Big Data NoSQL-järjestelmissä

Relaatiotietokannat ovat olleet vallitseva suunta suurissa tietokantajärjestelmissä jo 80-luvulta lähtien. Viimeisen vuosikymmenen aikana lähes kaikki teollinen ja henkilökohtainen tiedonvaihto on siirtynyt sähköiseen maailmaan. Tämä on aiheuttanut valtaisan kasvun datamäärissä. Sama kasvu jatkuu edelleen eksponentiaalisesti. Samalla ei-relaatiotietokannat eli NoSQL-tietokannat ovat nousseet huomattavaan asemaan. Monet organisaatiot käsittelevät suuria määriä järjestämätöntä dataa, jolloin perinteisen relaatiotietokannan käyttö yksin ei välttämättä ole paras, tai edes riittävä vaihtoehto. Web 2.0 -termin takana oleva internet-kulttuurin muutos tukee mukautuvampia ja skaalautuvia NoSQL-järjestelmiä. Internetin käyttäjät, erityisesti sosiaalisessa mediassa tuottavat valtavia määriä järjestymätöntä dataa. Kerättävä tieto ei ole enää tietyn mallin mukaan muotoiltua, vaan yksittäiseen tietueeseen saattaa liittyä esimerkiksi kuvia, videoita, viittauksia muiden käyttäjien luomiin instansseihin tai osoitetietoja. Tässä tutkielmassa käsitellään NoSQL-järjestelmien rakennetta sekä asemaa erityisesti suurissa tietojärjestelmissä ja vertaillaan niiden hyötyjä ja haittoja relaatiotietokantojen suhteen.

Magnetic resonance spectroscopy. Data analysis for clinical applications

This text is taken from the postgraduate thesis, which one of the authors (A.B.) developed for the degree of Medical Physicist in the School on Medical Physics of the University of Florence. The text explores the feasibility of quantitative Magnetic Resonance Spectroscopy as a tool for daily clinical routine use. The results and analysis comes from two types of hyper spectral images: the first set are hyper spectral images coming from a standard phantom (reference images); and hyper spectral images obtained from a group of patients who have undergone MRI examinations at the Santa Maria Nuova Hospital. This interdisciplinary work stems from the IFAC-CNR know how in terms of data analysis and nanomedicine, and the clinical expertise of Radiologists and Medical Physicists. The results reported here, which were the subject of the thesis, are original, unpublished, and represent independent work.

Estimation of whole body muscle, adipose/fat mass, validation in health and during weight loss. Development of prediction equations using MRI as reference method

Background: Body composition is affected by diseases, and affects responses to medical treatments, dosage of medicines, etc., while an abnormal body composition contributes to the causation of many chronic diseases. While we have reliable biochemical tests for certain nutritional parameters of body composition, such as iron or iodine status, and we have harnessed nuclear physics to estimate the body’s content of trace elements, the very basic quantification of body fat content and muscle mass remains highly problematic. Both body fat and muscle mass are vitally important, as they have opposing influences on chronic disease, but they have seldom been estimated as part of population health surveillance. Instead, most national surveys have merely reported BMI and waist, or sometimes the waist/hip ratio; these indices are convenient but do not have any specific biological meaning. Anthropometry offers a practical and inexpensive method for muscle and fat estimation in clinical and epidemiological settings; however, its use is imperfect due to many limitations, such as a shortage of reference data, misuse of terminology, unclear assumptions, and the absence of properly validated anthropometric equations. To date, anthropometric methods are not sensitive enough to detect muscle and fat loss. Aims: The aim of this thesis is to estimate Adipose/fat and muscle mass in health disease and during weight loss through; 1. evaluating and critiquing the literature, to identify the best-published prediction equations for adipose/fat and muscle mass estimation; 2. to derive and validate adipose tissue and muscle mass prediction equations; and 3.to evaluate the prediction equations along with anthropometric indices and the best equations retrieved from the literature in health, metabolic illness and during weight loss. Methods: a Systematic review using Cochrane Review method was used for reviewing muscle mass estimation papers that used MRI as the reference method. Fat mass estimation papers were critically reviewed. Mixed ethnic, age and body mass data that underwent whole body magnetic resonance imaging to quantify adipose tissue and muscle mass (dependent variable) and anthropometry (independent variable) were used in the derivation/validation analysis. Multiple regression and Bland-Altman plot were applied to evaluate the prediction equations. To determine how well the equations identify metabolic illness, English and Scottish health surveys were studied. Statistical analysis using multiple regression and binary logistic regression were applied to assess model fit and associations. Also, populations were divided into quintiles and relative risk was analysed. Finally, the prediction equations were evaluated by applying them to a pilot study of 10 subjects who underwent whole-body MRI, anthropometric measurements and muscle strength before and after weight loss to determine how well the equations identify adipose/fat mass and muscle mass change. Results: The estimation of fat mass has serious problems. Despite advances in technology and science, prediction equations for the estimation of fat mass depend on limited historical reference data and remain dependent upon assumptions that have not yet been properly validated for different population groups. Muscle mass does not have the same conceptual problems; however, its measurement is still problematic and reference data are scarce. The derivation and validation analysis in this thesis was satisfactory, compared to prediction equations in the literature they were similar or even better. Applying the prediction equations in metabolic illness and during weight loss presented an understanding on how well the equations identify metabolic illness showing significant associations with diabetes, hypertension, HbA1c and blood pressure. And moderate to high correlations with MRI-measured adipose tissue and muscle mass before and after weight loss. Conclusion: Adipose tissue mass and to an extent muscle mass can now be estimated for many purposes as population or groups means. However, these equations must not be used for assessing fatness and categorising individuals. Further exploration in different populations and health surveys would be valuable.

Differences in pelvic floor morphology between continent, stress urinary incontinent, and mixed urinary incontinent elderly women : an MRI study

Aims To compare magnetic resonance imaging (MRI) of the pelvic floor musculature (PFM), bladder neck and urethral sphincter morphology under three conditions (rest, PFM maximal voluntary contraction (MVC), and straining) in older women with symptoms of stress (SUI) or mixed urinary incontinence (MUI) or without incontinence. Methods This 2008–2012 exploratory observational cohort study was conducted with community-dwelling women aged 60 and over. Sixty six women (22 per group), mean age of 67.7 ± 5.2 years, participated in the study. A 3 T MRI examination was conducted under three conditions: rest, PFM MVC, and straining. ANOVA or Kruskal–Wallis tests (data not normally distributed) were conducted, with Bonferroni correction, to compare anatomical measurements between groups. Results Women with MUI symptoms had a lower PFM resting position (M-Line P = 0.010 and PC/H-line angle P = 0.026) and lower pelvic organ support (urethrovesical junction height P = 0.013) than both continent and SUI women. Women with SUI symptoms were more likely to exhibit bladder neck funneling and a larger posterior urethrovesical angle at rest than both continent and MUI women (P = 0.026 and P = 0.008, respectively). There were no significant differences between groups on PFM MVC or straining. Conclusions Women with SUI and MUI symptoms present different morphological defects at rest. These observations emphasize the need to tailor UI interventions to specific pelvic floor defects and UI type in older women.

Evaluation of tumor recurrences after radical prostatectomy using 18F-Choline PET/CT and 3T multiparametric MRI without endorectal coil: a single center experience

The aim os this study is to evaluate and compare the utility of 18F-fluorocholine (18F-CH) PET/CT versus 3-Tesla multiparametric MRI (mpMRI) without endorectal coil to detect tumor recurrences in patients with biochemical relapse following radical prostatectomy (RP). Secondarily, to identify possible prognostic variables associated with mpMRI and 18F-CH PET/CT findings. Retrospective study of 38 patients who developed biochemical recurrence after RP between the years 2011 and 2015 at our institution. PET/CT and mpMRI were both performed within 30 days of each other in all patients. The PET/CT was reviewed by a nuclear medicine specialist while the mpMRI was assessed by a radiologist, both of whom were blinded to outcomes. The median prostate-specific antigen (PSA) value pre-MRI/PET-CT was 0.9 ng/mL (interquartile range 0.4–2.2 ng/mL). There were no differences in the detection rate between 18F-CH PET/CT and mpMRI for local recurrence (LR), lymph node recurrence (LNR) and bone metastases (BM). Separately, mpMRI and 18F-CH PET/CT were positive for recurrence in 55.2% and 52.6% of cases, respectively, and in 65.7% of cases when findings from both modalities were considered together. The detection of LR was better with combined mpMRI and choline PET/CT versus choline PET/CT alone (34.2% vs 18.4%, p = 0.04). Salvage treatment was modified in 22 patients (57.8%) based on the imaging findings. PSA values on the day of biochemical failure were significantly associated with mpMRI positivity (adjusted odds ratio (OR): 30.9; 95% confidence interval (CI): 1.5–635.8). Gleason score > 7 was significantly associated with PET/CT positivity (OR: 13.9; 95% CI: 1.5–125.6). A significant association was found between PSA doubling time (PSADT) (OR: 1.3; 95% CI: 1.0–1.7), T stage (OR: 21.1; 95% CI: 1.6–272.1), and LR. Multiparametric MRI and 18F-CH PET/CT yield similar detection rates for LR, LNR and pelvic BM. The combination of both imaging techniques provides a better LR detection versus choline PET/CT alone. The initially planned salvage treatment was modified in 57.8% of patients due to imaging findings. In addition to PSA values, Gleason score, T stage, and PSADT may provide valuable data to identify those patients that are most likely to benefit from undergoing both imaging procedures.

Differences in pelvic floor morphology between continent, stress urinary incontinent, and mixed urinary incontinent elderly women : an MRI study

Aims To compare magnetic resonance imaging (MRI) of the pelvic floor musculature (PFM), bladder neck and urethral sphincter morphology under three conditions (rest, PFM maximal voluntary contraction (MVC), and straining) in older women with symptoms of stress (SUI) or mixed urinary incontinence (MUI) or without incontinence. Methods This 2008–2012 exploratory observational cohort study was conducted with community-dwelling women aged 60 and over. Sixty six women (22 per group), mean age of 67.7 ± 5.2 years, participated in the study. A 3 T MRI examination was conducted under three conditions: rest, PFM MVC, and straining. ANOVA or Kruskal–Wallis tests (data not normally distributed) were conducted, with Bonferroni correction, to compare anatomical measurements between groups. Results Women with MUI symptoms had a lower PFM resting position (M-Line P = 0.010 and PC/H-line angle P = 0.026) and lower pelvic organ support (urethrovesical junction height P = 0.013) than both continent and SUI women. Women with SUI symptoms were more likely to exhibit bladder neck funneling and a larger posterior urethrovesical angle at rest than both continent and MUI women (P = 0.026 and P = 0.008, respectively). There were no significant differences between groups on PFM MVC or straining. Conclusions Women with SUI and MUI symptoms present different morphological defects at rest. These observations emphasize the need to tailor UI interventions to specific pelvic floor defects and UI type in older women.

Longitudinal Analysis Of Hippocampal T2 Relaxometry In Fmtle.

To investigate the degree of T2 relaxometry changes over time in groups of patients with familial mesial temporal lobe epilepsy (FMTLE) and asymptomatic relatives. We conducted both cross-sectional and longitudinal analyses of T2 relaxometry with Aftervoxel, an in-house software for medical image visualization. The cross-sectional study included 35 subjects (26 with FMTLE and 9 asymptomatic relatives) and 40 controls; the longitudinal study was composed of 30 subjects (21 with FMTLE and 9 asymptomatic relatives; the mean time interval of MRIs was 4.4 ± 1.5 years) and 16 controls. To increase the size of our groups of patients and relatives, we combined data acquired in 2 scanners (2T and 3T) and obtained z-scores using their respective controls. General linear model on SPSS21® was used for statistical analysis. In the cross-sectional analysis, elevated T2 relaxometry was identified for subjects with seizures and intermediate values for asymptomatic relatives compared to controls. Subjects with MRI signs of hippocampal sclerosis presented elevated T2 relaxometry in the ipsilateral hippocampus, while patients and asymptomatic relatives with normal MRI presented elevated T2 values in the right hippocampus. The longitudinal analysis revealed a significant increase in T2 relaxometry for the ipsilateral hippocampus exclusively in patients with seizures. The longitudinal increase of T2 signal in patients with seizures suggests the existence of an interaction between ongoing seizures and the underlying pathology, causing progressive damage to the hippocampus. The identification of elevated T2 relaxometry in asymptomatic relatives and in patients with normal MRI suggests that genetic factors may be involved in the development of some mild hippocampal abnormalities in FMTLE.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Feasibility And Reproducibility Of Diffusion-weighted Magnetic Resonance Imaging Of The Fetal Brain In Twin-twin Transfusion Syndrome.

The aim of this study is to test the feasibility and reproducibility of diffusion-weighted magnetic resonance imaging (DW-MRI) evaluations of the fetal brains in cases of twin-twin transfusion syndrome (TTTS). From May 2011 to June 2012, 24 patients with severe TTTS underwent MRI scans for evaluation of the fetal brains. Datasets were analyzed offline on axial DW images and apparent diffusion coefficient (ADC) maps by two radiologists. The subjective evaluation was described as the absence or presence of water diffusion restriction. The objective evaluation was performed by the placement of 20-mm(2) circular regions of interest on the DW image and ADC maps. Subjective interobserver agreement was assessed by the kappa correlation coefficient. Objective intraobserver and interobserver agreements were assessed by proportionate Bland-Altman tests. Seventy-four DW-MRI scans were performed. Sixty of them (81.1%) were considered to be of good quality. Agreement between the radiologists was 100% for the absence or presence of diffusion restriction of water. For both intraobserver and interobserver agreement of ADC measurements, proportionate Bland-Altman tests showed average percentage differences of less than 1.5% and 95% CI of less than 18% for all sites evaluated. Our data demonstrate that DW-MRI evaluation of the fetal brain in TTTS is feasible and reproducible.

[gait Speed, Grip Strength And Self-rated Health Among The Elderly: Data From The Fibra Campinas Network, São Paulo, Brazil].

The article seeks to investigate patterns of performance and relationships between grip strength, gait speed and self-rated health, and investigate the relationships between them, considering the variables of gender, age and family income. This was conducted in a probabilistic sample of community-dwelling elderly aged 65 and over, members of a population study on frailty. A total of 689 elderly people without cognitive deficit suggestive of dementia underwent tests of gait speed and grip strength. Comparisons between groups were based on low, medium and high speed and strength. Self-related health was assessed using a 5-point scale. The males and the younger elderly individuals scored significantly higher on grip strength and gait speed than the female and oldest did; the richest scored higher than the poorest on grip strength and gait speed; females and men aged over 80 had weaker grip strength and lower gait speed; slow gait speed and low income arose as risk factors for a worse health evaluation. Lower muscular strength affects the self-rated assessment of health because it results in a reduction in functional capacity, especially in the presence of poverty and a lack of compensatory factors.

Correlation Between Cephalometric Data And Severity Of Sleep Apnea.

Obstructive sleep apnea syndrome has a high prevalence among adults. Cephalometric variables can be a valuable method for evaluating patients with this syndrome. To correlate cephalometric data with the apnea-hypopnea sleep index. We performed a retrospective and cross-sectional study that analyzed the cephalometric data of patients followed in the Sleep Disorders Outpatient Clinic of the Discipline of Otorhinolaryngology of a university hospital, from June 2007 to May 2012. Ninety-six patients were included, 45 men, and 51 women, with a mean age of 50.3 years. A total of 11 patients had snoring, 20 had mild apnea, 26 had moderate apnea, and 39 had severe apnea. The distance from the hyoid bone to the mandibular plane was the only variable that showed a statistically significant correlation with the apnea-hypopnea index. Cephalometric variables are useful tools for the understanding of obstructive sleep apnea syndrome. The distance from the hyoid bone to the mandibular plane showed a statistically significant correlation with the apnea-hypopnea index.

Spinal Cord Atrophy Correlates With Disease Duration And Severity In Amyotrophic Lateral Sclerosis.

Our objective was to investigate spinal cord (SC) atrophy in amyotrophic lateral sclerosis (ALS) patients, and to determine whether it correlates with clinical parameters. Forty-three patients with ALS (25 males) and 43 age- and gender-matched healthy controls underwent MRI on a 3T scanner. We used T1-weighted 3D images covering the whole brain and the cervical SC to estimate cervical SC area and eccentricity at C2/C3 level using validated software (SpineSeg). Disease severity was quantified with the ALSFRS-R and ALS Severity scores. SC areas of patients and controls were compared with a Mann-Whitney test. We used linear regression to investigate association between SC area and clinical parameters. Results showed that mean age of patients and disease duration were 53.1 ± 12.2 years and 34.0 ± 29.8 months, respectively. The two groups were significantly different regarding SC areas (67.8 ± 6.8 mm² vs. 59.5 ± 8.4 mm², p < 0.001). Eccentricity values were similar in both groups (p = 0.394). SC areas correlated with disease duration (r = - 0.585, p < 0.001), ALSFRS-R score (r = 0.309, p = 0.044) and ALS Severity scale (r = 0.347, p = 0.022). In conclusion, patients with ALS have SC atrophy, but no flattening. In addition, SC areas correlated with disease duration and functional status. These data suggest that quantitative MRI of the SC may be a useful biomarker in the disease.

Censored Linear Regression Models For Irregularly Observed Longitudinal Data Using The Multivariate-t Distribution.

In acquired immunodeficiency syndrome (AIDS) studies it is quite common to observe viral load measurements collected irregularly over time. Moreover, these measurements can be subjected to some upper and/or lower detection limits depending on the quantification assays. A complication arises when these continuous repeated measures have a heavy-tailed behavior. For such data structures, we propose a robust structure for a censored linear model based on the multivariate Student's t-distribution. To compensate for the autocorrelation existing among irregularly observed measures, a damped exponential correlation structure is employed. An efficient expectation maximization type algorithm is developed for computing the maximum likelihood estimates, obtaining as a by-product the standard errors of the fixed effects and the log-likelihood function. The proposed algorithm uses closed-form expressions at the E-step that rely on formulas for the mean and variance of a truncated multivariate Student's t-distribution. The methodology is illustrated through an application to an Human Immunodeficiency Virus-AIDS (HIV-AIDS) study and several simulation studies.