1,211 research outputs found
Do logarithmic proximity measures outperform plain ones in graph clustering?
We consider a number of graph kernels and proximity measures including
commute time kernel, regularized Laplacian kernel, heat kernel, exponential
diffusion kernel (also called "communicability"), etc., and the corresponding
distances as applied to clustering nodes in random graphs and several
well-known datasets. The model of generating random graphs involves edge
probabilities for the pairs of nodes that belong to the same class or different
predefined classes of nodes. It turns out that in most cases, logarithmic
measures (i.e., measures resulting after taking logarithm of the proximities)
perform better while distinguishing underlying classes than the "plain"
measures. A comparison in terms of reject curves of inter-class and intra-class
distances confirms this conclusion. A similar conclusion can be made for
several well-known datasets. A possible origin of this effect is that most
kernels have a multiplicative nature, while the nature of distances used in
cluster algorithms is an additive one (cf. the triangle inequality). The
logarithmic transformation is a tool to transform the first nature to the
second one. Moreover, some distances corresponding to the logarithmic measures
possess a meaningful cutpoint additivity property. In our experiments, the
leader is usually the logarithmic Communicability measure. However, we indicate
some more complicated cases in which other measures, typically, Communicability
and plain Walk, can be the winners.Comment: 11 pages, 5 tables, 9 figures. Accepted for publication in the
Proceedings of 6th International Conference on Network Analysis, May 26-28,
2016, Nizhny Novgorod, Russi
Metabolism regulates exposure of pancreatic islets to circulating molecules in vivo.
International audiencePancreatic β-cells modulate insulin secretion through rapid sensing of blood glucose and integration of gut-derived signals. Increased insulin demand during pregnancy and obesity alters islet function and mass and leads to gestational diabetes mellitus and type 2 diabetes in predisposed individuals. However, it is unclear how blood-borne factors dynamically access the islets of Langerhans. Thus, understanding the changes in circulating molecule distribution that accompany compensatory β-cell expansion may be key to developing novel antidiabetic therapies. Here, using two-photon microscopy in vivo in mice, we demonstrate that islets are almost instantly exposed to peaks of circulating molecules, which rapidly pervade the tissue before clearance. In addition, both gestation and short-term high-fat-diet feeding decrease molecule extravasation and uptake rates in vivo in islets, independently of β-cell expansion or islet blood flow velocity. Together, these data support a role for islet vascular permeability in shaping β-cell adaptive responses to metabolic demand by modulating the access and sensing of circulating molecules
Anterior pituitary cell networks
Both endocrine and non-endocrine cells of the pituitary gland are organized into structural and functional
networks which are formed during embryonic development but which may be modified throughout life.
Structural mapping of the various endocrine cell types has highlighted the existence of distinct network
motifs and relationships with the vasculature which may relate to temporal differences in their output.
Functional characterization of the network activity of growth hormone and prolactin cells has revealed a
role for cell organization in gene regulation, the plasticity of pituitary hormone output and remarkably
the ability to memorize altered demand. As such, the description of these endocrine cell networks alters
the concept of the pituitary from a gland which simply responds to external regulation to that of an oscillator
which may memorize information and constantly adapt its coordinated networks’ responses to the
flow of hypothalamic inputs
Outlier Edge Detection Using Random Graph Generation Models and Applications
Outliers are samples that are generated by different mechanisms from other
normal data samples. Graphs, in particular social network graphs, may contain
nodes and edges that are made by scammers, malicious programs or mistakenly by
normal users. Detecting outlier nodes and edges is important for data mining
and graph analytics. However, previous research in the field has merely focused
on detecting outlier nodes. In this article, we study the properties of edges
and propose outlier edge detection algorithms using two random graph generation
models. We found that the edge-ego-network, which can be defined as the induced
graph that contains two end nodes of an edge, their neighboring nodes and the
edges that link these nodes, contains critical information to detect outlier
edges. We evaluated the proposed algorithms by injecting outlier edges into
some real-world graph data. Experiment results show that the proposed
algorithms can effectively detect outlier edges. In particular, the algorithm
based on the Preferential Attachment Random Graph Generation model consistently
gives good performance regardless of the test graph data. Further more, the
proposed algorithms are not limited in the area of outlier edge detection. We
demonstrate three different applications that benefit from the proposed
algorithms: 1) a preprocessing tool that improves the performance of graph
clustering algorithms; 2) an outlier node detection algorithm; and 3) a novel
noisy data clustering algorithm. These applications show the great potential of
the proposed outlier edge detection techniques.Comment: 14 pages, 5 figures, journal pape
Comparative Population Genetics of the Immunity Gene, Relish: Is Adaptive Evolution Idiosyncratic?
The frequency of adaptive evolution acting on common loci in distant lineages remains an outstanding question in evolutionary biology. We asked whether the immunity factor, Relish, a gene with a history of directional selection in Drosophila simulans, shows evidence of a similar selective history in other Drosophila species. We found only weak evidence of recurrent adaptive protein evolution at the Relish locus in three sister species pairs, suggesting that this key component of the insect immune system has an idiosyncratic evolutionary history in Drosophila
Pelvic tenderness is not limited to the prostate in chronic prostatitis/chronic pelvic pain syndrome (CPPS) type IIIA and IIIB: comparison of men with and without CP/CPPS
Background: We wished to determine if there were differences in pelvic and non-pelvic tenderness between men with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) Type III and men without pelvic pain.
Methods: We performed the Manual Tender Point Survey (MTPS) as described by the American College of Rheumatology on 62 men with CP/CPPS Type IIIA and IIIB and 98 men without pelvic pain. We also assessed tenderness of 10 external pelvic tender points (EPTP) and of 7 internal
pelvic tender points (IPTP). All study participants completed the National Institutes of Health Chronic Prostatitis Symptom Inventory (NIH CPSI).
Results: We found that men with CPPS were significantly more tender in the MTPS, the EPTPS and the IPTPS. CPSI scores correlated with EPTP scale but not with IPTP scale or prostate tenderness. Prostatic tenderness was present in 75% of men with CPPS and in 50% of men without
CPPS. Expressed prostatic fluid leukocytosis was not associated with prostatic tenderness.
Conclusion: Men with CP/CPPS have more tenderness compared to men without CPPS. Tenderness in men with CPPS is distributed throughout the pelvis and not specific to the prostate
The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing
In nature, closely related species may hybridize while still retaining their distinctive identities. Chromosomal regions that experience reduced recombination in hybrids, such as within inversions, have been hypothesized to contribute to the maintenance of species integrity. Here, we examine genomic sequences from closely related fruit fly taxa of the Drosophila pseudoobscura subgroup to reconstruct their evolutionary histories and past patterns of genic exchange. Partial genomic assemblies were generated from two subspecies of Drosophila pseudoobscura (D. ps.) and an outgroup species, D. miranda. These new assemblies were compared to available assemblies of D. ps. pseudoobscura and D. persimilis, two species with overlapping ranges in western North America. Within inverted regions, nucleotide divergence among each pair of the three species is comparable, whereas divergence between D. ps. pseudoobscura and D. persimilis in non-inverted regions is much lower and closer to levels of intraspecific variation. Using molecular markers flanking each of the major chromosomal inversions, we identify strong crossover suppression in F1 hybrids extending over 2 megabase pairs (Mbp) beyond the inversion breakpoints. These regions of crossover suppression also exhibit the high nucleotide divergence associated with inverted regions. Finally, by comparison to a geographically isolated subspecies, D. ps. bogotana, our results suggest that autosomal gene exchange between the North American species, D. ps. pseudoobscura and D. persimilis, occurred since the split of the subspecies, likely within the last 200,000 years. We conclude that chromosomal rearrangements have been vital to the ongoing persistence of these species despite recent hybridization. Our study serves as a proof-of-principle on how whole genome sequencing can be applied to formulate and test hypotheses about species formation in lesser-known non-model systems
GFS, a preparation of Tasmanian Undaria pinnatifida is associated with healing and inhibition of reactivation of Herpes
BACKGROUND: We sought to assess whether GFS, a proprietary preparation of Tasmanian Undaria pinnatifida, has effects on healing or re-emergence of Herpetic infections, and additionally, to assess effects of GFS in vitro. Undaria is the most commonly eaten seaweed in Japan, and contains sulphated polyanions and other components with potential anti-viral activity. Herpes simplex virus type 1 (HSV-1) infections have lower reactivation rates and Herpes type 2 (HSV-2) infections have lower incidence in Japan than in the west. METHODS: Patients with active (15 subjects) or latent (6 subjects) Herpetic infections (HSV-1, 2, EBV, Zoster) were monitored for response to ingestion of GFS. GFS extract was tested in vitro for human T cell mitogenicity and anti-Herpes activity. RESULTS: Ingestion of GFS was associated with increased healing rates in patients with active infections. In addition, patients with latent infection remained asymptomatic whilst ingesting GFS. GFS extract inhibited Herpes viruses in vitro and was mitogenic to human T cells in vitro. CONCLUSIONS: Ingestion of GFS has inhibitory effects on reactivation and is associated with increased rate of healing after Herpetic outbreaks. GFS extract potently inhibited Herpes virus in vitro, and had mitogenic effects on human T cells
Unity between God and mind? A study on the relationship between panpsychism and pantheism
The author thanks the John Templeton Foundation and The Pantheism and Panentheism Project for sponsoring this paperA number of contemporary philosophers have suggested that the recent revival of interest in panpsychism within philosophy of mind could reinvigorate a pantheistic philosophy of religion. This project explores whether the combination and individuation problems, which have dominated recent scholarship within panpsychism, can aid the pantheist’s articulation a God/Universe Unity. Constitutive holistic panpsychism is seen to be the only type of panpsychism suited to aid pantheism in articulating this type of unity. There are currently no well-developed solutions to the individuation problem for this type of panpsychism. Moreover, the gestures towards a solution appear costly to the religious significance of pantheism. This article concludes that any hope that the contemporary panpsychism might aid pantheists in articulating Unity is premature and possibly misplaced.Publisher PDFPeer reviewe
The chromosomal polymorphism of Drosophila subobscura: a microevolutionary weapon to monitor global change
The Palaearctic species Drosophila subobscura recently invaded the west coast of Chile and North America. This invasion helped to corroborate the adaptive value of the rich chromosomal polymorphism of the species, as the same clinal patterns than those observed in the original Palaearctic area were reproduced in the colonized areas in a relatively short period of time. The rapid response of this polymorphism to environmental conditions makes it a good candidate to measure the effect of the global rising of temperatures on the genetic composition of populations. Indeed, the long-term variation of this polymorphism shows a general increase in the frequency of those inversions typical of low latitudes, with a corresponding decrease of those typical of populations closer to the poles. Although the mechanisms underlying these changes are not well understood, the system remains a valid tool to monitor the genetic impact of global warming on natural populations. Heredity ( 2009) 103, 364-367; doi: 10.1038/hdy.2009.86; published online 29 July 200
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