94 research outputs found
Weighted and unweighted network of amino acids within protein
The information regarding the structure of a single protein is encoded in the
network of interacting amino acids. Considering each protein as a weighted and
unweighted network of amino acids we have analyzed a total of forty nine
protein structures that covers the three branches of life on earth. Our results
show that the probability degree distribution of network connectivity follows
Poisson's distribution; whereas the probability strength distribution does not
follow any known distribution. However, the average strength of amino acid node
depends on its degree (k). For some of the proteins, the strength of a node
increases linearly with k. On the other hand, for a set of other proteins,
although the strength increases linaerly with k for smaller values of k, we
have not obtained any clear functional relationship of strength with degree at
higher values of k. The results also show that the weight of the amino acid
nodes belonging to the highly connected nodes tend to have a higher value. The
result that the average clustering coefficient of weighted network is less than
that of unweighted network implies that the topological clustering is generated
by edges with low weights. The ratio of average clustering coefficients of
protein network to that of the corresponding classical random network varies
linearly with the number (N) of amino acids of a protein; whereas the ratio of
characteristic path lengths varies logarithmically with N. The power law
behaviour of clustering coefficients of weighted and unweighted network as a
function of degree k indicates that the network has a signature of hierarchical
network. It has also been observed that the network is of assortative type
The topology of a discussion: the #occupy case
We analyse a large sample of the Twitter activity developed around the social
movement 'Occupy Wall Street' to study the complex interactions between the
human communication activity and the semantic content of a discussion. We use a
network approach based on the analysis of the bipartite graph @Users-#Hashtags
and of its projections: the 'semantic network', whose nodes are hashtags, and
the 'users interest network', whose nodes are users In the first instance, we
find out that discussion topics (#hashtags) present a high heterogeneity, with
the distinct role of the communication hubs where most the 'opinion traffic'
passes through. In the second case, the self-organization process of users
activity leads to the emergence of two classes of communicators: the
'professionals' and the 'amateurs'. Moreover the network presents a strong
community structure, based on the differentiation of the semantic topics, and a
high level of structural robustness when a certain set of topics are censored
and/or accounts are removed. Analysing the characteristics the @Users-#Hashtags
network we can distinguish three phases of the discussion about the movement.
Each phase corresponds to specific moment of the movement: from declaration of
intent, organisation and development and the final phase of political
reactions. Each phase is characterised by the presence of specific #hashtags in
the discussion. Keywords: Twitter, Network analysisComment: 13 pages, 9 figure
Hydrophobic, hydrophilic and charged amino acids' networks within Protein
The native three dimensional structure of a single protein is determined by
the physico chemical nature of its constituent amino acids. The twenty
different types of amino acids, depending on their physico chemical properties,
can be grouped into three major classes - hydrophobic, hydrophilic and charged.
We have studied the anatomy of the weighted and unweighted networks of
hydrophobic, hydrophilic and charged residues separately for a large number of
proteins. Our results show that the average degree of the hydrophobic networks
has significantly larger value than that of hydrophilic and charged networks.
The average degree of the hydrophilic networks is slightly higher than that of
charged networks. The average strength of the nodes of hydrophobic networks is
nearly equal to that of the charged network; whereas that of hydrophilic
networks has smaller value than that of hydrophobic and charged networks. The
average strength for each of the three types of networks varies with its
degree. The average strength of a node in charged networks increases more
sharply than that of the hydrophobic and hydrophilic networks. Each of the
three types of networks exhibits the 'small-world' property. Our results
further indicate that the all amino acids' networks and hydrophobic networks
are of assortative type. While maximum of the hydrophilic and charged networks
are of assortative type, few others have the characteristics of disassortative
mixing of the nodes. We have further observed that all amino acids' networks
and hydrophobic networks bear the signature of hierarchy; whereas the
hydrophilic and charged networks do not have any hierarchical signature.Comment: Corresponding author: Sudip Kund
Impact of Vitamin D Supplementation on Arterial Vasomotion, Stiffness and Endothelial Biomarkers in Chronic Kidney Disease Patients
Background: Cardiovascular events are frequent and vascular endothelial function is abnormal in patients with chronic
kidney disease (CKD). We demonstrated endothelial dysfunction with vitamin D deficiency in CKD patients; however the impact of cholecalciferol supplementation on vascular stiffness and vasomotor function, endothelial and bone biomarkers in CKD patients with low 25-hydroxy vitamin D [25(OH)D] is unknown, which this study investigated.
Methods: We assessed non-diabetic patients with CKD stage 3/4, age 17–80 years and serum 25(OH)D ,75 nmol/L. Brachial
artery Flow Mediated Dilation (FMD), Pulse Wave Velocity (PWV), Augmentation Index (AI) and circulating blood biomarkers were evaluated at baseline and at 16 weeks. Oral 300,000 units cholecalciferol was administered at baseline and 8-weeks.
Results: Clinical characteristics of 26 patients were: age 50614 (mean61SD) years, eGFR 41611 ml/min/1.73 m2, males
73%, dyslipidaemia 36%, smokers 23% and hypertensives 87%. At 16-week serum 25(OH)D and calcium increased (43616
to 84629 nmol/L, p,0.001 and 2.3760.09 to 2.4260.09 mmol/L; p = 0.004, respectively) and parathyroid hormone
decreased (10.868.6 to 7.464.4; p = 0.001). FMD improved from 3.163.3% to 6.163.7%, p = 0.001. Endothelial biomarker
concentrations decreased: E-Selectin from 566662123 to 525662058 pg/mL; p = 0.032, ICAM-1, 3.4560.01 to
3.1061.04 ng/mL; p = 0.038 and VCAM-1, 54633 to 42633 ng/mL; p = 0.006. eGFR, BP, PWV, AI, hsCRP, von Willebrand
factor and Fibroblast Growth Factor-23, remained unchanged.
Conclusion: This study demonstrates for the first time improvement of endothelial vasomotor and secretory functions with vitamin D in CKD patients without significant adverse effects on arterial stiffness, serum calcium or FGF-23.
Trial Registration: ClinicalTrials.gov NCT0200571
Network 'small-world-ness': a quantitative method for determining canonical network equivalence
Background: Many technological, biological, social, and information networks fall into the broad class of 'small-world' networks: they have tightly interconnected clusters of nodes, and a shortest mean path length that is similar to a matched random graph (same number of nodes and edges). This semi-quantitative definition leads to a categorical distinction ('small/not-small') rather than a quantitative, continuous grading of networks, and can lead to uncertainty about a network's small-world status. Moreover, systems described by small-world networks are often studied using an equivalent canonical network model-the Watts-Strogatz (WS) model. However, the process of establishing an equivalent WS model is imprecise and there is a pressing need to discover ways in which this equivalence may be quantified.
Methodology/Principal Findings: We defined a precise measure of 'small-world-ness' S based on the trade off between high local clustering and short path length. A network is now deemed a 'small-world' if S. 1-an assertion which may be tested statistically. We then examined the behavior of S on a large data-set of real-world systems. We found that all these systems were linked by a linear relationship between their S values and the network size n. Moreover, we show a method for assigning a unique Watts-Strogatz (WS) model to any real-world network, and show analytically that the WS models associated with our sample of networks also show linearity between S and n. Linearity between S and n is not, however, inevitable, and neither is S maximal for an arbitrary network of given size. Linearity may, however, be explained by a common limiting growth process.
Conclusions/Significance: We have shown how the notion of a small-world network may be quantified. Several key properties of the metric are described and the use of WS canonical models is placed on a more secure footing
Mesoscopic organization reveals the constraints governing C. elegans nervous system
One of the biggest challenges in biology is to understand how activity at the
cellular level of neurons, as a result of their mutual interactions, leads to
the observed behavior of an organism responding to a variety of environmental
stimuli. Investigating the intermediate or mesoscopic level of organization in
the nervous system is a vital step towards understanding how the integration of
micro-level dynamics results in macro-level functioning. In this paper, we have
considered the somatic nervous system of the nematode Caenorhabditis elegans,
for which the entire neuronal connectivity diagram is known. We focus on the
organization of the system into modules, i.e., neuronal groups having
relatively higher connection density compared to that of the overall network.
We show that this mesoscopic feature cannot be explained exclusively in terms
of considerations, such as optimizing for resource constraints (viz., total
wiring cost) and communication efficiency (i.e., network path length).
Comparison with other complex networks designed for efficient transport (of
signals or resources) implies that neuronal networks form a distinct class.
This suggests that the principal function of the network, viz., processing of
sensory information resulting in appropriate motor response, may be playing a
vital role in determining the connection topology. Using modular spectral
analysis, we make explicit the intimate relation between function and structure
in the nervous system. This is further brought out by identifying functionally
critical neurons purely on the basis of patterns of intra- and inter-modular
connections. Our study reveals how the design of the nervous system reflects
several constraints, including its key functional role as a processor of
information.Comment: Published version, Minor modifications, 16 pages, 9 figure
Resilience management during large-scale epidemic outbreaks
Assessing and managing the impact of large-scale epidemics considering only the individual risk and severity of the disease is exceedingly difficult and could be extremely expensive. Economic consequences, infrastructure and service disruption, as well as the recovery speed, are just a few of the many dimensions along which to quantify the effect of an epidemic on society's fabric. Here, we extend the concept of resilience to characterize epidemics in structured populations, by defining the system-wide critical functionality that combines an individual’s risk of getting the disease (disease attack rate) and the disruption to the system’s functionality (human mobility deterioration). By studying both conceptual and data-driven models, we show that the integrated consideration of individual risks and societal disruptions under resilience assessment framework provides an insightful picture of how an epidemic might impact society. In particular, containment interventions intended for a straightforward reduction of the risk may have net negative impact on the system by slowing down the recovery of basic societal functions. The presented study operationalizes the resilience framework, providing a more nuanced and comprehensive approach for optimizing containment schemes and mitigation policies in the case of epidemic outbreaks
Holographic Vitrification
We establish the existence of stable and metastable stationary black hole
bound states at finite temperature and chemical potentials in global and planar
four-dimensional asymptotically anti-de Sitter space. We determine a number of
features of their holographic duals and argue they represent structural
glasses. We map out their thermodynamic landscape in the probe approximation,
and show their relaxation dynamics exhibits logarithmic aging, with aging rates
determined by the distribution of barriers.Comment: 100 pages, 25 figure
Understanding the implementation of evidence-based care: A structural network approach
<p>Abstract</p> <p>Background</p> <p>Recent study of complex networks has yielded many new insights into phenomenon such as social networks, the internet, and sexually transmitted infections. The purpose of this analysis is to examine the properties of a network created by the 'co-care' of patients within one region of the Veterans Health Affairs.</p> <p>Methods</p> <p>Data were obtained for all outpatient visits from 1 October 2006 to 30 September 2008 within one large Veterans Integrated Service Network. Types of physician within each clinic were nodes connected by shared patients, with a weighted link representing the number of shared patients between each connected pair. Network metrics calculated included edge weights, node degree, node strength, node coreness, and node betweenness. Log-log plots were used to examine the distribution of these metrics. Sizes of k-core networks were also computed under multiple conditions of node removal.</p> <p>Results</p> <p>There were 4,310,465 encounters by 266,710 shared patients between 722 provider types (nodes) across 41 stations or clinics resulting in 34,390 edges. The number of other nodes to which primary care provider nodes have a connection (172.7) is 42% greater than that of general surgeons and two and one-half times as high as cardiology. The log-log plot of the edge weight distribution appears to be linear in nature, revealing a 'scale-free' characteristic of the network, while the distributions of node degree and node strength are less so. The analysis of the k-core network sizes under increasing removal of primary care nodes shows that about 10 most connected primary care nodes play a critical role in keeping the <it>k</it>-core networks connected, because their removal disintegrates the highest <it>k</it>-core network.</p> <p>Conclusions</p> <p>Delivery of healthcare in a large healthcare system such as that of the US Department of Veterans Affairs (VA) can be represented as a complex network. This network consists of highly connected provider nodes that serve as 'hubs' within the network, and demonstrates some 'scale-free' properties. By using currently available tools to explore its topology, we can explore how the underlying connectivity of such a system affects the behavior of providers, and perhaps leverage that understanding to improve quality and outcomes of care.</p
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