When resources collide: Towards a theory of coincidence in information spaces

This paper is an attempt to lay out foundations for a general theory of coincidence in information spaces such as the World Wide Web, expanding on existing work on bursty structures in document streams and information cascades. We elaborate on the hypothesis that every resource that is published in an information space, enters a temporary interaction with another resource once a unique explicit or implicit reference between the two is found. This thought is motivated by Erwin Shroedingers notion of entanglement between quantum systems. We present a generic information cascade model that exploits only the temporal order of information sharing activities, combined with inherent properties of the shared information resources. The approach was applied to data from the world's largest online citizen science platform Zooniverse and we report about findings of this case study

The role of DNA methylation in cancer development.

Epigenetic modifications include DNA methylation and covalent modification of histones. These alterations are reversible but very stable and exert a significant impact on the regulation of gene expression. Changes in methylation of promoter or first exon may mimic the effect of mutations of various tumor suppressor genes (TSGs) or protooncogenes. Carcinogenesis can also result from aberrations in genomic DNA methylation that include hypermethylation and hypomethylation of promoter or first exon of cancer-related genes. Hypermethylation of promoter of various TSGs causes their transcriptional silencing. However, hypomethylation of regulatory DNA sequences activates transcription of protooncogenes, retrotransposons, as well as genes encoding proteins involved in genomic instability and malignant cell metastasis. The methylation of genomic DNA in malignant cells is catalyzed by DNA methyltransferases DNMT1 and DNMT3B, revealing significantly elevated expression in different types of cancers. The reversibility of hypermethylation can be used as target of therapeutic treatment in cancer. DNMT 1 and DNMT3B inhibitors including 5-Aza-2'-deoxycytidine and antisense oligonucleotides have been applied in clinical trials of such treatment. Identification of aberrations of DNA methylation in cancer cells is a new field of investigation in carcinogenesis. We believe that epigenetic cancer diagnostic and therapy will be achieved in the next decades

How Many and What Types of SPARQL Queries can be Answered through Zero-Knowledge Link Traversal?

The current de-facto way to query the Web of Data is through the SPARQL protocol, where a client sends queries to a server through a SPARQL endpoint. Contrary to an HTTP server, providing and maintaining a robust and reliable endpoint requires a significant effort that not all publishers are willing or able to make. An alternative query evaluation method is through link traversal, where a query is answered by dereferencing online web resources (URIs) at real time. While several approaches for such a lookup-based query evaluation method have been proposed, there exists no analysis of the types (patterns) of queries that can be directly answered on the live Web, without accessing local or remote endpoints and without a-priori knowledge of available data sources. In this paper, we first provide a method for checking if a SPARQL query (to be evaluated on a SPARQL endpoint) can be answered through zero-knowledge link traversal (without accessing the endpoint), and analyse a large corpus of real SPARQL query logs for finding the frequency and distribution of answerable and non-answerable query patterns. Subsequently, we provide an algorithm for transforming answerable queries to SPARQL-LD queries that bypass the endpoints. We report experimental results about the efficiency of the transformed queries and discuss the benefits and the limitations of this query evaluation method.Comment: Preprint of paper accepted for publication in the 34th ACM/SIGAPP Symposium On Applied Computing (SAC 2019

Expression of HOXA-10 and HOXA-11 in the endometria of women with idiopathic infertility

In fertile women, HOXA-10 and HOXA-11 expression rises during the luteal phase, with the peak occurring during the implantation window, and stays at a high level until the end of the cycle. We evaluated the transcript and protein levels of HOXA-10 and HOXA-11 in the endometria of patients with idiopathic infertility (n = 15) and control patients (n = 10). The amounts of mRNA were determined by reverse transcription and real-time quantitative PCR. The protein levels were evaluated by Western blotting analysis. Using immunohistochemical techniques, we compared the localization of HOXA-10 and HOXA-11 proteins in the implantation window between the study and control groups. We observed statistically significantly decreased HOXA-10 and HOXA-11 transcript levels (p = 0.003, p = 0.012 respectively) in infertile patients compared to controls. There was no significant decrease in HOXA-10 protein levels between these groups (p = 0.074). However, we observed a significantly higher level of HOXA-11 protein in the endometria of infertile patients compared to controls (p = 0.015). HOXA-10 and HOXA-11 proteins were localized in the nuclei of the endometrial stromal cells. Immunohistochemical analyses did not reveal differences between amounts of HOXA-10 and HOXA-11 protein levels in infertility and control groups. Our results suggest that HOXA-10 and HOXA-11 gene expression in the endometrium during the implantation window may not be altered in patients with idiopathic infertility. (Folia Histochemica et Cytobiologica 2011; Vol. 49, No. 1, pp. 111–118

Coloring random graphs

We study the graph coloring problem over random graphs of finite average connectivity $c$. Given a number $q$ of available colors, we find that graphs with low connectivity admit almost always a proper coloring whereas graphs with high connectivity are uncolorable. Depending on $q$, we find the precise value of the critical average connectivity $c_q$. Moreover, we show that below $c_q$ there exist a clustering phase $c\in [c_d,c_q]$ in which ground states spontaneously divide into an exponential number of clusters and where the proliferation of metastable states is responsible for the onset of complexity in local search algorithms.Comment: 4 pages, 1 figure, version to app. in PR

A law of large numbers approximation for Markov population processes with countably many types

When modelling metapopulation dynamics, the influence of a single patch on the metapopulation depends on the number of individuals in the patch. Since the population size has no natural upper limit, this leads to systems in which there are countably infinitely many possible types of individual. Analogous considerations apply in the transmission of parasitic diseases. In this paper, we prove a law of large numbers for rather general systems of this kind, together with a rather sharp bound on the rate of convergence in an appropriately chosen weighted $\ell_1$ norm.Comment: revised version in response to referee comments, 34 page

Sleep deprivation causes memory deficits by negatively impacting neuronal connectivity in hippocampal area CA1

Brief periods of sleep loss have long-lasting consequences such as impaired memory consolidation. Structural changes in synaptic connectivity have been proposed as a substrate of memory storage. Here, we examine the impact of brief periods of sleep deprivation on dendritic structure. In mice, we find that five hours of sleep deprivation decreases dendritic spine numbers selectively in hippocampal area CA1 and increased activity of the filamentous actin severing protein cofilin. Recovery sleep normalizes these structural alterations. Suppression of cofilin function prevents spine loss, deficits in hippocampal synaptic plasticity, and impairments in long-term memory caused by sleep deprivation. The elevated cofilin activity is caused by cAMP-degrading phosphodiesterase-4A5 (PDE4A5), which hampers cAMP-PKA-LIMK signaling. Attenuating PDE4A5 function prevents changes in cAMP-PKA-LIMK-cofilin signaling and cognitive deficits associated with sleep deprivation. Our work demonstrates the necessity of an intact cAMP-PDE4-PKA-LIMK-cofilin activation-signaling pathway for sleep deprivation-induced memory disruption and reduction in hippocampal spine density