Over the last few decades, research concerning the insight of patients with schizophrenia and its relationships with other clinical variables has been given much attention in the clinical setting. Since that time, a series of instruments assessing insight have been developed. The purpose of this study was to examine the reliability and validity of the Taiwanese version of the Beck Cognitive Insight Scale (BCIS). The BCIS is a self-administered instrument designed to evaluate cognitive processes that involves reevaluating patients' anomalous experiences and specific misinterpretations.The English language version of the BCIS was translated into Taiwanese for use in this study. A total of 180 subjects with and without psychosis completed the Taiwanese version of the BCIS and additional evaluations to assess researcher-rated insight scales and psychopathology. Psychometric properties  were assessed for this translated questionnaire.Overall, the Taiwanese version of the BCIS showed good reliability and stability over time. This translated scale comprised a two-factor solution corresponding to reflective attitude and certain attitude subscales. Following the validation of the internal structure of the scale, we obtained an R-C (reflective attitude minus certain attitude) index of the translated BCIS, representing the measurement of cognitive insight by subtracting the score of the certain attitude subscale from that of the reflective attitude subscale. As predicted, the differences in mean reflective attitude, certain attitude and R-C index between subjects with and without psychosis were significant. Our data also demonstrated that psychotic patients were significantly less reflective, more confident in their beliefs, and had less cognitive insight compared with nonpsychotic control groups.In light of these findings, we believe that the Taiwanese version of BCIS is a valid and reliable instrument for the assessment of cognitive insight in psychotic patients. To fully understand the issues related to the clinical course of schizophrenia, patients' perspectives, beliefs, and values should be taken into consideration when assessing something as complex as insight. This will provide the clinician and researcher with a better understanding of the different models of psychotic illness, help-seeking, and mental health care acceptability ,2. InsigOver the past few decades, researchers have focused their attention on the complex nature of insight ,2. AlthoThe initial study by Beck et al. found that the BCIS is composed of two subscales: self-reflectiveness and self-certainty . The forThe majority of studies that have investigated the relationship between overall cognitive insight of schizophrenic patients as measured by the composite index scale of the BCIS and clinical insight as measured by the Scale to Assess Unawareness of Mental Disorder (SUMD) ,14 and tTo our knowledge, no similar instrument has been published and validated in the Taiwanese language. Consequently, the goal of our study was to describe the reliability and validity of the Taiwanese version of the BCIS originally developed by Beck et al. . ParticiThe repeated forward-backward translation procedure was applied to translate the BCIS from English into Taiwanese language. One clinical psychologist and one psychiatrist translated the questionnaire into Taiwanese and two professional translators backward translated the Taiwanese into English. Any inconsistencies were resolved by retaining only the translated items that perfectly matched the original BCIS after back-translating the items into English. Subsequently, a provisional version of the Taiwanese questionnaire was developed, and a pilot study was performed with ten respondents with and without schizophrenia. Small revisions have been made to the translated version as a result of the pilot study's findings. Ultimately, a final Taiwanese version of the BCIS was used in this study.A cross-sectional study using the translated BCIS was conducted across three subgroups of study subjects. Group 1 consisted of 60 health control subjects , including practical nursing students and staff members at a general hospital with no history of psychiatric disorders, who served as a general population comparison group. Group 2 comprised 60 patients  with the diagnosis of major depressive disorder (MDD) without psychotic features, single episode or recurrent, and were outpatients who had been referred by the psychiatric department of a general hospital. Group 3 included 60 outpatients  with the diagnosis of schizophrenia or schizoaffective disorder; the patients were recruited from the outpatient department of a general hospital. All of the diagnoses in our sample were made according to DSM-IV criteria  by a resThe following assessments were administrated in a single session with reference to the respondent's behaviour and experience over the previous 12 months. To identify the test-retest reliability of the BCIS measure in this study, 30 subjects, including 10 from each diagnostic group, completed the BCIS again four weeks after the initial assessment. All 30 patients were closely followed up by the same investigator during the time between assessments, permitting a longer interval to complete the test-retest procedure.To assess the convergent validity of the Taiwanese version of the BCIS, we evaluated how the BCIS results compared with clinicians' and researchers' assessments of insight among people with schizophrenia or schizoaffective disorder. The researchers first assessed Item G12, "judgment and insight," of the PANSS ,18. ThisThe PANSS was developed in an attempt to provide a more comprehensive assessment of the psychopathology of schizophrenic patients and is widely used in clinical and research settings; it is regarded as a reliable means of symptom assessment ,18. In tAll statistical tests were carried out using the Statistical Package for the Social Science (SPSS) version 15.0 for Windows with the significance level set at P = 0.05 (two-tailed test).We conducted an exploratory principal components analysis (PCA) on the correlation matrix of the 15 items of the Taiwanese version of the BCIS. To clarify the interpretation, a varimax orthogonal rotation was employed. The exploratory approach of this study was justified by the extraction of factors with eigenvalues greater than or equal to 1.0. Construct validity and reliability were evaluated by calculating Cronbach's alpha coefficient for each factor.The score for each factor  obtained using the present factor analysis and was utilised. Two researcher-rated insight scales, selected specific variables from the PANSS, and demographic and clinical characteristics were correlated with the analysed factor scores of the translated BCIS. Correlation analyses were performed using the Pearson coefficient when data were normally distributed; elsewhere, Spearman rank correlation was calculated.One-way analysis of variance (ANOVA) was used to test for differences between selected groups of BCIS subscales and index scores. To ensure that the BCIS subscales and index scores might differentiate patients (n = 60) with schizophrenia or schizoaffective disorder from patients (n = 60) with MDD without psychotic features and healthy controls (n = 60), independent t-tests were then performed to compare the mean BCIS subscale and index scores of patients with psychosis to those of subjects without psychosis. In considering the differences in the levels of education among the three selected groups, it should be noted that we attempted to statistically control for such differences. An analysis of covariance (ANCOVA) was performed to compare the three selected subgroups with level of education as a covariate (concomitant variable) that could influence the cognitive insight among the three studied groups.The demographic and clinical characteristics of the participants in the study are presented in Table The results of the factor analysis indicated that the Kaiser-Meyer-Olkin measure of sampling adequacy was at an acceptable level of 0.72, and the Bartlett's test of sphericity was 483.89, P < 0.001, indicating that all of the correlations that were tested simultaneously were significantly different from zero. According to the principal components analysis (PCA) with varimax rotation, the first two eigenvalues were 4.24 and 2.66, accounting for 46.03% of the total variance. These eigenvalues indicated that two factors should be extracted and inspected for simple structure.Each of the subscales was developed based on the factor loadings and applied in the subsequent analysis. For each item, the highest factor loading determined subscale inclusion. These two subscales can most suitably be described as the reflective attitude subscale and the certain attitude subscale Table .Based on concepts regarding self-correction derived from previous studies -22, it wAn internal consistency analysis was conducted on each of the two subscales. The reliabilities  of the two subscales of the translated BCIS for the 180 subjects were 0.7 for the reflective attitude subscale and 0.72 for the certain attitude subscale. Test-retest reliability was determined using the assessments of the 30 patients who repeated the BCIS after four weeks. The test-retest reliability coefficient over a four-week interval ranged from 0.75 to 0.79 at the subscales and R-C index level. . Given the results obtained, these two subscales were considered acceptable for the purpose of the research ,24. For The correlation of the BCIS subscale scores with the psychosocial/clinical characteristics and psychopathology for the selected groups are presented in Table In addition, an intercorrelation matrix was calculated for patients with schizophrenia or schizoaffective disorder. There was no significant correlation between the other BCIS subscales and the psychosocial variables except for a significant negative correlation between the R-C index and gender . The correlations of the BCIS subscale scores with use of particular medications did not reach statistical significance.Pearson correlations between the BCIS and two researcher-rated clinical insight scales were independently examined to evaluate the validity of the translated BCIS. The BCIS was uncorrelated with the two researcher-rated insight scales, SUMD and G12 item of the PANSS. Nevertheless, we had to note that the awareness, consequence, and medication subscales as well as the total SUMD scale were significantly correlated with all of the psychopathology measures , except for the depression component of the PANSS. The two researcher-rated insight scales, namely the SUMD subscales and the G12 item of the PANSS, demonstrated positive significant correlations  for the 60 schizophrenic or schizoaffective outpatients.We examined whether correlations existed between subscales and index scores derived from the scale and positive, negative, cognitive, depressed, and excited components derived from the factor analysis studies of the PANSS. The BCIS R-C index and its subscale scores did not correlate significantly with the PANSS total score, positive, negative, depressed, and excited factors. The cognitive factor of the five-factor model of the PANSS was not significantly correlated with the BCIS R-C index and subscale scores.To assess the discriminative validity of the Taiwanese BCIS, we used ANOVA to compare the mean test scores of the BCIS subscales and composite index for the patients and controls. The results are presented in Table Using education as a covariate, the results of the ANCOVA were not comparable to the findings just mentioned. The difference in the reflective attitude subscale scores among the three groups of subjects was significant . However, there was no significant difference between patients and controls on the certain attitude subscale  and the R-C index . In view of our findings, we then consider the determinative confounding factor in the selected subgroups. The results, therefore, should be treated circumspectly.Independent t-tests identified significant main effects of group for each of the two BCIS subscales and the index score. For the reflective attitude and R-C index scores, the patients diagnosed with schizophrenic disorders reported lower scores than subjects diagnosed with MDD and controls (P < 0.05) Figure . AdditioAs shown in Figure The intent of this article was to develop and validate a cultural adaptation of the BCIS scale to measure Taiwanese schizophrenia patients' cognitive insight. The Taiwanese version of the BCIS, which is easy to administer in less than 15 minutes, proved to be acceptable to participants and clinicians, and its internal consistency and test-retest reliability were satisfactory. A R-C index of the BCIS was used to estimate a patient's level of cognitive insight.There is general consensus that cognitive insight should be considered a multidimensional construct. This concept was also supported by our study. Exploratory factor analysis (EFA) of the Taiwanese version of the BCIS in the current study identified two factors that accounted for 46.03% of the variance, which resembled the two-factor structure of the original version. Additionally, note that these 15 items all had factor loadings higher than 0.3 in this study, which is consistent with previous studies . HoweverThe amounts of variance explained by the factors are somewhat different between the three cohorts in the present study and also found in previous studies ,25. The For internal consistency, the reliability  in our study  was higher than those in the original BCIS  as reported by Beck et al. (2004)  and PedrComparing the factor loadings of the original BCIS and the Taiwanese version, although the magnitudes of each factor were different, items measuring self-reflectiveness were gathered in the "reflective attitude" factor, and items of self-certainty were aggregated in the "certain attitude" factor for both subscales. In addition, the factor congruence coefficient indicated satisfactory factor agreement between the original and the Taiwanese version. These findings lead us to believe that that the original BCIS and the Taiwanese version are similar in their factor structures. Cronbach's alpha for each factor was high. This suggests that all factors were internally consistent. The equivalence between the BCIS and the translated BCIS was demonstrated through a similar factor structure and similar factor loading on particular items. However, as pointed out by Beck  and PedrAlthough our principal components analysis yielded a two-factor solution, the observed pattern of intercorrelation supported the hypothesis that cognitive insight is not a unitary construct but one that comprises two or more related yet partially independent components. We hypothesised that patients' level of certainty about their beliefs might diminish their ability or willingness to be introspective and that the R-C index would reflect such a dampening of self-reflectiveness . TherefoOur study also aimed to establish the convergent validity of the translated BCIS and its relationship with other traditional researcher-rated insight scales for insight evaluation in psychosis. The BCIS R-C index and its subscales did not significantly correlate with SUMD or the G12 item of the PANSS. The authors of the latter emphasise, in fact, that they are specifically examining attitudes towards illness and treatment. This contrasts markedly with previous studies' findings, which indicated moderate correlations between the R-C index score and the Birchwood Insight Scale relabel subscale score and total score . One reaIn fact, in our study, no correlation was found between the subscales and index score of the translated BCIS and the PANSS cognitive component which could also point to the fact that self-assessment of cognitive insight is independent of the clinical evaluation of cognitive functions. The correlation of cognitive insight with subjective perception of cognition in schizophrenia deserves to be considered and analysed.It is, perhaps, unexpected that the BCIS subscales and index scores were not consistently related to positive and negative symptoms of the PANSS in this study. These finding are not in line with those of previous studies , in whicClinical insight is known to be associated with depression in patients with psychosis ,27. PatiA patient's understanding of his/her mental illness and its treatment is often influenced by his/her social and cultural background. A patient may have various culturally based beliefs that explain his/her illness and influence his/her coping strategies. Interestingly, a growing number of non-Western studies  that havLike any study attempting to capture complex clinical realties, our study is limited in several ways. First, our sample was restricted, rather than employing randomly chosen subjects, and it consisted of mostly patients with chronic mental illnesses. It is possible that the results of this study may not generalise to all patients with psychosis outside of the selected group. Second, because the present study required informed consent and involved the psychopathological assessments, we did not include subjects who were very uncooperative. Because subjects who were very uncooperative were not included in the present study, demographic characteristics of non-volunteers are not available. However, it should be noted that uncooperative subjects were demographically different from the volunteers, so the generalisability of our result might be limited. Third, we readily acknowledge that our research was exploratory and that our recruitment procedure could be improved upon. Those participants who agreed to participate in the insight assessment may have had better relationships with the staff, may have more clearly perceived the beneficial effects of treatment, or may have had a higher insight level than those who did not. Fourth, in psychotic patients, cognitive deficit or dysfunction is probably the strongest predictor of insight assessment and future functional adaptability . DetermiThe results show that the Taiwanese version of the BCIS is a measurement instrument with adequate psychometric properties that can assess the impairments of cognitive insight present in patients with psychosis in research and clinical settings; this instrument can therefore improve the detection and prevention of these impairments. However, because the scale showed a two-factor structure that does not confirm perfectly to the theoretical basis for the BCIS, we intend to continue pursuing this line of investigation in a series of explorative studies. Accordingly, we recommend that the approach used in this study be replicated on larger and different populations.The authors declare that they have no competing interests.YCK wrote the draft of this manuscript. YCK and YPL conceptualised and designed the study. YCK collected and analysed the data. YPL supervised the study. YCK analysed the data further and wrote the final manuscript. YPL helped to revise the manuscript. All authors read and approved the paper.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-244X/10/27/prepub


Breast cancer is one of the most common cancer types. Due to the complexity of this disease, it is important to face its study with an integrated and multilevel approach, from genes, transcripts and proteins to molecular networks, cell populations and tissues. According to the systems biology perspective, the biological functions arise from complex networks: in this context, concepts like molecular pathways, protein-protein interactions (PPIs), mathematical models and ontologies play an important role for dissecting such complexity.http://www.itb.cnr.it/breastcancer.In this work we present the Genes-to-Systems Breast Cancer (G2SBC) Database, a resource which integrates data about genes, transcripts and proteins reported in literature as altered in breast cancer cells. Beside the data integration, we provide an ontology based query system and analysis tools related to intracellular pathways, PPIs, protein structure and systems modelling, in order to facilitate the study of breast cancer using a multilevel perspective. The resource is available at the URL The G2SBC Database represents a systems biology oriented data integration approach devoted to breast cancer. By means of the analysis capabilities provided by the web interface, it is possible to overcome the limits of reductionist resources, enabling predictions that can lead to new experiments. Cancer is a complex disease in which both genomic and environmental factors affect the functioning of the molecular circuits leading to the so-called acquired capabilities of cancer . Due to To realise a multilevel and systems oriented approach about a disease, it is crucial to collect and integrate data stored in several dedicated resources. Currently, this process is characterised by some issues. First, data required to realise this perspective are still sparse on the web: despite some existing databases (such as those developed by the NCBI and the EBI) collect data from several projects, data provided by specific resources dedicated to particular pathologies are not yet integrated and therefore are difficult to exploit. Moreover, the accessible information is by far too heterogeneous: for example, some resources make their content available relying on identifiers that do not match directly. Another issue concerns the relevance of data produced by using high-throughput technologies, which represent a useful source of information and, therefore, are essential in a data integration approach: this is the case, for instance, of protein-protein interactions (PPIs) data, that enable the study of cellular networks structure by means of graph theory approaches. Lastly, even if several mathematical models have been developed in the cancer research field, many of them are not coded in standard languages and thus they are not directly available for simulations. In this systems biology perspective, we chose to focus our research on one of the most common cancer types, the breast cancer, which has a high impact on the population and is studied within our institute .Generic as well as scientifically relevant resources exist concerning this pathology. "Oncomine"  was deveTo fill this gap we developed the Genes-to-Systems Breast Cancer (G2SBC) Database. This resource realises the integration of information concerning molecular components related to breast cancer and the overlying molecular and cellular layers, even providing a series of tools for the analysis of the available data.The G2SBC Database relies on a MySQL server. The database structure follows a data warehouse approach, which consists in collecting and formatting heterogeneous data from different sources, in order to make them accessible by the scientific community through a unified query schema using a web interface. This approach is typical of data integration, while normalised databases, designed to support data integrity, are widely used to maintain primary resources. From the data integration point of view, a series of perl scripts have been developed to retrieve different datasets from remote and sparse data sources. The architecture of the G2SBC Database is illustrated in Figure Data has been retrieved from literature, both relying on a manual curation process and exploiting automated methods for data integration from datasets available on the web ,10-22.Breast cancer genes are annotated by gene symbol, description, aliases and sequences. The list of molecular alterations found in breast cancer spans the genome, transcriptome and proteome layers and comes from both clinical data and cell line experiments. Gene characterisation is enriched with information about the related Single Nucleotide Polymorphisms (SNPs), downloaded from dbSNP . SNPs arGene products have been collected as list of mRNAs sequences and related protein isoforms according to the NCBI RefSeq annotations (NCBI Nucleotide ). Gene ein situ breast cancer, lobular breast cancer, malignant neoplasy, hyperplasia). Each image is associated with information concerning the protein detected on the tissue, its spatial localisation (nuclei or cytoplasm/membrane), some patients clinical information, staining intensity  and quantity of stained cells . Similarly to what has been done in the HPA database, values of the cartesian product of intensity and quantity , , , ..., ) have been mapped to natural numbers belonging to the set {1, 2, ..., 16}. These numbers represent a score for the protein expression, where 1 is associated with  and 16 with . Following this operation it has been possible to calculate average protein expression and to infer protein differential expression between breast cancer tissues and normal tissues as difference between two protein expression scores.Data about proteins include all the identifiers suitable to download the related sequences, functional domains according to InterPro , structuConsidering the molecular systems layer, the G2SBC Database lists the biochemical pathways , all-pairs shortest paths (a shortest path in a graph is the path connecting two vertices such that the sum of the weights of its edges is minimised) and their lengths (the number of edges that belong to the path) have been calculated. Other interesting information related to molecular systems is represented by the association of the breast cancer genes with the cell cycle process , incConsidering the cellular systems level, the database includes data about breast cancer types, tissue images and mathematical models  available in literature, which focus on carcinogenesis, tumour growth and tumour response.Gi =  , that undergo the hierarchically structured terms, represent a crucial instrument to shed light on relationships between biological components, thus performing more accurate queries and even promoting the deduction of new relations. Ontologies have been exploited even to better define the scientific context of the developed resource. Human disease ontology [To provide a standard framework for data integration and to enhance a systemic view of breast cancer information, a rich ontology layer underlies the database structure. Where available, genes are annotated using the GO and biochemical pathways by the KEGG Pathway  ontologyontology , BRENDA ontology  and cellontology  are inclontology , an EBI The web interface of the G2SBC Database (implemented employing PHP and JavaScript languages), provides a series of tools to show and analyse data collected in the resource. An extensive help section is available through the left side menu of the web site and shows detailed examples on how to explore the database content and how to exploit the tools integrated in the resource: use cases are described for illustrating what kind of predictions are allowed by the G2SBC database.query system, that is structured in the molecular components, the molecular systems and the cellular systems level. The second section concerns the data analysis tools available through the web interface. This area includes: the "Neighbourhood density and hubs" and the "Shortest paths" tools, both relying on the PPIs network analysis; the gene-annotation enrichment analysis (GEA); the Blast tool [model oriented section, which involves two aspects. The first one concerns the interaction among cell cycle regulation and breast cancer: due to this connection it is possible to retrieve the breast cancer genes involved in cell cycle control and simulate the associated mathematical models. The second regards the mathematical models related to carcinogenesis, tumour growth and response to treatments.The web site pages are grouped into three main sections, listed in the left side menu. The first group concerns the ast tool , which aAt the molecular components level, it is possible to query the G2SBC Database through gene or protein identifiers, synonyms and descriptions, in order to directly retrieve the breast cancer gene report. In this page users can find the information related to each gene that has been integrated into the database. This data includes gene and gene product identifiers, SNPs, molecular alterations involved in breast cancer, microRNAs, tissue expression, drugs, molecular interactions established by gene products, molecular pathways regulated by the listed protein and cell cycle associated kinetic models.Moreover, it is possible to query the system starting from information about gene products function, represented by the protein domains and the GO molecular functions. An interesting application of this query concerns the knowledge about proteins involved in a key biological function, which is often under aberrant control in cancer conditions: transcription regulation. In fact, through this query, it is possible to list the transcription factors associated with molecular alterations in breast cancer.Another possibility is to query the system considering the spatial localisation. This information includes the knowledge related to the gene localisation within the genome by means of spatial coordinates: in this case, the G2SBC Database provides the interactive visualisation of the genome by means of the UCSC Genome browser . SpatialThe G2SBC Database contains several types of molecular alterations associated with breast cancer. These alterations encompass the genome (mutations and SNPs), the transcriptome (RNA expression level and splicing variations) and the proteome , as shown in Table The list of alterations associated with a particular gene is available in the gene report. Each alteration is annotated through some features - that vary according to the type of molecular alteration - such as the contig number, the direction of gene expression variation (up/down), the experimental method used, the cancer type or the cell line. Lastly, each molecular alteration is reported along with the reference to the paper where its experimental identification has been described.top-down approach, which leads to the "building blocks" starting from the systems. In this context, the user interested in a particular biological process can retrieve the list of genes that may affect its normal activity leading to cancer conditions. An example is the response to lowered oxygen tension, an important process for tumour progression; searching through the keyword "hypoxia" it is possible to understand that the GO BP term "response to hypoxia" includes 30 genes which have at least one evidence of association with breast cancer.Considering the molecular systems layer, it is possible to query the G2SBC Database starting from a specific biochemical pathway name, exploiting data from KEGG, Reactome and GO BP. This system level query follows a For what concerns the information that can be retrieved from cellular and tissue levels, the query system lists a series of breast cancer types  and subtypes . A specific breast cancer type can be selected in order to obtain the list of genes products (i) found expressed in the considered breast cancer type according to the HPA data and/or (ii) associated with molecular alterations identified in the selected breast cancer type.Breast cancer types supported by HPA data are provided with information concerning protein differential expression with respect to the normal tissue, Figure In this context, the multilevel data integration realised by the G2SBC Database provides some insights on the characterisation of the different breast cancer types in terms of genes and biochemical pathways.Other than representing an important instrument for generating new hypotheses and producing novel knowledge , the ontThe G2SBC Database provides a series of tools which can be used to analyse the database content. By means of the sequential use of these tools it is possible to create analysis pipelines, which in some cases can lead to new predictions.G2SBC Database web interface provides two tools that rely on the application of the graph theory to biological networks.The first tool retrieves breast cancer genes that have a particular neighbourhood density in the PPIs network and establish a specific number of interactions. On one hand, a protein with a high neighbourhood density, measurable by means of the so called clustering coefficient, is potentially part of a protein complex  and, morThe second tool concerns the "Shortest paths analysis", which is particularly useful in systems biology since it enables the reconstruction of biochemical pathways (an example of the use of shortest paths for the reconstruction of metabolic networks can be found in ). The G2P value  indicating the probability of obtaining the observed distribution of terms among the whole gene set in a hypergeometric experiment. This measure identifies annotation terms that are significantly enriched in a specific gene set. These terms represent distinctive properties of the gene set and constitute the starting point for further functional characterisation. The GEA tool is integrated in the web interface of G2SBC Database and is available whenever a gene list is obtained. Results can be downloaded in a text file. For instance, by performing an appropriate query on the clustering coefficients and the number of interactions, the user discovers that the protein inhibin, encoded by the gene INHBC, is part of a highly interconnected module of proteins which involves the activins (ACV proteins), as shown in Figure P values and, hence, these terms represent the annotation signature that characterises the gene set.The G2SBC Database provides a tool for GEA. The application finds the set of annotations associated with the input gene set. Each annotation term is coupled with a P value 3.66E-8), "skin morphogenesis" , "skeletal system development" , a series of annotations which suggest more detailed biological roles of DCN. Another case is represented by the gene MTA1 (metastasis associated 1), that is currently annotated with two general GO BP terms: "regulation of transcription, DNA-dependent" and "signal transduction". The analysis of MTA1 protein neighbours shows that it interacts with proteins that regulate "histone deacetylation" , "nucleotide-excision repair, DNA damage removal"  and "chromatin modification" , that are all processes related to the DNA transcription.It is worth noting that the GEA tool is useful whenever the selected breast cancer gene is poorly annotated. In this case, the tool provides a way to study the annotations of its interacting partners and gain some insights, according to the concept of network-based function prediction   are highlighted. By selecting the desired SNP, the web interface lists the IDs of the available PDB structures whose chains contain a model of the wild type sequence associated with the selected allele variant. The user can choose one chain and the complete structure is automatically downloaded from the PDB web site. Starting from this PDB structure, the polymorphic model is created using an automatic approach based on a customised python script from Modeller . It replThis tool provides a statistical approach to tissue-related information. Tissue data maintained in the database, which allows vertical integration among proteomic and cellular levels, are analysed by considering the association between genes and breast cancer types. By means of the data collected in the HPA, we calculated the frequency of detection of a specific gene product among the breast cancers types, in order to show its distribution over them. This content is shown in a dedicated web page reachable from the gene report, where the list of the antibodies exploited to detect the specific gene product is provided, together with a pie-chart plot which visualises the calculated percentage distribution.Since the cell cycle process is often affected by misregulations that can lead to cancer onset , the G2SMoreover, some mathematical models related to breast cancer development and response to treatment have been encoded in the Systems Biology Markup Language (SBML)  in orderThe G2SBC Database is a freely available resource developed with the aim of supporting research on breast cancer in a systems biology context. Using data integration a large amount of records have been collected in this database: therefore, enhanced query solutions and web tools are provided to infer non trivial knowledge, e.g. the proteins differentially expressed in each breast cancer type. The contents and tools provided encompass molecular components, molecular systems and cell systems layers. The G2SBC Database provides systems level queries (enabling a top down approach), tools based on PPIs network (e.g. the shortest paths) and a mathematical models section. Due to these features, it is possible to overcome the limits of a resource dedicated only to data exploration, enabling predictions that may induce new experiments.M. musculus and R. norvegicus, making cross-species comparisons possible.The G2SBC Database will be periodically updated according to the publication of new research, biological data and mathematical models about breast cancer. We plan to integrate data from other sources, e.g. the Human Protein Reference Database (HPRD)  , and tohttp://www.itb.cnr.it/breastcancer.The G2SBC Database is freely available at the URL EM implemented the programs for data integration, PPIs network analysis, developed the web interface and the database; RA implemented the database, the web interface; IM implemented the SNP-related contents, developed the sequence and structure retrieving system and provided a complete overview on the work; FV created the ontological layer, the tissue contents and the molecular alterations section; AC contributed to data integration development; LM managed and directed the work. All authors read and approved the final manuscript.


There is strong evidence that athletes have a twofold risk for re-injury after a previous ankle sprain, especially during the first year post-injury. These ankle sprain recurrences could result in disability and lead to chronic pain or instability in 20 to 50% of these cases. When looking at the high rate of ankle sprain recurrences and the associated chronic results, ankle sprain recurrence prevention is important.To evaluate the effect of a proprioceptive balance board training programme on ankle sprain recurrences, that was applied to individual athletes after rehabilitation and treatment by usual care.This study was designed as a randomized controlled trial with a follow-up of one year. Healthy individuals between 12 and 70 years of age, who were actively participating in sports and who had sustained a lateral ankle sprain up to two months prior to inclusion, were eligible for inclusion in the study. The intervention programme was compared to usual care. The intervention programme consisted of an eight-week proprioceptive training, which started after finishing usual care and from the moment that sports participation was again possible. Outcomes were assessed at baseline and every month for 12 months. The primary outcome of this study was the incidence of recurrent ankle injuries in both groups within one year after the initial sprain. Secondary outcomes were severity and etiology of re-injury and medical care. Cost-effectiveness was evaluated from a societal perspective. A process evaluation was conducted for the intervention programme.The 2BFit trial is the first randomized controlled trial to study the effect of a non-supervised home-based proprioceptive balance board training programme in addition to usual care, on the recurrence of ankle sprains in sports. Results of this study could possibly lead to changes in practical guidelines on the treatment of ankle sprains. Results will become available in 2009.ISTRCN34177180. Ankle injuries are the most common injuries across a wide variety of sports -5. It haRecent research showed that the mean total costs (direct and indirect costs) of one ankle sprain are approximately € 360 . This woThe relatively high rate of ankle sprains across all sports, as well as the severity and subsequent negative consequences of ankle sprains on future sports participation motivates attention for preventive measures against this type of injury.The most commonly used preventive measures against ankle sprains, i.e. tape and braces, have been evaluated in previous research. An overall ankle sprain reduction of approximately 50% can be attributed to any of these measures . More reSuch a prolonged rehabilitation does not need to be supervised by a (sports) physician or (sports) physical therapist and might also suffice if the injured athletes are encouraged to follow a specific preventive programme for a certain period of time after their usual care. Such an unsupervised preventive programme would keep the medical costs associated with a prolonged rehabilitation period to a minimum, would put no additional demand on medical practitioners, and would have large potential positive effects in terms of health improvement and savings of direct medical costs due to ankle sprain recurrences. Another potential strength of an unsupervised programme lies in the fact that not all athletes with ankle sprains seek medical attention. However, the twofold-increased risk for an ankle sprain recurrence also exists in these athletes. Therefore, an unsupervised preventive programme targeted at ankle sprain recurrences would also benefit these athletes, and the unsupervised nature of such a programme makes it possible to administer the programme to these athletes through non-medical channels.Proprioceptive balance board training is the most promising of the three mentioned preventive measures for such an unsupervised preventive programme . WhereasThe objective of this randomised controlled trial was to evaluate the effect of an unsupervised proprioceptive balance board training programme on ankle sprain recurrences, that was applied after the usual care of individual athletes who had sustained an acute sports-related lateral ankle ligament injury.The CONSORT statement was followed to describe the design of this study ,26. ThisThe Balance Board Functional Instability Training (2BFit) study was a randomized controlled trial (RCT) with a one year follow-up. The study design and flow of participants are shown in Figure The focus of this study was to examine the effectiveness of an extended treatment procedure, on top of the standard usual care after an ankle sprain. Therefore, subjects in the intervention group received an eight week training programme following treatment by usual care, whereas the control group received usual care only.The study was funded by the Netherlands Organization for Health Research and Development (ZonMW). The study design, procedures and informed consent procedure were approved by the Medical Ethics Committee (number 06/085) of the VU University Medical Center, The Netherlands. All participants provided written informed consent.The first hypothesis of this study was that the intervention would lead to a 50% reduction of ankle sprain recurrence incidence. The second hypothesis was that the intervention would additionally lead to ankle sprain cost-reduction, mediated through a decrease of productivity loss and prevention of direct medical costs related to recurrent ankle sprains.Healthy participants between 12 and 70 years of age, who were actively participating in sports and who had sustained a lateral ankle sprain up to two months prior to inclusion, were eligible for inclusion in the study. Participants were excluded if they did not master the Dutch language, had a history of vestibular complaints, or in case of a diagnosis of a different injury than a lateral ankle sprain (e.g. fracture of the ankle).This resulted in a diverse source population of athletes from all types and levels of sports were involved in the study. The intervention was considered to be appropriate for all athletes and to have no negative side-effects.A power calculation was carried out for the main outcome variable ankle sprain recurrences. A difference of 50% in the incidence of recurrent ankle sprains between the intervention and control group after a follow up of 12 months was considered to be clinically relevant and was found previously in a volleyball setting .The prevalence of ankle sprain recurrences being about 13% in 12 months , 275 subRecruitment was carried out at eleven hospital emergency rooms (ER's), five general practices, and four physical therapy offices throughout the Netherlands, assisted by advertisements in Dutch media . An information brochure was handed to individuals, participating in sports, who had sustained an ankle sprain and visited the cooperating (para-)medical institutes. If individuals were interested in participating in the study, they returned an answer form to the researchers. Enrolment through the internet was possible as well. The total number of positive reactions is shown as step 1 in Figure Recruitment of participants for the 2BFit trial took place between August 2006 and August 2007. A total of 796 people were interested to participate in the 2BFit trial and reacted on the call for subjects with a recent ankle sprain. A total of 166 athletes were classified as non-responders after a maximum of ten attempts to contact them through telephone or email failed. Of 630 people who were available for inclusion, 101 were excluded. Reasons for exclusion were: no return of baseline questionnaire (63), still undergoing treatment at the end of inclusion period (12), no agreement on informed consent (9), not participating in sports (9), and private reasons (8). After baseline measurements and stratification, 529 athletes were randomly assigned to the intervention group (n = 261) and to the control group (n = 268).After informed consent and baseline questionnaire, participants were randomized to the intervention training programme or the control group. To ensure that both groups were equal in terms of re-injury risk, a stratified randomization was performed  guideline. High-level athletes could have a treatment duration of up to twelve weeks . TherefoThe Dutch College of General Practitioners (NHG) practice guideline for ankle sprains states that follow-ups are not necessary for an individual with a mild sprain . A mild The Dutch Institute for Healthcare Improvement (CBO) has formulated a consensus statement on diagnostics and treatment of acute ankle sprains . This guIn this study the aim was to compare usual care of athletes with a recent lateral ankle sprain with a proprioceptive training programme after usual care. Usual care of the ankle sprain was by choice of the athlete; there was no interference from the authors.The intervention programme consisted of an eight-week proprioceptive training, which started after finishing the complete ankle sprain treatment procedure and from the moment that sports participation was again possible. From that moment athletes completed the baseline questionnaire and commenced their one-year follow-up.The programme was a modification of the programme previously proven effective for the prevention of ankle sprain recurrences in volleyball . The preAll participants of the intervention group received the same balance board, and general written and visual information on the duration and intensity of the programme. In addition, a website was created including basic information on the project and a section only accessible for intervention group subjects .The frequency of exercising was consistent throughout the full eight weeks: three training sessions per week , and type of sport. Sports participation was assessed in part two by means of questions concerning mean training hours per week, number of matches played per month, and participation in other sports. Part three covered the working situation including questions on mean working hours a week and type of occupation. For stratification purposes, part four consisted of a question about treatment after the initial diagnosis of ankle injury. Preventive measures were assessed in part five, with questions concerning use of braces, tape, and/or socks. Information about medical history was collected by the last part of the baseline questionnaire. Questions about previous ankle and knee injuries were assessed as well as other injuries of the lower extremities.The monthly questionnaires gathered information on sports participation, on the use of preventive means and sustained knee or ankle injuries in the past month. Per training or match session the total minutes of participation, type of sports and participation percentage of total session duration were registered. In case of absence from a training or match session, the reason  for it was asked.During the 8 weeks proprioceptive training programme, the intervention group completed an additional questionnaire on the subjective response to the proprioceptive and balance board training programme, and reasons of (non-)compliance.If participants did not fill in their questionnaires or forms after one week, a reminder was sent by email. If the questionnaires or forms were not returned after two weeks, contact was made by telephone.In case of an ankle sprain, athletes were asked to fill in a web-based ankle sprain registration form. This form consisted of questions concerning the diagnosis, the cause, and the etiology of the re-injury. Furthermore, the advised treatment and the person who treated the injury were registered. Based on this form, a cost diary was sent to the athlete.To evaluate the cost-effectiveness of the intervention programme subjects (intervention and control group) who sustained an ankle sprain received a cost-diary.The cost-diary was a log, which registered all absence from work, school and other chores of life, and (para-)medical treatment (including use of medication) from the moment of injury onwards until full recovery. From these cost-diaries direct and indirect costs resulting from the sustained ankle sprain could be calculated for use in an economic evaluation.The economic evaluation was performed from a societal perspective. Table A process evaluation was conducted for the intervention programme. The supplement questionnaires, which were sent to intervention group participants in questionnaires two and three, contained questions on the subjective response to the programme, the expected effect of the intervention, and the compliance to the programme.To evaluate the success of the randomization, baseline values were analyzed for differences between intervention group and control group, using a chi-square for categorical data and a student's t-test for numerical data. Cox-regression analysis was used to compare ankle sprain recurrence risk between the intervention and control group. Other variables were checked for confounding and/or effect-modification and were adjusted accordingly. Severity of re-injury was tested between groups using a Mann-Whitney test, since it is shown to be not normally distributed ,11,14,20All analyses were carried out according to the 'intention to treat' principle. Differences were considered statistically significant at p < 0.05.Mean direct, indirect and total costs were estimated and compared between the two groups, both for the costs per subject in the injured population and for the costs per subject in the total population. Because costs were not normally distributed, 95% confidence intervals for the differences in mean costs was obtained by bias corrected and accelerated bootstrapping (2000 replications) . DiffereThe 2BFit trial is the first randomized controlled trial to study the effect of a non-supervised home-based proprioceptive balance board training programme in addition to usual care, on the recurrence of ankle sprains in sports.The recruitment of athlete participants in the 2BFit study was the most challenging task. Although a total of eleven participating hospitals was deemed sufficient to reach the desired number of participants within one year, the way of enrolment had to be adjusted. This total number of hospitals was based on the estimated annual number of acute ankle sprains in the Netherlands. The partaking hospitals had an estimated total of 4000 acute ankle sprains in 2003. A two-month pilot study was performed at one of the participating hospitals to identify the strong and weak points and feasibility aspects of the intended way of recruitment at the ER's. This pilot resulted in a high number of positive reactions from hospital employees as well as from athletes, and encouraged us to state that eleven hospitals was sufficient.Nevertheless actual inclusion of participants through participating ER's was below expectations, namely 26 participants after two months, where 100 participants were expected. Therefore, it was chosen to approach general practitioners and physical therapists to participate in the project. Additionally, the internet was used as a mean to increase awareness of the existence of our programme. It was also possible to enroll through the webpage of the study.In conclusion, although the recruitment of participants started of slow, appropriate measures were taken, and the number of responders was adequate at the end of the recruitment period.It is striking that the only Dutch medical guideline explicitly describing the use of proprioceptive training for the treatment of acute ankle sprains is the KNGF guideline. This guideline states that proprioceptive balance board training could be useful as part of an ankle sprain treatment protocol . It was Between step 1 and step 2 of the study flow (see Figure Once athletes had given informed consent it turned out to be a struggle to retain them. As discussed, re-injury risk is highest in the first year after the initial ankle sprain . TherefoThe compliance to the intervention programme was difficult to assess, since the proprioceptive balance board training was performed at home, without supervision. Athletes completed a compliance questionnaire each month during their training. Effort was made to make the training programme as appealing as possible: a parcel including a balance board, an instructional DVD, and instructional forms was sent to the athlete. Furthermore, athletes could log on to the internet and watch the training programme online.The results of this study could possibly lead to a change in the treatment of ankle sprains. Positive results on secondary outcomes could offer extended possibilities for implementation of the intervention in usual care. Positive study results could also lead to changes in the three practical guidelines on the treatment of ankle sprains. Results of this study will become available in 2009.The authors declare that they have no competing interests.EALMV conceived of the idea and obtained funding for the study. EALMV and MDWH developed the intervention, developed the design of this trial, and MDWH recruited participants. WvM provided advice on the study design and contributed to the content of the article. MDWH is the study investigator, was responsible for data acquisition, and wrote the article. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


A multiplicative combination of tuning to interaural time difference (ITD) and interaural level difference (ILD) contributes to the generation of spatially selective auditory neurons in the owl's midbrain. Previous analyses of multiplicative responses in the owl have not taken into consideration the frequency-dependence of ITD and ILD cues that occur under natural listening conditions. Here, we present a model for the responses of ITD- and ILD-sensitive neurons in the barn owl's inferior colliculus which satisfies constraints raised by experimental data on frequency convergence, multiplicative interaction of ITD and ILD, and response properties of afferent neurons. We propose that multiplication between ITD- and ILD-dependent signals occurs only within frequency channels and that frequency integration occurs using a linear-threshold mechanism. The model reproduces the experimentally observed nonlinear responses to ITD and ILD in the inferior colliculus, with greater accuracy than previous models. We show that linear-threshold frequency integration allows the system to represent multiple sound sources with natural sound localization cues, whereas multiplicative frequency integration does not. Nonlinear responses in the owl's inferior colliculus can thus be generated using a combination of cellular and network mechanisms, showing that multiple elements of previous theories can be combined in a single system. The barn owl is able to pinpoint sound sources with great accuracy after hearing only a short burst of sound Space-specific neurons in the barn owl's auditory space map gain spatial selectivity as a result of tuning to combinations of the interaural time difference (ITD) and interaural level difference ILD; . In the While the owl's auditory system provides one of the best examples of multiplication in a neural circuit, how the sound localization cues are processed under natural listening conditions and what mechanisms produce the responses of neurons in the owl's inferior colliculus remain unanswered questions. Peña and Konishi Here, we develop a model for the responses of ITD- and ILD-sensitive neurons in the barn owl's inferior colliculus. This work combines multiple experimental data sets Guide for the Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee of the California Institute of Technology.Experimental procedures followed the National Institutes of Health Methods for surgery, stimulus delivery, and data collection have been described previously We present a model for the responses of ITD- and ILD-sensitive neurons in the barn owl's inferior colliculus. The model is constructed in three stages: (1) a front end for extracting binaural localization cues from the auditory inputs, (2) ICcl, and (3) ICx.In the first stage of the model, the input signals to the left and right ears are filtered with a bank of band-pass filters t, For an input signal ITD is extracted from the outputs of the band-pass filterbank using a cross-correlation-based operation The input to the cross-correlation in each frequency channel is a gain-modulated version of the filterbank output c = 1 causes the input to the squaring nonlinearity to be positive so that responses are consistent with phase-locking in NL by having only one peak per stimulus cycle In the barn owl, cross-correlation is performed over a short time window mentally .ILD is extracted from the auditory input signals using a level subtraction operation. Specifically, ILD is computed using the interaural difference of a logarithmic function of the energy of the signals in each frequency channel The front end of the model therefore follows the form taken by many sound localization models and includes a bandpass filterbank followed by a cross-correlation and level subtraction operation in each frequency channel thi neuron at frequency Previous theoretical studies have shown that multiplicative spiking responses can occur in neurons where input variables are combined additively in subthreshold responses if the input-output function of the neuron follows a power-law The ILD-dependent component here is a difference of sigmoids; selection of different parameters can produce ILD tuning curves that range from sigmoidal to peaked, as is seen in ICcl max,ir is the maximum firing rate and ibias determines where the center of the dynamic range of the membrane potential response falls relative to the fixed spiking threshold of −68.2 mV. Both of these parameters are neuron-specific. The fixed parameters are found by fitting the curve to the measured ICx data shown in threshold. Spikes are produced using a non-homogeneous Poisson process with underlying rate The membrane potential Spikes are produced for each ICx neuron using a linear-nonlinear-Poisson model. ICx neurons have broad frequency tuning The two central properties of this ICx model are, first, that frequency integration in the membrane potential is linear We also considered simple static models of ICx responses to ITD and ILD in order to compare the responses of ICx neurons under the assumption of either additive or multiplicative frequency integration. This analysis is complementary to that involving the spiking model presented in the previous section.ITD, ILD, and A, respectively. For both additive and multiplicative models, we assume that the response of a neuron is determined by its preferred ITD and ILD spectra, denoted bITD and bILD. Each neuron's best ITD and ILD spectra are given by the ITD and ILD spectra derived from barn owl head-related transfer functions at a given direction In the static model, the stimulus is completely specified by the ITD, ILD, and average binaural intensity (ABI) at an array of frequencies. The vectors of ITD, ILD, and ABI are denoted by a = max(A)/200 is included so that the absence of energy in a single frequency channel does not eliminate the response.In both the additive and multiplicative models, the response to ITD and ILD at each frequency is given by the product of a Gaussian-shaped function of ILD and a circular Gaussian-shaped function of ITD. Under the additive model, the response of the ICx neuron isThese static models are not directly fit to data, but are used to illustrate the different predictions generated under the assumptions of linear and multiplicative frequency combination.We used additional analysis to determine the degree of nonlinearity in the interaction between ITD and ILD. Following previous studies R, is approximated as the minimum mean square model of the formIn the additive fit, the matrix of responses to pairs of stimulus ITD and ILD, denoted The multiplicative fit is specified in terms of the SVD of the response matrix, after the subtraction of a constant bias The constant mult − nRMSadd)/(nRMSmult + nRMSadd), where nRMSadd is the normalized RMS error between the response and the additive fit and nRMSmult is the normalized RMS error between the response and the multiplicative fit.The accuracy of the additive and multiplicative fits is given by the root mean squared (RMS) error between the response and the model fit, normalized by the dynamic range of the neuron's response. The dynamic range is the difference between the maximum and minimum of the response. The relative accuracy of the additive and multiplicative fits is summarized by a multiplication index defined as MI = . A low Δthreshold value places the membrane potential dynamic range near the saturation point, a middle Δthreshold value places the membrane potential dynamic range in the linear portion of the curve, and a high Δthreshold places the membrane potential dynamic range near the expansive portion of the curve. Overall, neurons with the highest Δthreshold values had the most multiplicative responses. However, the multiplication index did not vary monotonically with Δthreshold. The multiplication index is a measure of the relative accuracy of additive and multiplicative models of ITD-ILD interaction. Over a range of low Δthreshold values, the spiking response was better described by a multiplicative fit than by an additive fit, but the accuracy of the multiplicative fit decreased as the Δthreshold increased  (n = 14). Thus, there is near equivalent performance of the spiking and SVD-based models even though the former is the result of combining populations of Poisson responses and the latter is a direct fit of the data.Experimentally observed membrane potential responses to ITD and ILD could be produced in model ICx neurons using a linear combination of ICcl spiking responses . We propn = 14) . In the Peña and Konishi Under natural listening conditions with broadband stimuli, the sounds received at the left and right ears contain a spectrum of ITDs and ILDs The ICx model produced nonlinear spiking responses to multi-tone stimuli . NonlineThis model also leads to the prediction that, in ICx, subthreshold responses to narrowband sounds are more multiplicative than responses to broadband sounds. For example, according to the model, the subthreshold response of an ICx neuron to ITD and ILD of a tone should appear more multiplicative than the response to a sound consisting of two frequency components, where ITD is varied in one frequency channel and ILD is varied in the second . In the We hypothesize that non-multiplicative frequency integration facilitates the representation of multiple, spectrally distinct sources in the auditory space map. Listening in natural environments requires the localization of multiple distinct sound sources. Neurophysiological studies show that spectrally distinct sound sources create distinct patterns of activity in the auditory space map n = 9). In three of nine neurons, the half-width increased with stimulus intensity.In our linear model of frequency integration, simultaneous, spectrally distinct sounds can be represented in the space map in such a way that the more intense source dominates the response. This means that information about the individual frequency components of the sound is not lost in the responses of spatially selective auditory neurons. This cannot occur with a purely multiplicative model of frequency convergence, where stimulus intensity only modulates the overall gain. However, similar results to the linear model would be obtained with a sum and square model that includes linear and nonlinear frequency integration We described a model for the processing of sound localization cues in the barn owl's midbrain. In this model, ITD- and ILD-dependent signals are combined multiplicatively within frequency channels, and signals are combined across frequency channels using a linear-threshold operation. The model is consistent with neurophyiological studies of both ITD-ILD coding and the representation of multiple sound sources in the owl's midbrain.The model presented here better captures the ICcl spiking responses and ICx subthreshold responses to sounds than previous models. As in previous models This model, along with previous ones, leaves several issues open. First, how are the connections between ICcl and ICx neurons learned? There are several proposals for the mechanisms underlying learning in the owl's auditory system We propose that the population of neurons in each frequency channel of ICcl acts as the layer that performs multiplication of ITD- and ILD-dependent signals. This model makes simple biophysical assumptions: subthreshold integration of signals is linear, and nonlinearity between ITD and ILD is introduced by the spiking input-output function. Under this model, the responses to ITD and ILD in ICcl are only approximately multiplicative, which is consistent with the data There are several previously proposed models for the generation of multiplicative neural responses. These models show that the mechanism that produces multiplicative responses may be the property of a single cell A study by Poirazi et al. Based on the model, we make three specific predictions about responses of neurons in the midbrain of the owl to ITD and ILD. First, in ICcl, spiking responses to ITD and ILD will be more multiplicative than subthreshold responses. This prediction is based on our hypothesis that multiplicative responses emerge in ICcl neurons as a result of the spiking nonlinearity. In our model, subthreshold integration of ITD and ILD is purely linear, but this may not be satisfied in the owl because of synaptic nonlinearities that the model does not account for. Nevertheless, we predict that spiking responses will be more multiplicative than will subthreshold responses. This prediction can be tested by recording intracellularly the responses of ICcl neurons to ITD and ILD. Second, in ICx, neurons with preferred directions away from the center of gaze will have less multiplicative subthreshold responses to ITD and ILD than will neurons with preferred directions near the center of gaze. This occurs in our model because addition and multiplication across frequency are clearly distinguished for neurons with highly frequency-dependent preferred ITD and ILD spectra. This prediction can be tested by recording intracellularly the responses of ICx neurons with preferred directions away from the center of gaze to ITD and ILD. Third, we predict that frequency integration is not multiplicative in the spiking responses of neurons in ICx and the optic tectum; the response to two tones should appear as a linear-threshold combination of the responses to the individual tones Figure S1(A) Linear output of the gain-modulated gammatone filter , as a function of average binaural level of a broadband noise. (B) Cross-correlation vector as a function of average binaural level. (C) Tolerance to ILD of the cross-correlation vector.(0.17 MB PDF)Click here for additional data file.


Caenorhabditis elegans as it crawls on an agar plate. We characterize the statistics of the trajectories through the correlation functions of the orientation angular velocity, orientation angle and the mean-squared displacement, and we find that the loss of orientational memory has significant contributions from both abrupt, large amplitude turning events and the continuous dynamics between these events. Further, we discover long-time persistence of orientational memory in the intervals between abrupt turns. Building on recent work demonstrating that C. elegans movements are restricted to a low-dimensional shape space, we construct a map from the dynamics in this shape space to the trajectory of the worm along the agar. We use this connection to illustrate that changes in the continuous dynamics reveal subtle differences in movement strategy that occur among mutants defective in two classes of dopamine receptors.Organisms move through the world by changing their shape, and here we explore the mapping from shape space to movements in the nematode  E. coliFrom the swimming motions of In general, the connection between transformations in shape space and movement through the world is complicated. There is a long tradition of work which tries to make this connection through analytic approximations of the equations describing the mechanics of the organism's interaction with the outside world. This approach is perhaps best developed for swimming and flying organisms Caenorhabditis elegans provides an example of this dimensionality reduction. In previous work, we found that the shapes taken on by the worm's body are well-approximated by a four dimensional space spanned by elementary shapes or ‘eigenworms’ The motion of the nematode E. coli, consisting of long, relatively straight runs punctuated by tumbles, which randomly reorient the cell C. elegansTo understand how changes in the worm's shape determines its motion, we first characterize the motion itself. In Trajectories are characterized by the speed of motion,  in time . The stainset to . ExcursiIf worms lose orientational memory then their movements will look diffusive at long times. One signature of such behavior is contained in the mean–square distance between two points on the trajectory,E. coli these events are the tumbles, and it is natural to think that for C. elegans these events are the reorientation events. If turns occur randomly at rate A sequence of uncorrelated runs and tumbles translates into a mathematical model in which the orientation angle We can disentangle the contributions of continuous and discrete reorientation by looking at the orientation correlation of the trajectory between reorientation events. As in previous work C. elegans movement.If the continuous dynamics within intervals are independent of reorientation events then the angular correlation function is the product of two termsWorms move in the world by changing their posture and here we show that the centroid trajectories are quantitatively captured by the dynamics of body shape. Following general practice, we generated trajectories by tracking the center of mass of the worm's silhouette, s speed  , illustrC. elegans during free locomotion is low-dimensional with four principal dimensions (eigenworms) capturing approximately In previous work In general we expect the worm's reorientation dynamics to be connected to changes in its shape, and we can construct this connection between modes and movement using the four intrinsic shape modes. The simplest model is a linear one,The curvature is dominated by contributions from the amplitude of the third mode, which is connected to bending of the worm's body lane  cf . Taken tlane  cf .C. elegans behavior is modulated by experience. As an example, the rate of dop-2 (vs105) and dop-3 (vs106).As with all organisms, The distribution of times between reorientation events changes as the worms spend more time away from food. As before we identify reorientation events as moments when dop-2 is similar to the wild type, but dop-3 exhibits a faster oscillation. Recalling that this corresponds to the undulatory wave along the body dop-3 mutant should move more quickly, and this is observed when we track the center-of-mass motions: mean speeds of the three variants are dop-2 and dop-3 respectively. The mode dynamics also combine though Eq 9 to produce different turning dynamics and, in particular, dop-3 animals make longer-lasting turns which result in curvier trajectories. While these pheonotypic differences are subtle and have not been reported before, they are immediately apparent in the dynamics in shape space. Taken together we find continuous motion, including gradual re–orientation, and discrete turning behaviors are under genetic control.Our analysis above shows that continuous re–orientation in between turns is a significant component of the worm's motion, and that this behavior is driven by the dynamics in shape space. Indeed, the correlation time of the bending mode te times , showingE. coli, we can see these discrete events reflected directly in the trajectory of the organism's center-of-mass motion C. elegans, discrete behaviors are roughly only half of the story: the exploratory trajectories of the worm get approximately equal contributions from discrete turning events and from continuous re–orientational motions in between the turns. Further, we can trace these continuous motions back to the underlying dynamics in the space of body shapes. Finally, we see that these different components of the motion are under independent genetic and adaptive control.It is tempting to think of behavior as a sequence of discrete actions, each taken in consequence of a specific decision. In the simplest cases, such as the running and tumbling of C. elegans are composed of two principle reorientation elements: abrupt events, including classical C. elegans controls more aspects of its motion than the stochastic rate of abrupt events. Evidence for this sort of continuous control has also recently been observed during C. elegans chemotaxis Quantitatively, we found that the exploratory motions of C. elegans are captured by four modes dop-2 and dop-3, which contain defective receptors for the neurotransmitter dopamine, an important component in the modulation of foraging strategy. Although these mutants have nearly identical statistics when we look at their discrete turning behaviors, their continuous motions, as seen in the dynamics of fluctuations along four different shape dimensions, show substantial differences. This suggests that the goal of mapping genes to behavior Extending previous work showing that the body shapes of dop-2 (vs105) worms and dop-3 (vs106) worms, each tracked for 35 minutes. The worms were transferred to the agar plate using a platinum worm pick and we excluded the first 400 seconds of each tracking run to avoid any influences due to mechanical stimulation. Following The image centroid and worm shape data were collected as in Ref Figure S1Reconstructed trajectories. To explicitly demonstrate that the shape modes provide sufficient information to reconstruct the worm trajectories in real space, we show 16 trajectory reconstructions from (randomly chosen) continuous intervals in the data that are longer than 60 seconds. In these reconstructions, red trajectories are generated from the mode model (Eq 9) while blue trajectories are measured from centroid motion. Arrows denote the direction of motion and the black scale bar is 1 mm in each plot. For these reconstructions, we model the worms trajectory orientation dynamics entirely through (0.81 MB EPS)Click here for additional data file.


Statistical algorithms are routinely used to detect outbreaks of well-defined syndromes, such as influenza-like illness. These methods cannot be applied to the detection of emerging diseases for which no preexisting information is available.This paper presents a method aimed at facilitating the detection of outbreaks, when there is no a priori knowledge of the clinical presentation of cases.nd version (ICPC-2). The surveillance data are transformed into color-coded cells, ranging from white to red, reflecting the increasing frequency of observed signs. They are placed in a graphic reference frame mimicking body anatomy. Simple visual observation of color-change patterns over time, concerning a single code or a combination of codes, enables detection in the setting of interest.The method uses a visual representation of the symptoms and diseases coded during a patient consultation according to the International Classification of Primary Care 2The method is demonstrated through retrospective analyses of two data sets: description of the patients referred to the hospital by their general practitioners (GPs) participating in the French Sentinel Network and description of patients directly consulting at a hospital emergency department (HED).Informative image color-change alert patterns emerged in both cases: the health consequences of the August 2003 heat wave were visualized with GPs' data , and the flu epidemics, which are routinely detected by standard statistical techniques, were recognized visually with HED data.Using human visual pattern-recognition capacities to detect the onset of unexpected health events implies a convenient image representation of epidemiological surveillance and well-trained "epidemiology watchers". Once these two conditions are met, one could imagine that the epidemiology watchers could signal epidemiological alerts, based on "image walls" presenting the local, regional and/or national surveillance patterns, with specialized field epidemiologists assigned to validate the signals detected. Interest in syndromic surveillance was fueled in the recent years by the 9/11 attack on the US that revived fears of bioterrorism and by the threat of emerging diseases. Syndromic surveillance is defined as "an investigational approach where health department staff, assisted by automated data acquisition and generation of statistical alerts, monitor disease indicators in real-time or near real-time to detect outbreaks of disease earlier than would otherwise be possible with traditional public health methods",3.Once the databases are available in appropriate settings, outbreak-analysis algorithms are needed. An outbreak is an unexpected cluster of cases of a certain category, given the past experience in the same place and under the same conditions. Thus, outbreak detection can be considered a problem of pattern recognition.Since the advent of artificial neural network methods of pattern recognition , it has While the supervised approach is straightforward, by definition, it only identifies those events that have been defined a priori. A second class of pattern-recognition techniques is the class of "unsupervised methods". In this class, the patterns to separate have not been defined previously. The challenge is to distinguish them – when they exist – from background "noise". In epidemiological terms, unsupervised approaches are suited to the detection of outbreaks of emerging diseases, for which no prior description is available, or bioterrorist attacks using unconventional biological weapons, i.e., modified biological agents causing novel unknown symptoms. Supervised methods are inapplicable in this critical role of epidemiological surveillance.Herein, we describe an unsupervised outbreak-detection method that relies on the human visual capacity to detect new patterns . This stnd version (ICPC-2), which was specifically developed to code the clinical consultations patients in general practice. Then, these code counts, corresponding to number of consultations with those symptoms, are presented within a graphic reference frame, which contains all the codes of the terminology ordered in such a way as to mimic body anatomy. This ordering facilitates the epidemiology watcher's interpretation of the images, that we call ICPCviews.The principle of the method relies on the translation of medical linguistic information collected during the consultation into a visual signal. To do so, the first step is to encode that information using standardized medical terminology. For this study, we chose the International Classification of Primary Care, 2Each patient-practitioner encounter is described with a chain of linguistic information describing the chief purpose of the consultation. That information is then translated into ICPC-2 code . It can th International Classification of Diseases (ICD-10). In this study, we used the symptoms and diagnoses corresponding to 685 codes.In ICPC-2, the codes are ranged according to three axes: symptoms, diagnoses and processes. Within these axes, 17 social-nosological categories  are defined. A total of 745 different codes comprise ICPC-2, compared to the 10,795 codes making up the 10The aim of the method is to provide an instantaneous visualization of the whole set of codes. Herein, we applied an approach that we previously used for other medical classifications ,22: eachThe graphic reference frame Figure  was builEach color is coded by a number reflecting the frequency of the diagnosis/symptom, from white (absent) to bright red (= 255). Let's assume that, in a given cell, a frequency x was observed. The color code N(x) assigned to x is defined by N(x) = integer part of [(x/(Max - Min)) × 255], where Max and Min are the respective maximum and minimum numbers of medical consultations associated with the symptom codes corresponding to the image cells for this population of patients.We used two databases to illustrate our method: one from GPs in private practice and the other from an HED.Data from GPs were obtained through the French Sentinel Network which has monitored online a series of common communicable diseases since 1984  and, allData on outpatients consulting at an HED were obtained during 2006  in a major university hospital in Paris. The chief complaints of every consulting patient during 2006 were recorded in free text by the triage nurse. To determine whether characteristic patterns of influenza were visible before the 2006 outbreak, we selected 4 random subsets of 200 consultations each, corresponding respectively to: the week just before the flu period (week 3/2006), the week of the flu outbreak peak (week 6/2006), the week after the flu period (week 14/2006) and the rest of the year. The time of the epidemic peak and its duration were provided by the routine periodic regression software used for real-time data from the Sentinel Network . The chiThe first example of epidemiological detection of events of interest obtained with the GPs' data, shown in Figure We also analyzed the GPs' data concerning influenza-like surveillance over a 7-year period  can be used in the present application. We examined the ICPCviews corresponding, as above, to: the week just before the outbreak (week 3/2006), the week at the outbreak peak (week 6/2006), the week after the outbreak (week 14/2006), and the rest of the year taken as a control period. We then subtracted the control ICPCview from the three ICPCviews being considered. The pattern for the week preceding the outbreak ICPCview clearly foresees that seen during the week of the outbreak peak Figures  and 3B . This paThe usual syndromic surveillance methods are supervised and based on statistical tools. Herein, we described a novel method that could be used when the supervised approach is not applicable. That situation occurs when we are faced with the detection of "unexpected" events, which, by definition, are of major interest for epidemiological alert. Indeed, our primary goal is to help recognize, as early as possible, totally unexpected epidemiological patterns. The detection-triggering signal can be the mere increase of an isolated diagnosis code. Pertinently, in this case, a regression method with a threshold would have performed better only under the very restrictive condition that this code would have been identified in advance. However, the signal can also be an unusual association of different color patches on the monitor, which appear to be novel to the observer, and trigger an in depth epidemiological investigation.Our proposed model is similar to what already happens in an air-traffic-control room: most of the routine tasks are now automated and the attention of the human observers is now focused on "unexpected" events. Likewise, we propose relying on the classical supervised methods for the usual situations that happen regularly , and we seek to improve our detection of the unexpected epidemiological events that are extremely critical from a public health perspective, precisely because they are unexpected.An important technical problem is the choice of the time resolution of the display on the monitor. For the French Sentinel Network, resolution time was the month: that timeframe is clearly irrelevant for prospective surveillance and was only used to show the potential of our method to recognize a very special event . Similarly, for the HED, the choice of weekly resolution was only illustrative and was imposed by the numbers of data available per day, keeping in mind that several hundred cases are needed to create an informative image. In a real-world application, the choice of the temporal resolution would depend on the nature of the class of events to be identified: hourly resolution or, at worst, daily resolution would be desirable to recognize a terrorist attack-associated disease. The temporal resolution chosen also reflects the spatial resolution, with the number of cases observed indeed being a decreasing function of both spatial and temporal resolutions.For example, the HED data we used in our example was collected in real time. The hospital that provided those data has ~150 consultations per day. Using a surveillance system based on the network of all Paris region public hospitals (Assistance Publique-Hôpitaux de Paris), which collects real-time data on 4000 patients per day  would, in contrast, empower a much shorter timeframe, of the order of a few hours.Furthermore, for the method we propose, we chose to code diagnoses and symptoms with the ICPC-2 system, because it was developed precisely for primary care patients, who are the best target for surveillance of emerging diseases or bioterrorist attacks. However, the same paradigm developed herein could be used with other classification methods.In a first test example, we showed that visual inspection of the ICPCviews obtained based on Sentinel Network GPs' transmissions during the 2003 heat wave in France would have likely raised suspicion that something unusual was occurring at that time. Indeed, in light of the public health and political scandal that ensued, it is highly rewarding that the images generated with our model heralded the high morbidity and mortality (later documented) that passed unnoticed. At the time of the event, the only public health warnings came from newspapers and funeral parlors, not from the health information systems, which were therefore far from the ideal real-time systems we described above. Imagine that the wall of monitors would have generated patterns similar to those seen in Figure The second example we used was the detection of a flu-like outbreak. Flu-like symptoms are observed at the onset of many diseases, during bioterrorist attacks , and for emerging diseases . Numerous supervised techniques proved successful at recognizing seasonal influenza outbreaks, and the goal of our technique is not to compete with those methods in this situation.Now, imagine an outbreak of influenza-like syndromes occurring in August, or the onset of a new disease heralded by symptoms, like epistaxis or purpura; the supervised methods would be, by definition, unsuited to detect them, while an unsupervised technique, like the one we proposed here, could work. Finally, the method is designed to have the highest sensitivity possible, in order to detect rare, unusual and unexpected signals. To achieve good positive-predictive value would require, in addition, a "back room", where human experts would validate the signals based on appropriate field epidemiological investigations.One caveat of the method is that it relies, by definition, on human observers. Hence, its effectiveness will depend upon the quality of these observers and their training. The system's quality and that of the epidemiology watcher could be measured with a research protocol based on simulated datasets. This approach has been successfully used in epidemiological surveillance to test new algorithms . SimulatIf one accepts that an epidemiological alert system must be able to detect unexpected events, then huge efforts must be made to develop unsupervised methods precisely designed with this effect in mind. Herein, we described an attempt in this direction. The use of visual perception that we advocate here is not the only possible solution. Unsupervised pattern recognition is a prolific field of research that takes advantage of the ever-increasing power of computers and the new methods of machine learning. Those will be new avenues for epidemiological research into efficient warning systems.The authors declare that they have no competing interests.A-JV proposed using the present visual method for outbreak detection. PL defined the visual graphic reference frame and selected the databases used to exemplify the method. A-JV and PL wrote the paper jointly.The pre-publication history for this paper can be accessed here:ICPC-body. ICPC classification with our visual reference frameClick here for fileMovie of flu epidemics. This slide show is composed of 82 successive images of the graphic reference frame corresponding to the ~7-year period and illustrates the visual changes of the color patterns of the disease-associated ICPC-2 codes generated by the successively entered codes that paralleled flu epidemics.Click here for file