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1.  Are Frontal Cognitive and Atrophy Patterns Different in PSP and bvFTD? A Comparative Neuropsychological and VBM Study 
PLoS ONE  2013;8(11):e80353.
Progressive supranuclear palsy (PSP) and frontotemporal lobar degeneration (FTD) are two clinicohistological entities that share a severe prefrontal syndrome. To what extent do the cognitive syndrome and the location of the underlying brain atrophy unify or segregate these entities? Here, we examined the clinical and radiological patterns of frontal involvement and the neural bases of the cognitive dysfunctions observed in the Richardson form of PSP and the behavioral variant of FTD (bvFTD). The cognitive profile and grey and white matter volume of PSP (n = 19) and bvFTD (n = 16) patients and control participants (n = 18) were compared using a standard battery of neuropsychological tests and voxel-based morphometry (VBM), respectively. Analyses of correlations between neuropsychological and morphometric data were additionally performed. The severity and qualitative pattern of cognitive dysfunction was globally similar between the two patient groups. Grey matter volume was decreased in widespread frontal areas and in the temporal uncus in bvFTD, while it was decreased in the frontal and temporal lobes as well as in the thalamus in PSP. We also found an unexpected involvement of the frontal rectal gyrus in PSP patients compared to controls. Correlation analyses yielded different results in the two groups, with no area showing significant correlations in PSP patients, while several frontal and some temporal areas did so in bvFTD patients. In spite of minor neuropsychological and morphological differences, this study shows that the patterns of cognitive dysfunction and atrophy are very similar in PSP and bvFTD. However, executive dysfunction in these diseases may stem from partially divergent cortical and subcortical neural circuits.
doi:10.1371/journal.pone.0080353
PMCID: PMC3835584  PMID: 24278277
2.  Landscape of transcription in human cells 
Djebali, Sarah | Davis, Carrie A. | Merkel, Angelika | Dobin, Alex | Lassmann, Timo | Mortazavi, Ali M. | Tanzer, Andrea | Lagarde, Julien | Lin, Wei | Schlesinger, Felix | Xue, Chenghai | Marinov, Georgi K. | Khatun, Jainab | Williams, Brian A. | Zaleski, Chris | Rozowsky, Joel | Röder, Maik | Kokocinski, Felix | Abdelhamid, Rehab F. | Alioto, Tyler | Antoshechkin, Igor | Baer, Michael T. | Bar, Nadav S. | Batut, Philippe | Bell, Kimberly | Bell, Ian | Chakrabortty, Sudipto | Chen, Xian | Chrast, Jacqueline | Curado, Joao | Derrien, Thomas | Drenkow, Jorg | Dumais, Erica | Dumais, Jacqueline | Duttagupta, Radha | Falconnet, Emilie | Fastuca, Meagan | Fejes-Toth, Kata | Ferreira, Pedro | Foissac, Sylvain | Fullwood, Melissa J. | Gao, Hui | Gonzalez, David | Gordon, Assaf | Gunawardena, Harsha | Howald, Cedric | Jha, Sonali | Johnson, Rory | Kapranov, Philipp | King, Brandon | Kingswood, Colin | Luo, Oscar J. | Park, Eddie | Persaud, Kimberly | Preall, Jonathan B. | Ribeca, Paolo | Risk, Brian | Robyr, Daniel | Sammeth, Michael | Schaffer, Lorian | See, Lei-Hoon | Shahab, Atif | Skancke, Jorgen | Suzuki, Ana Maria | Takahashi, Hazuki | Tilgner, Hagen | Trout, Diane | Walters, Nathalie | Wang, Huaien | Wrobel, John | Yu, Yanbao | Ruan, Xiaoan | Hayashizaki, Yoshihide | Harrow, Jennifer | Gerstein, Mark | Hubbard, Tim | Reymond, Alexandre | Antonarakis, Stylianos E. | Hannon, Gregory | Giddings, Morgan C. | Ruan, Yijun | Wold, Barbara | Carninci, Piero | Guigó, Roderic | Gingeras, Thomas R.
Nature  2012;489(7414):101-108.
Summary
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific sub-cellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic sub-cellular localizations are also poorly understood. Since RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modifications and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations taken together prompt to a redefinition of the concept of a gene.
doi:10.1038/nature11233
PMCID: PMC3684276  PMID: 22955620
3.  Challenges for the understanding of the dynamics of social coordination 
The way people interact can be examined by looking at the way they move relative to each other. Seeking the principles behind those interactions have consequences potentially related to any type of interpersonal function, far beyond the so-called “motor” processes typically associated with the study of movements, be it perceptive, cognitive, affective, pragmatic, or epistemic. Here, we present the way the framework of coordination dynamics define and addresses the interactive actions in a dyad. We first introduce the basics of pattern formation as the roots of the theoretical approach of coordination dynamics, and then the way this framework may contribute to establish a solution to classify behaviors. Thereafter we review promising empirical results on the dynamics of interpersonal coordination, and finally discuss were to go next to decipher the way the coordination between two people and the way each individual contribute may be disentangled.
doi:10.3389/fnbot.2013.00018
PMCID: PMC3795308  PMID: 24130526
coordination dynamics; perception–action coupling; asymmetric roles; creation of information; taxonomy
4.  Behavioral Impact of Unisensory and Multisensory Audio-Tactile Events: Pros and Cons for Interlimb Coordination in Juggling 
PLoS ONE  2012;7(2):e32308.
Recent behavioral neuroscience research revealed that elementary reactive behavior can be improved in the case of cross-modal sensory interactions thanks to underlying multisensory integration mechanisms. Can this benefit be generalized to an ongoing coordination of movements under severe physical constraints? We choose a juggling task to examine this question. A central issue well-known in juggling lies in establishing and maintaining a specific temporal coordination among balls, hands, eyes and posture. Here, we tested whether providing additional timing information about the balls and hands motions by using external sound and tactile periodic stimulations, the later presented at the wrists, improved the behavior of jugglers. One specific combination of auditory and tactile metronome led to a decrease of the spatiotemporal variability of the juggler's performance: a simple sound associated to left and right tactile cues presented antiphase to each other, which corresponded to the temporal pattern of hands movement in the juggling task. A contrario, no improvements were obtained in the case of other auditory and tactile combinations. We even found a degraded performance when tactile events were presented alone. The nervous system thus appears able to integrate in efficient way environmental information brought by different sensory modalities, but only if the information specified matches specific features of the coordination pattern. We discuss the possible implications of these results for the understanding of the neuronal integration process implied in audio-tactile interaction in the context of complex voluntary movement, and considering the well-known gating effect of movement on vibrotactile perception.
doi:10.1371/journal.pone.0032308
PMCID: PMC3288083  PMID: 22384211
5.  Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells 
PLoS ONE  2012;7(1):e28213.
The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5′ and 3′ transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network.
doi:10.1371/journal.pone.0028213
PMCID: PMC3251577  PMID: 22238572
6.  Efficient targeted transcript discovery via array-based normalization of RACE libraries 
Nature methods  2008;5(7):629-635.
RACE (Rapid Amplification of cDNA Ends) is a widely used approach for transcript identification. Random clone selection from the RACE mixture, however, is an ineffective sampling strategy if the dynamic range of transcript abundances is large. Here, we describe a strategy that uses array hybridization to improve sampling efficiency of human transcripts. The products of the RACE reaction are hybridized onto tiling arrays, and the exons detected are used to delineate a series of RT-PCR reactions, through which the original RACE mixture is segregated into simpler RT-PCR reactions. These are independently cloned, and randomly selected clones are sequenced. This approach is superior to direct cloning and sequencing of RACE products: it specifically targets novel transcripts, and often results in overall normalization of transcript abundances. We show theoretically and experimentally that this strategy leads indeed to efficient sampling of novel transcripts, and we investigate multiplexing it by pooling RACE reactions from multiple interrogated loci prior to hybridization.
doi:10.1038/nmeth.1216
PMCID: PMC2713501  PMID: 18500348
7.  Social coordination dynamics: Measuring human bonding 
Social neuroscience  2008;3(2):178-192.
Spontaneous social coordination has been extensively described in natural settings but so far no controlled methodological approaches have been employed that systematically advance investigations into the possible self-organized nature of bond formation and dissolution between humans. We hypothesized that, under certain contexts, spontaneous synchrony -a well-described phenomenon in biological and physical settings- could emerge spontaneously between humans as a result of information exchange. Here, a new way to quantify interpersonal interactions in real time is proposed. In a simple experimental paradigm, pairs of participants facing each other were required to actively produce actions, while provided (or not) with the vision of similar actions being performed by someone else. New indices of interpersonal coordination, inspired by the theoretical framework of coordination dynamics (based on relative phase and frequency overlap between movements of individuals forming a pair) were developed and used. Results revealed that spontaneous phase synchrony (i.e., unintentional in-phase coordinated behavior) between two people emerges as soon as they exchange visual information, even if they are not explicitly instructed to coordinate with each other. Using the same tools, we also quantified the degree to which the behavior of each individual remained influenced by the social encounter even after information exchange had been removed, apparently a kind of social memory.
doi:10.1080/17470910701563392
PMCID: PMC2156197  PMID: 18552971
Social memory; Interpersonal; Spontaneous Synchronization; Coupling; Emergence; Vision; Entrainment
8.  EGASP: the human ENCODE Genome Annotation Assessment Project 
Genome Biology  2006;7(Suppl 1):S2.
Background
We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment.
Results
The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified.
Conclusion
This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.
doi:10.1186/gb-2006-7-s1-s2
PMCID: PMC1810551  PMID: 16925836
9.  GENCODE: producing a reference annotation for ENCODE 
Genome Biology  2006;7(Suppl 1):S4.
Background
The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.
Results
The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions.
Conclusion
In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.
doi:10.1186/gb-2006-7-s1-s4
PMCID: PMC1810553  PMID: 16925838
10.  ArrayProspector: a web resource of functional associations inferred from microarray expression data 
Nucleic Acids Research  2004;32(Web Server issue):W445-W448.
DNA microarray experiments have provided vast amounts of data which can be used for inferring gene function. However, most methods for predicting functional associations between genes from expression data are not suited to simultaneous analysis of multiple datasets, and a comprehensive resource of coexpression-based predictions is currently lacking. Here, we present an interactive web resource of gene associations predicted by applying a novel algorithm to all expression data in the Stanford Microarray Database. The underlying pre-computed database currently contains more than 200 000 high-confidence gene associations in 12 different species sampled from a broad taxonomic range. The resource allows every association to be inspected visually and can be accessed at http://www.bork.embl.de/ArrayProspector.
doi:10.1093/nar/gkh407
PMCID: PMC441545  PMID: 15215427

Results 1-10 (10)