d-matrix – database exploration, visualization and analysis

BACKGROUND: Motivated by a biomedical database set up by our group, we aimed to develop a generic database front-end with embedded knowledge discovery and analysis features. A major focus was the human-oriented representation of the data and the enabling of a closed circle of data query, exploration, visualization and analysis. RESULTS: We introduce a non-task-specific database front-end with a new visualization strategy and built-in analysis features, so called d-matrix. d-matrix is web-based and compatible with a broad range of database management systems. The graphical outcome consists of boxes whose colors show the quality of the underlying information and, as the name suggests, they are arranged in matrices. The granularity of the data display allows consequent drill-down. Furthermore, d-matrix offers context-sensitive categorization, hierarchical sorting and statistical analysis. CONCLUSIONS: d-matrix enables data mining, with a high level of interactivity between humans and computer as a primary factor. We believe that the presented strategy can be very effective in general and especially useful for the integration of distinct data types such as phenotypical and molecular data

Influence of Climate on Emergency Department Visits for Syncope: Role of Air Temperature Variability

BACKGROUND: Syncope is a clinical event characterized by a transient loss of consciousness, estimated to affect 6.2/1000 person-years, resulting in remarkable health care and social costs. Human pathophysiology suggests that heat may promote syncope during standing. We tested the hypothesis that the increase of air temperatures from January to July would be accompanied by an increased rate of syncope resulting in a higher frequency of Emergency Department (ED) visits. We also evaluated the role of maximal temperature variability in affecting ED visits for syncope. METHODOLOGY/PRINCIPAL FINDINGS: We included 770 of 2775 consecutive subjects who were seen for syncope at four EDs between January and July 2004. This period was subdivided into three epochs of similar length: 23 January-31 March, 1 April-31 May and 1 June-31 July. Spectral techniques were used to analyze oscillatory components of day by day maximal temperature and syncope variability and assess their linear relationship. There was no correlation between daily maximum temperatures and number of syncope. ED visits for syncope were lower in June and July when maximal temperature variability declined although the maximal temperatures themselves were higher. Frequency analysis of day by day maximal temperature variability showed a major non-random fluctuation characterized by a ∼23-day period and two minor oscillations with ∼3- and ∼7-day periods. This latter oscillation was correlated with a similar ∼7-day fluctuation in ED visits for syncope. CONCLUSIONS/SIGNIFICANCE: We conclude that ED visits for syncope were not predicted by daily maximal temperature but were associated with increased temperature variability. A ∼7-day rhythm characterized both maximal temperatures and ED visits for syncope variability suggesting that climate changes may have a significant effect on the mode of syncope occurrence

OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control [preprint]

MOTIVATION: Particle tracking coupled with time-lapse microscopy is critical for understanding the dynamics of intracellular processes of clinical importance. Spurred on by advances in the spatiotemporal resolution of microscopy and automated computational methods, this field is increasingly amenable to multi-dimensional high-throughput data collection schemes (Snijder et al, 2012). Typically, complex particle tracking datasets generated by individual laboratories are produced with incompatible methodologies that preclude comparison to each other. There is therefore an unmet need for data management systems that facilitate data standardization, meta-analysis, and structured data dissemination. The integration of analysis, visualization, and quality control capabilities into such systems would eliminate the need for manual transfer of data to diverse downstream analysis tools. At the same time, it would lay the foundation for shared trajectory data, particle tracking, and motion analysis standards. RESULTS: Here, we present Open Microscopy Environment inteGrated Analysis (OMEGA), a cross-platform data management, analysis, and visualization system, for particle tracking data, with particular emphasis on results from viral and vesicular trafficking experiments. OMEGA provides easy to use graphical interfaces to implement integrated particle tracking and motion analysis workflows while keeping track of error propagation and data provenance. Specifically, OMEGA: 1) imports image data and metadata from data management tools such as Open Microscopy Environment Remote Objects (OMERO; Allan et al., 2012); 2) tracks intracellular particles moving across time series of image planes; 3) facilitates parameter optimization and trajectory results inspection and validation; 4) performs downstream trajectory analysis and motion type classification; 5) estimates the uncertainty associated with motion analysis; and, 6) facilitates storage and dissemination of analysis results, and analysis definition metadata, on the basis of our newly proposed Minimum Information About Particle Tracking Experiments (MIAPTE; Rigano & Strambio-De-Castillia, 2016; 2017) guidelines in combination with the OME-XML data model (Goldberg et al, 2005)

Cerebral blood flow and cerebrovascular reactivity correlate with severity of motor symptoms in Parkinson’s disease

Background: Parkinson’s disease (PD) is a progressive neurodegenerative disorder that is mainly characterized by movement dysfunction. Neurovascular unit (NVU) disruption has been proposed to be involved in the disease, but its role in PD neurodegenerative mechanisms is still unclear. The aim of this study was to investigate cerebral blood flow (CBF) and cerebrovascular reactivity (CVR) within the regions belonging to the motor network, in patients with mild to moderate stages of PD. Methods: Twenty-eight PD patients (66.6 ± 8.6 years, 22 males, median [interquartile range, IQR] Hoehn & Yahr = 1.5 [1–1.9]) and 32 age- and sex-matched healthy controls (HCs) were scanned with arterial spin labeling (ASL) magnetic resonance imaging (MRI) for CBF assessment. ASL MRI was also acquired in hypercapnic conditions to induce vasodilation and subsequently allow for CVR measurement in a subgroup of 13 PD patients and 13 HCs. Median CBF and CVR were extracted from cortical and subcortical regions belonging to the motor network and compared between PD patients and HCs. In addition, the correlation between these parameters and the severity of PD motor symptoms [quantified with Unified Parkinson’s Disease Rating Scale part III (UPDRS III)] was assessed. The false discovery rate (FDR) method was used to correct for multiple comparisons. Results: No significant differences in terms of CBF and CVR were found between PD patients and HCs. Positive significant correlations were observed between CBF and UPDRS III within the precentral gyrus, postcentral gyrus, supplementary motor area, striatum, pallidum, thalamus, red nucleus, and substantia nigra (pFDR < 0.05). Conversely, significant negative correlation between CVR and UPDRS III was found in the corpus striatum (pFDR < 0.05). Conclusion: CBF and CVR assessment provides information about NVU integrity in an indirect and noninvasive way. Our findings support the hypothesis of NVU involvement at the mild to moderate stages of PD, suggesting that CBF and CVR within the motor network might be used as either diagnostic or prognostic markers for PD

Frequency domain analyses of Maximal Temperature spontaneous fluctuations (variability), during the three epochs.

<p>Max Temperature Variance is the variance of the values of Maximal Temperature corresponding to each epoch. DO₂₃ , DO₇ and DO₃ are the powers of Max Temperature rhythmic fluctuations with a period of ≈23, ≈7 and ≈3 days, respectively. (%) indicates % of total variance. Other abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022719#pone-0022719-t002" target="_blank">table 2</a>.</p

Day by day values of maximal and minimal air temperature, heat index and of syncope observed from January 23^rd, 2004 to July 31^st, 2004.

<p>The expected progressive increase of air temperature from January diverged from Emergency Department (ED) visits for syncope which remained stable until May, before decreasing. Maximal and minimal air temperatures fluctuate (temperature variability) on a day by day basis. The temperature variability was lower in June and July compared to the cooler months. Heat index has been computed only for values of maximal temperature >20°C and its spontaneous variability mirrors maximal temperature fluctuations.</p

Modifications of the rate of syncope, in all the patients who presented to ED for syncope and in subpopulations of different age and gender, grouped according to three epochs.

<p>Max Temperature is the mean ± SD of daily Maximal Temperatures. Max Temperature Variability is the mean ± SD of day by day Maximal Temperatures variations in each epoch. Admitted Syncope refers to patients admitted to hospital for syncope. n is the number; ‰ is the number of Syncope ED visits per thousand, in respect to Total ED visits; % is the percentage of Admitted Syncope in respect to Syncope ED visits and of Syncope aged >75 yrs in respect to Syncope ED visits.</p><p>*p<0.05 vs epoch 2 and epoch 1;</p>§<p>p<0.001 vs epoch 2 and epoch 1;</p>#<p>p<0.001 vs epoch 1.</p