A multi-layered Bayesian network model for structured document retrieval

New standards in document representation, like for example SGML, XML, and MPEG-7, compel Information Retrieval to design and implement models and tools to index, retrieve and present documents according to the given document structure. The paper presents the design of an Information Retrieval system for multimedia structured documents, like for example journal articles, e-books, and MPEG-7 videos. The system is based on Bayesian Networks, since this class of mathematical models enable to represent and quantify the relations between the structural components of the document. Some preliminary results on the system implementation are also presented

2q37 deletions in patients with an albright hereditary osteodystrophy phenotype and PTH resistance

Pseudohypoparathyroidism (PHP) is a rare endocrine disorder derived from the defective activation of the cAMP pathway by the parathyroid hormone secondary to GNAS molecular defects. PHP subtypes are defined by the presence/absence of specific clinical/biochemical features. PHP1A is characterized by resistance to multiple hormones with features of Albright hereditary osteodystrophy (AHO), while pseudopseudohypoparathyroidism (PPHP) is characterized by AHO in the absence of PTH resistance. Small subsets of PHP and PPHP patients without known molecular defects have been re-diagnosed as being affected by the brachydactyly-mental retardation syndrome (BDMR), also known as the AHO-like syndrome. This study aimed to analyse 24 PHP1A and 51 PPHP patients without a molecular diagnosis for the presence of BDMR-associated 2q37 deletions to improve the differential diagnosis and to identify features that might help to avoid a misdiagnosis. Molecular investigations identified 4 deletions in 4 unrelated patients. The affected patients showed a combination of the most pathognomonic AHO features. Of note, 3 of the patients also displayed mild PTH resistance, and none of the patients developed ectopic ossifications. Our work confirmed the rarity of the misdiagnosis of BDMR in PHP patients through the identification of 4 patients bearing a 2q37 deletion in a cohort of 73 PHP patients (5.3%). Three patients with the deletion presented a PHP1A phenotype in the absence of any BDMR-specific findings. Further studies on larger case series are needed to elucidate the overlap between these clinical entities and to allow the early identification of patients

Mosaicism for GNAS methylation defects associated with pseudohypoparathyroidism type 1B arose in early post-zygotic phases

BACKGROUND: Pseudohypoparathyroidism type 1B (PHP1B; MIM#603233) is a rare imprinting disorder (ID), associated with the GNAS locus, characterized by parathyroid hormone (PTH) resistance in the absence of other endocrine or physical abnormalities. Sporadic PHP1B cases, with no known underlying primary genetic lesions, could represent true stochastic errors in early embryonic maintenance of methylation. Previous data confirmed the existence of different degrees of methylation defects associated with PHP1B and suggested the presence of mosaicism, a phenomenon already described in the context of other IDs. RESULTS: With respect to mosaic conditions, the study of multiple tissues is a necessary approach; thus, we investigated somatic cell lines (peripheral blood and buccal epithelium and cells from the urine sediment) descending from different germ layers from 19 PHP patients (11 spor-PHP1B, 4 GNAS mutated PHP1A, and 4 PHP with no GNAS (epi)genetic defects) and 5 healthy controls. We identified 11 patients with epigenetic defects, further subdivided in groups with complete or partial methylation defects. The recurrence of specific patterns of partial methylation defects limited to specific CpGs was confirmed by checking methylation profiles of spor-PHP1B patients diagnosed in our lab (n\u2009=\u200956). Underlying primary genetic defects, such as uniparental disomy or deletion, potentially causative for the detected partial methylation were excluded in all samples. CONCLUSIONS: Our data showed no differences of methylation levels between organs and tissues from the same patient, so we concluded that the epimutation occurred in early post-zygotic phases and that the partial defects were mosaics. The number of patients with no detectable (epi)genetic GNAS defects was too small to exclude epimutations occurring in later post-zygotic phases, affecting only selected tissues different from blood, thus leading to underdiagnosis during routine molecular diagnosis. Finally, we found no correlation between methylation ratios, representing the proportion of epimutated cells, and the clinical presentation, further confirming the hypothesis of a threshold effect of the GNAS loss of imprinting leading to an "all-or-none" phenotype

A Survey of Volunteered Open Geo-Knowledge Bases in the Semantic Web

Over the past decade, rapid advances in web technologies, coupled with innovative models of spatial data collection and consumption, have generated a robust growth in geo-referenced information, resulting in spatial information overload. Increasing 'geographic intelligence' in traditional text-based information retrieval has become a prominent approach to respond to this issue and to fulfill users' spatial information needs. Numerous efforts in the Semantic Geospatial Web, Volunteered Geographic Information (VGI), and the Linking Open Data initiative have converged in a constellation of open knowledge bases, freely available online. In this article, we survey these open knowledge bases, focusing on their geospatial dimension. Particular attention is devoted to the crucial issue of the quality of geo-knowledge bases, as well as of crowdsourced data. A new knowledge base, the OpenStreetMap Semantic Network, is outlined as our contribution to this area. Research directions in information integration and Geographic Information Retrieval (GIR) are then reviewed, with a critical discussion of their current limitations and future prospects

An Interactive Approach Based on Alternative Achievement Scale and Alternative Comprehensive Scale for Multiple Attribute Decision Making under Linguistic Environment

The aim of this paper is to develop an interactive approach for multiple attribute decision making with incomplete weight information under linguistic environment. Some of the concepts are defined, such as the distance between two 2-tuple linguistic variables, the expectation level of alternative, the achievement scale, the alternative comprehensive scale under linguistic environment. Based on these concepts, we establish some linear programming models, through which the decision maker interacts with the analyst. Furthermore, we establish a practical interactive approach for selecting the most desirable alternative(s). The interactive process can be realized by giving and revising the achievement scale and comprehensive scale of alternatives till the achievement scale and the comprehensive scale are achieved to the decision maker’s request. Finally, an illustrative example is also given.The author is very grateful to the associated editor and two anonymous referees for their insightful and constructive comments and suggestions that have led to an improved version of this paper. This work was partly supported by the National Natural Science Foundation of China (No. 90924027, No. 71101043), National Basic Research Program of China (973 Program, No. 2010C B951104), Key Program of National Social Science Foundation of China (No. 10AJY005), College Philosophy and Social Science Research Project of Jiangsu Province under Grant 2011SJD630007.Xu, Y.; Wang, H.; Palacios Marqués, D. (2013). An Interactive Approach Based on Alternative Achievement Scale and Alternative Comprehensive Scale for Multiple Attribute Decision Making under Linguistic Environment. International Journal of Computational Intelligence Systems. 6(1):87-95. https://doi.org/10.1080/18756891.2013.756226S87956

Boundary spanning as identity work in university business engagement roles

The study explores how boundary-spanning is carried out to further community engagement in 15 universities of differing sizes/ages across the United Kingdom. Fifteen interviewees participated in a series of four semi-structured interviews, aged between 35–50 and with a first degree (with almost half with an MSc). One third were women. All managed their own teams and felt these were their base in negotiating difficult internal territory.. Here, boundary spanning is found to be synonymous with identity work, carried out to enable individuals to adapt to different internal and external conditions and requirements through processes of interaction and learning. It also suggests the strategic construction of identities to address perceived threats and insecurities - and the impacts of change, dominant organisational discourse and senior management on this process. Their job titles were not useful as identity badges to signal meaning, due to these being outside ‘what universities are for’

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society