305 research outputs found
Stability of graph communities across time scales
The complexity of biological, social and engineering networks makes it
desirable to find natural partitions into communities that can act as
simplified descriptions and provide insight into the structure and function of
the overall system. Although community detection methods abound, there is a
lack of consensus on how to quantify and rank the quality of partitions. We
show here that the quality of a partition can be measured in terms of its
stability, defined in terms of the clustered autocovariance of a Markov process
taking place on the graph. Because the stability has an intrinsic dependence on
time scales of the graph, it allows us to compare and rank partitions at each
time and also to establish the time spans over which partitions are optimal.
Hence the Markov time acts effectively as an intrinsic resolution parameter
that establishes a hierarchy of increasingly coarser clusterings. Within our
framework we can then provide a unifying view of several standard partitioning
measures: modularity and normalized cut size can be interpreted as one-step
time measures, whereas Fiedler's spectral clustering emerges at long times. We
apply our method to characterize the relevance and persistence of partitions
over time for constructive and real networks, including hierarchical graphs and
social networks. We also obtain reduced descriptions for atomic level protein
structures over different time scales.Comment: submitted; updated bibliography from v
Perceived importance of components of asynchronous music in circuit training
This study examined regular exercisers’ perceptions of specific components of music
during circuit training. Twenty-four men (38.8 years, s = 11.8 years) and 31 women
(32.4 years, s = 9.6 years) completed two questionnaires immediately after a circuit
training class. Participants rated the importance of 13 components of music (rhythm,
melody, etc.) in relation to exercise enjoyment, and each completed the Affect Intensity
Measure (Larsen, 1984) to measure emotional reactivity. Independent t tests were used
to evaluate gender differences in perceptions of musical importance. Pearson
correlations were computed to evaluate the relationships between affect intensity, age
and importance of musical components. Consistent with previous research and
theoretical predictions, rhythm response components (rhythm, tempo, beat) were rated
as most important. Women rated the importance of melody significantly higher than did
men, while men gave more importance to music associated with sport. Affect intensity
was found to be positively and significantly related to the perceived importance of
melody, lyrical content, musical style, personal associations and emotional content.
Results suggest that exercise leaders need to be sensitive to personal factors when
choosing music to accompany exercise. Qualitative research that focuses on the
personal meaning of music is encouraged
A Music-Related Quality of Life measure to guide music rehabilitation for adult CI users
Purpose: A music-related quality of life (MuRQoL) questionnaire was developed for the evaluation of music rehabilitation for adult cochlear implant (CI) users. The present studies were aimed at refinement and validation. Method: Twenty-four experts reviewed the MuRQoL items for face validity. A refined version was completed by 147 adult CI users and psychometric techniques were used for item selection, assessment of reliability and definition of the factor structure. The same participants completed the Short Form Health Survey for construct validation. MuRQoL responses from 68 CI users were compared with those of a matched group of normal-hearing (NH) adults. Results: Eighteen items measuring music perception & engagement and 18 items measuring their importance were selected; they grouped together into two domains. The final questionnaire has high internal consistency and repeatability. Significant differences between CI users and NH adults and a correlation between music engagement and quality of life (QoL) support construct validity. Scores of music perception & engagement and importance for the 18 items can be combined to assess the impact of music on the QoL. Conclusion: The MuRQoL questionnaire is a reliable and valid measure of self-reported music perception, engagement and their importance for adult CI users with potential to guide music aural rehabilitation
Revisiting the exercise heart rate-music tempo preference relationship
In the present study, we investigated a hypothesized quartic relationship (meaning three inflection points) between exercise heart rate (HR) and preferred music tempo. Initial theoretical predictions suggested a positive linear relationship (Iwanaga, 1995a, 1995b); however, recent experimental work has shown that as exercise HR increases, step changes and plateaus that punctuate the profile of music tempo preference may occur (Karageorghis, Jones, & Stuart, 2008). Tempi bands consisted of slow (95–100 bpm), medium
(115–120 bpm), fast (135–140 bpm), and very fast (155–160 bpm) music. Twenty-eight active undergraduate students cycled at exercise intensities representing 40, 50, 60, 70, 80, and 90% of their maximal HR reserve while their music preference was assessed using a 10-point scale. The Exercise Intensity x Music Tempo interaction was significant, F(6.16, 160.05) = 7.08, p < .001, ηp 2 =.21, as was the test for both cubic and quartic trajectories in the exercise HR–preferred-music-tempo relationship (p < .001). Whereas slow tempo music was not preferred at any exercise intensity, preference for fast tempo increased, relative to medium and very fast tempo music, as exercise intensity increased. The implications for the prescription of music in exercise and physical activity contexts are discussed
Node-weighted measures for complex networks with spatially embedded, sampled, or differently sized nodes
When network and graph theory are used in the study of complex systems, a
typically finite set of nodes of the network under consideration is frequently
either explicitly or implicitly considered representative of a much larger
finite or infinite region or set of objects of interest. The selection
procedure, e.g., formation of a subset or some kind of discretization or
aggregation, typically results in individual nodes of the studied network
representing quite differently sized parts of the domain of interest. This
heterogeneity may induce substantial bias and artifacts in derived network
statistics. To avoid this bias, we propose an axiomatic scheme based on the
idea of node splitting invariance to derive consistently weighted variants of
various commonly used statistical network measures. The practical relevance and
applicability of our approach is demonstrated for a number of example networks
from different fields of research, and is shown to be of fundamental importance
in particular in the study of spatially embedded functional networks derived
from time series as studied in, e.g., neuroscience and climatology.Comment: 21 pages, 13 figure
Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation
In this paper, we investigate the conformational dynamics of alanine
dipeptide under an external electric field by nonequilibrium molecular dynamics
simulation. We consider the case of a constant and of an oscillatory field. In
this context we propose a procedure to implement the temperature control, which
removes the irrelevant thermal effects of the field. For the constant field
different time-scales are identified in the conformational, dipole moment, and
orientational dynamics. Moreover, we prove that the solvent structure only
marginally changes when the external field is switched on. In the case of
oscillatory field, the conformational changes are shown to be as strong as in
the previous case, and non-trivial nonequilibrium circular paths in the
conformation space are revealed by calculating the integrated net probability
fluxes.Comment: 23 pages, 12 figure
Beyond the Binding Site: The Role of the β2 – β3 Loop and Extra-Domain Structures in PDZ Domains
A general paradigm to understand protein function is to look at properties of isolated well conserved domains, such as SH3 or PDZ domains. While common features of domain families are well understood, the role of subtle differences among members of these families is less clear. Here, molecular dynamics simulations indicate that the binding mechanism in PSD95-PDZ3 is critically regulated via interactions outside the canonical binding site, involving both the poorly conserved loop and an extra-domain helix. Using the CRIPT peptide as a prototypical ligand, our simulations suggest that a network of salt-bridges between the ligand and this loop is necessary for binding. These contacts interconvert between each other on a time scale of a few tens of nanoseconds, making them elusive to X-ray crystallography. The loop is stabilized by an extra-domain helix. The latter influences the global dynamics of the domain, considerably increasing binding affinity. We found that two key contacts between the helix and the domain, one involving the loop, provide an atomistic interpretation of the increased affinity. Our analysis indicates that both extra-domain segments and loosely conserved regions play critical roles in PDZ binding affinity and specificity
A Systematic Analysis of Metal and Metalloid Concentrations in Eight Zebrafish Recirculating Water Systems
Metals and metalloids are integral to biological processes and play key roles in physiology and metabolism. Nonetheless, overexposure to some metals or lack of others can lead to serious health consequences. In this study, eight zebrafish facilities collaborated to generate a multielement analysis of their centralized recirculating water systems. We report a first set of average concentrations for 46 elements detected in zebrafish facilities. Our results help to establish an initial baseline for trouble-shooting purposes, and in general for safe ranges of metal concentrations in recirculating water systems, supporting reproducible scientific research outcomes with zebrafish
ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome
<p>Abstract</p> <p>Background</p> <p>Maize (<it>Zea mays </it>ssp. <it>mays </it>L.) is an important model for plant basic and applied research. In 2009, the B73 maize genome sequencing made a great step forward, using clone by clone strategy; however, functional annotation and gene classification of the maize genome are still limited. Thus, a well-annotated datasets and informative database will be important for further research discoveries. Signal transduction is a fundamental biological process in living cells, and many protein families participate in this process in sensing, amplifying and responding to various extracellular or internal stimuli. Therefore, it is a good starting point to integrate information on the maize functional genes involved in signal transduction.</p> <p>Results</p> <p>Here we introduce a comprehensive database 'ProFITS' (Protein Families Involved in the Transduction of Signalling), which endeavours to identify and classify protein kinases/phosphatases, transcription factors and ubiquitin-proteasome-system related genes in the B73 maize genome. Users can explore gene models, corresponding transcripts and FLcDNAs using the three abovementioned protein hierarchical categories, and visualize them using an AJAX-based genome browser (JBrowse) or Generic Genome Browser (GBrowse). Functional annotations such as GO annotation, protein signatures, protein best-hits in the <it>Arabidopsis </it>and rice genome are provided. In addition, pre-calculated transcription factor binding sites of each gene are generated and mutant information is incorporated into ProFITS. In short, ProFITS provides a user-friendly web interface for studies in signal transduction process in maize.</p> <p>Conclusion</p> <p>ProFITS, which utilizes both the B73 maize genome and full length cDNA (FLcDNA) datasets, provides users a comprehensive platform of maize annotation with specific focus on the categorization of families involved in the signal transduction process. ProFITS is designed as a user-friendly web interface and it is valuable for experimental researchers. It is freely available now to all users at <url>http://bioinfo.cau.edu.cn/ProFITS</url>.</p
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