A report on the meeting Comparative Genomics of Eukaryotic Microorganisms: understanding the complexity of diversity. Sant Feliu de Guíxols, Spain. October 15-20, 2011. EvoDevo.'We scientists are like the lovers in 1950s films, absolutely insatiable. After one genome will come another, and another, and we will not stop until we have sequenced all of them' said microbiologist Antonio Lazcano more than a decade ago. The truth is that this year's EMBO conference series on the Comparative Genomics of Eukaryotic Microorganisms has proven Lazcano to be somehow right. Importantly, however, these new genomes are giving us useful insights into eukaryotic diversity, biology and evolution. Even more importantly, thanks to high-throughput sequencing technologies the cost of sequencing is rapidly dropping providing researchers with the opportunity not only to analyze hundreds of genomes but to obtain the first genome data from previously neglected eukaryotic taxa. Below we report some of the highlights of the meeting that both emphasize this trend and are potentially relevant to the readers of Trypanosoma brucei . Moreover, Patrick Keeling  presented comparative genomic analyses of several species of microsporidians, as well as three different strains of Encephalitozoon. Microsporidians have among the smallest eukaryotic genomes as a result of their adaptation to intracellular parasitism. Keeling's analysis revealed higher variation in subtelomeric regions than in the rest of the genome, and a high degree of conservation in synteny and intergenic regions.It is clear that there exists a huge bias in genomic sampling efforts across the diversity of the eukaryotic tree. For example, the Opisthokonta, the clade that includes Fungi and Metazoa, continues to be by far the most well-sampled eukaryotic superclade, whereas genomic data on Excavata and Rhizaria remain scarce. In this meeting more than half of the presentations concerned the analysis of genomes and/or transcriptomes of Fungi, which is not surprising given that more than 200 fungal genomes have been sequenced to date. Such comprehensive genome sampling enables studies at the level of population genomics, some of which are providing important insights into the subtelomeric regions. It is becoming widely accepted that subtelomeric genes show increased rates of duplication and undergo frequent ectopic recombination without the need for meiosis. Thus, these subtelomeric regions may play important roles in the origin of evolutionary innovation and, specifically, in the generation of genetic diversity. Good examples of this, presented by Kevin Verstrepen , are the yeast MAL genes that show interesting patterns of subfunctionalitzation of the resulting duplicates. Another good example is the evolution of variant surface glycoprotein (VSG) genes, which produce an important surface glycoprotein, in the kinetoplastid parasite Yarrowia lipolytica inside Saccharomyces cerevisiae, causing a severely unfit phenotype. They subsequently grew this strain for hundreds of generations in non-limiting media, eventually observing an increase in fitness. By genomic re-sequencing they discovered that the insert had been amplified by multiple episomes, which were later re-introduced in tandem repeats inside the genome, allowing an increase in sequence changes. Finally, Jure Piskur  presented a case of parallel evolution in yeast, in which two distantly related lineages had evolved a convergent lifestyle by re-wiring cis-regulatory motifs of the same metabolic pathway.Another good reason to study fungi relates to the interesting field of experimental evolution. Sophisticated molecular biology techniques and extensive genomic sampling enables experiments to be conducted across hundreds of generations in lab conditions. Bernard Dujon  presented an interesting series of evolutionary experiments designed to unravel how adaptation works. He reported that they had introduced a metabolic gene from Phytophtora infestants, which shares a very similar lifestyle with fungi. More importantly, the bulk of transferred genes are involved in the processes of osmotrophy and plant parasitic mechanisms  suggesting that HGT played a significant role in the convergent evolution towards the osmotrophic capacity of the oomycetes. Interestingly, following the same pipeline they were only able to infer nine ancient transfers between fungi and plants.A remarkable example of the role that horizontal gene transfer (HGT) plays in eukaryotic evolution was presented by Tom Richards . His group analyzed the role of HGT in the evolution of the osmotrophic lifestyle. Their genome-wide analysis revealed at least 34 HGT events from Fungi to the oomycote Another important subject that arose during the conference was the importance of whole genome duplications (WGD) in eukaryotes. Some examples, besides plants and vertebrates, are the Saccharomycotina, in which WGD was followed by a rapid loss of duplicates, or the ancestral duplication of Zigomycota, in which Rhizopus suffered a third round of WGD. Analyses of the dynamics of paralog retention and synteny loss shed some light both on sex-chromosome evolution and sensory perception .Andalucia godoyi) to be fully sequenced, by Marek Elias . This is particularly important if Discoba really are the most basal eukaryotic group. Elias presented a very compelling argument for why it is worth sequencing previously neglected taxa such as Andalucia or other jakobids. Within this same clade (Discoba), Lillian Fritz-Laylin  showed how the genome of Naegleria gruberi has changed our views of the last common ancestor of Eukaryotes and presented promising results on the development of molecular techniques for this organism.The tree of life and the efforts to obtain a well-supported tree of eukaryotes was one of the main topics of the conference with four consecutive sessions. Toni Gabaldón  presented a promising automatic method of iterative and nested phylogenetic reconstruction, in which after every node a new dataset of shared genes is re-calculated allowing a scalable resolution at more recent nodes (the tips). The deeper nodes of eukaryotes, however, remain problematic and unsupported. The pipeline allows continuous update as more data become available, so it remains to be seen whether trimming unnecessary taxa and incorporating new genomes from basal nodes will provide better-supported trees. A different strategy was proposed by Céline Brochier-Armanet , who suggested constructing phylogenies with concatenated datasets of operational rather than informational genes. Although operational genes have been considered unsuitable for phylogenies given that they evolve faster, Brochier-Armanet showed a well-supported eukaryote tree inferred using concatenated genes from the midbody toolkit. In her tree, deeper eukaryotic nodes had better resolution than in trees reconstructed from published datasets that are based on informational genes . A study to unravel the root of eukaryotes was presented by Ding He . He showed how they had used a concatenated dataset of 40 nuclear-encoded proteins of bacterial origin (euBacs), mainly of mitochondrial origin, to reconstruct the tree of eukaryotes. The use of euBacs allowed the tree to be rooted using alpha-proteobacteria as an out-group. The topology showed that Discoba  is the sister-group to the remaining eukaryotes. Then Andrew J. Roger  nicely introduced us to the long-standing problem of long branch attraction as well as other systematic errors and the possible solutions for overcoming them. He emphasized the use of improved phylogenetic models and improved taxonomic sampling. For example, he showed how the addition of several slowly evolving excavates radically changed the topology on the deeper nodes of the eukaryotic tree. For this reason it was good to learn of the first jakobid  presented the epigenomic map of DNA methylation in the diatom P. tricornutum. Bowler reported a set of convincing experiments that clearly show that methylation is found preferentially on transposable elements, such that these are silenced by default. Transposable elements are later unsilenced allowing an increase in evolutionary rates, when the organism faces stressful conditions.Two talks discussed work on diatoms, which are ecologically relevant microorganisms. Andrew Allen  reported the presence of genes involved in the urea cycle in the genomes of both Two successful symposiums dealt with mitochondrial genomes and metagenomics. In the first one, Gertraud Burger  and Michael W. Gray  presented examples of degenerate mitochondrial genomes among diplonemids and euglenids. The mitochondrial genomes of diplonemids demonstrate an extremely complex behavior, with all genes being partitioned among hundreds of small chromosomes. These fragments are transcribed and trans-spliced, as well as heavily edited, making the adaptive value of this process a big mystery. All this seems to be led by some kind of 'guiding RNAs', the nature of which has been investigated in a series by Burger.It is probably the field of metagenomics that best emphasizes the role that high-throughput sequencing technologies are playing in shaping this, as well as other, disciplines. Patrick Wincker  gave an overview of the ambitious Tara Oceans project, the goal of which is to explore global ocean biodiversity and ecosystems with the use of high-throughput sequencing, imaging methods and modeling tools. A recurrent technical issue throughout the talk was the importance of the single-celled amplified genomes in order to better understand the main players of marine ecological environments. Finally, Alexandra Z. Worden  focused on eukaryotic phytoplankton, pinpointing the importance of linking organism and gene function in order to increase our current understanding of marine ecosystems.Given the enormous amount of genomic data that is currently being generated, Lazcano's statement certainly bears some truth. However, one wonders whether in the future, and with the limits of data processing, we will have to think carefully about which organisms it will be worth obtaining the genome from. Nevertheless, we should enjoy and celebrate the power that technology is providing us to understand the diversity of eukaryotes in unforeseen ways.The authors declare that they have no competing interests.Both AdM and IRT wrote the manuscript. Both authors read and approved the final manuscript.


The aim of the current study was to evaluate the innervation of the acetabular labrum in the various zones and to understand its potential role in nociception and proprioception in hips with labral pathology.A total of twenty hip labrums were tagged and excised intraoperatively from patients undergoing a total hip replacement. After preparation, the specimens were cut to a thickness of 10 μm and divided into four quadrants (zones) using a clock face pattern. Neurosensory structure distribution was then evaluated using Hematoxylin and Eosin (H and E), and immunoreactivity to S-100.All specimens had abundant free nerve endings (FNEs). These were seen predominantly superficially and on the chondral side of the labrum. In addition, predominantly three different types of nerve end organs (NEOs) were identified in all twenty specimens. FNEs and NEOs were more frequently seen in the antero-superior and postero-superior zones. Four specimens had abundant vascularity and disorganised architecture of FNEs in the deeper zones of the antero-superior quadrant suggestive of a healed tear. Myofibroblasts were present in abundance in all the labral specimens and were distributed uniformly throughout all labral zones and depth.The current study shows that the human acetabular labrum has abundant FNEs and NEOs. These are more abundant in the antero-superior and postero-superior zones. The labrum, by virtue of its neural innervation, can potentially mediate pain as well as proprioception of the hip joint, and be involved in neurosecretion that can influence connective tissue repair. The acetabular labrum is a complex fibro-cartilaginous structure that is attached to the acetabular rim. It has Over the last decade, hip arthroscopy has emerged as an important procedure for addressing labral pathology,7. DespiA better understanding of the innervation of the human labrum may help address many questions related to symptomology and management of various hip pathologies. Very few studies in the English literature have investigated the sensory innervation of the human labrum-13. AlthThe aim of the current study was to evaluate the innervation of the acetabular labrum in the various zones and to understand its potential role in nociception and proprioception in hips with labral pathology.Following institutional review board approval from the University of Calgary office of medical bioethics, an informed consent was obtained from all the patients undergoing total hip arthroplasty (THA) or hip resurfacing. Twenty labrums were excised intraoperatively from the acetabular rim with the aid of a scalpel. Care was taken to resect a single large segment of labrum. Any specimen not resected in toto because of significant deficiency of the labrum in any part was discarded. Labrums having calcific deposits were also discarded.After the harvest, all the specimens were tagged by a suture placed at the edge of the antero-inferior segment of the labrum Figure . The speAn analysis of the distribution of neurosensory structures in the labrum involved dividing the labrum into four quadrants (zones) using a clock face pattern: Antero-superior (AS), Postero-Superior (PS), Antero-Inferior (AI) and Postero-Inferior (PI) as shown in Figure A total of 20 specimens were harvested for evaluation. The mean age of these patients was 60.5 (range 42–78) and the primary diagnosis in all was symptomatic end stage osteoarthritis of hip.All specimens had abundant free nerve endings (FNE). These were seen predominantly superficially and on the chondral side of the labrum. In addition, predominantly three different types of nerve end organs (NEO) were identified in all twenty specimens. These included Vater-Pacini, Golgi-Mazonian and Ruffini corpuscles. The articular corpuscles (Krause Corpuscles) were not consistently seen and were identified in only 2 specimens. Representative histological sections with specific NEOs are shown in Figures Although difficult to quantify precisely, FNEs were clearly more abundant in the AS and PS zones of the labrum as compared to the AI and PI zones. NEOs were also more frequently seen in the AS and PS zones. All the specimens had one or more NEOs in AS and PS zones. However, NEOs were identified in only 20-40% of specimens in the AI (8 specimens) or SI (4 specimens) zones. These findings have been summarized in Table There were no appreciable differences in the innervation based on patient age. FNEs and NEOs were predominantly distributed in the superficial layer and on the articular  side of the labrum. These extended from the junction of the capsular and articular zone of the labrum towards the chondro-labral junction  accompanied the FNEs in these 4 specimens Figures  and7.Fibroblasts were present in abundance in all the labral specimens and were distributed uniformly throughout all labral zones and depth. These fibroblasts had elongated cell processes that extended into the extracelluar matrix Figure .The most important finding of this study was a consistent demonstration of FNEs and sensory NEOs in all the labral specimens with a higher prevalence in the antero-superior and postero-superior zones of the labrum. The presence of both FNEs and NEOs in the human labrum as demonstrated by the study clearly shows that the human labrum plays a role not just in transmitting nociception (through FNEs), but also providing proprioception to the hip joint (through NEOs).To the best of our knowledge, this is the second study in the literature after the study by Gerhardt et al. describiLabral innervation primarily comes from a branch of the nerve to the quadratus femoris as well as the obturator nerve. The ramIn FAI, the labrum gets crushed between the acetabular rim and femoral neck with different patterns of involvement in cam and pincer lesions. On examWyss et al. reportedThe neural and vascular anatomy of the hip labrum differs from that of knee menisci. The anterior and the posterior horns of menisci in the knee have a rich vascularity associated with numerous nerve endings. HoweverAn interesting finding in the current study was the presence of loosely organised FNEs in the deeper layers of the labrum in the antero-superior zones of 4 of the specimens. These nerve fibers had more oblique and radial orientation, and were associated with abdundant vascularity. These findings have not been described by any of the previously published studies-13. We bAnother important finding in the current study was the presence of microfilaments rich fibroblasts in the labrum giving them the appearance of myofibroblasts. These were found to be dispersed uniformly through the acetabular labrum. These myofibroblasts are specialized contractile fibroblasts, which contribute to the reconstruction of injured tissue by secreting extracellular matrix and exerting high contractile forces that help in healing of many tissues including open wounds and avascular tissues like the cornea-23. TheoThe strength of the current study included larger numbers than the previously published study. Kim and Azuma evaluateOne clear limitation of the study was evaluation of the labrum harvested from hips with end stage symptomatic osteoarthritis. Although all the specimens had consistent variation in density of FNEs and NEOs, this may not be truly representative of a labrum from a non-pathological hip or a labrum from a young adult with FAI with or without a labral tear.Nevertheless, the study provides useful new information regarding the innervation of the hip labrum. Our study shows that human acetabular labrum has abundant FNEs and NEOs. These are more abundant in the antero-superior and postero-superior zones. The labrum, by virtue of its neural innervation, can potentially mediate pain arising in the hip joint, mediate proprioception of the hip joint, and be involved in neursecretion that can influence connective tissue repair. HealingIn conclusion, from a clinical point of view, arthroscopic labral debridement  may lead to more predictable pain relief than labral repair because of excision of pain-mediating FNEs in the torn labrum. However, labral repair might be a better option in the long run as it preserves the proprioceptive function of the hip joint and this might in turn increase the longevity of a pathological hip.The authors on this study wish to declare that they have no competing interests.Conception, design of study, preparation and submission of application for ethics: JP, AA, PR, RG. Acquisition of data: JP, AA, PR. Preparation of specimens, analysis and interpretation of data: AA, JM, DP, KB. Manuscript preparation and revisions: JP, KB, AA, PR, RG, JM. Final Manuscript edit and approval: JP, AA, PR, RG, KB, DP, JM.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2474/15/41/prepub


The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets. Here, we present DC-ATLAS, a novel and versatile resource for the interpretation of high-throughput data generated perturbing the signaling network of dendritic cells (DCs).Pathways are annotated using a novel data model, the Biological Connection Markup Language (BCML), a SBGN-compliant data format developed to store the large amount of information collected. The application of DC-ATLAS to pathway-based analysis of the transcriptional program of DCs stimulated with agonists of the toll-like receptor family allows an integrated description of the flow of information from the cellular sensors to the functional outcome, capturing the temporal series of activation events by grouping sets of reactions that occur at different time points in well-defined functional modules.The initiative significantly improves our understanding of DC biology and regulatory networks. Developing a systems biology approach for immune system holds the promise of translating knowledge on the immune system into more successful immunotherapy strategies. Dendritic cells (DCs) orchestrate a repertoire of immune responses that endow resistance to infections and tolerance to self. DC plasticity has a prominent role in eliciting the proper immune response. Different DC subsets display different receptors and surface molecules and express different sets of cytokines/chemokines, all of which lead to distinct immunological outcomes. Among the receptors are the innate pattern recognition receptors (PRRs) that mediate the initial sensing of an infection. These include Toll-like receptors (TLRs), RIG-I-like receptors (RLRs), NOD-like receptors (NLRs), and C-type lectin receptors (CLRs) . TLRs reBecause of their essential role in the initiation of an adaptive immune response, DCs are an attractive target for therapeutic manipulation of the immune system . In factImmune systems biology is defined as the comprehensive and quantitative study of interactions between hosts and microbes over time, leading to the generation of models describing their dynamic behavior of immune cells and pathogens.Many studies investigated immune cell since these cells are particularly suited to functional genomics analyses because their responses to specific stimuli in a controlled environment can be clearly categorized. Innate responses against pathogens however cannot be considered as a set of discrete signaling pathways activated by a pathogen binding to a receptor; but rather such responses are composed of many interconnected pathways depending on multiple factors.Important initiatives based on systems biology are arising to collect high throughput data and to develop sophisticated bioinformatic methods to compare and analyze these data. In this respect, the Immunological Genome Project initiative  represenhttp://www.dc-atlas.net and they cover a plethora of cell surface receptors  and DC-relevant processes . To illustrate the potential of this new resource, we have selected as paradigmatic the set of TLRs pathways. We describe how they were curated and show the advantages of our approach through their validation both "in silico" and "in vitro".Here we describe DC-ATLAS, a collection of pathways specifically curated in DC, that can be exploited, using pathway analysis based approach, in deciphering the complex network of interactions occurring in DCs upon activation. The pathways are available at The database contains both human and mice data and the modular structure of DC-ATLAS led to unravel of the major differences between these two systems. The knowledge provided by DC-ATLAS permits the conversion of genomic research into accurate and robust biological hypotheses by generating signatures that serve as valuable tools to understand DC physiology and contribute to the design of new strategies in immunotherapy.DC-ATLAS is one of the first immunological and bioinformatics integrated project which complies with the Systems Biology Graphical Notation (SBGN) . It is cEvery specific gene and reaction were annotated providing information on the organism, the organism part, the cell type and the experimental details in which the evidence has been obtained. The community of curators within DC-ATLAS manually annotated the pathways providing also the most updated reference available in existing databases and literature, as well as generating experimental proofs in their own laboratories where these were lacking. The curation procedure itself is described in more detail in Additional file To ensure that the results of the curation process would also be fully used for representation and data analysis, a DC specific data format, the Biological Connection Markup Language (BCML), was developed to represent pathways according to the specification proposed by the Systems Biology Graphical Notation (SBGN). BCML prIn addition to a full implementation of the PD specification, BCML provides a series of optional features. First of all, BCML can include additional information on the entities that compose the network: each entity can be described by a series of species specific database identifiers, e.g. Entrez Gene or Uniprot accession numbers. Furthermore, each entity or reaction can have a set of facts or "Findings" associated. "Findings" are collections of biological information that are relevant to that entity or reaction. The current specification includes support for organism, organism part (tissue), cell type, the specific biological environment in which the evidence was proven, and the type of the experiment used to gather evidence. To reduce ambiguity and promote consistency among different "findings", the schema enforces a controlled vocabulary built from current medical ontologies.The specification of BCML is accompanied by a series of programs (BCML software suite) that enable the use and manipulation of the format both for the bioinformatician and the biologist. First of all, the software suite permits validation of pathways described using BCML, to ensure consistency and the proper enforcement of the SBGN rules. Secondly, the software can create a fully SBGN compliant graphical representations by transforming the BCML XML into other formats (GraphML) which can be then saved as images with third-party software.The format also permits filtering of the pathway data creating a new network containing only elements with user-defined characteristics, allowing the production of tailored made pathways, allowing individualized analyses. The tools in the BCML software suite allow specific "filtering" of the pathway, taking advantage of all the information stored. For example, nodes and edges can be selected for a specific cell type or organism, permitting the construction of customized network maps to represent specific biological contexts. When a filter is applied to the pathway, elements are marked as "included", "excluded", or "affected". An element of the pathway is included or excluded in the resulting map if it matches with the selected filter criteria or not. The "affected" state is used to indicate elements that may not be present depending on the filtering; for example. in a specific cell type a complex may not form if one or more of its proteins are not present. Filtering may be used to assist data analysis and interpretation and might point to gaps in current knowledge.The BCML format can incorporate any kind of experimental measurements that can be matched to the identifiers of an element. This allows modification of the BCML map, facilitating incorporation of high-throughput data coming from transcriptomic or proteomic experiments. The outcome will be visualized in different color on the graphical map.Finally, BCML allows transformation of the pathways into different data formats, which may be needed for further analysis. Tools provided within the suite allow the generation of identifier (gene) lists from a BCML file, enabling their use with analysis tools such as Gene Set Enrichment Analysis (GSEA), Fisher's Exact Test. Additionally, the format can be converted to a form amenable for impact analysis through the SPIA R package. This conversion can take into account the filtering applied to the elements of the pathway, to carry out individualized analyses.A detailed description of BCML format is available as Additional file At present, the human TLR pathway set in DC-ATLAS is a network organized in an ensemble of 8 pathways , subdivided in 10 sensing modules, 32 signal transduction modules and 30 outcome modules. In contrast to what is present in existing databases, TLR7 and TLR8 were curated separately. Although their genes lie in close proximity on chromosome X and are highly homologous, recent evidences suggest they have distinct roles in DC mediated immune response -13. For Expert-guided, manual curation of the pathways has been a crucial part of the DC-ATLAS initiative, leading to a substantial "reshaping" of the existing pathways. For example, curation of TLR3 pathway led to the validation of only about 50% of the genes included in the list originally retrieved from public databases Figure  and 1B. Another example demonstrating the importance of DC-ATLAS curation is exemplified by the fact that in the sensing module of TLR9 we found a new element, UNC93B1, whose involvement in signaling was demonstrated already in 2007 . All theA summary of all the new genes and/or connections, not previously annotated in TLR pathways, and present in DC-ATLAS is presented in Table To facilitate meaningful analysis of "omics" data, the pathways in DC-ATLAS are organized in a modular structure. Every signaling cascade downstream a specific receptor was divided into 3 types of modules in which the very last component of one module is also the first component of the subsequent module. The first type of module is the receptor and sensing module and comprises component(s) of the pathway directly interacting with the stimulus. The second transduction module, encompasses all components transducing the incoming signal from the sensing module downstream to the nucleus. This module generally starts with a molecule interacting with the receptor and ends with a transcription factor. The third and final module is the outcome module: it describes the end result of the signaling process. This last module begins with a transcription factor and includes target genes whose expression is altered after activation of the receptor. Complex cell functions, such as apoptosis, migration and differentiation are also described as outcomes.According to the previous module definition, the pathways in DC-ATLAS may contain more than one of each type of modules. As an example, Figure The modules, as we defined them, have been subsequently tested using gene expression data as described in the following paragraphs. It should be emphasized that the transduction modules are not independent but are highly interconnected and partially overlapping. Furthermore, a given outcome may result from activation of more than one transduction module.The data format we used to describe the pathway allowed us to depict interactions in the cellular organelles where they occur as well as to specifically mark genes and interactions according to the biological system  where they took place. Thus, we were able to create a map of the TLR3 pathway for example clearly showing which genes and interactions were described in DCs and which were not  that respectively activate TLR4 and TLR7/8. We calculated pathway signatures for each of these datasets and subsequently clustered resulting pathways (see Methods).By clustering pathway signatures using publically available TLR pathways, it proved virtually impossible to obtain information of individual potentially affected elements within the TLR pathway, despite clear up-regulation at the pathway level. Instead, clustering of DC-ATLAS based results readily showed a separation of different stimulatory conditions Figure . The totAs we expected both the TLR7/8 and TLR4 modules were affected upon specific stimulation, with R848 and LPS respectively . At earlAlso in time course experiments, the modular structure of DC-ATLAS allows to appreciate time-dependent changes in expression providing a more informative analysis. The TLR4-sensing module is repressed at 3 hours of LPS stimulation. After 12 hours of stimulation, the MyD88 dependent signaling module is less abundant when compared to MyD88 independent transduction modules during the earliest time points. As can be seen in Figure As can be seen from the analysis, in addition to a single TLR specific pathway, a number of other TLR pathways can be affected by the stimuli used. This is because several of the TLR pathways, such as the TLR4 and TLR7/8 pathways, share some elements, although this does not necessarily mean that their engagement leads to identical outcome. When analyzing the LPS dataset at 3 hours, 135 genes were found to be differentially expressed within the DC-ATLAS pathways and 47 of them belonged to the TLR4 signaling pathway Figure . Among tGiven the modular structure and DC specific annotations of DC-ATLAS we can also evaluate individual elements involved in TLR specific signaling. For example, we mapped differentially expressed genes upon 3 hours-LPS stimulation from our data set to the TLR4 pathway Figure  and becaThese results thus illustrate that the modular structure of DC-ATLAS allows a better and more detailed understanding of TLR mediated signaling in time course experiments.Currently, studies on mouse DCs outnumber those on human cells; however, comparisons between mouse and human models have been somewhat biased due to biological differences between both species  as well An immune response forms a complex biological system with many possible inputs, influences and outcomes, in which DCs play a critical role. The relationship among the different immune cells subsets and model systems are currently under active debate, highlighting the importance of annotating signaling pathways in respect of both the cell type and the species in which the pathway was found.Zanoni et al. reviewed the divergent responses of DCs and macrophages upon LPS , and desStudying DCs using an immune systems biology approach facilitated by DC-ATLAS, holds promise to dissect the integrated signals from these cells. This allows us to build models of the complex process of DC regulation and generate predictions and hypotheses about DC function under physiological and pathological conditions. However, the road forward is not without obstacles. There is a strong need of a greater coverage of network data, improved accuracy and standardization of annotation. The extraction of signal transduction maps from gene expression data requires well-structured pathway definitions. Similarly to the recently published DC pathway map , DC ATLAThe presented results show how DC-ATLAS allows temporal dissection of events within the signal, represented by 3 different modules grouping the sensing/receptor, the transduction of the signal and outcome pool. The pathway analysis perturbations, with these modular pathways, visualize the signal propagation, keeping track of the flow of information.As demonstrated by LPS and R848 stimulation of DCs Figure , the uprThis type of dissection of the flow of information described as changes in gene expression is made possible solely by the use of BCML. It provides a suitable format to store the information collected and organized by the curators and to build the modular pathways. Our goal was to provide a data format that was easily extensible and manipulable for computational analyses, but at the same time intuitive and user friendly for both cell biologist and immunologist communities. BCML satisfies these needs thanks to its flexibility, which permits its use in computational analysis and in the conversion to a SBGN compliant graphical map. The possibility of filtering permits the creation of "customized" networks, better suited to identify specific biological problems or to highlight gaps in current knowledge. At this moment, BCML only covers the SBGN Process Description. In the near future we will also integrate. the SBGN Entity Relationship and Activity Flow representation. in order to provide a complete representation of SBGN at the data level.We developed our own format since neither of the many existing formats such as KGML, BioPAX  or SBML Being SBGN compliant and machine readable, BCML provides a convenient and precise way to represent biological pathways, in an intuitive and user friendly format to both the biologist and the bioinformatician.Because of the more refined modular description of pathways in DC-ATLAS, the results of statistical analysis are much improved with respect to the results one can obtain from existing pathway databases.The modular pathway of DC-ATLAS allows more accurate capture of signaling pathways. In many cases pathway modules are not specific for just one stimulus. This overlap is expected given the combinatorial nature of the module structure and definition that describes the biological nature of signal transduction in DCs. This is an important feature, as the decision making process of DCs often integrates signaling from multiple receptors and temporal integration of multiple sets of stimuli.New computational methods such as DC-ATLAS will contribute to fill in current gaps in the analysis of genomic data. Furthermore, the ability of DC-ATLAS to identify gaps in our current knowledge will foster future research within the immune system, and lead to the design of novel experiments aimed at reconciling interactions and findings documented in human and mouse DCs. In addition, DC-ATLAS will establish the relationships between pathways operating within DCs and other cell types of different species.In conclusion, DC-ATLAS provides a knowledge base on DC biology with the potential to decipher the complex network of interactions occurring within these cells in response to activation stimuli. This knowledge allows the conversion of genomic research into accurate and robust biological hypotheses. Extracting results from large expression datasets using DC-ATLAS will enable us to validate experimentally defined pathways and generate signatures that will serve as valuable tools in the design of new strategies for DC-based immunotherapy.We selected several pathways of interest for immunology, in particular for DC activation, as TLRs pathways and curated them. We handled the currently available information from the literature and from public available pathway databases, such as KEGG, Reactome and GenMAPP, evaluating the quality of the data, as well as experimental evidence generated in our laboratories to curate/design the pathways in a cell specific manner. Detailed information are available on line as Additional file Pathways were drawn following the SBGN Process Description (PD) 1.1 specification . Followihttp://www.inoh.org), (http://www.dc-atlas.net).The DC-ATLAS pathways were also represented in GPML (using an in-house modified version of the PathVisio program ) and INO6 DCs were cultivated with LPS (100 ng/ml) or R848  or without any stimuli. After 3, 6, 12 and 24 hr, cells were collected. RNA preparation, labeling with Cy5, hybridization on a Human HT12 array (Illumina), and scanning were performed according to the Illumina reference protocols.Peripheral blood mononucleated cells (PBMC) were isolated from buffy coat blood sample from healthy donors from the Transfusion Unit Erlangen hospital  by Ficoll-Hypaque density gradient centrifugation (Biochrom AG). The experimental plan was approved by the local Ethical Committee, and informed consent was obtained from all donors. Monocytes were isolated from low density PBMCs by magnetic enrichment with anti-CD14 beads (Miltenyi Biotec). Cells were cultured in the presence of granulocyte macrophage colony stimulating factor  and recombinant IL-4 (1000 U/ml) for 6 days to allow DC differentiation . 2 × 106Bead-summary data saved from Illumina BeadStudio was pre-processed in several steps. Firstly, the background signal was assessed and corrected using the intensity signal from the control probes present on the array, then quantile normalization was performed. In addition to background correction, Illumina probe identifiers were converted to nucleotide universal IDentifiers (nuIDs)  specificMicroarray data have been submitted to the Array Express repository, with the accession number E-MTAB-448.http://rmaexpress.bmbolstad.com) or with the R programming language (other platforms).Publicly available data sets were retrieved from the Gene Expression Omnibus (GEO) database. After retrieving, they were normalized with the Robust Multi-array Average (RMA) method  in the cet al., unpublished data), over the compendium of DC-ATLAS TLR pathways. Prior to the analysis, microarray raw data were transformed into absolute-scale values and processed following the procedure outlined by [Pathway analysis was performed with PathStudio ; grey elements indicate entities whose presence has not been demonstrated in DCs. Blue elements highlight reactions that depend on non present (grey) elements and thus may not occur.Click here for fileFigure S2: SBGN representation of the TLR3 signaling pathway highlighting the reactions that occur only in macrophages. Black elements are entities whose presence has been demonstrated in dendritic cells (DCs); grey elements indicate entities whose presence has not been demonstrated in DCs. Blue elements highlight reactions that depend on non present (grey) elements and thus may not occur.Click here for filePathways analysis results of LPS vs R848 comparison: input matrix. A matrix of Pathway Enrichment Factors (PEFs) obtained from the transformation of the signed p-values derived from the pathway analysis. This matrix can be used for clustering using multiscale bootstrap resampling or other methods.Click here for fileFigure S3: Enriched genes found to be part of TLR4 signaling upon LPS stimulation superimposed to the SBGN pathway map. Differentially expressed genes of DCs stimulated for 3 hours with LPS present in the TLR4 signaling superimposed to the pathway map. Red nodes indicate that the respective genes are up-regulated, and green nodes indicate down-regulated genes.Click here for fileFigure S4: Enriched genes found to be part of TLR4 signaling upon LPS stimulation superimposed to the SBGN pathway map. Differentially expressed genes of DCs stimulated for 6 hours with LPS present in the TLR4 signaling superimposed to the pathway map. Red nodes indicate that the respective genes are up-regulated, and green nodes indicate down-regulated genes.Click here for filePathways analysis results of human vs mouse comparison: input matrix. A matrix of Pathway Enrichment Factors (PEFs) obtained from the transformation of the signed p-values derived from the pathway analysis. This matrix can be used for clustering using multiscale bootstrap resampling or other methods.Click here for file


This review examined whether the combination of pharmacological treatments and psychotherapy is associated with higher effectiveness than pharmacotherapy alone A systematic search was conducted in the following databases: Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, ISI Web of Science, BIOSIS, PsycINFO, and CINAHL. Primary efficacy outcome was a response to treatment; primary acceptance outcome was dropping out of the study. Only randomized controlled trials were considered.We identified 8 studies with a total of 9 relevant comparisons. Our analysis revealed small, but statistically not significant effects of combined therapies on outcomes directly related to depression (BR = 1.20) with substantial heterogeneity between studies (I² = 67%). Three treatment effect modifiers were identified: target disorders, the type of psychotherapy and the type of pharmacotherapy. Small but statistically significant effects of combined therapies on quality of life (SMD = 0.18) were revealed. No differences in acceptance rates and the long-term effects between combined treatments and pure pharmacological interventions were observed.This systematic review could not provide clear evidence for the combination of pharmacotherapy and psychotherapy. However, due to the small amount of primary studies further research is needed for a conclusive decision. Approximately 20% of all patients who experience a major depressive episode develop a chronic course  and apprChronic depression is associated with increased functional impairment , increasAn increasing number of studies have assessed the effectiveness of several pharmacological, psychotherapeutic, and combined pharmacological and psychotherapeutic interventions for the treatment of chronic depression in the last several decades. Several meta-analyses have confirmed the effectiveness of pharmacological treatments ,7 and syBecause different effective interventions are available for the treatment of chronic depression, a comparative analysis of the effectiveness of these different interventions is of great clinical interest. Although, both systematic reviews and current treatment guidelines recommend combined psychotherapeutic and pharmacological interventions for the treatment of chronic depression, these recommendations are based on a limited amount of evidence -11.Psychotherapy continues to face numerous barriers, such as limited access in underserved areas and higher short-term costs when delivered by mental health care professionals . Therefoversus pharmacotherapy alone are available from a large randomized controlled trial [e.g. according to diagnosis).Because new data on the comparative effectiveness of combined interventions ed trial , we decii.e. factors that may influence the size of effects of augmentation of pharmacological treatments with psychotherapy.The objectives of this systematic review are to examine whether the augmentation of pharmacological treatments with psychotherapy is associated with higher effectiveness compared to pharmacotherapy alone and identify possible treatment effect modifiers, a priori in a freely accessible review protocol that included a detailed description of the methods, which are summarized briefly here [The methods and results are reported in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) statement . Methodsfly here .e.g. predefined comorbidities) of chronically depressed patients were excluded.Studies that were conducted in adults with a diagnosis of chronic major depression, dysthymia, double depression, or recurrent depression without complete remission between episodes were included. The diagnosis of depression had to rely on a formal classification system. Studies focusing on preselected samples  were included. Psychotherapeutic interventions had to fulfill the following criteria: 1) the intervention must be based on a scientific theory; 2) a minimum of one contact between therapist and patient must take place; and 3) the intervention must consider the personal needs of the patient and must be individually tailored in an interpersonal process. Combined interventions included the administration of one or more antidepressant pharmacological agents combined with one or more psychotherapeutic interventions. Somatic, non-pharmacological, and organizational interventions were not considered.The comparator treatment needed to be an antidepressant pharmacological intervention alone.Only studies that reported at least one outcome to assess the efficacy of the interventions and only randomized controlled trials (RCTs) were included.(((chron$ adj3 depress$) or dysthym$ or (double adj1 depress$) or (treatment adj1 resist$ adj1 depress$) or (non adj1 respon$ adj3 depress$) or (recurrent adj3 depress$)).ab,ti,sh.) AND ((random$ or rct).ab,ti. or random$.sh.) . No language restrictions were applied and all publications from 1970 forward were considered.An electronic database search was conducted in the following databases on January 18, 2010: Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, ISI Web of Science, BIOSIS, PsycINFO, and CINAHL. A disease component was combined (AND) with a design component for all searches: Additionally, all volumes of the Archives of General Psychiatry, the Journal of Consulting and Clinical Psychology, and the Journal of Affective Disorders were searched by hand beginning with the year 1970. The reference lists of all included studies and relevant reviews were searched and a cited reference search in the Social Sciences and Science Citation Index was performed for all included studies. The first author of all included studies was contacted for further information regarding published and unpublished trials.a priori defined. Disagreement was resolved by discussion.Two reviewers independently screened title and abstract of all identified articles. Next two reviewers independently examined the full texts of all potentially relevant studies using inclusion criteria that were A data extraction form of study characteristics, treatment characteristics, sample characteristics and outcomes was developed.Risk of bias was assessed in accordance with the Cochrane Collaboration’s Risk of Bias tool . Two resThe primary efficacy outcome was the response to treatment, which was defined as an at least 50% decrease on a depression scale from baseline to the end of treatment. Secondary efficacy outcomes included metric outcomes of depression scales at the end of intervention and at follow-up, the dichotomous outcome remission, and metric outcomes on any quality of life scale. The primary acceptance outcome was dropping out of the study due to any reason. The primary endpoint was the end of intervention for all outcomes irrespective of intervention duration. Follow-up was defined as at least 6 months after the end of intervention.The statistical analysis followed actual guidelines -18. EffeEffect sizes were calculated using the intention-to-treat principle for all studies. All randomized patients were included in the analyses of primary outcomes irrespective of how the authors of the primary studies defined their intention-to-treat sample. For secondary outcomes the definition of the intention-to-treat sample provided by the authors was followed. In all analyses a random effects model with inverse variance weights were applied .Statistical heterogeneity between study results was tested for significance using Cochran’s Q-test and quantified using the I² statistic .Possible publication bias was investigated using visual examination of funnel plots and applying Egger’s test .A priori defined analyses were performed according to the type of psychotherapeutic intervention (brief supportive psychotherapy (BSP), cognitive behavioural therapy (CBT), Cognitive Behavioural Analysis System of Psychotherapy (CBASP), Interpersonal Psychotherapy (IPT)), the subtype of chronic depression , the onset and severity of the target disorder (percentage of patients who reported an early onset of the disorder and baseline severity of depression), and study quality  [a posteriori analyses were performed according to the total number of patients included, setting (outpatient vs. inpatient), the number of sessions, treatment duration (in weeks), the use of selective serotonin reuptake inhibitors (SSRIs) as antidepressant medication, mean age of the sample, and the percentage of females in the sample.Heterogeneity among primary study findings was explored using meta-regression analyses that examined a series of possible effect modifiers. quality) . Additiovia the restricted information maximum likelihood procedure. We chose to conduct meta-regression analysis instead of subgroup analysis for categorical effect modifiers because this method allows applying a random effects model and provides a consistent framework for all analyses . All analyses were conducted for two types of outcome measures: benefit ratios for treatment response and standardized mean differences for depressive symptoms at end of intervention. Bivariate association of treatment effect modifiers were examined to reveal possible multicollinearity.Inverse variance-weighted meta-regression models were used to test possible effect modifiers formally -24. RandIn order to examine the influence of single studies on the findings leave-one-out sensitivity analyses were conducted for the primary outcomes response and dropout. Additional leave-one-out sensitivity analyses were performed for the meta-regression-analyses.Analyses were performed using Review Manager 5  and PASW Statistics 18  with an additional macro by Wilson .versus pharmacotherapy alone.After the removal of 1,710 duplicates 2,417 potentially relevant publications were identified through the electronic database research  used SSRIs as the pharmacological intervention. IPT was used as the psychotherapeutic intervention in four studies, CBASP and CBT were each used in two studies and one study used BSP. Half of the studies (4/8) were conducted in the United States. Most studies focused on samples with a majority of dysthymic patients. The average age of the study participants ranged from 37 to 45 years. All studies included a majority of women. The detailed characteristics of each study are presented in Table The overall risk of bias was evaluated as “low” for five studies and as “medium” for two studies. Only one study was judged to have a “high” risk of bias. Knowledge of allocation was adequately concealed in nearly all studies (7/8), whereas an adequate concealment of the allocation was reported in only four of the studies. The results of the methodological quality assessment are presented for individual studies in Table One study reported two intervention arms with a combined treatment and one arm with a pharmacological treatment and thus provided two comparisons of interest for the current meta-analysis . We cut The results of one study  proved tNo statistically significant difference (at p < 0.05) in response rates between combined treatments and pharmacological interventions alone were found. However, combined treatments tended to be superior to pharmacological therapies . This result corresponds with a number needed to treat (NNT) of 20. Leave-one-out sensitivity analysis showed the greatest increase of the overall effect  after removal of the study by Browne and colleagues  and the Substantial statistical heterogeneity among the results of the primary studies was observed for all outcomes .Combined treatment showed statistically significantly better quality of life outcomes than pure pharmacological interventions at the end of active treatment .Dropout rates did not differ statistically between combined treatments and pharmacological interventions alone . These results were not heterogeneous across studies (I² = 0%). Leave-one-out sensitivity analysis showed the greatest increase of the overall effect  after removal of the study by Keller and colleagues  and the Four studies provided data of depressive symptoms at follow-up. Long-term effectiveness at an average of 12.5 months after end of active treatment was not statistically significantly different between combined and pharmacological treatments .Results for each individual study concerning each outcome as well as overall effects are displayed in Table response to treatment by visual examination of the funnel plot was observed . This result did not reach statistical significance for the outcome depressive symptoms at end of intervention (p = 0.252), but it accounted for nearly 70% of the effect variance across studies (as suggested by the R-squared estimate). Expressed in differences of benefit ratios this result indicates, that in a study with only dysthymic patients the estimated benefit risk for response between a combined treatment and a pure pharmacological treatment would be 0.95, whereas in a study with patients suffering from chronic major depression the estimated benefit ratio would be 4.02. Leave-one-out sensitivity analysis revealed that the diagnostic subgroup did not serve as a statistically significant treatment effect moderator when the study by Keller and colleagues [The results of the meta-regression analysis are presented in Table a p = 0.0. This relleagues  were remApart from diagnostic subgroups the sample characteristics of the studies such as mean age, percentage of women, or percentage of patients reporting an early onset of their disorder were not associated statistically significantly with differences in effect sizes between combined treatments and pure pharmacological interventions.Second, in studies that added CBASP to a pharmacological intervention, differences between the combined intervention and the pharmacological intervention were significantly greater than in studies that used IPT . IPT was used as reference intervention because it was the most frequently used form of psychotherapy. This effect corresponds to a benefit ratio of 1.07 for IPT compared to an estimated benefit ratio of 1.49 for CBASP. No effect of the number of psychotherapeutic sessions or the duration of treatment was observed. Leave-one-out sensitivity analysis revealed that the type of psychotherapeutic intervention did not serve as a statistically significant treatment effect moderator when the study by Keller and colleagues  were remThird, in studies that used SSRIs as the pharmacological intervention, the add-on effect of the psychotherapeutic intervention was diminished compared to studies that used other antidepressant medications . This effect corresponds to an estimated benefit ratio of 1.02 in a study that uses SSRIs s the antidepressant medication  compared to an estimated BR of 1.52 in study with other types of medication. Leave-one-out sensitivity analysis revealed that the type of medication did not serve as a statistically significant treatment effect moderator when the study by Keller and colleagues  was remoThe risk of bias of the individual studies and the number of patients that were included in the analysis did not serve as treatment effect modifiers.response to treatment. No statistically significant effect was found for the outcome depressive symptoms at end of intervention after removal of the study by Keller and colleagues [We conducted further exploratory multiple regression analyses testing all three relevant effect modifiers  in one model. The results indicated that SSRIs significantly reduced the effect of combined psychotherapeutic and pharmacological interventions compared to a pure pharmacological intervention . However, the use of CBASP as the psychotherapeutic intervention and the percent of patients with chronic major depression did not influence the differences in effect sizes between combined interventions and pharmacological interventions alone. Inter-correlations between the three treatment effect modifiers were small to moderate and not statistically significant (Spearman’s rho: -0.33 to 0.34). Leave-one-out sensitivity analysis revealed that the type of medication did not serve as a statistically significant treatment effect moderator when the study by deMello  was remolleagues  or the slleagues .A small and statistically not significant effect of combined psychotherapeutic and pharmacological interventions on outcomes that are directly related to depression  with a substantial variation of effect sizes between studies was revealed. A more detailed meta-regression-analysis demonstrated that this variation can be partly explained by differences in target disorders (studies of patients suffering from chronic major depression showed greater effects for combined therapies than studies with dysthymic patients), psychotherapy (CBASP yielded greater effects for combined therapies than IPT), and pharmacotherapy (SSRIs decreased the add-on effect of any psychotherapy). Exploratory multiple regression analyses suggested that the most important treatment effect modifier is the use of SSRIs as the pharmacological intervention. The finding of a small add-on effect of psychotherapy on depressive symptoms in the treatment of chronic depression is consistent with previous findings , yet we Small but statistically significant add-on effects of psychotherapy on the quality of life of chronically depressed patients were demonstrated. No differences in acceptance rates (dropout rates) or long-term effects between combined treatments and pure pharmacological interventions were observed.a priori defined treatment effect modifiers we conducted additional explorative meta-regression analyses whose interpretation needs to be considered preliminary. Altogether the number of examined effect moderators was large, particularly in relation to the small number of studies. Therefore we advise careful interpretation of these findings as causal evidence and consider them as observational hypotheses that need further investigation.Several limitations of the current literature emerged upon this review. First, the sample sizes of primary studies varied greatly and the overall number of studies that were suitable for the systematic review was rather small. Therefore, our analyses were primarily dominated by three large-scale studies ,26,28. LAnother shortcoming of our review is that the presented evidence is based on clinical trials which focus on high internal validity, yet implementation of combined treatments in routine care is connected to certain challenges. For example patients may perceive practical and emotional barriers prior to psychotherapeutic treatment  and the Third, results of the long-term add-on effect of psychotherapy are preliminary, as only four studies provided relevant data. More research is required because of the high risk of relapse in chronic depression.This systematic review could not provide clear evidence for the augmentation of pharmacotherapy with psychotherapy in the treatment of chronic depression. Our findings indicate that the role of add-on psychotherapy may be of more limited value than suggested in current literature  and cline.g., moclobemide, nefazodone) are in combination with psychotherapeutic interventions less effective than SSRIs in combination with psychotherapeutic interventions, yet further evidence on the direct comparison of the different types of antidepressants is needed to conclusively interpret this finding. Therefore, in further studies of the combination of pharmacotherapy with psychotherapy SSRIs should be used as a comparator. The heterogeneity across studies further indicated that the category chronic depression subsumes clinically heterogeneous subgroups. Especially patients suffering from dysthymia and chronic major depression seem to respond differently to certain treatment strategies.The heterogeneity across studies further highlighted the relevance of the optimization of both psychotherapeutic and pharmacological interventions to increase treatment effects. Our analysis revealed a high impact of SSRIs on the comparative effectiveness of treatment strategies. One explanation for this finding could be that the non-SSRI antidepressants (Further research on the cost-effectiveness, long-term outcomes and the role of psychotherapy in the continuation and maintenance treatment of chronically depressed patients is required to conclusively assess the value of psychotherapy as an add-on treatment to pharmacotherapy.The authors declare that they have no competing interests.LH, MH, and LK designed the study. AvW, LH, and LK prepared the study protocol. AvW and AW managed the literature searches and the reference database. AvW, LH, AW and LK screened potentially relevant publications. AvW, LH, and LK examined studies for inclusion. AvW and LK performed data extraction. AvW and LK undertook the statistical analyses. All authors contributed to the interpretation of results. AvW wrote the first draft of the manuscript. LH, AW, MH, and LK revised the article critically for important intellectual content. All authors have approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-244X/12/61/prepub


Osteochondroma is a disease of growing bone and thus typically presents in younger patients. It has rarely been described in middle-aged and elderly patients. Data on the occurrence of osteochondroma show that the reported incidence of costal osteochondroma is very low. Moreover, costal osteochondroma arising at the costovertebral junction with neural foraminal extension and spinal cord compression is extremely rare.This study reports the case of a 58-year-old patient with a solitary osteochondroma of the 12th rib with intraspinal extension and spinal cord compression. The clinical history, plain radiographs, computed tomography (CT), magnetic resonance imaging, and pathologic findings of the reported patient have been reviewed. The relevant medical literature has also been reviewed. The patient was treated with surgery for complete tumour excision to avoid tumour recurrence. After surgery, the patient's symptoms improved. An additional CT scan obtained at 1 year after surgery did not show any evidence of recurrence.This patient is the oldest patient reported to have this rare form of costal osteochondroma. The age of the patient and the erosion of the adjacent bones raised clinical suspicion of malignancy; therefore, surgical management involved complete tumour excision with thoracolumbar fixation and fusion. Osteochondromas are the most common benign tumours of the bone and may present as either a solitary lesion or as multiple lesions ,2. SolitWe report a case that is unusual in many aspects such as the site of tumour origin within the rib; associated myelopathic symptoms; occurrence in a middle-aged patient; and the erosion and fusion of the vertebral pedicle, facet, and body due to tumour extension. Extension of the tumour necessitated total pediculectomy of T12, total facetectomy of T12-L1, and partial unilateral vertebrectomy of T12 with thoracolumbar fixation and fusion.A 58-year-old man presented with a 3-month history of right lower extremity weakness and numbness. He also reported progressive gait disturbance of 1-month duration. He denied bowel and bladder incontinence and sexual dysfunction. There was no medical or family history of neurologic dysfunction or bony tumour. Neurologic examination showed profound weakness, decreased pinprick sensation, and hyperreflexia of his right lower extremity. Right ankle clonus and positive Babinski response were also elicited.Plain radiographs of the lower thoracic and lumbar spine regions showed an exophytic bony mass on the right side of T12-L1 Figure . The difA posterior midline skin incision was used to expose the posterior elements of T11 to L1, and the exposure was extended to both ribs. After dissection, the large outer fragment of the multilobulated osseous mass was completely exposed Figure . This frPathologic examination of the tissues of the lesion showed proliferated hyaline cartilage but atypical changes indicative of myxoid degeneration were not observed. The histologic examination results indicated the strong possibility of osteochondroma, but low-grade chondrosarcoma could not be excluded because of the age of the patient and the erosion of adjacent bones Figure . After sThe reported incidence of costal osteochondroma is very low ,4. HowevOsteochondroma is a disease of growing bone, and thus typically presents in younger patients . Tumour Although the location of the bony portion of the osteochondroma can be reliably determined using multiplanar CT reconstruction, the exact size of the tumour may be underestimated because the cartilage cap of the tumour is not detectable by CT ,4. MR imMalignant transformation, usually into a chondrosarcoma, occurs in approximately 1% of solitary osteochondromas and 10% of HMEs ,12. A suThe type of osteochondroma described in this case, which arose at the costovertebral junction with neural foraminal extension and spinal cord compression, is extremely rare. Only 7 such cases have been previously reported in the English-language literature. This is the first report of this form of rare costal osteochondroma occurring in a middle-aged patient and requiring surgical management involving complete tumour excision with thoracolumbar fixation and fusion. Malignancy remained a possibility throughout because of the patient's age and erosion of adjacent bones.Written informed consent was obtained from the patient for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.The authors declare that they have no competing interests.JH Shim provided major contributions to writing and editing the manuscript. CK Park supervised the writing of the manuscript. SH Shin contributed to analysis of the data. HS Jeong interpreted the radiologic results. JH Hwang contributed to conception and design of the data. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2474/13/57/prepub


The neuropsychological exam plays a central role in the assessment of elderly patients with cognitive complaints. It is particularly relevant to differentiate patients with mild dementia from those subjects with mild cognitive impairment. Formal education is a critical factor in neuropsychological performance; however, there are few studies that evaluated the psychometric properties, especially criterion related validity, neuropsychological tests for patients with low formal education. The present study aims to investigate the validity of an unstructured neuropsychological assessment protocol for this population and develop cutoff values for clinical use.A protocol composed by the Rey-Auditory Verbal Learning Test, Frontal Assessment Battery, Category and Letter Fluency, Stick Design Test, Clock Drawing Test, Digit Span, Token Test and TN-LIN was administered to 274 older adults  with predominantly low formal education. Factor analysis showed a four factor structure related to Executive Functions, Language/Semantic Memory, Episodic Memory and Visuospatial Abilities, accounting for 65% of explained variance. Most of the tests showed a good sensitivity and specificity to differentiate the diagnostic groups. The neuropsychological protocol showed a significant ecological validity as 3 of the cognitive factors explained 31% of the variance on Instrumental Activities of Daily Living.The study presents evidence of the construct, criteria and ecological validity for this protocol. The neuropsychological tests and the proposed cutoff values might be used for the clinical assessment of older adults with low formal education. The neuropsychological evaluation plays an important role in the differential diagnostic between normal and pathological aging cognitive processes Formal education has a major impact in the performance on cognitive tests and can bias the interpretation of test results. Educational level influences the performance on cognitive screening test, such as the Mini-Mental State Examination and the Category Fluency Test, and cut-off scores for dementia diagnosis based on the educational level have been widely used In clinical neuropsychology the use of an unstructured assessment protocol allows the clinician to carefully choose the neuropsychological tests according to a cognitive model and his clinical hypothesis, mapping different cognitive domains in a comprehensive way In the present study 274 consecutive older adults were assessed. Participants were enrolled in an ongoing work evaluating the relationship of depression and dementia in the elderly. The participants or caregivers who did not show interest in joining the study were referred and treated normally by the patient service center, not suffering any burden with the non-participation. This study was approved by the local Ethics Committee (registry 334/06) and carried out in accordance with the Helsinki declaration. All the participants (and caregivers for patients with suspected dementia) gave written consent for the participation. Participants with less than 60 years, previous history of neurological or psychiatric disorders (except for depression), use of typical and atypical antipsychotics, evidence of major vascular events on brain computed tomography scans, severe sensorial or motor impairments or other clinical conditions which may influence the neuropsychological performance (such as hypothyroidism or B12 vitamin depletion), history of alcohol or other substance abuse and patients which a close caregiver was not present on the assessment were excluded from the present study.All subjects underwent a comprehensive gerontological evaluation which included the cognitive assessment with the administration of the Mattis Dementia Rating Scale The performance on neuropsychological tests used for diagnosis was interpreted based on cut-off values for the Mini-Mental State Examination . For the Mattis Dementia Rating total score and Subscales the “-2 Standard-Deviations” guideline  was used. For the CERAD Neuropsychological Battery, we adopted as cut-off the first quartile stratified by education, following Nitrini and colleagues Neurocognitive status was adjudicated at expert multidisciplinary meetings, taking into account all clinical, cognitive assessment, laboratorial, and neuroimaging data when available. Functional status was investigated based on caregiver's reports about activities of daily living and by the functional components of the Clinical Dementia Rating A total of 85 subjects were identified as MCI and 93 with AD. Ninety-six subjects with no evidence of cognitive impairment were included as a comparison group . Normal aging and MCI participants had MMSE scores above the cutoff for dementia according to formal education The protocol used in the present study was designed to assess episodic memory, attention, executive functions, visuospatial abilities and language. It was designed to be fully administered in one session of 90 minutes, increasing its usefulness in the clinical contexts where the time and human resources for the neuropsychological assessment are scarce. The tests were selected based on Brazilian studies which investigated their psychometric properties on older adults with low formal education. Two neuropsychologists (LFM-D and JJP) searched the Brazilian and international literature for neuropsychological tests which: 1) may be suitable for older adults with low formal education ; 2) have previous studies reporting, at least partially, validity for this population, 3) could be all applied on a 90 minutes assessment section, 4) tests did not have copyright agreements, with stimuli and application procedures freely available. The following tests were selected:Rey Auditory Verbal Learning Test (RAVLT): a measure of episodic memory containing five learning trials of a 15 word list followed by a distractor, an immediate recall (RAVLT IR), a 25-minutes delayed recall (RAVLT DR) and a recognition Trial (RAVLT Rec). The Brazilian version of the test proposed by Malloy-Diniz and colleagues Frontal Assessment Battery: designed as a bedside screening test for frontal-executive impairment Short version of the Token Test: this language comprehension test designed for the detection of aphasia involves verbal orders of increasing difficulty (input) and motor sequences on colored tokens (output). The short version (36 items) is adapted Category Fluency and Letter Fluency: The verbal fluency tests are classical screening tests for cognitive impairment, usually associated with the executive functions. Two categories and one letter were chosen for the protocol, based on the normative and validity studies for the Brazilian population: AnimalsFruitsS”Digit Span: a classical measure of verbal working memory, a cognitive process related to storage and manipulation of verbal information. Kessels, van den Berg, Ruis and Brands Clock Drawing Test: A classical drawing task designed for the assessment of cognitive impairment in older adults and a widely used test for cognitive screening. The Shulman's Stick Design Test: a test used for the assessment of visuospatial abilities consisted of four bi-dimensional models where the subject must reproduce them using four matches The Neuropsychological Investigations Laboratory Naming Test (TN-LIN): developed as a measure of naming abilities in children and older adults with low formal education Activities of Daily Living: we used the Basic Daily Life Activities Index and the Instrumental Daily Life Activities Index, based on the Katz Performance on neuropsychological assessment tests and socio-demographic characteristics were assessed by one-way ANOVA, and the Sidak's post hoc test was used to assess pairwise group differences. Effect sizes for this analysis were computed by the eta-squared. Keeping in mind the hierarchical structure of the cognitive system The ecological validity of the neuropsychological assessment was investigated by linear regression models, containing the ADL measures as dependent variables and the components of the factor analysis  as predictors. We adopted stepwise procedures to reduce multicollinearity.forward entry, entering criteria: 0.05 and exclusion criteria 0.10).We carried out Receiver Operator Characteristic (ROC) curve analyses to compare the performance of each neuropsychological test to differentiate the diagnostic groups. Cutoffs for clinical use considering the best ration between sensitivity and specificity were calculated. Finally, we performed a multinomial logistic regression analysis, with diagnosis as dependent variable and the neuropsychological tests as independent variables; to evaluate which neuropsychological tests best differentiate the diagnostic groups. To reduce multicollinearity, we adopted a stepwise procedure  and statistical significance was set at α<5%.The three groups did not differ in clinical and socio-demographic and clinical characteristics. As expected, we found significant differences in the scores of all neuropsychological tests among diagnostic groups, with effect sizes ranging from small to large .Executive Functions Factor). The second component contained the three TN-LIN variables, a test designed to assess the naming skills (Language/Semantic Memory Factor). The third component contained the RAVLT items (Episodic Memory Factor). The last component contained tests designed to assess visuospatial abilities, visual search . Unexpectedly, a verbal comprehension test was also present in this fourth factor. These four factors explained 65% of the total variance. The internal consistency of the individual factors and the protocol as a whole was 0.83 satisfactory.The Neuropsychological battery formed four related factors . The fir2 = 31%) and contained three steps. The final model (third step) consisted of Executive Functions , Episodic Memory  and Language/Semantic Memory , but not Visuospatial abilities . The ecological validity of the neuropsychological assessment was assessed by a stepwise linear regression model. The model was significant , was significant . Six steps were performed by the model starting with RAVLT-DR , then adding, Mini-Mental State Examination , Category Fluency Animals , RAVLT-Rec , TN-LIN-Nouns  and the Frontal Assessment Battery . The participant's classification, considering chance, the final regression model and error are shown in The multinomial logistic regression model, which seeks to correctly classify the participants . This is in accordance with the expected protocol structure given the tests chosen included in the neuropsychological protocol. Therefore, our results show that this protocol has good construct validity and is appropriate for administration in older adults with low educational level. This is particularly important as most of these tests were developed in countries with population with higher educational attainment level.Three of the four cognitive components of our study correlated with functional performance and only visuospatial abilities were not correlated with functional performance. Previous studies, nonetheless, reported significant associations between visuospatial tests and functional measures This neuropsychological protocol showed good criterion related validity, and the cutoff values found on this study could be used on clinical setting for discriminating AD, MCI and healthy older subjects. The best sensitivity and specificity values were observed for AD vs. healthy controls. The sensitivity and specificity for AD vs. MCI and MCI vs. NA was lower than those observed for AD vs. NA, but still at an acceptable range to be used in clinical practice. Our results are in accordance with other studies, with minor differences in the proposed cut-off value, and differences might be explained by sample particularities The neuropsychological assessment protocol proposed by this study significantly improved the classification of the three groups. A multinomial regression model included tests of delayed and recognition memory (RAVLT), global cognitive functioning , executive functions  and language/semantic processing (TN-LIN Nouns). These results support the hypothesis that adding cognitive tests of different cognitive domains increase diagnostic power Our study was performed with a very particular and vulnerable population, and the proposed cutoff scores might improve the clinical use of the neuropsychological testes for patients with similar characteristics. In this sense, the study is clinically relevant, with different cutoffs for several neuropsychological tests for three different comparisons, and could be used along with other methods to the diagnosis of AD and MCI, as well for the differentiation of these two conditions. However the cutoffs must be used cautiously, since the accuracy of each test independently is usually moderate, especially on the MCI x AD differentiation.The present results should be viewed in light of study limitations. This is a cross-sectional study and the MCI patients were not followed-up to assess the progression to dementia. Previous studies suggest that there are significant baseline differences in cognitive performance between MCI converters and non-converters what may significantly influence the definition of cut-off scores to differentiate MCI from normal aging and dementia subjects The present study shows strong evidence of the validity of a neuropsychological protocol designed for the cognitive assessment of older adults with low educational level. The measures are valid for the assessment of executive functions, language, memory and visuospatial abilities. It has good accuracy for the diagnosis of AD and MCI patients. Future studies are necessary to replicate these finding, to verify its applicability under other clinical conditions and to develop population-based norms for this protocol.


Intraorbital foreign bodies are frequently the result of high-velocity injuries with varying clinical presentations. The resultant diagnosis, management, and outcome depend on the type of foreign body present, anatomical location, tissue disruption, and symptomatology. A patient who presented to the Emergency Department with a large intraorbital foreign body projectile that was not evident clinically, but found incidentally on computed tomography and subsequent plain films is reported. The emergency room physician needs to be aware of the differential diagnosis of a unilateral irregular pupil with or without visual acuity changes. The differential diagnosis for any trauma patient with an irregular pupil with significant visual loss must include intraorbital foreign body and associated injury to the optic nerve directly or via orbital compartment syndrome secondary to hemorrhage and/or edema. Patients with significantly decreased visual acuity may benefit from emergent surgical intervention. In patients with intact visual acuity, the patient must be monitored closely for any visual changes as this may require emergent surgical intervention. Research has shown that 3% of all visits to the Emergency Department (ED) in the US are related to ocular trauma . Rapid aPupillary irregularity resulting from orbital trauma can be ocular or orbital in nature. Blunt or penetrating trauma to the globe can result in iris sphincter muscle disruption or disintertion of the iris from its origin . PartialA 39-year-old Caucasian male lumber mill saw operator presented to the ED with the chief complaint of "I got hit in the face with a piece of wood." The initial triage report stated that there was no "significant" visual loss, left periorbital edema, and no other injuries. On initial evaluation the patient was noted to be alert and oriented, and to have "an isolated injury to the left eye and orbit area with normal neurologic exam." There was a "left fixed and dilated pupil with minimal extraocular motion," a "small amount of red blood in the anterior chamber," and "no light sensation whatsoever." An emergent ophthalmology consultation was placed, and a CT of the head and cervical spine was ordered. The CT of the head revealed artifact from a large metallic IFB. Emergent oculoplastics and neurosurgery consults were then ordered.The patient expanded on the history, adding that he had been using a saw consisting of a large metal disc with smaller C-shaped blades bolted onto it when something flew off and hit him on the left side of the face. He denied loss of consciousness but did describe pain in the left orbital area. He again reiterated that initially he was able to see out of the affected eye, but his vision went away quickly until he was unable to see anything. The patient denied having any significant previous ocular history.Upon ophthalmologic examination, the patient had an uncorrected Rosenbaum near card visual acuity of J1+ (20/20) in the right eye and no light perception in the left eye. Intraocular pressures were 15 mmHg in the right eye and 17 mmHg in the left by Perkins tonometer. Extraocular motility was full in the right eye and severely reduced in all directions of gaze in the left eye. The right pupil was 3 mm and constricted to 2 mm with direct light. The left eye had a 7-mm pupil that did not react to direct or consensual light. A "swinging-flashlight test" confirmed a reverse afferent pupillary defect in the left eye. Confrontation visual fields were full in the right eye and not present in the left eye. External, slit lamp, and fundoscopic examination of the right eye was unremarkable.External exam of the left eye revealed significant edema and ecchymosis of the upper and lower eyelids. There was a 1-cm laceration lateral and inferior to the lateral canthus Figure . Slit laPlain film radiographs and CT of the head revealed a large sickle-shaped metallic density extending through the left orbital roof superiorly into the left frontal lobe Figure . FragmenThe metallic IFB projectile was removed by neurosurgery and oculoplastics the next day. The item removed was a 3 × 0.25-inch solid steel, sickle-shaped saw component Figure . PostopeThis case presents numerous teaching points of properly assessing periorbital/orbital injuries as well as an often overlooked differential diagnosis for unilateral pupillary defect. The clinical course of the patient underscores the importance of a detailed history and thorough examination. There are multiple "clues" within the history and presentation that point to an increased likelihood of an IFB. The patient's employment and mode of injury should raise suspicion for a potential IFB projectile. The small laceration adjacent to the lateral canthus was not documented during the ED evaluation, suggesting a penetrating injury was absent from the differential diagnosis.The patient reported having acuity immediately following the injury with subsequent loss. This is suggestive for the onset of orbital compartment syndrome causing traumatic optic neuropathy, not transection of the optic nerve. Anatomically, posterior to the globe the extraocular muscles and their surrounding fascia form a conical structure encasing vital vessels, lymphatics, and the optic nerve sheath, which contains the ophthalmic artery and optic nerve [5.8]. Direct trauma or secondary compression to these structures may cause a dilated and fixed pupil. Patients can also sustain decreased acuity following the initial injury from a worsening hypehma or vitreous hemorrhage. While these were noted in this patient, their extent was not consistent with his level of acuity. It is likely the patient had orbital compartment syndrome secondary to retrobulbar hemorrhage and generalized tissue edema. In cases such as this, an emergent canthotomy/canthal cutdown may preserve visual function; however, time is imperative as permanent optic nerve injury can occur within minutes .Patients who have sustained high-velocity periorbital or orbital injuries should be suspected of having an IFB. Their presentation ranges from being asymptomatic to varying degrees of visual disturbance and/or periorbital pain, edema, and ecchymosis. A detailed history and clinical examination are imperative as the severity of a penetrating orbital injury is often underestimated on physical exam . RadioloSurgical intervention in the patient with intraorbital foreign body is indicated in the presence of a sharp foreign body, signs of infection, proptosis, restricted motility, chemosis, palpable orbital mass, optic nerve compression, abscess, suspicion of organic material , fistula formation, presence of copper, or when adjacent structures are compromised. Inorganic foreign bodies that are asymptomatic and not easily accessible can sometimes be safely left in place ,3,6.IFB: intraorbital foreign body; ED: emergency department; CT: computed tomography; MRI: magnetic resonance imagingWritten informed consent was obtained from the patient for publication and/or presentation of his medical data, including this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.JF is the president elect of the American Society of Ophthalmic Plastic and Reconstructive Surgery. JF and KC serve as section editors for the American Academy of Ophthalmology board review book series. JF is an oral examiner for the American Academy of Ophthalmology. KC is an oral examiner for the American Society of Ophthalmic Plastic and Reconstructive Surgery. CC is an assistant professor and Department Chair of Ophthalmology and Oculofacial Plastic and Reconstructive Surgery Section Head at Ohio University/Doctors Hospital. JF and KC are assistant professors of Ophthalmology at Ohio State University. CC, JF, and KC are all fellows of the American Academy of Ophthalmology and American Society of Ophthalmic Plastic and Reconstructive Surgeons. JF and KC are fellows of the American College of Surgeons, and CC is a fellow of the American College of Osteopathic Surgeons.The authors declare that they have no competing interests.CC was involved in direct patient care, concept, drafting, and critically revising the manuscript. TP was involved in drafting the manuscript and reviewing the pertinent literature. JH was involved in direct clinical care of the patient and aiding in drafting the manuscript. KC was involved in critically revising the manuscript for important intellectual content. JF was involved in critically revising the manuscript for important intellectual content. All authors read and approved the final manuscript.