a mass balance for better understanding of the occurrence, fate and distribution of antibiotics in the environment. Finally, all the antibiotics detected in reclaimed and surface waters were investigated to assess the potential risk to the aquatic organisms. The surface water antibiotic concentrations that represented the real time exposure conditions revealed that the macrolide antibiotics, erythromycin, clarithromycin and tylosin along with quinolone antibiotic, ciprofloxacin were suspected to induce high toxicity to aquatic biota. Preliminary results showing that, among the antibiotic groups tested, macrolides posed the highest ecological threat, and therefore, they may need to be further evaluated with, long-term exposure studies considering bioaccumulation factors and more number of species selected. Overall, the occurrence of antibiotics in aquatic environment is posing an ecological health concern.

Assessment of MALDI-TOF MS as Alternative Tool for Streptococcus suis Identification

The accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identifying Streptococcus suis isolates obtained from pigs, wild animals, and humans was evaluated using a PCR-based identification assay as the gold standard. In addition, MALDI-TOF MS was compared with the commercial multi-tests Rapid ID 32 STREP system. From the 129 S. suis isolates included in the study and identified by the molecular method, only 31 isolates (24.03%) had score values ≥2.300 and 79 isolates (61.24%) gave score values between 2.299 and 2.000. After updating the currently available S. suis MALDI Biotyper database with the spectra of three additional clinical isolates of serotypes 2, 7, and 9, most isolates had statistically significant higher score values (mean score: 2.65) than those obtained using the original database (mean score: 2.182). Considering the results of the present study, we suggest using a less restrictive threshold score of ≥2.000 for reliable species identification of S. suis. According to this cut-off value, a total of 125 S. suis isolates (96.9%) were correctly identified using the updated database. These data indicate an excellent performance of MALDI-TOF MS for the identification of S. suis.

Assessment of the sensitivity and specificity of serological (IFAT) and molecular (direct PCR) techniques for diagnosis of leishmaniasis in lagomorphs using a Bayesian approach

Leishmaniasis, caused by Leishmania infantum, is a vector-borne zoonotic disease that is endemic to the Mediterranean basin. The potential of rabbits and hares to serve as competent reservoirs for the disease has recently been demonstrated, although assessment of the importance of their role on disease dynamics is hampered by the absence of quantitative knowledge on the accuracy of diagnostic techniques in these species. A Bayesian latent-class model was used here to estimate the sensitivity and specificity of the Immuno-fluorescence antibody test (IFAT) in serum and a Leishmania-nested PCR (Ln-PCR) in skin for samples collected from 217 rabbits and 70 hares from two different populations in the region of Madrid, Spain. A two-population model, assuming conditional independence between test results and incorporating prior information on the performance of the tests in other animal species obtained from the literature, was used. Two alternative cut-off values were assumed for the interpretation of the IFAT results: 1/50 for conservative and 1/25 for sensitive interpretation. Results suggest that sensitivity and specificity of the IFAT were around 70–80%, whereas the Ln-PCR was highly specific (96%) but had a limited sensitivity (28.9% applying the conservative interpretation and 21.3% with the sensitive one). Prevalence was higher in the rabbit population (50.5% and 72.6%, for the conservative and sensitive interpretation, respectively) than in hares (6.7% and 13.2%). Our results demonstrate that the IFAT may be a useful screening tool for diagnosis of leishmaniasis in rabbits and hares. These results will help to design and implement surveillance programmes in wild species, with the ultimate objective of early detecting and preventing incursions of the disease into domestic and human populations.

Structured professional judgement approach to risk assessment: generalisability across patient groups for the prediction of adverse outcomes in secure mental health care

This is a redacted version of the the final thesis. Copyright material has been removed to comply with UK Copyright Law.

Assessment of resting energy expenditure in pediatric mitochondrial diseases with indirect calorimetry

Mitochondrial diseases (MD) are the most frequent inborn errors of metabolism. In affected tissues, MD can alter cellular oxygen consumption rate leading to potential decreases in whole-body resting energy expenditure (REE), but data on pediatric children are absent. We determined, using indirect calorimetry (IC), whole-body oxygen consumption (VO2), carbon dioxide production (VCO2), respiratory quotient (RQ) and REE in pediatric patients with MD and healthy controls. Another goal was to assess the accuracy of available predictive equations for REE estimation in this patient population. IC data were obtained under fasting and resting conditions in 20 MD patients and 27 age and gender-matched healthy peers. We determined the agreement between REE measured with IC and REE estimated with Schofield weight and FAO/WHO/UNU equations. Mean values of VO2, VCO2 (mL·min-1·kg-1) or RQ did not differ significantly between patients and controls (P = 0.085, P = 0.055 and P = 0.626 respectively). Accordingly, no significant differences (P = 0.086) were found for REE (kcal·day-1 kg-1) either. On the other hand, although we found no significant differences between IC-measured REE and Schofield or FAO/WHO/UNU-estimated REE, Bland-Altman analysis revealed wide limits of agreement and there were some important individual differences between IC and equation-derived REE. VO2, VCO2, RQ and REE are not significantly altered in pediatric patients with MD compared with healthy controls. The energy demands of pediatric patients with MD should be determined based on IC data in order to provide the best possible personalized nutritional management for these children.

Assessment of interstitial lung disease in Sjögren’s syndrome by lung ultrasound: a pilot study of correlation with high-resolution chest tomography

The background of this study is to assess the accuracy of lung ultrasound (LUS) to diagnose interstitial lung disease (ILD) in Sjögren’s syndrome (Sjs), in patients who have any alterations in pulmonary function tests (PFT) or respiratory symptoms. LUS was correlated with chest tomography (hrCT), considering it as the imaging gold standard technique to diagnose ILD. This is a pilot, multicenter, cross-sectional, and consecutive-case study. The inclusion criteria are ≥18 years old, Signs and symptoms: according to ACEG 2002 criteria, respiratory symptoms (dyspnea, cough), or any alterations in PFR. LUS was done following the International Consensus Conference on Lung Ultrasound protocol for interstitial syndrome (B pattern). Of the 50 patients in follow-up, 13 (26%) met the inclusion criteria. All were women with age 63.62 years (range 39–88). 78.6% of the cases had primary Sjs (SLE, RA, n = 2). The intra-rater reliability k is 1, according to Gwet’s Ac1 and GI index (probability to concordance—e(K)—, by Cohen, of 0.52). LUS has a sensitivity of 1 (95% CI 0.398–1.0), specificity of 0.89 (95% CI 0.518–0.997), and a positive probability reason of 9.00 (95% CI 7.1–11.3) to detect ILD. The correlation of Pearson is r = 0.84 (p < 0.001). To check the accuracy of LUS to diagnose ILD, a completely bilateral criterion of yes/no for interstitial pattern was chosen, AUC reaches significance, 0.94 (0.07) (95% CI 0.81–1.0, p = 0.014). LUS reaches an excellent correlation to hrCT in Sjs affected with ILD, and might be a useful technique in daily clinical practice for the assessment of pulmonary disease in the sicca syndrome. © 2016 SIMI

A micro-extraction technique using a new digitally controlled syringe combined with UHPLC for assessment of urinary biomarkers of oxidatively damaged DNA

The formation of reactive oxygen species (ROS) within cells causes damage to biomolecules, including membrane lipids, DNA, proteins and sugars. An important type of oxidative damage is DNA base hydroxylation which leads to the formation of 8-oxo-7,8-dihydro-29-deoxyguanosine (8-oxodG) and 5-hydroxymethyluracil (5-HMUra). Measurement of these biomarkers in urine is challenging, due to the low levels of the analytes and the matrix complexity. In order to simultaneously quantify 8-oxodG and 5-HMUra in human urine, a new, reliable and powerful strategy was optimised and validated. It is based on a semi-automatic microextraction by packed sorbent (MEPS) technique, using a new digitally controlled syringe (eVolH), to enhance the extraction efficiency of the target metabolites, followed by a fast and sensitive ultrahigh pressure liquid chromatography (UHPLC). The optimal methodological conditions involve loading of 250 mL urine sample (1:10 dilution) through a C8 sorbent in a MEPS syringe placed in the semi-automatic eVolH syringe followed by elution using 90 mL of 20% methanol in 0.01% formic acid solution. The obtained extract is directly analysed in the UHPLC system using a binary mobile phase composed of aqueous 0.1% formic acid and methanol in the isocratic elution mode (3.5 min total analysis time). The method was validated in terms of selectivity, linearity, limit of detection (LOD), limit of quantification (LOQ), extraction yield, accuracy, precision and matrix effect. Satisfactory results were obtained in terms of linearity (r2 . 0.991) within the established concentration range. The LOD varied from 0.00005 to 0.04 mg mL21 and the LOQ from 0.00023 to 0.13 mg mL21. The extraction yields were between 80.1 and 82.2 %, while inter-day precision (n=3 days) varied between 4.9 and 7.7 % and intra-day precision between 1.0 and 8.3 %. This approach presents as main advantages the ability to easily collect and store urine samples for further processing and the high sensitivity, reproducibility, and robustness of eVolHMEPS combined with UHPLC analysis, thus retrieving a fast and reliable assessment of oxidatively damaged DNA.

Field-oriented assessment of agricultural crops through temporal segmentation of modis VI data.

Monitoring agricultural crops constitutes a vital task for the general understanding of land use spatio-temporal dynamics. This paper presents an approach for the enhancement of current crop monitoring capabilities on a regional scale, in order to allow for the analysis of environmental and socio-economic drivers and impacts of agricultural land use. This work discusses the advantages and current limitations of using 250m VI data from the Moderate Resolution Imaging Spectroradiometer (MODIS) for this purpose, with emphasis in the difficulty of correctly analyzing pixels whose temporal responses are disturbed due to certain sources of interference such as mixed or heterogeneous land cover. It is shown that the influence of noisy or disturbed pixels can be minimized, and a much more consistent and useful result can be attained, if individual agricultural fields are identified and each field's pixels are analyzed in a collective manner. As such, a method is proposed that makes use of image segmentation techniques based on MODIS temporal information in order to identify portions of the study area that agree with actual agricultural field borders. The pixels of each portion or segment are then analyzed individually in order to estimate the reliability of the temporal signal observed and the consequent relevance of any estimation of land use from that data. The proposed method was applied in the state of Mato Grosso, in mid-western Brazil, where extensive ground truth data was available. Experiments were carried out using several supervised classification algorithms as well as different subsets of land cover classes, in order to test the methodology in a comprehensive way. Results show that the proposed method is capable of consistently improving classification results not only in terms of overall accuracy but also qualitatively by allowing a better understanding of the land use patterns detected. It thus provides a practical and straightforward procedure for enhancing crop-mapping capabilities using temporal series of moderate resolution remote sensing data.

A framework for the environmental risk assessment of offshore carbon storage in CCS systems

Carbon capture and storage (CCS) represents an interesting climate mitigation option, however, as for any other human activity, there is the impelling need to assess and manage the associated risks. This study specifically addresses the marine environmental risk posed by CO2 leakages associated to CCS subsea engineering system, meant as offshore pipelines and injection / plugged and abandoned wells. The aim of this thesis work is to start approaching the development of a complete and standardized practical procedure to perform a quantified environmental risk assessment for CCS, with reference to the specific activities mentioned above. Such an effort would be of extreme relevance not only for companies willing to implement CCS, as a methodological guidance, but also, by uniformizing the ERA procedure, to begin changing people’s perception about CCS, that happens to be often discredited due to the evident lack of comprehensive and systematic methods to assess the impacts on the marine environment. The backbone structure of the framework developed consists on the integration of ERA’s main steps and those belonging to the quantified risk assessment (QRA), in the aim of quantitatively characterizing risk and describing it as a combination of magnitude of the consequences and their frequency. The framework developed by this work is, however, at a high level, as not every single aspect has been dealt with in the required detail. Thus, several alternative options are presented to be considered for use depending on the situation. Further specific studies should address their accuracy and efficiency and solve the knowledge gaps emerged, in order to establish and validate a final and complete procedure. Regardless of the knowledge gaps and uncertainties, that surely need to be addressed, this preliminary framework already finds some relevance in on field applications, as a non-stringent guidance to perform CCS ERA, and it constitutes the foundation of the final framework.