Googling the brain: discovering hierarchical and asymmetric network structures, with applications in neuroscience

Hierarchical organisation is a common feature of many directed networks arising in nature and technology. For example, a well-defined message-passing framework based on managerial status typically exists in a business organisation. However, in many real-world networks such patterns of hierarchy are unlikely to be quite so transparent. Due to the nature in which empirical data is collated the nodes will often be ordered so as to obscure any underlying structure. In addition, the possibility of even a small number of links violating any overall “chain of command” makes the determination of such structures extremely challenging. Here we address the issue of how to reorder a directed network in order to reveal this type of hierarchy. In doing so we also look at the task of quantifying the level of hierarchy, given a particular node ordering. We look at a variety of approaches. Using ideas from the graph Laplacian literature, we show that a relevant discrete optimization problem leads to a natural hierarchical node ranking. We also show that this ranking arises via a maximum likelihood problem associated with a new range-dependent hierarchical random graph model. This random graph insight allows us to compute a likelihood ratio that quantifies the overall tendency for a given network to be hierarchical. We also develop a generalization of this node ordering algorithm based on the combinatorics of directed walks. In passing, we note that Google’s PageRank algorithm tackles a closely related problem, and may also be motivated from a combinatoric, walk-counting viewpoint. We illustrate the performance of the resulting algorithms on synthetic network data, and on a real-world network from neuroscience where results may be validated biologically

Understanding edge-connectivity in the Internet through core-decomposition

Internet is a complex network composed by several networks: the Autonomous Systems, each one designed to transport information efficiently. Routing protocols aim to find paths between nodes whenever it is possible (i.e., the network is not partitioned), or to find paths verifying specific constraints (e.g., a certain QoS is required). As connectivity is a measure related to both of them (partitions and selected paths) this work provides a formal lower bound to it based on core-decomposition, under certain conditions, and low complexity algorithms to find it. We apply them to analyze maps obtained from the prominent Internet mapping projects, using the LaNet-vi open-source software for its visualization

Fast matrix computations for pair-wise and column-wise commute times and Katz scores

We first explore methods for approximating the commute time and Katz score between a pair of nodes. These methods are based on the approach of matrices, moments, and quadrature developed in the numerical linear algebra community. They rely on the Lanczos process and provide upper and lower bounds on an estimate of the pair-wise scores. We also explore methods to approximate the commute times and Katz scores from a node to all other nodes in the graph. Here, our approach for the commute times is based on a variation of the conjugate gradient algorithm, and it provides an estimate of all the diagonals of the inverse of a matrix. Our technique for the Katz scores is based on exploiting an empirical localization property of the Katz matrix. We adopt algorithms used for personalized PageRank computing to these Katz scores and theoretically show that this approach is convergent. We evaluate these methods on 17 real world graphs ranging in size from 1000 to 1,000,000 nodes. Our results show that our pair-wise commute time method and column-wise Katz algorithm both have attractive theoretical properties and empirical performance.Comment: 35 pages, journal version of http://dx.doi.org/10.1007/978-3-642-18009-5_13 which has been submitted for publication. Please see http://www.cs.purdue.edu/homes/dgleich/publications/2011/codes/fast-katz/ for supplemental code

Unprocessed red meat and processed meat consumption: Dietary guideline recommendations from the NutriRECS Consortium

Description: Dietary guideline recommendations require consideration of the certainty in the evidence, the magnitude of potential benefits and harms, and explicit consideration of people's values and preferences. A set of recommendations on red meat and processed meat consumption was developed on the basis of 5 de novo systematic reviews that considered all of these issues. Methods: The recommendations were developed by using the Nutritional Recommendations (NutriRECS) guideline development process, which includes rigorous systematic review methodology, and GRADE methods to rate the certainty of evidence for each outcome and to move from evidence to recommendations. A panel of 14 members, including 3 community members, from 7 countries voted on the final recommendations. Strict criteria limited the conflicts of interest among panel members. Considerations of environmental impact or animal welfare did not bear on the recommendations. Four systematic reviews addressed the health effects associated with red meat and processed meat consumption, and 1 systematic review addressed people's health-related values and preferences regarding meat consumption. Recommendations: The panel suggests that adults continue current unprocessed red meat consumption (weak recommendation, low-certainty evidence). Similarly, the panel suggests adults continue current processed meat consumption (weak recommendation, low-certainty evidence)

Synthesis and evaluation of novel antifungal agents targeted to the plasma membrane H[+]-ATPase

A library of dienones were synthesized as candidate antifungal agents. These compounds were screened against Saccharomyces cerevisiae and Candida albicans using macro-broth susceptibility assay. The dienones exhibited a broad range of inhibition against S. cerevisiae (0.2-99%) and C. albicans (0-99%). 3,5-bis(p- trifluoromethylbenzylidene)-1-methyl-piperidine-4-one was identified as the most potent inhibitor of S. cerevisiae. Whereas, the most promising inhibitor of C. albicans was 2,6-bis(pyridine-3ylmethylene)cyclohexan-1-one

Euclidean versus hyperbolic congestion in idealized versus experimental networks

This paper proposes a mathematical justification of the phenomenon of extreme congestion at a very limited number of nodes in very large networks. It is argued that this phenomenon occurs as a combination of the negative curvature property of the network together with minimum length routing. More specifically, it is shown that, in a large n-dimensional hyperbolic ball B of radius R viewed as a roughly similar model of a Gromov hyperbolic network, the proportion of traffic paths transiting through a small ball near the center is independent of the radius R whereas, in a Euclidean ball, the same proportion scales as 1/R^{n-1}. This discrepancy persists for the traffic load, which at the center of the hyperbolic ball scales as the square of the volume, whereas the same traffic load scales as the volume to the power (n+1)/n in the Euclidean ball. This provides a theoretical justification of the experimental exponent discrepancy observed by Narayan and Saniee between traffic loads in Gromov-hyperbolic networks from the Rocketfuel data base and synthetic Euclidean lattice networks. It is further conjectured that for networks that do not enjoy the obvious symmetry of hyperbolic and Euclidean balls, the point of maximum traffic is near the center of mass of the network.Comment: 23 pages, 4 figure

Global, regional, and national disability-adjusted life-years (DALYs) for 359 diseases and injuries and healthy life expectancy (HALE) for 195 countries and territories, 1990-2017: a systematic analysis for the Global Burden of Disease Study 2017.

How long one lives, how many years of life are spent in good and poor health, and how the population's state of health and leading causes of disability change over time all have implications for policy, planning, and provision of services. We comparatively assessed the patterns and trends of healthy life expectancy (HALE), which quantifies the number of years of life expected to be lived in good health, and the complementary measure of disability-adjusted life-years (DALYs), a composite measure of disease burden capturing both premature mortality and prevalence and severity of ill health, for 359 diseases and injuries for 195 countries and territories over the past 28 years. Methods We used data for age-specific mortality rates, years of life lost (YLLs) due to premature mortality, and years lived with disability (YLDs) from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 to calculate HALE and DALYs from 1990 to 2017. We calculated HALE using age-specific mortality rates and YLDs per capita for each location, age, sex, and year. We calculated DALYs for 359 causes as the sum of YLLs and YLDs. We assessed how observed HALE and DALYs differed by country and sex from expected trends based on Socio-demographic Index (SDI). We also analysed HALE by decomposing years of life gained into years spent in good health and in poor health, between 1990 and 2017, and extra years lived by females compared with males. Findings Globally, from 1990 to 2017, life expectancy at birth increased by 7·4 years (95% uncertainty interval 7·1-7·8), from 65·6 years (65·3-65·8) in 1990 to 73·0 years (72·7-73·3) in 2017. The increase in years of life varied from 5·1 years (5·0-5·3) in high SDI countries to 12·0 years (11·3-12·8) in low SDI countries. Of the additional years of life expected at birth, 26·3% (20·1-33·1) were expected to be spent in poor health in high SDI countries compared with 11·7% (8·8-15·1) in low-middle SDI countries. HALE at birth increased by 6·3 years (5·9-6·7), from 57·0 years (54·6-59·1) in 1990 to 63·3 years (60·5-65·7) in 2017. The increase varied from 3·8 years (3·4-4·1) in high SDI countries to 10·5 years (9·8-11·2) in low SDI countries. Even larger variations in HALE than these were observed between countries, ranging from 1·0 year (0·4-1·7) in Saint Vincent and the Grenadines (62·4 years [59·9-64·7] in 1990 to 63·5 years [60·9-65·8] in 2017) to 23·7 years (21·9-25·6) in Eritrea (30·7 years [28·9-32·2] in 1990 to 54·4 years [51·5-57·1] in 2017). In most countries, the increase in HALE was smaller than the increase in overall life expectancy, indicating more years lived in poor health. In 180 of 195 countries and territories, females were expected to live longer than males in 2017, with extra years lived varying from 1·4 years (0·6-2·3) in Algeria to 11·9 years (10·9-12·9) in Ukraine. Of the extra years gained, the proportion spent in poor health varied largely across countries, with less than 20% of additional years spent in poor health in Bosnia and Herzegovina, Burundi, and Slovakia, whereas in Bahrain all the extra years were spent in poor health. In 2017, the highest estimate of HALE at birth was in Singapore for both females (75·8 years [72·4-78·7]) and males (72·6 years [69·8-75·0]) and the lowest estimates were in Central African Republic (47·0 years [43·7-50·2] for females and 42·8 years [40·1-45·6] for males). Globally, in 2017, the five leading causes of DALYs were neonatal disorders, ischaemic heart disease, stroke, lower respiratory infections, and chronic obstructive pulmonary disease. Between 1990 and 2017, age-standardised DALY rates decreased by 41·3% (38·8-43·5) for communicable diseases and by 49·8% (47·9-51·6) for neonatal disorders. For non-communicable diseases, global DALYs increased by 40·1% (36·8-43·0), although age-standardised DALY rates decreased by 18·1% (16·0-20·2)