SIRIUS: Dual, Symmetric, Interactive Dimension Reductions

Much research has been done regarding how to visualize and interact with observations and attributes of high-dimensional data for exploratory data analysis. From the analyst's perceptual and cognitive perspective, current visualization approaches typically treat the observations of the high-dimensional dataset very differently from the attributes. Often, the attributes are treated as inputs (e.g., sliders), and observations as outputs (e.g., projection plots), thus emphasizing investigation of the observations. However, there are many cases in which analysts wish to investigate both the observations and the attributes of the dataset, suggesting a symmetry between how analysts think about attributes and observations. To address this, we define SIRIUS (Symmetric Interactive Representations In a Unified System), a symmetric, dual projection technique to support exploratory data analysis of high-dimensional data. We provide an example implementation of SIRIUS and demonstrate how this symmetry affords additional insights.

Observation-Level and Parametric Interaction for High-Dimensional Data Analysis

Exploring high-dimensional data is challenging. Dimension reduction algorithms, such as weighted multidimensional scaling, support data exploration by projecting datasets to two dimensions for visualization. These projections can be explored through parametric interaction, tweaking underlying parameterizations, and observation-level interaction, directly interacting with the points within the projection. In this article, we present the results of a controlled usability study determining the differences, advantages, and drawbacks among parametric interaction, observation-level interaction, and their combination. The study assesses both interaction technique effects on domain-specific high-dimensional data analyses performed by non-experts of statistical algorithms. This study is performed using Andromeda, a tool that enables both parametric and observation-level interaction to provide in-depth data exploration. The results indicate that the two forms of interaction serve different, but complementary, purposes in gaining insight through steerable dimension reduction algorithms.

Towards a Systematic Combination of Dimension Reduction and Clustering in Visual Analytics

Dimension reduction algorithms and clustering algorithms are both frequently used techniques in visual analytics. Both families of algorithms assist analysts in performing related tasks regarding the similarity of observations and finding groups in datasets. Though initially used independently, recent works have incorporated algorithms from each family into the same visualization systems. However, these algorithmic combinations are often ad hoc or disconnected, working independently and in parallel rather than integrating some degree of interdependence. A number of design decisions must be addressed when employing dimension reduction and clustering algorithms concurrently in a visualization system, including the selection of each algorithm, the order in which they are processed, and how to present and interact with the resulting projection. This paper contributes an overview of combining dimension reduction and clustering into a visualization system, discussing the challenges inherent in developing a visualization system that makes use of both families of algorithms.

A system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature

A broadly accepted and stable biological classification system is a prerequisite for biological sciences. It provides the means to describe and communicate about life without ambiguity. Current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. The current system is thus inadequate to classify and name the immense genetic diversity within species that is now being revealed by genome sequencing on a daily basis. To address this lack of a general intra-species classification and naming system adequate for today's speed of discovery of new diversity, we propose a classification and naming system that is exclusively based on genome similarity and that is suitable for automatic assignment of codes to any genome-sequenced organism without requiring any phenotypic or phylogenetic analysis. We provide examples demonstrating that genome similarity-based codes largely align with current taxonomic groups at many different levels in bacteria, animals, humans, plants, and viruses. Importantly, the proposed approach is only slightly affected by the order of code assignment and can thus provide codes that reflect similarity between organisms and that do not need to be revised upon discovery of new diversity. We envision genome similarity-based codes to complement current biological nomenclature and to provide a universal means to communicate unambiguously about any genome-sequenced organism in fields as diverse as biodiversity research, infectious disease control, human and microbial forensics, animal breed and plant cultivar certification, and human ancestry research.

Semantics of directly manipulating spatializations

When high-dimensional data is visualized in a 2D plane by using parametric projection algorithms, users may wish to manipulate the layout of the data points to better reflect their domain knowledge or to explore alternative structures. However, few users are well-versed in the algorithms behind the visualizations, making parameter tweaking more of a guessing game than a series of decisive interactions. Translating user interactions into algorithmic input is a key component of Visual to Parametric Interaction (V2PI) [13]. Instead of adjusting parameters, users directly move data points on the screen, which then updates the underlying statistical model. However, we have found that some data points that are not moved by the user are just as important in the interactions as the data points that are moved. Users frequently move some data points with respect to some other 'unmoved' data points that they consider as spatially contextual. However, in current V2PI interactions, these points are not explicitly identified when directly manipulating the moved points. We design a richer set of interactions that makes this context more explicit, and a new algorithm and sophisticated weighting scheme that incorporates the importance of these unmoved data points into V2PI.

Allelic variation in two distinct Pseudomonas syringae flagellin epitopes modulates the strength of plant immune responses but not bacterial motility

The bacterial flagellin (FliC) epitopes flg22 and flgII-28 are microbe-associated molecular patterns (MAMPs). Although flg22 is recognized by many plant species via the pattern recognition receptor FLS2, neither the flgII-28 receptor nor the extent of flgII-28 recognition by different plant families is known. Here, we tested the significance of flgII-28 as a MAMP and the importance of allelic diversity in flg22 and flgII-28 in plant-pathogen interactions using purified peptides and a Pseudomonas syringae ∆fliC mutant complemented with different fliC alleles. The plant genotype and allelic diversity in flg22 and flgII-28 were found to significantly affect the plant immune response, but not bacterial motility. The recognition of flgII-28 is restricted to a number of solanaceous species. Although the flgII-28 peptide does not trigger any immune response in Arabidopsis, mutations in both flg22 and flgII-28 have FLS2-dependent effects on virulence. However, the expression of a tomato allele of FLS2 does not confer to Nicotiana benthamiana the ability to detect flgII-28, and tomato plants silenced for FLS2 are not altered in flgII-28 recognition. Therefore, MAMP diversification is an effective pathogen virulence strategy, and flgII-28 appears to be perceived by an as yet unidentified receptor in the Solanaceae, although it has an FLS2-dependent virulence effect in Arabidopsis.

Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens

While the existence of environmental reservoirs of human pathogens is well established, less is known about the role of nonagricultural environments in emergence, evolution, and spread of crop pathogens. Here, we analyzed phylogeny, virulence genes, host range, and aggressiveness of Pseudomonas syringae strains closely related to the tomato pathogen P. syringae pv. tomato (Pto), including strains isolated from snowpack and streams. The population of Pto relatives in nonagricultural environments was estimated to be large and its diversity to be higher than that of the population of Pto and its relatives on crops. Ancestors of environmental strains, Pto, and other genetically monomorphic crop pathogens were inferred to have frequently recombined, suggesting an epidemic population structure for P. syringae. Some environmental strains have repertoires of type III-secreted effectors very similar to Pto, are almost as aggressive on tomato as Pto, but have a wider host range than typical Pto strains. We conclude that crop pathogens may have evolved through a small number of evolutionary events from a population of less aggressive ancestors with a wider host range present in nonagricultural environments.

The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity

Recently, genome sequencing of many isolates of genetically monomorphic bacterial human pathogens has given new insights into pathogen microevolution and phylogeography. Here, we report a genome-based micro-evolutionary study of a bacterial plant pathogen, Pseudomonas syringae pv. tomato. Only 267 mutations were identified between five sequenced isolates in 3,543,009 nt of analyzed genome sequence, which suggests a recent evolutionary origin of this pathogen. Further analysis with genome-derived markers of 89 world-wide isolates showed that several genotypes exist in North America and in Europe indicating frequent pathogen movement between these world regions. Genome-derived markers and molecular analyses of key pathogen loci important for virulence and motility both suggest ongoing adaptation to the tomato host. A mutational hotspot was found in the type III-secreted effector gene hopM1. These mutations abolish the cell death triggering activity of the full-length protein indicating strong selection for loss of function of this effector, which was previously considered a virulence factor. Two non-synonymous mutations in the flagellin-encoding gene fliC allowed identifying a new microbe associated molecular pattern (MAMP) in a region distinct from the known MAMP flg22. Interestingly, the ancestral allele of this MAMP induces a stronger tomato immune response than the derived alleles. The ancestral allele has largely disappeared from today's Pto populations suggesting that flagellin-triggered immunity limits pathogen fitness even in highly virulent pathogens. An additional non-synonymous mutation was identified in flg22 in South American isolates. Therefore, MAMPs are more variable than expected differing even between otherwise almost identical isolates of the same pathogen strain.

Abstract P6-05-06: Clinical Presentation of Molecular Apocrine Subgroup of Breast Cancer: A Rather Aggressive Group of Tumor

Background: Estrogen receptor negative (ER-) breast cancer represents 30% of breast cancers. This heterogeneous group comprises at least the basal and HER2+ subgroups. Recent data, as well as our own, has observed that the HER2+ subtype is highly heterogeneous. Several teams have identified a new “apocrine” molecular subgroup of cancer, characterized by androgen receptor (AR) expresion in an ER-context. Here, we have retrospectively identified, based on a transcriptionnal signature, these apocrine molecular tumours and described their clinical presentation and evolution.

Material and Methods:

We retrospectively identified 60 patients treated in St Louis Hospital (Paris) from 1995 to 2008 and presenting the signature of the molecular apocrine subgroup (ERA-, AR+, FOXA1+) by Q-RT-PCR.

Results:

Mean age at diagnosis was 53,5 y.o. Tumours size were T2 or more in 78% cases. Histological types were ductal invasive with intraductal component (n=22), histological apocrine (n=3), and paget disease (n=4). Tumor grade was 3 in 68%, and 2 in 21%, with lymphovascular invasion in 37%. Excluding patients receiving neo-adjuvant chemotherapy, lymph node status was negative in 41%, and positive in 52% (1 to 3, 32%, more than 4N+, 20%). By immunohistochemistry 97.4% were PR-and 58.72% overexpressed HER2.

Surgery was conservative in 46%, and 48% patients underwent mastectomy. Sixteen patients received neoadjuvant chemotherapy (27%), 41 received adjuvant chemotherapy (68%), 16 received hormonal therapy (27%), and

16 received trastuzumab (27%). With a median follow up of 60 months, 34 events (local recurrence n=9, contralateral n=3, distant metastasis n=22), and 13 deaths occurred. Median disease free survival was 48 months.

Discussion:

In this cohort of apocrine molecular carcinomas, tumor phenotypes appears to be rather aggressive, with a high proportion of poor prognosis factors (grade SBR3, lymphovascular invasion, node involvement), and are generally well-correlated to a poor clinical outcome in this population that received heterogeneous treatments. Further data are needed to precisely characterise this particular breast cancer subtype, notably patients who are not eligible to Herceptin-based regimen.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-05-06.

PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes

Although there are adequate DNA sequence differences among plant-associated and plant-pathogenic bacteria to facilitate molecular approaches for their identification, identification at a taxonomic level that is predictive of their phenotype is a challenge. The problem is the absence of a taxonomy that describes genetic variation at a biologically relevant resolution and of a database containing reference strains for comparison. Moreover, molecular evolution, population genetics, ecology, and epidemiology of many plant-pathogenic and plant-associated bacteria are still poorly understood. To address these challenges, a database with web interface was specifically designed for plant-associated and plant-pathogenic microorganisms. The Plant-Associated Microbes Database (PAMDB) comprises, thus far, data from multilocus sequence typing and analysis (MLST/MLSA) studies of Acidovorax citrulli, Pseudomonas syringae, Ralstonia solanacearum, and Xanthomonas spp. Using data deposited in PAMDB, a robust phylogeny of Xanthomonas axonopodis and related bacteria has been inferred, and the diversity existing in the Xanthomonas genus and in described Xanthomonas spp. has been compared with the diversity in P. syringae and R. solanacearum. Moreover, we show how PAMDB makes it easy to distinguish between different pathogens that cause almost identical diseases. The scalable design of PAMDB will make it easy to add more plant pathogens in the future.

Lack of serotonin1B receptor expression leads to age-related motor dysfunction, early onset of brain molecular aging and reduced longevity

Normal aging of the brain differs from pathological conditions and is associated with increased risk for psychiatric and neurological disorders. In addition to its role in the etiology and treatment of mood disorders, altered serotonin (5-HT) signaling is considered a contributing factor to aging; however, no causative role has been identified in aging. We hypothesized that a deregulation of the 5-HT system would reveal its contribution to age-related processes and investigated behavioral and molecular changes throughout adult life in mice lacking the regulatory presynaptic 5-HT(1B) receptor (5-HT(1B)R), a candidate gene for 5-HT-mediated age-related functions. We show that the lack of 5-HT(1B)R (Htr1b(KO) mice) induced an early age-related motor decline and resulted in decreased longevity. Analysis of life-long transcriptome changes revealed an early and global shift of the gene expression signature of aging in the brain of Htr1b(KO) mice. Moreover, molecular changes reached an apparent maximum effect at 18-months in Htr1b(KO) mice, corresponding to the onset of early death in that group. A comparative analysis with our previous characterization of aging in the human brain revealed a phylogenetic conservation of age-effect from mice to humans, and confirmed the early onset of molecular aging in Htr1b(KO) mice. Potential mechanisms appear independent of known central mechanisms (Bdnf, inflammation), but may include interactions with previously identified age-related systems (IGF-1, sirtuins). In summary, our findings suggest that the onset of age-related events can be influenced by altered 5-HT function, thus identifying 5-HT as a modulator of brain aging, and suggesting age-related consequences to chronic manipulation of 5-HT.

Neuropeptides in psychiatric diseases: an overview with a particular focus on depression and anxiety disorders

This paper aimed at reviewing the involvement of neuropeptides in various psychiatric diseases, particularly in depression, and anxiety disorders. General features of neuropeptides are first described, including the history of their discovery, their definition, classification, biosynthesis, transport, release, inactivation, as well as their interaction with specific neuronal receptors. The differences with classical neurotransmitters are mentioned, as well as the different patterns of co-transmission. Finally, different mechanisms, both at the cellular and at the systemic level, are proposed that may explain the involvement of these molecules in various psychiatric diseases. Indeed, at the cellular level, a neuropeptide can be involved in a psychiatric disease, either because it is co-localized with a classical neurotransmitter involved in a disease, or because the neuropeptide-containing neuron projects on a target neuron involved in the disease. At the systemic level, a neuropeptide can play a direct role in the expression of a symptom of the disease. This is illustrated by different examples.

Effect of dorsal periaqueductal gray lesions on cardiovascular and behavioral responses to cat odor exposure in rats

Previously we demonstrated Fos expression in the dorsal periaqueductal gray (DPAG) of the rat following cat odor exposure. Further work correlated the response to cat odor with a sustained blood pressure increase and deployment of defense behavior. It was therefore of interest to determine whether lesions of the DPAG would abolish these two effects of cat odor exposure. Male Wistar rats were given excitotoxic NMDA (N-methyl-D-aspartate) lesions of the DPAG and anterior tectum under halothane, then implanted with blood pressure telemetric probes. Sham lesions were made with saline. Rats were then exposed to cat odor with a hide option, followed 2 weeks later by re-exposure to cat odor without a hide option. Controls were exposed to rat odor in the same way. Trends toward attenuation in defense and cardiovascular indices were found in lesioned rats for cat odor exposure with a hide option, but these were not significant. Re-exposure to cat fur without a hide option enhanced the cardiovascular response and under these conditions, lesioned rats showed a significant change of the heart rate and locomotor activity response to cat fur. However, the blood pressure response was not significantly attenuated. Thus, the present results support the Fos data and indicate that the DPAG is involved in the expression of some but not all of the cardiovascular and behavioral components of the response to cat odor.

Effect of dorsal periaqueductal gray lesion on cardiovascular and behavioural responses to contextual conditioned fear in rats

Contextual conditioned fear in the rat is characterized by a freezing immobility associated with a marked increase in blood pressure, a slow increase in heart rate, and ultrasonic vocalizations. A previous Fos study also revealed a marked activation of the ventrolateral part of the periaqueductal gray (VLPAG) and a much smaller activation of its dorsal part (DPAG). Recent chemical blockade experiments indicate that the main role of the VLPAG in the response is to impose the immobility necessary for the expression of the freezing component. We now test the role of the DPAG to see if its small activation (as revealed by Fos) is of any functional significance in the contextual fear response. Large N-methyl-D-aspartate (NMDA) excitotoxic lesions that destroyed most of the DPAG were made in 10 rats. Another group of 10 rats had sham lesions with saline. The animals were then implanted with blood pressure telemetric probes, fear conditioned, and finally tested. There was no significant difference in the amount of freezing and in the blood pressure response between the two groups. However, there was a complete abolition of ultrasonic vocalizations and a significantly greater increase in heart rate in the DPAG-lesioned group. The effect on vocalization and heart rate may be explained by lesion of adjacent structures: the lateral PAG and the superior colliculus (baroreflex alteration), respectively. Thus, most of DPAG appears to play little role in the expression of the contextual fear response.

Activation of ventrolateral medullary neurons projecting to spinal autonomic areas after chemical stimulation of the central nucleus of amygdala: a neuroanatomical study in the rat

Several studies have shown that the central nucleus of amygdala is involved in cardiovascular regulation. The control of this function may be mediated by activation of the ventrolateral medulla neurons that project to preganglionic neurons located in the intermediolateral nucleus of the spinal cord. The aim of the present study was to examine whether stimulation of the central nucleus of amygdala activated ventrolateral medulla neurons projecting to the intermediolateral nucleus. For this purpose, the injection of a retrograde tracer, the cholera toxin b subunit (CTb), into the intermediolateral nucleus of the T2 segment was combined with immunohistochemical detection of Fos protein following chemical stimulation of the central nucleus of amygdala. Results showed that retrogradely labeled neurons were found throughout the ventrolateral medulla. Moreover, chemical stimulation of the central nucleus of amygdala induced: (1) a decrease of arterial blood pressure; (2) an expression of Fos protein mainly in sub-populations of neurons located in the intermediate and caudal parts of the ventrolateral medulla; (3) a significantly higher number of double labeled neurons (CTb-immunoreactive/Fos-immunoreactive) in the rostral part of the ventrolateral medulla than in the other parts of this region. These results show that the central nucleus of amygdala influences the activity of brainstem neurons projecting to the intermediolateral nucleus. Data were discussed in terms of descending amygdalofugal pathways involved in the hypotension.

Double immunocytochemistry for the detection of Fos protein in retrogradely identified neurons using cholera toxin B subunit

The focus of this paper was to describe a method combining the neuroanatomical technique of retrograde transport of cholera toxin B subunit (CTB) with the technique of Fos functional labeling. This method allowed us to evaluate whether neurons identified by retrograde tracing were activated following chemical stimulation of another brain area. We have used this method at the light microscopic level to determine whether the stimulation of the rostral ventrolateral medulla activated retrogradely labeled adrenal sympathetic preganglionic neurons in the spinal cord. CTB-containing neurons, Fos immunoreactive neurons and double labeled neurons were observed in spinal autonomic areas. These results suggest that the rostral ventrolateral medulla exerts a descending activation upon identified adrenal preganglionic neurons. The method described in this protocol can be applied for other brain areas in order to establish if a given structure can activate an identified population of neurons linked with a particular target of central or peripheral nervous system.

Autonomic dysreflexia increases plasma adrenaline level in the chronic spinal cord-injured rat

Autonomic dysreflexia (AD) occurs in up to 80% of quadriplegics and high paraplegics and is characterized by exaggerated sympathetic reflexes which induced paroxysmal hypertension. The aim of this study was to determine if plasma catecholamine levels increased during autonomic dysreflexia in the chronic spinal cord-injured (SCI) rats with special care to adrenaline. Catecholamine samples were collected before, during and 1 h after AD induced hypertension with colorectal distension. Results showed that plasma noradrenaline and adrenaline levels increased respectively 1.5-fold and 5-fold during AD in the chronic SCI rats. This suggests substantial roles for these two hormones in mediating the cardiovascular changes during AD. Knowledge of catecholamine levels during AD may thus aid in determining pathophysiology and potential pharmacologic treatments of this autonomic dysfunction.

Expression of Fos protein in adrenal preganglionic neurons following chemical stimulation of the rostral ventrolateral medulla of the rat

The ventrolateral medulla is known to be involved in the regulation of arterial blood pressure, especially via its connections with sympathetic preganglionic neurons (SPNs) mainly located in the intermediolateral nucleus of the spinal cord. It has been shown that stimulation of the rostral part of the ventrolateral medulla (RVLM) elicits a release of catecholamines from the adrenal medulla. The aim of the present study was to demonstrate the existence of a functional pathway between the RVLM and adrenal SPNs using the combination of a retrograde tract tracing technique (cholera toxin B subunit) with the immunohistochemical detection of Fos protein following the chemical stimulation of RVLM. The data obtained showed that: (1) chemical stimulation of the RVLM induced Fos immunoreactivity in the intermediolateral nucleus and particularly in SPNs projecting to the adrenal medulla; (2) along the thoracic segments T2-T12, 26.1% of retrogradely identified adrenal SPNs were Fos-immunoreactive with the greatest percentage (30.9%) in the T8 segment. These results favored a functional control of the RVLM on adrenal SPNs which may contribute to a substantial activation of the cardiovascular system via the release of adrenal catecholamines.

[Interobserver variation of the Global Assessment Scale. Study of 59 patients at admission to a general adult psychiatric unit]

In France, an analysis of the evaluation of psychiatric activity was done by a work group representing thirteen hospitals spread over the entire country. The group just recently published their final report in the form of an experimentation protocol for the description of psychiatric activity. The proposed methodology leads to some modifications of the existing data collection based on individual patient information sheets "fiche par patient", more particularly concerning new items such as the Global Assessment Scale (GAS or Axis V of DSM III-R): our first impression was that this new type of evaluation seemed to us somewhat subjective. We therefore decided to analyze the reliability of the score established by psychiatrists not familiar with its use. In the beginning the GAS score was evaluated in clinical cases (patients seen at their admission by two or three psychiatrists and scored afterwards independently), then in theoretical cases (34 cases types taken from the Health-Sickness Rating Scale of Luborsky) with the objective to improve the consensus between clinicians.

RESULTS

The clinical case studies made in an adult psychiatry pavilion permitted evaluating 59 patients at admission, of which 25 by three judges and respectively 40, 28 and 41 by pairs. The global accuracy of the score obtained with the clinical cases seems satisfactory for a discipline such as psychiatry (Kappa of Cohen's coefficient = 0.51, p < 0.001 for 25 patients by three judges--Kappa = 0.45, p < 0.001 for the 109 pairs of evaluations). The more detailed study of the classes obtained a satisfactory consensus for the scores below 40 and above 60 (K = 0.46 to 0.59) but not entirely satisfactory for the scores in the mid range of the scale between 40 and 60 (K = 0.22 to 0.29) which represents 39% of the patients in the study; this is improved by grouping into larger classes this part of the scale and it is therefore advisable to use it that way. For the 34 theoretical cases taken from the Luborsky HSRS evaluated independently by three judges the results obtained are clearly not as good (global Kappa = 0.29, p < 0.01). That is perhaps due to the fact that these "case types" don't use the descriptive patient models generally used in France. Keeping in mind that the mid range of the scale should be interpreted prudently, the GAS scale can nevertheless be credited with a certain global objectivity in the case of neutral study. Would it be the same if the GAS study could influence the allocation of resources? Taking into account all the clinical practices in mental health, the question of how all the data of this type evaluation could be recorded and updated should also examined.