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PubMed2006

Testing effective connectivity changes with structural equation modeling: what does a bad model tell us?

Structural equation modeling (SEM) is a statistical method that can assess changes in effective connectivity across tasks or between groups. In its initial application to neuroimaging data, anatomical connectivity provided the constraints to decompose interregional covariances to estimate effective connections. There have been concerns expressed, however, with the validity of interpreting effective connections for a model that does not adequately fit the data. We sought to address this concern by creating two population networks with different patterns of effective connectivity, extracting three samples sizes (N = 100, 60, 20), and then assessing whether the ability to detect effective connectivity differences depended on absolute model fit. Four scenarios were assessed: (1) elimination of a region showing no task differences; (2) elimination of connections with no task differences; (3) elimination of connections that carried task differences, but could be expressed through alternative indirect routes; (4) elimination of connections that carried task differences, and could not be expressed through indirect routes. We were able to detect task differences in all four cases, despite poor absolute model fit. In scenario 3, total effects captured the overall task differences even though the direct effect was no longer present. In scenario 4, task differences that were included in the model remained, but the missing effect was not expressed. In conclusion, it seems that when independent information (e.g., anatomical connectivity) is used to define the causal structure in SEM, inferences about task- or group-dependent changes are valid regardless of absolute model fit.

Algorithms↗

PubMed2007

Issues in applied statistics for public health bioterrorism surveillance using multiple data streams: research needs.

The objective of this report is to provide a basis to inform decisions about priorities for developing statistical research initiatives in the field of public health surveillance for emerging threats. Rapid information system advances have created a vast opportunity of secondary data sources for information to enhance the situational and health status awareness of populations. While the field of medical informatics and initiatives to standardize healthcare-seeking encounter records continue accelerating, it is necessary to adapt analytic and statistical methodologies to mature in sync with sibling information science technologies. One major right-of-passage for statistical inference is to advance the optimal application of analytic methodologies for using multiple data streams in detecting and characterizing public health population events of importance. This report first describes the problem in general and the data context, then delineates more specifically the practical nature of the problem and the related issues. Approaches currently applied to data with time-series, statistical process control and traditional inference concepts are described with examples in the section on Statistics and the Role of the Analytic Surveillance Data Monitor. These are the techniques that are providing substance to surveillance professionals and enabling use of multiple data streams. The next section describes use of a more complex approach that takes temporal as well as spatial dimensions into consideration for detection and situational awareness regarding event distributions. The space-time statistic has successfully been used to detect and track public health events of interest. Important research questions which are summarized at the end of this report are described in more detail with respect to the methodological application in the respective sections. This was thought to help elucidate the research requirements as summarized later in the report. Following the description of the space-time scan statistical application; this report extends to a less traditional area of promise given what has been observed in recent application of analytic methods. Bayesian networks (BNs) represent a conceptual step with advantages of flexibility for the public health surveillance community. Progression from traditional to the more extending statistical concepts in the context of the dynamic status quo of responsibility and challenge, leads to a conclusion consisting of categorical research needs. The report is structured by design to inform judgment about how to build on practical systems to achieve better analytic outcomes for public health surveillance. There are references to research issues throughout the sections with a summarization at the end, which also includes items previously unmentioned in the report.

Algorithms↗

PubMed2026

Integrative transcriptomic, spatial and functional-genomic analysis identifies a UFMylation-related vascular-stromal program and prioritizes WWTR1 in glioblastoma.

Glioblastoma (GBM) contains spatially organized stress-adaptive and vascular niches. Because transcript abundance does not measure UFM1 conjugation, we asked whether a UFMylation-related transcriptional axis identifies a reproducible tissue program and alters candidate prioritization. In 518 unique primary TCGA-GBM tumors profiled on the Affymetrix HT Human Genome U133A array, weighted gene co-expression network analysis of 8,000 variable genes yielded 12 modules. The 278-gene green module ranked first across nine prespecified traits (mean |r|=0.637). Direct overlap comprised 1/3 measurable UFMylation-core, 5/19 ER-stress/UPR, and 2/15 proteostasis genes; after excluding overlapping genes, correlations with the green eigengene remained significant (r = 0.373, 0.831, 0.639, and 0.699 for UFMylation-core, ER-stress/UPR, proteostasis, and composite scores, respectively). The green score was associated with overall survival per standard-deviation increase (HR 1.17, 95% CI 1.07-1.28), although clinical adjustment attenuated the estimate. In a 10-sample single-cell dataset, sample-level scores were higher in pericytes and endothelial cells than in malignant cells. Donor-aware IvyGAP analysis supported regional organization, whereas one Visium section showed stronger concordance with ER-stress/UPR and mesenchymal scores than with the UFMylation-core score. CellChat indicated pathway-selective rather than global remodeling of inferred vascular communication. Layer ablation moved WWTR1 from rank 48 using WGCNA alone to rank 4 overall and rank 1 among non-common-essential genes after cross-platform integration. These findings define an ER-stress/mesenchymal-weighted, UFMylation-related vascular-stromal transcriptional association and nominate WWTR1 for experimental testing.

Humans↗

PubMed1995

Paleolakes on Mars.

Observational evidence such as outflow channels and valley networks suggest that in the past there was flowing water on Mars. The images of fluvial features on Mars logically suggest that there must exist downstream locations in which the water pooled and the sediment load deposited (i.e. lakes). Sediments and morphological features associated with the martian paleolakes are believed to occur in Valles Marineris, and several large basins including Amazonis, Chryse and Elysium planitia. As Mars became progressively colder over geological time, any lakes on its surface would have become seasonally, and eventually perennially ice-covered. We know from polar lakes on Earth that ice-covered lakes can persist even when the mean annual temperature falls below freezing. Thus, the most recent lacustrine sediments on Mars were probably deposited in ice-covered lakes. While life outside of the Earth's atmosphere has yet to be observed, there is a general consensus among exobiologists that the search for extraterrestrial life should be based upon liquid water. The inference that there was liquid water on Mars during an earlier epoch is the primary motivation for considering the possibility of life during this time. It would be of enormous interest from both an exobiological and paleolimnological perspective to discover lakes or the evidence of former lakes on another planet such as Mars. Limnology would then become an interplanetary science.

Atmosphere↗

PubMed2006

Demographic history of HIV-1 subtypes B and F in Brazil.

The reconstruction of the epidemic history of several HIV populations, by using methods that infer the population history from sampled gene sequence data, has revealed important subtype-specific and regional-specific differences in patterns of epidemic growth. Here, we employ Bayesian coalescent-based methods to compare the population history of the HIV-1 subtype B and F1 epidemics in Brazil from non-contemporary env and pol gene sequences. Our results suggest that after the introduction of the subtypes B and F1 into Brazilian population, around mid to late 1960s and late 1970s, respectively, these subtypes experienced an initial period of exponential growth with similar epidemic growth rates ( approximately 0.5-0.6year(-1)). Later, the spreading rate of both subtypes seems to have slowed-down since mid to late 1980s. This demographic pattern is very similar to that reported for the subtype B epidemics in high-income countries where HIV was initially transmitted through homosexual intercourse and injecting drug use, as in Brazil; suggesting that the characteristics of transmission networks may be a key determinant of the HIV epidemic growth pattern. It is important to note that most of the subtype B and F1 sequences used in this study come from the Southeast region that has been the most affected by the AIDS epidemic in Brazil, being responsible for around 63% of all AIDS cases reported since the early eighties; but may not represent the demographic trend of the HIV-1 epidemic in other Brazilian regions.

Bayes Theorem↗

PubMed2006

Surface structure smoothing effect of polysaccharide on a heat-set protein particle gel.

This work investigates surface properties of a protein particle gel and effects of polysaccharide on the surface microstructure of such a protein gel. Whey protein isolate (WPI) was used as the primary gelling agent, and a polysaccharide (xanthan) was investigated for its surface smoothing effects. The surface properties of heat-set WPI gels with and without the presence of xanthan (0, 0.05, and 0.25%) were characterized using a surface friction technique. The surface friction force of a gel against a stainless steel substrate was found to be highly dependent on the sliding speed for all three gel samples, and the addition of xanthan caused a general reduction of surface friction. The gel containing no xanthan has the largest surface friction and behaved in the most load-dependent manner, whereas the gel containing 0.25% xanthan has the lowest surface friction and showed the least load dependency. It was inferred that the WPI gel containing no xanthan has the roughest surface among the three samples and the presence of xanthan leads to a smoother surface with probably a thinner layer of surface water. Surface features derived from surface friction tests were confirmed by surface microstructure observation from confocal laser scanning microscopy (CLSM) and environmental electron scanning microscopy (ESEM). Surface profiles from CLSM images were used to quantify the surface roughness of these gels. The mean square root surface roughness R(q) was calculated to be 3.8 +/- 0.2, 3.0 +/- 0.2, and 1.5 +/- 0.2 microm for gels containing 0, 0.05, and 0.25% xanthan, respectively. The dual excitation images of protein and xanthan from CLSM observation and images from ESEM observation indicate a xanthan-rich layer at the surfaces of the xanthan-containing gel samples. We speculate that the creation of the outer surface of a particle gel is based on a different particle aggregation mechanism from that leading to network formation in the bulk.

Friction↗

PubMed2001

ADP-ribosylation factors (ARFs) and ARF-like 1 (ARL1) have both specific and shared effectors: characterizing ARL1-binding proteins.

Despite the 40-60% identity between ADP-ribosylation factors (ARFs) and ARF-like (ARL) proteins, distinct functional roles have been inferred from findings that ARLs lack the biochemical or genetic activities characteristic of ARFs. The potential for functional overlap between ARFs and ARLs was examined by comparing effects of expression on intact cells and the ability to bind effectors. Expression of [Q71L]ARL1 in mammalian cells led to altered Golgi structure similar to, but less dramatic than, that reported previously for [Q71L]ARF1. Two previously identified partners of ARFs, MKLP1 and Arfaptin2/POR1, also bind ARL1 but not ARL2 or ARL3. Two-hybrid screens of human cDNA libraries with dominant active mutants of human ARL1, ARL2, and ARL3 identified eight different but overlapping sets of binding partners. Specific interactions between ARL1 and two binding proteins, SCOCO and Golgin-245, are defined and characterized in more detail. Like ARFs and ARL1, the binding of SCOCO to Golgi membranes is rapidly reversed by brefeldin A, suggesting the presence of a brefeldin A-sensitive ARL1 exchange factor. These data reveal a complex network of interactions between GTPases in the ARF family and their effectors and reveal a potential for cross-talk not demonstrated previously.

ADP-Ribosylation Factors↗

PubMed2025

Efficient detection and characterization of targets of natural selection using transfer learning.

Natural selection leaves detectable patterns of altered spatial diversity within genomes, and identifying affected regions is crucial for understanding species evolution. Recently, machine learning approaches applied to raw population genomic data have been developed to uncover these adaptive signatures. Convolutional neural networks (CNNs) are particularly effective for this task, as they handle large data arrays while maintaining element correlations. However, shallow CNNs may miss complex patterns due to their limited capacity, while deep CNNs can capture these patterns but require extensive data and computational power. Transfer learning addresses these challenges by utilizing a deep CNN pre-trained on a large dataset as a feature extraction tool for downstream classification and evolutionary parameter prediction. This approach reduces extensive training data generation requirements and computational needs while maintaining high performance. In this study, we developed TrIdent, a tool that uses transfer learning to enhance detection of adaptive genomic regions from image representations of multilocus variation. We evaluated TrIdent across various genetic, demographic, and adaptive settings, in addition to unphased data and other confounding factors. TrIdent demonstrated improved detection of adaptive regions compared to recent methods using similar data representations. We further explored model interpretability through class activation maps and adapted TrIdent to infer selection parameters for identified adaptive candidates. Using whole-genome haplotype data from European and African populations, TrIdent effectively recapitulated known sweep candidates and identified novel cancer, and other disease-associated genes as potential sweeps.

Journal Article↗

PubMed2003

Lack of monosynaptic corticomotoneuronal EPSPs in rats: disynaptic EPSPs mediated via reticulospinal neurons and polysynaptic EPSPs via segmental interneurons.

In the rat, some findings have been taken to suggest the existence of monosynaptic corticomotoneuronal (CM) connections. Because this connection is believed to be largely responsible for the ability to make independent digit movements in primates and man, it has been inferred that the monosynaptic CM connection in the rat is likewise important for skilled prehension. Comparison of intra- and extracellular recordings from forelimb motoneurons in anesthetized rats, revealed no monosynaptic CM excitatory postsynaptic potentials (EPSPs). The fastest descending excitation in forelimb motoneurons was disynaptically mediated via a corticoreticulospinal pathway and slowly conducted excitation via corticospinal fibers and segmental interneurons. The findings stress the importance of di- and trisynaptic excitatory corticofugal pathways to forelimb motoneurons in the control of skillful digit movements.

Animals↗

PubMed2003

Combined functional MRI and tractography to demonstrate the connectivity of the human primary motor cortex in vivo.

In this study, we combined advanced MR techniques to explore primary motor cortex (M1) connectivity in the human brain. We matched functional and anatomical information using motor functional MRI (fMRI) and white matter tractography inferred from diffusion tensor imaging (DTI). We performed coregistered DTI and motor task fMRI in 8 right-handed healthy subjects and in 1 right-handed patient presenting with a left precentral tumour. We used the fast-marching tractography (FMT) algorithm to define 3D connectivity maps within the whole brain, from seed points selected in the white matter adjacent to the location of the maximum of fMRI activation. Connectivity maps were then anatomically normalised and analysed using statistical parametric mapping software (SPM99) allowing group comparisons (left versus right hemisphere in control subjects and patient versus control subjects). The results demonstrated, in all control subjects, strong connections from M1 to the pyramidal tracts, premotor areas, parietal cortices, thalamus, and cerebellum. M1 connectivity was asymmetric, being more extensive in the dominant hemisphere. The patient had differences in M1 connectivity from the control group. Thus, fMRI-correlated DTI-FMT is a promising tool to study the structural basis of functional networks in the human brain in vivo.

Adult↗

PubMed1993

Blood supply to the amphibian mesonephros.

The purpose of the present study was to describe geometry of branching, topography and sources of blood vessels supplying the mesonephros of three different species of amphibia and to infere from the results their common and species-specific features. The detailed information on arrangement of portal and arterial blood supply to mesonephros is necessary for better understanding of the conditions under which these kidneys function. For this reason the blood vessels of the mesonephros of adult Hynobius Keyserlingi, Triturus vulgaris and Rana temporaria were injected with stained gelatin. The urodelian kidneys were shown to be supplied by numerous segmental arteries. Three types of arterial supply to glomeruli were distinguished: those mediated by short, medium and long branches, which create different physical conditions for the glomerular filtration in pertinent nephrons--as the blood pressure necessarily decreases with the increasing distance from the aorta. The tributaries to the renal portal vein were identified in all three species as the veins draining hind limbs, tail, pelvis and body wall. It is being suggested that the purpose of this large drainage area is to secure a sufficient volume of blood to the peritubular network.

Amphibians↗

PubMed1979

A viscosity model of polyacrylamide gel electrophoresis.

In current theories of polyacrylamide gel electrophoresis, the idea prevails that molecular sieving relies on different accessibility of volume fractions and of cross-sectional area fractions (denoted "pores") to different-sized ions due to the effect of "geometric exclusion". This correlates with the assumption that all elements of a polyacrylamide network occupy fixed and unchangeable positions thus forcing colliding macro-ions to diffuse laterally in order to find an "accessible pore" and to resume motion in direction of the electrical field. However, the alternative conception would be equally well justified, i.e. the assumption that polyacrylamide chains represent smooth obstacles cleared aside under the electrokinetic pressure of a macro-ion. This explanation would even be preferable with respect to the molecular sieving effects occurring in solutions of "liquid polyacrylamide". Yet no theory exists as to describe such effects in quantitative terms. In the present article, a parameter is defined and discussed, which can be estimated by experiment, and which seems to be apt to characterize local resistivity of polymer structures against dislocation and deformation: the "fractional specific resistance". Definition of this parameter is based on the model of a "viscosity-emulsion" composed of two interpenetrating liquid compartments which are characterized by different levels of hydrodynamic friction and the spatial dimensions of which are inferred from Ogston's theory. This concept of "localized viscosity" may also serve as a link between theories of molecular sieving and of "macroscopic viscosity" of flexible polymers. The data of Morris, formerly taken as verifications of the "rigid-pore" concept, are now interpreted in terms of four factors responsible for sizediscrimination: collision frequency, duration of single contacts, size-dependent frictional force, and the extent of cooperation among fibres, due to crosslinking and to simultanous contacts of several fibres to a single macro-ion. Some functions relevant for problems of molecular weight determination by gel electrophoresis are discussed in relation to the suggested model.

Acrylamides↗

PubMed1998

NMR determination of the global structure of the 113Cd derivative of desulforedoxin: investigation of the hydrogen bonding pattern at the metal center.

Desulforedoxin (Dx) is a simple homodimeric protein isolated from Desulfovibrio gigas (Dg) containing a distorted rubredoxin-like center with one iron coordinated by four cysteinyl residues (7.9 kDa with 36 amino acids per monomer). In order to probe the geometry and the H-bonding at the active site of Dx, the protein was reconstituted with 113Cd and the solution structure determined using 2D NMR methods. The structure of this derivative was initially compared with the NMR solution structure of the Zn form (Goodfellow BJ et al., 1996, J Biol Inorg Chem 1:341-353). Backbone amide protons for G4, D5, G13, L11 NH, and the Q14 NH side-chain protons, H-bonded in the X-ray structure, were readily exchanged with solvent. Chemical shift differences observed for amide protons near the metal center confirm the H-bonding pattern seen in the X-ray model (Archer M et al., 1995, J Mol Biol 251:690-702) and also suggest that H-bond lengths may vary between the Fe, Zn, and 113Cd forms. The H-bonding pattern was further probed using a heteronuclear spin echo difference (HSED) experiment; the results confirm the presence of NH-S H-bonds inferred from D2O exchange data and observed in the NMR family of structures. The presence of "H-bond mediated" coupling in Dx indicates that the NH-S H-bonds at the metal center have significant covalent character. The HSED experiment also identified an intermonomer "through space" coupling for one of the L26 methyl groups, indicating its proximity to the 113Cd center in the opposing monomer. This is the first example of an intermonomer "through space" coupling. Initial structure calculations produced subsets of NMR families with the S of C28 pointing away from or toward the L26 methyl: only the subset with the C28 sulfur pointing toward the L26 methyl could result in a "through space" coupling. The HSED result was therefore included in the structure calculations. Comparison of the Fe, Zn, and 113Cd forms of Dx suggests that the geometry of the metal center and the global fold of the protein does not vary to any great extent, although the H-bond network varies slightly when Cd is introduced. The similarity between the H-bonding pattern seen at the metal center in Dx, Rd (including H-bonded and through space-mediated coupling), and many zinc-finger proteins suggests that these H-bonds are structurally vital for stabilization of the metal centers in these proteins.

Amino Acid Sequence↗

PubMed2006

Kinetics of the formation and dissociation of actin filament branches mediated by Arp2/3 complex.

The actin filament network at the leading edge of motile cells relies on localized branching by Arp2/3 complex from "mother" filaments growing near the plasma membrane. The nucleotide bound to the mother filaments (ATP, ADP and phosphate, or ADP) may influence the branch dynamics. To determine the effect of the nucleotide bound to the subunits of the mother filament on the formation and stability of branches, we compared the time courses of actin polymerization in bulk samples measured using the fluorescence of pyrene actin with observations of single filaments by total internal reflection fluorescence microscopy. Although the branch nucleation rate in bulk samples was nearly the same regardless of the nucleotide on the mother filaments, we observed fewer branches by microscopy on ADP-bound filaments than on ADP-P(i)-bound filaments. Observation of branches in the microscope depends on their binding to the slide. Since the probability that a branch binds to the slide is directly related to its lifetime, we used counts of branches to infer their rates of dissociation from mother filaments. We conclude that the nucleotide on the mother filament does not affect the initial branching event but that branches are an order of magnitude more stable on the sides of new ATP- or ADP-P(i) filaments than on ADP-actin filaments.

Actin Cytoskeleton↗

PubMed1997

Molecular Rigidity in Dry and Hydrated Onion Cell Walls.

Solid-state nuclear magnetic resonance relaxation experiments can provide information on the rigidity of individual molecules within a complex structure such as a cell wall, and thus show how each polymer can potentially contribute to the rigidity of the whole structure. We measured the proton magnetic relaxation parameters T2 (spin-spin) and T1p (spin-lattice) through the 13C-nuclear magnetic resonance spectra of dry and hydrated cell walls from onion (Allium cepa L.) bulbs. Dry cell walls behaved as rigid solids. The form of their T2 decay curves varied on a continuum between Gaussian, as in crystalline solids, and exponential, as in more mobile materials. The degree of molecular mobility that could be inferred from the T2 and T1p decay patterns was consistent with a crystalline state for cellulose and a glassy state for dry pectins. The theory of composite materials may be applied to explain the rigidity of dry onion cell walls in terms of their components. Hydration made little difference to the rigidity of cellulose and most of the xyloglucan shared this rigidity, but the pectic fraction became much more mobile. Therefore, the cellulose/xyloglucan microfibrils behaved as solid rods, and the most significant physical distinction within the hydrated cell wall was between the microfibrils and the predominantly pectic matrix. A minor xyloglucan fraction was much more mobile than the microfibrils and probably corresponded to cross-links between them. Away from the microfibrils, pectins expanded upon hydration into a nonhomogeneous, but much softer, almost-liquid gel. These data are consistent with a model for the stress-bearing hydrated cell wall in which pectins provide limited stiffness across the thickness of the wall, whereas the cross-linked microfibril network provides much greater rigidity in other directions.

Journal Article↗

PubMed2026

Complete genomes from a xenic Dolichospermum flosaquae FBCC-A233 culture reveal genome-inferred metabolic asymmetry with associated bacteria.

Cyanobacteria form phycosphere communities with associated bacteria, but genome-resolved resources are needed to formulate testable hypotheses about their metabolic interactions. Here, we reconstructed three complete circular genomes from a unialgal xenic culture, including Dolichospermum flosaquae FBCC-A233 and two associated alphaproteobacterial genomes assigned to Sphingorhabdus sp. and Brevundimonas sp. Genome-wide read mapping and genome-quality assessment supported the three recovered genomes as high-quality circular reconstructions. Comparative genome analysis placed the cyanobacterial genome within the Dolichospermum flosaquae species cluster under the GTDB framework, while the associated bacterial genomes represented Sphingorhabdus sp. and a putative undescribed Brevundimonas species-level lineage. Genome architecture analysis indicated reduced genome size and gene content in Brevundimonas relative to genus-level references although additional metrics did not support a strong conclusion of classical genome streamlining. Selected KEGG module and KO-level reconstructions indicated genome-inferred metabolic asymmetries across the consortium. FBCC-A233 encoded photosynthesis- and nitrogen-related modules and a BioU-mediated de novo biotin biosynthesis route, whereas the associated bacteria lacked complete de novo biotin biosynthesis but retained biotin-dependent carboxylase genes. FBCC-A233 also encoded extensive anaerobic corrinoid biosynthesis potential; however, canonical DMB-containing cobalamin completion, cobamide identity, and complete transporter systems were not resolved. Together, these complete genomes provide a genome-resolved resource for investigating genome-inferred metabolic differentiation and ecological interactions in cyanobacteria-associated bacterial consortia.IMPORTANCEPhycosphere interactions between cyanobacteria and associated bacteria can shape aquatic microbial communities, but many proposed interactions remain difficult to evaluate without genome-resolved resources. This study provides three complete circular genomes from a unialgal xenic Dolichospermum flosaquae culture, capturing the cyanobacterium and two co-maintained bacterial associates. Our analysis identifies genome-inferred metabolic asymmetries, particularly in biotin- and cobamide-related pathways. D. flosaquae FBCC-A233 encoded candidate de novo biotin and corrinoid biosynthesis capacity, whereas the associated bacteria lacked complete de novo pathways but retained cofactor-dependent enzymes. These findings nominate cofactor-related dependencies as experimentally testable hypotheses while emphasizing unresolved uptake, export, cobamide identity, and growth-dependence mechanisms. The complete genomes and KO-level reconstructions generated here provide a resource for future studies of cyanobacteria-associated consortia.

Genome, Bacterial↗

PubMed2006

Seeing or doing? Influence of visual and motor familiarity in action observation.

The human brain contains specialized circuits for observing and understanding actions. Previous studies have not distinguished whether this "mirror system" uses specialized motor representations or general processes of visual inference and knowledge to understand observed actions. We report the first neuroimaging study to distinguish between these alternatives. Purely motoric influences on perception have been shown behaviorally, but their neural bases are unknown. We used fMRI to reveal the neural bases of motor influences on action observation. We controlled for visual and knowledge effects by studying expert dancers. Some ballet moves are performed by only one gender. However, male and female dancers train together and have equal visual familiarity with all moves. Male and female dancers viewed videos of gender-specific male and female ballet moves. We found greater premotor, parietal, and cerebellar activity when dancers viewed moves from their own motor repertoire, compared to opposite-gender moves that they frequently saw but did not perform. Our results show that mirror circuits have a purely motor response over and above visual representations of action. We understand actions not only by visual recognition, but also motorically. In addition, we confirm that the cerebellum is part of the action observation network.

Adolescent↗

PubMed2006

Prediction of protein secondary structure content using amino acid composition and evolutionary information.

Knowing protein structure and inferring its function from the structure are one of the main issues of computational structural biology, and often the first step is studying protein secondary structure. There have been many attempts to predict protein secondary structure contents. Previous attempts assumed that the content of protein secondary structure can be predicted successfully using the information on the amino acid composition of a protein. Recent methods achieved remarkable prediction accuracy by using the expanded composition information. The overall average error of the most successful method is 3.4%. Here, we demonstrate that even if we only use the simple amino acid composition information alone, it is possible to improve the prediction accuracy significantly if the evolutionary information is included. The idea is motivated by the observation that evolutionarily related proteins share the similar structure. After calculating the homolog-averaged amino acid composition of a protein, which can be easily obtained from the multiple sequence alignment by running PSI-BLAST, those 20 numbers are learned by a multiple linear regression, an artificial neural network and a support vector regression. The overall average error of method by a support vector regression is 3.3%. It is remarkable that we obtain the comparable accuracy without utilizing the expanded composition information such as pair-coupled amino acid composition. This work again demonstrates that the amino acid composition is a fundamental characteristic of a protein. It is anticipated that our novel idea can be applied to many areas of protein bioinformatics where the amino acid composition information is utilized, such as subcellular localization prediction, enzyme subclass prediction, domain boundary prediction, signal sequence prediction, and prediction of unfolded segment in a protein sequence, to name a few.

Amino Acid Sequence↗