Watershed Segmentation of Medical Volumes with Paint Drop Marking

We present an improvement of the classical marker-controlled watershed approach in the direction of a better exploitation of user-defined markers. The combined action of a partial flooding and paint drops falling downwards on the gray value relief from marker locations, leads to a robust and meaningful identification of the candidate basins, which is a prerequisite for an accurate segmentation. This is useful for user-controlled segmentation of biomedical volumes in that it facilitates robust identification of complex 3D structures with inhomogeneous borders. To this end, a visual interactive segmentation system has been implemented where different user-data interaction tools can be selected by physicians to generate machine-understandable knowledge in a quick and compact way. Experimental results on selected use-cases demonstrate the strengths of the proposed solutions

Petrology and geochemistry of the back-arc lithospheric mantle beneath eastern Payunia (La Pampa, Argentina): evidence from Agua Poca peridotite xenoliths

This paper presents the results of new petrochemical studies carried out on mantle xenoliths hosted in Pleistocene basaltic rocks from the Agua Poca volcano in central-western Argentina. Mantle xenoliths studied are shown to be mainly anhydrous spinel lherzolites with minor amounts of harzburgite and banded pyroxenite, showing highly variable equilibrium temperatures ranging from 820°C to 1030°C at 1.0 to 2.0 GPa. This constitutes evidence that the mantle xenoliths are representative of a large portion of the lithospheric mantle column and that the geothermal gradient is not very elevated as reported in some other Patagonian provinces. Geochemical characteristics of clinopyroxene in the mantle xenoliths allow classification into two groups; Groups 1 and 2. Group 1 contains most of the lherzolites and has light-REE depletion, with slightly positive anomalies of Eu in some samples and extreme Nb and Ta depletion. Group 2 consists of two harzburgitic samples, has flat REE patterns with lower Sm to Lu concentrations, with enriched Sr and negative HFSE anomalies. Based on mineral and residua compositions estimated assuming equilibrium with clinopyroxenes, Group 1 can be considered to be refractory residua after up to 7%, non-modal, near-fractional melting of a spinel-facies Primitive Mantle. Group 2 can be considered to be after ca. 13% of partial melting. It is inferred that partial melting events in the lithospheric mantle beneath the Agua Poca occurred in different ages since the Proterozoic, but compared with Group 1, the metasomatic overprint is dominant in Group 2 mantle xenoliths. The calculated melt compositions from Group 2 are interpreted to be transient liquid compositions developed during melt-peridotite interaction, and are different from the host alkaline basalts. The HFSE-depleted composition estimated for the rising melt suggests the presence of a slab-derived component, although the possibility cannot be disregarded (on the basis of present data) that such a geochemical feature is due to segregation of HFSE-bearing minerals during the interaction with the peridotite. Thus, we attribute the metasomatic agent to a basaltic melt and to a minor amount of slab-derived fluids.Fil: Bertotto, Gustavo Walter. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Mazzucchelli, Maurizio. Università di Modena e Reggio Emilia. Dipartimento di Scienze Chimiche e Geologiche; ItaliaFil: Zanetti, Alberto. Università di Pavia. Istituto di Geoscienze e Georisorse; Italia. Consiglio Nazionale delle Ricerche; ItaliaFil: Vannucci, Riccardo. Università di Pavia. Dipartamento di Scienze della Terra; Itali

Petrology and geochemistry of the back-arc lithospheric mantle beneath eastern Payunia (La Pampa, Argentina): evidence from Agua Poca peridotite xenoliths

This paper presents the results of new petrochemical studies carried out on mantle xenoliths hosted in Pleistocene basaltic rocks from the Agua Poca volcano in central-western Argentina. Mantle xenoliths studied are shown to be mainly anhydrous spinel lherzolites with minor amounts of harzburgite and banded pyroxenite, showing highly variable equilibrium temperatures ranging from 820°C to 1030°C at 1.0 to 2.0 GPa. This constitutes evidence that the mantle xenoliths are representative of a large portion of the lithospheric mantle column and that the geothermal gradient is not very elevated as reported in some other Patagonian provinces. Geochemical characteristics of clinopyroxene in the mantle xenoliths allow classification into two groups; Groups 1 and 2. Group 1 contains most of the lherzolites and has light-REE depletion, with slightly positive anomalies of Eu in some samples and extreme Nb and Ta depletion. Group 2 consists of two harzburgitic samples, has flat REE patterns with lower Sm to Lu concentrations, with enriched Sr and negative HFSE anomalies. Based on mineral and residua compositions estimated assuming equilibrium with clinopyroxenes, Group 1 can be considered to be refractory residua after up to 7%, non-modal, near-fractional melting of a spinel-facies Primitive Mantle. Group 2 can be considered to be after ca. 13% of partial melting. It is inferred that partial melting events in the lithospheric mantle beneath the Agua Poca occurred in different ages since the Proterozoic, but compared with Group 1, the metasomatic overprint is dominant in Group 2 mantle xenoliths. The calculated melt compositions from Group 2 are interpreted to be transient liquid compositions developed during melt-peridotite interaction, and are different from the host alkaline basalts. The HFSE-depleted composition estimated for the rising melt suggests the presence of a slab-derived component, although the possibility cannot be disregarded (on the basis of present data) that such a geochemical feature is due to segregation of HFSE-bearing minerals during the interaction with the peridotite. Thus, we attribute the metasomatic agent to a basaltic melt and to a minor amount of slab-derived fluids.Fil: Bertotto, Gustavo Walter. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Mazzucchelli, Maurizio. Università di Modena e Reggio Emilia. Dipartimento di Scienze Chimiche e Geologiche; ItaliaFil: Zanetti, Alberto. Università di Pavia. Istituto di Geoscienze e Georisorse; Italia. Consiglio Nazionale delle Ricerche; ItaliaFil: Vannucci, Riccardo. Università di Pavia. Dipartamento di Scienze della Terra; Itali

Multivariate correlation measures reveal structure and strength of brain–body physiological networks at rest and during mental stress

In this work, we extend to the multivariate case the classical correlation analysis used in the field of network physiology to probe dynamic interactions between organ systems in the human body. To this end, we define different correlation-based measures of the multivariate interaction (MI) within and between the brain and body subnetworks of the human physiological network, represented, respectively, by the time series of delta, theta, alpha, and beta electroencephalographic (EEG) wave amplitudes, and of heart rate, respiration amplitude, and pulse arrival time (PAT) variability (eta, rho, pi). MI is computed: (i) considering all variables in the two subnetworks to evaluate overall brain-body interactions; (ii) focusing on a single target variable and dissecting its global interaction with all other variables into contributions arising from the same subnetwork and from the other subnetwork; and (iii) considering two variables conditioned to all the others to infer the network topology. The framework is applied to the time series measured from the EEG, electrocardiographic (ECG), respiration, and blood volume pulse (BVP) signals recorded synchronously via wearable sensors in a group of healthy subjects monitored at rest and during mental arithmetic and sustained attention tasks. We find that the human physiological network is highly connected, with predominance of the links internal of each subnetwork (mainly eta-rho and delta-theta, theta-alpha, alpha-beta), but also statistically significant interactions between the two subnetworks (mainly eta-beta and eta-delta). MI values are often spatially heterogeneous across the scalp and are modulated by the physiological state, as indicated by the decrease of cardiorespiratory interactions during sustained attention and by the increase of brain-heart interactions and of brain-brain interactions at the frontal scalp regions during mental arithmetic. These findings illustrate the complex and multi-faceted structure of interactions manifested within and between different physiological systems and subsystems across different levels of mental stress

QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Background: Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results: Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions: QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/

AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts

An increasing number of eukaryotic and prokaryotic genes are being found to have natural antisense transcripts (NATs). There is also growing evidence to suggest that antisense transcription could play a key role in many human diseases. Consequently, there have been several recent attempts to set up computational procedures aimed at identifying novel NATs. Our group has developed the AntiHunter program for the identification of expressed sequence tag (EST) antisense transcripts from BLAST output. In order to perform an analysis, the program requires a genomic sequence plus an associated list of transcript names and coordinates of the genomic region. After masking the repeated regions, the program carries out a BLASTN search of this sequence in the selected EST database, reporting via email the EST entries that reveal an antisense transcript according to the user-supplied list. Here, we present the newly developed version 2.0 of the AntiHunter tool. Several improvements have been added to this version of the program in order to increase its ability to detect a larger number of antisense ESTs. As a result, AntiHunter can now detect, on average, >45% more antisense ESTs with little or no increase in the percentage of the false positives. We also raised the maximum query size to 3 Mb (previously 1 Mb). Moreover, we found that a reasonable trade-off between the program search sensitivity and the maximum allowed size of the input-query sequence could be obtained by querying the database with the MEGABLAST program, rather than by using the BLAST one. We now offer this new opportunity to users, i.e. if choosing the MEGABLAST option, users can input a query sequence up to 30 Mb long, thus considerably improving the possibility to analyze longer query regions. The AntiHunter tool is freely available at

Soluzioni Open Source per la linearizzazione del problema di integrazione di applicativi nei sistemi informativi ospedalieri

2008-04-17Sardegna Ricerche, Edificio 2, Località Piscinamanna 09010 Pula (CA) - ItaliaPAAL 2008 - Pubblica Amministrazione Aperta e Libera: dalle tecnologie aperte alla libera circolazione dei contenuti digital

Comparison and potential determinants of health-related quality of life among rheumatoid arthritis, psoriatic arthritis, and spondyloarthritis: A cross-sectional study

Objectives: This study aimed to compare the health-related quality of life scores among rheumatoid arthritis, psoriatic arthritis, and spondyloarthritis and to evaluate socio-demographic and clinical determinantes of quality of life across diseases. Methods: The sample comprised 490 patients with rheumatoid arthritis, 198 with psoriatic arthritis, and 119 with spondyloarthritis who completed a series of health examinations and self-reported questionnaires. Quality of life was evaluated using the Short-Form 36 Health Survey, disease activity by DAS28-CRP, DAPSA, and ASDAS-CRP (for rheumatoid arthritis, psoriatic arthritis, and spondyloarthritis, respectively), depression and anxiety using the Hospital Anxiety and Depression Scale. ANOVA was used to compare the quality of life dimensions and their physical and mental summary measures among rheumatic diseases, and multivariate analysis was used to explore their potential determinants. Results: Rheumatoid arthritis had significantly worse scores than spondyloarthritis in the following dimensions: physical functioning, role limitation due to physical health, physical component score, and mental health. Psoriatic arthritis was not significantly different from the other two diseases. Multivariate analysis revealed that physical quality of life was mainly associated with disease activity across rheumatic diseases, rheumatological treatment and depression in rheumatoid arthritis and psoriatic arthritis. Mental quality of life is primarily associated with depression and anxiety across rheumatic diseases. Conclusion: There were differences in quality of life among patients with inflammatory rheumatic diseases, but overall, approximately uniform factors explained the variance in quality of life across diseases. Clinicians should develop general approaches and strategies for inflammatory rheumatic diseases to improve patients' quality of life