A Validation Study for the Use of ROS1 Immunohistochemical Staining in Screening for ROS1 Translocations in Lung Cancer

INTRODUCTION: The presence of ROS proto-oncogene 1, receptor tyrosine kinase gene (ROS1) rearrangements in lung cancers confers sensitivity to ROS kinase inhibitors, including crizotinib. However, they are rare abnormalities (in ∼1% of non-small cell lung carcinomas) that are typically identified by fluorescence in situ hybridization (FISH), and so screening using immunohistochemical (IHC) staining would be both cost- and time-efficient.

METHODS: A cohort of lung tumors negative for other common mutations related to targeted therapies were screened to assess the sensitivity and specificity of IHC staining in detecting ROS1 gene rearrangements, enriched by four other cases first identified by FISH. A review of published data was also undertaken.

RESULTS: IHC staining was 100% sensitive (95% confidence interval: 48-100) and 83% specific (95% confidence interval: 86-100) overall when an h-score higher than 100 was used. Patients with ROS1 gene rearrangements were younger and typically never-smokers, with the tumors all being adenocarcinomas with higher-grade architectural features and focal signet ring morphologic features (two of five). Four patients treated with crizotinib showed a partial response, with three also showing a partial response to pemetrexed. Three of four patients remain alive at 13, 27, and 31 months, respectively.

CONCLUSION: IHC staining can be used to screen for ROS1 gene rearrangements, with patients herein showing a response to crizotinib. Patients with tumors that test positive according to IHC staining but negative according to FISH were also identified, which may have implications for treatment selection.

STOPPFrail (Screening Tool of Older Persons Prescriptions in Frail Adults with Limited Life Expectancy): Consensus Validation

Background: To validate STOPPFrail, a list of explicit criteria for potentially inappropriate medications (PIMs) in frailer older adults with limited life expectancy. A Delphi consensus survey of an expert panel (n = 17) comprising specialists in geriatric medicine, clinical pharmacology, palliative care, psychiatry of old age, clinical pharmacy and general practice.
Methods: STOPPFrail criteria was initially created by the authors based on clinical
experience and appraisal of the available literature. Criteria were organised according to physiological system. Each criterion was accompanied by an explanation. Panellists ranked their agreement with each criterion on a 5-point Likert scale and invited to provide written feedback. Criteria with a median Likert response of 4/5 (agree/strongly agree) and a 25th centile of ≥4 were included in the final criteria.
Results: Three Delphi rounds were required. All panellists completed all rounds. Thirty criteria were proposed for inclusion; 26 were accepted. No new criteria were added. The first two criteria suggest deprescribing medications with no indication or where compliance is poor. The remaining 24 criteria include lipid-lowering therapies, alpha-blockers for hypertension, anti-platelets, neuroleptics, proton pump inhibitors, H-2 receptor antagonists, anti-spasmodics, theophylline, leukotriene antagonists, calcium supplements, bone anti-resorptive therapy, selective oestrogen receptor modulators, non-steroidal antiinflammatories, corticosteroids, 5-alpha reductase inhibitors, alpha-1 selective blockers, muscarinic antagonists, oral diabetic agents, ACE-inhibitors, angiotensin receptor blockers, systemic oestrogens, multivitamins, nutritional supplements and prophylactic antibiotics. Anticoagulants and anti-depressants were excluded. Despite incorporation of panellists’ suggestions, memantine and acetyl-cholinesterase inhibitors remained inconclusive.
Conclusion: STOPPFrail comprises 26 criteria, which have been judged by broad consensus, to be potentially inappropriate in frailer older patients with limited life expectancy. STOPPFrail may assist in deprescribing medications in these patients.

New methods for movement technique development in cross-country skiing using mathematical models and simulation

This Licentiate Thesis is devoted to the presentation and discussion of some new contributions in applied mathematics directed towards scientific computing in sports engineering. It considers inverse problems of biomechanical simulations with rigid body musculoskeletal systems especially in cross-country skiing. This is a contrast to the main research on cross-country skiing biomechanics, which is based mainly on experimental testing alone. The thesis consists of an introduction and five papers. The introduction motivates the context of the papers and puts them into a more general framework. Two papers (D and E) consider studies of real questions in cross-country skiing, which are modelled and simulated. The results give some interesting indications, concerning these challenging questions, which can be used as a basis for further research. However, the measurements are not accurate enough to give the final answers. Paper C is a simulation study which is more extensive than paper D and E, and is compared to electromyography measurements in the literature. Validation in biomechanical simulations is difficult and reducing mathematical errors is one way of reaching closer to more realistic results. Paper A examines well-posedness for forward dynamics with full muscle dynamics. Moreover, paper B is a technical report which describes the problem formulation and mathematical models and simulation from paper A in more detail. Our new modelling together with the simulations enable new possibilities. This is similar to simulations of applications in other engineering fields, and need in the same way be handled with care in order to achieve reliable results. The results in this thesis indicate that it can be very useful to use mathematical modelling and numerical simulations when describing cross-country skiing biomechanics. Hence, this thesis contributes to the possibility of beginning to use and develop such modelling and simulation techniques also in this context.

Studies on Bio-Geochemistry, Bio-Optical Properties and Satellite Validation of Coastal Waters of South Eastern Arabian Sea

In situ methods used for water quality assessment have both physical and time constraints. Just a limited number of sampling points can be performed due to this, making it difficult to capture the range and variability of coastal processes and constituents. In addition, the mixing between fresh and oceanic water creates complex physical, chemical and biological environment that are difficult to understand, causing the existing measurement methodologies to have significant logistical, technical, and economic challenges and constraints. Remote sensing of ocean colour makes it possible to acquire information on the distribution of chlorophyll and other constituents over large areas of the oceans in short periods. There are many potential applications of ocean colour data. Satellite-derived products are a key data source to study the distribution pattern of organisms and nutrients (Guillaud et al. 2008) and fishery research (Pillai and Nair 2010; Solanki et al. 2001. Also, the study of spatial and temporal variability of phytoplankton blooms, red tide identification or harmful algal blooms monitoring (Sarangi et al. 2001; Sarangi et al. 2004; Sarangi et al. 2005; Bhagirathan et al., 2014), river plume or upwelling assessments (Doxaran et al. 2002; Sravanthi et al. 2013), global productivity analyses (Platt et al. 1988; Sathyendranath et al. 1995; IOCCG2006) and oil spill detection (Maianti et al. 2014). For remote sensing to be accurate in the complex coastal waters, it has to be validated with the in situ measured values. In this thesis an attempt to study, measure and validate the complex waters with the help of satellite data has been done. Monitoring of coastal ecosystem health of Arabian Sea in a synoptic way requires an intense, extensive and continuous monitoring of the water quality indicators. Phytoplankton determined from chl-a concentration, is considered as an indicator of the state of the coastal ecosystems. Currently, satellite sensors provide the most effective means for frequent, synoptic, water-quality observations over large areas and represent a potential tool to effectively assess chl-a concentration over coastal and oceanic waters; however, algorithms designed to estimate chl-a at global scales have been shown to be less accurate in Case 2 waters, due to the presence of water constituents other than phytoplankton which do not co-vary with the phytoplankton. The constituents of Arabian Sea coastal waters are region-specific because of the inherent variability of these optically-active substances affected by factors such as riverine input (e.g. suspended matter type and grain size, CDOM) and phytoplankton composition associated with seasonal changes.

Isolation and Validation of Anti-B7-H4 scFvs from an Ovarian Cancer scFv Yeast-Display Library.

B7-H4 (VTCN1, B7x, B7s) is an inhibitory modulator of T-cell response implicated in antigen tolerization. As such, B7-H4 is an immune checkpoint of potential therapeutic interest. To generate anti-B7-H4 targeting reagents, we isolated antibodies by differential cell screening of a yeast-display library of recombinant antibodies (scFvs) derived from ovarian cancer patients and we screened for functional scFvs capable to interfere with B7-H4-mediated inhibition of antitumor responses. We found one antibody binding to B7-H4 that could restore antitumor T cell responses. This chapter gives an overview of the methods we developed to isolate a functional anti-B7-H4 antibody fragment.

External Validation of the ProACS Score for Risk Stratification of Patients with Acute Coronary Syndromes

INTRODUCTION: The ProACS risk score is an early and simple risk stratification score developed for all-cause in-hospital mortality in acute coronary syndromes (ACS) from a Portuguese nationwide ACS registry. Our center only recently participated in the registry and was not included in the cohort used for developing the score. Our objective was to perform an external validation of this risk score for short- and long-term follow-up. METHODS: Consecutive patients admitted to our center with ACS were included. Demographic and admission characteristics, as well as treatment and outcome data were collected. The ProACS risk score variables are age (≥72 years), systolic blood pressure (≤116 mmHg), Killip class (2/3 or 4) and ST-segment elevation. We calculated ProACS, Global Registry of Acute Coronary Events (GRACE) and Canada Acute Coronary Syndrome risk score (C-ACS) risk scores for each patient. RESULTS: A total of 3170 patients were included, with a mean age of 64±13 years, 62% with ST-segment elevation myocardial infarction. All-cause in-hospital mortality was 5.7% and 10.3% at one-year follow-up. The ProACS risk score showed good discriminative ability for all considered outcomes (area under the receiver operating characteristic curve >0.75) and a good fit, similar to C-ACS, but lower than the GRACE risk score and slightly lower than in the original development cohort. The ProACS risk score provided good differentiation between patients at low, intermediate and high mortality risk in both short- and long-term follow-up (p<0.001 for all comparisons). CONCLUSIONS: The ProACS score is valid in external cohorts for risk stratification for ACS. It can be applied very early, at the first medical contact, but should subsequently be complemented by the GRACE risk score.

Evaluating statistical and machine learning methods to predict risk of in-hospital child mortality in Uganda

Thesis (Master's)--University of Washington, 2016-08

Développement et validation d’un questionnaire sur les connaissances en nutrition pour une population Canadienne-française

Plusieurs facteurs d’ordre environnemental, social ou individuel peuvent influencer l’adhésion à une saine alimentation. Parmi les déterminants individuels, les connaissances en nutrition ont un rôle à jouer. D’ailleurs, de nombreux programmes de promotion de la saine alimentation se basent sur une amélioration des connaissances en nutrition pour engendrer des changements positifs dans les comportements et les apports alimentaires de la population. Plusieurs études ont associé positivement le niveau de connaissances en nutrition et l’alimentation saine, mais il a été observé que les associations sont plus marquées avec l’utilisation de questionnaires validés sur les connaissances en nutrition. Une validation rigoureuse des questionnaires est donc primordiale pour assurer la validité des résultats obtenus. Au Canada, il n’existe pas d’outil spécifiquement conçu pour mesurer les connaissances en nutrition et plus précisément l’adhésion à la saine alimentation telle que présentée par le Guide alimentaire canadien (GAC), et ce mémoire illustre la pertinence d’un tel instrument pour la population canadienne. Les résultats de la validation ont mené à l’obtention d’un questionnaire valide et fiable pour la population à l’étude. L’usage de documents reconnus dans la littérature pour la conception du questionnaire de même que l’application de plusieurs méthodes de validation telles qu’utilisées par d’autres auteurs dans le domaine ont permis de bien valider l’instrument. Le questionnaire développé pourrait donc permettre la mesure adéquate des connaissances en nutrition dans un contexte canadien-français.

Insight assessment in psychosis and psychopathological correlates: validation of the Spanish version of the Schedule for Assessment of Insight - Expanded Version

Background and Objectives: Lack of insight is a cardinal feature of psycho­sis. Insight has been found to be a multidimensional concept, including awareness of having a mental illness, ability to relabel psychotic phenomena as abnormal and compliance with treatment., which can be measured with the Schedule for Assessment of Insight (SAI-E). The aim of this study was to validate the Spanish version of SAI-E. Methods: The SAI-E was translated into Spanish and back-translated into English, which was deemed appropriate by the original scale author. Next, the Spanish version of the SAI-E was administered to 39 patients with schizophrenia or schizoaffective disorder (DSM-IV criteria) from a North Peruvian psychiatric hospital. The Positive and Negative Syndrome Scale for Schizophrenia (PANSS) and the Scale of Unawareness of Mental Disorder (SUMD) were also administered. Specifically, internal consistency and convergent validity were assessed. Results: Internal consistency between the 11 items of the SAI-E was found to be good to excellent (α = 0.942). Compliance items did not contribute to internal consistency (A = 0.417, B = 572). Inter-rater reliability was excellent (ICC = 0.99). Regarding concurrent validity, the SAI-E total score correlated negatively with the lack of insight and judgement item of the PANNS (r = -0.91, p <0.01) and positively with the SUMD total score (r = 0.92, p <0.001). Conclusions: The Spanish version of the SAI-E scale was demonstrated to have both excellent reliability and external validity in our sample of South American Spanish-speaking patients with schizophrenia spectrum disorders.

Adaptation and validation into Portuguese language of the HIV Antibody Testing Attitude Scale

Objective. To culturally adapt and validate a version in European Portuguese language of the HIV Antibody Testing Attitude Scale. Methods. Study conducting a methodological investigation for the adaptation and validation of an attitude measurement instrument. The instrument translation and back-translation were performed. Then, a pre-test was conducted. The study used a sample of 317 subjects from the academic community - students, professors and other professionals - who were contacted in the campus. Ethical principles were observed. Results. Three analyses were conducted using the method of principal component analysis (PCA) with five, four and three factors. A three-factor solution was achieved, which presents 50.82% variance. In the analysis of inter-item correlation, values between -0.018 and 0.749 were observed. Internal consistency shows Cronbach’s alpha coefficients of 0.860 overall and between 0.865 and 0.659 in the three factors. Conclusion. The instrument version shows psychometric properties that allow its use in Portuguese-speaking countries.

STATISTICAL METHODS FOR ADVANCED ECONOMETRIC MODELS WITH APPLICATIONS TO VEHICLE HOLDING AND SPEED QUANTILES DISTRIBUTION

This dissertation proposes statistical methods to formulate, estimate and apply complex transportation models. Two main problems are part of the analyses conducted and presented in this dissertation. The first method solves an econometric problem and is concerned with the joint estimation of models that contain both discrete and continuous decision variables. The use of ordered models along with a regression is proposed and their effectiveness is evaluated with respect to unordered models. Procedure to calculate and optimize the log-likelihood functions of both discrete-continuous approaches are derived, and difficulties associated with the estimation of unordered models explained. Numerical approximation methods based on the Genz algortithm are implemented in order to solve the multidimensional integral associated with the unordered modeling structure. The problems deriving from the lack of smoothness of the probit model around the maximum of the log-likelihood function, which makes the optimization and the calculation of standard deviations very difficult, are carefully analyzed. A methodology to perform out-of-sample validation in the context of a joint model is proposed. Comprehensive numerical experiments have been conducted on both simulated and real data. In particular, the discrete-continuous models are estimated and applied to vehicle ownership and use models on data extracted from the 2009 National Household Travel Survey. The second part of this work offers a comprehensive statistical analysis of free-flow speed distribution; the method is applied to data collected on a sample of roads in Italy. A linear mixed model that includes speed quantiles in its predictors is estimated. Results show that there is no road effect in the analysis of free-flow speeds, which is particularly important for model transferability. A very general framework to predict random effects with few observations and incomplete access to model covariates is formulated and applied to predict the distribution of free-flow speed quantiles. The speed distribution of most road sections is successfully predicted; jack-knife estimates are calculated and used to explain why some sections are poorly predicted. Eventually, this work contributes to the literature in transportation modeling by proposing econometric model formulations for discrete-continuous variables, more efficient methods for the calculation of multivariate normal probabilities, and random effects models for free-flow speed estimation that takes into account the survey design. All methods are rigorously validated on both real and simulated data.

Multi-body simulation of a canine hind limb: model development, experimental validation and calculation of ground reaction forces

Background: Among other causes the long-term result of hip prostheses in dogs is determined by aseptic loosening. A prevention of prosthesis complications can be achieved by an optimization of the tribological system which finally results in improved implant duration. In this context a computerized model for the calculation of hip joint loadings during different motions would be of benefit. In a first step in the development of such an inverse dynamic multi-body simulation (MBS-) model we here present the setup of a canine hind limb model applicable for the calculation of ground reaction forces. Methods: The anatomical geometries of the MBS-model have been established using computer tomography- (CT-) and magnetic resonance imaging- (MRI-) data. The CT-data were collected from the pelvis, femora, tibiae and pads of a mixed-breed adult dog. Geometric information about 22 muscles of the pelvic extremity of 4 mixed-breed adult dogs was determined using MRI. Kinematic and kinetic data obtained by motion analysis of a clinically healthy dog during a gait cycle (1 m/s) on an instrumented treadmill were used to drive the model in the multi-body simulation. Results and Discussion: As a result the vertical ground reaction forces (z-direction) calculated by the MBS-system show a maximum deviation of 1.75%BW for the left and 4.65%BW for the right hind limb from the treadmill measurements. The calculated peak ground reaction forces in z- and y-direction were found to be comparable to the treadmill measurements, whereas the curve characteristics of the forces in y-direction were not in complete alignment. Conclusion: In conclusion, it could be demonstrated that the developed MBS-model is suitable for simulating ground reaction forces of dogs during walking. In forthcoming investigations the model will be developed further for the calculation of forces and moments acting on the hip joint during different movements, which can be of help in context with the in silico development and testing of hip prostheses.

A deformation model of flexible, high area-to-mass ratio debris under perturbations and validation method

A new type of space debris was recently discovered by Schildknecht in near -geosynchronous orbit (GEO). These objects were later identified as exhibiting properties associated with High Area-to-Mass ratio (HAMR) objects. According to their brightness magnitudes (light curve), high rotation rates and composition properties (albedo, amount of specular and diffuse reflection, colour, etc), it is thought that these objects are multilayer insulation (MLI). Observations have shown that this debris type is very sensitive to environmental disturbances, particularly solar radiation pressure, due to the fact that their shapes are easily deformed leading to changes in the Area-to-Mass ratio (AMR) over time. This thesis proposes a simple effective flexible model of the thin, deformable membrane with two different methods. Firstly, this debris is modelled with Finite Element Analysis (FEA) by using Bernoulli-Euler theory called “Bernoulli model”. The Bernoulli model is constructed with beam elements consisting 2 nodes and each node has six degrees of freedom (DoF). The mass of membrane is distributed in beam elements. Secondly, the debris based on multibody dynamics theory call “Multibody model” is modelled as a series of lump masses, connected through flexible joints, representing the flexibility of the membrane itself. The mass of the membrane, albeit low, is taken into account with lump masses in the joints. The dynamic equations for the masses, including the constraints defined by the connecting rigid rod, are derived using fundamental Newtonian mechanics. The physical properties of both flexible models required by the models (membrane density, reflectivity, composition, etc.), are assumed to be those of multilayer insulation. Both flexible membrane models are then propagated together with classical orbital and attitude equations of motion near GEO region to predict the orbital evolution under the perturbations of solar radiation pressure, Earth’s gravity field, luni-solar gravitational fields and self-shadowing effect. These results are then compared to two rigid body models (cannonball and flat rigid plate). In this investigation, when comparing with a rigid model, the evolutions of orbital elements of the flexible models indicate the difference of inclination and secular eccentricity evolutions, rapid irregular attitude motion and unstable cross-section area due to a deformation over time. Then, the Monte Carlo simulations by varying initial attitude dynamics and deformed angle are investigated and compared with rigid models over 100 days. As the results of the simulations, the different initial conditions provide unique orbital motions, which is significantly different in term of orbital motions of both rigid models. Furthermore, this thesis presents a methodology to determine the material dynamic properties of thin membranes and validates the deformation of the multibody model with real MLI materials. Experiments are performed in a high vacuum chamber (10-4 mbar) replicating space environment. A thin membrane is hinged at one end but free at the other. The free motion experiment, the first experiment, is a free vibration test to determine the damping coefficient and natural frequency of the thin membrane. In this test, the membrane is allowed to fall freely in the chamber with the motion tracked and captured through high velocity video frames. A Kalman filter technique is implemented in the tracking algorithm to reduce noise and increase the tracking accuracy of the oscillating motion. The forced motion experiment, the last test, is performed to determine the deformation characteristics of the object. A high power spotlight (500-2000W) is used to illuminate the MLI and the displacements are measured by means of a high resolution laser sensor. Finite Element Analysis (FEA) and multibody dynamics of the experimental setups are used for the validation of the flexible model by comparing with the experimental results of displacements and natural frequencies.

Knowledge about dietary fibres (KADF): development and validation of an evaluation instrument through structural equation modelling (SEM)

Objectives: Because there is scientific evidence that an appropriate intake of dietary fibre should be part of a healthy diet, given its importance in promoting health, the present study aimed to develop and validate an instrument to evaluate the knowledge of the general population about dietary fibres. Study design: The present study was a cross sectional study. Methods: The methodological study of psychometric validation was conducted with 6010 participants, residing in ten countries from 3 continents. The instrument is a questionnaire of self-response, aimed at collecting information on knowledge about food fibres. For exploratory factor analysis (EFA) was chosen the analysis of the main components using varimax orthogonal rotation and eigenvalues greater than 1. In confirmatory factor analysis by structural equation modelling (SEM) was considered the covariance matrix and adopted the Maximum Likelihood Estimation algorithm for parameter estimation. Results: Exploratory factor analysis retained two factors. The first was called Dietary Fibre and Promotion of Health (DFPH) and included 7 questions that explained 33.94 % of total variance ( = 0.852). The second was named Sources of Dietary Fibre (SDF) and included 4 questions that explained 22.46% of total variance ( = 0.786). The model was tested by SEM giving a final solution with four questions in each factor. This model showed a very good fit in practically all the indexes considered, except for the ratio 2/df. The values of average variance extracted (0.458 and 0.483) demonstrate the existence of convergent validity; the results also prove the existence of discriminant validity of the factors (r2 = 0.028) and finally good internal consistency was confirmed by the values of composite reliability (0.854 and 0.787). Conclusions: This study allowed validating the KADF scale, increasing the degree of confidence in the information obtained through this instrument in this and in future studies.

Biomarkers of Nitrosative Stress: Development and validation of a new analytical method for 3-Nitrotyrosine quantification

Background: The nitration of tyrosine residues in proteins is associated with nitrosative stress, resulting in the formation of 3-nitrotyrosine (3-NT). 3-NT levels in biological samples have been associated with numerous physiological and pathological conditions. For this reason, several attempts have been made in order to develop methods that accurately quantify 3-NT in biological samples. Regarding chromatographic methods, they seem to be very accurate, showing very good sensibility and specificity. However, accurate quantification of this molecule, which is present at very low concentrations both at physiological and pathological states, is always a complex task and a target of intense research. Objectives: We aimed to develop a simple, rapid, low-cost and sensitive 3-NT quantification method for use in medical laboratories as an additional tool for diagnosis and/or treatment monitoring of a wide range of pathologies. We also aimed to evaluate the performance of the HPLC-based method developed here in a wide range of biological matrices. Material and methods: All experiments were performed on a Hitachi LaChrom Elite® HPLC system and separation was carried out using a Lichrocart® 250-4 Lichrospher 100 RP-18 (5μm) column. The method was further validated according to ICH guidelines. The biological matrices tested were serum, whole blood, urine, B16 F-10 melanoma cell line, growth medium conditioned with the same cell line, bacterial and yeast suspensions. Results: From all the protocols tested, the best results were obtained using 0.5% CH3COOH:MeOH:H2O (15:15:70) as the mobile phase, with detection at wavelengths 215, 276 and 356 nm, at 25ºC, and using a flow rate of 1 mL/min. By using this protocol, it was possible to obtain a linear calibration curve (correlation coefficient = 1), limits of detection and quantification in the order of ng/mL, and a short analysis time (<15 minutes per sample). Additionally, the developed protocol allowed the successful detection and quantification of 3-NT in all biological matrices tested, with detection at 356 nm. Conclusion: The method described in this study, which was successfully developed and validated for 3-NT quantification, is simple, cheap and fast, rendering it suitable for analysis in a wide range of biological matrices.