Shared Information -- New Insights and Problems in Decomposing Information in Complex Systems

How can the information that a set ${X_{1},...,X_{n}}$ of random variables contains about another random variable $S$ be decomposed? To what extent do different subgroups provide the same, i.e. shared or redundant, information, carry unique information or interact for the emergence of synergistic information? Recently Williams and Beer proposed such a decomposition based on natural properties for shared information. While these properties fix the structure of the decomposition, they do not uniquely specify the values of the different terms. Therefore, we investigate additional properties such as strong symmetry and left monotonicity. We find that strong symmetry is incompatible with the properties proposed by Williams and Beer. Although left monotonicity is a very natural property for an information measure it is not fulfilled by any of the proposed measures. We also study a geometric framework for information decompositions and ask whether it is possible to represent shared information by a family of posterior distributions. Finally, we draw connections to the notions of shared knowledge and common knowledge in game theory. While many people believe that independent variables cannot share information, we show that in game theory independent agents can have shared knowledge, but not common knowledge. We conclude that intuition and heuristic arguments do not suffice when arguing about information.Comment: 20 page

Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

As human activity in the Arctic increases, so does the risk of hydrocarbon pollution events. On site bioremediation of contaminated soil is the only feasible clean up solution in these remote areas, but degradation rates vary widely between bioremediation treatments. Most previous studies have focused on the feasibility of on site clean-up and very little attention has been given to the microbial and functional communities involved and their ecology. Here, we ask the question: which microorganisms and functional genes are abundant and active during hydrocarbon degradation at cold temperature? To answer this question, we sequenced the soil metagenome of an ongoing bioremediation project in Alert, Canada through a time course. We also used reverse-transcriptase real-time PCR (RT-qPCR) to quantify the expression of several hydrocarbon-degrading genes. Pseudomonas species appeared as the most abundant organisms in Alert soils right after contamination with diesel and excavation (t = 0) and one month after the start of the bioremediation treatment (t = 1m), when degradation rates were at their highest, but decreased after one year (t = 1y), when residual soil hydrocarbons were almost depleted. This trend was also reflected in hydrocarbon degrading genes, which were mainly affiliated with Gammaproteobacteria at t = 0 and t = 1m and with Alphaproteobacteria and Actinobacteria at t = 1y. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in Arctic biopile soils. Taken together, these results indicated that biopile treatment leads to major shifts in soil microbial communities, favoring aerobic bacteria that can degrade hydrocarbons

Variation in Prices Charged to Patients for Specialty Intraocular Lenses Inserted during Universally Covered Cataract Surgery

Patients often pay for specialty intraocular lenses (IOLs) for cataract surgery covered by universal insurance. This practice creates the potential for inequitable pricing where the medical service provider is also the retailer. We measured the variation in prices between cataract surgeons for the same IOL and associated testing.We telephoned every cataract surgeon in Ontario, Canada, and asked their price for the most common type of specialty IOL as a prospective patient. We measured the total prices quoted and variation between providers.We contacted 404 ophthalmologists. There were 256 that performed cataract surgery but 127 offered the most commonly employed specialty IOL and would provide a price to patients over the telephone. We obtained prices from all 127 ophthalmologists. Prices for the same lens and associated testing varied substantially between ophthalmologists from $358 to$2790 (median $615, interquartile range$528-$915). There was variation in all components of the total out-of-pocket price, including the price for the IOL itself, charges for uninsured eye measurements, and non-specific supplemental fees.Although cataract surgery is covered by public health insurance, some ophthalmologists charge much more than others for the same specialty IOL and associated testing. Greater access to price information and better regulatory control could help ensure patients receive fair value for out-of-pocket health expenses

Interplay between Fermi gamma-ray lines and collider searches

We explore the interplay between lines in the gamma-ray spectrum and LHC searches involving missing energy and photons. As an example, we consider a singlet Dirac fermion dark matter with the mediator for Fermi gamma-ray line at 130 GeV. A new chiral or local U(1) symmetry makes weak-scale dark matter natural and provides the axion or Z 0 gauge boson as the mediator connecting between dark matter and electroweak gauge bosons. In these models, the mediator particle can be produced in association with a monophoton at colliders and it produces large missing energy through the decays into a DM pair or ZZ; Z with at least one Z decaying into a neutrino pair. We adopt the monophoton searches with large missing energy at the LHC and impose the bounds on the coupling and mass of the mediator field in the models. We show that the parameter space of the Z 0 mediation model is already strongly constrained by the LHC 8TeV data, whereas a certain region of the parameter space away from the resonance in axion-like mediator models are bounded. We foresee the monophoton bounds on the Z 0 and axion mediation models at the LHC 14 TeV

Accretion Disks Around Black Holes: Twenty Five Years Later

We study the progress of the theory of accretion disks around black holes in last twenty five years and explain why advective disks are the best bet in explaining varied stationary and non-stationary observations from black hole candidates. We show also that the recently proposed advection dominated flows are incorrect.Comment: 30 Latex pages including figures. Kluwer Style files included. Appearing in `Observational Evidence for Black Holes in the Universe', ed. Sandip K. Chakrabarti, Kluwer Academic Publishers (DORDRECHT: Holland

Shear Strength Parameters of Improved Peat by Chemical Stabilizer.

The present research aimed to discuss the applicability of cationic grouts in geotechnical engineering. The effects of several cationic stabilizers such as monovalent (sodium silicate), divalent (calcium oxide and calcium chloride), and trivalent (aluminum hydroxide) were investigated on shear strength improvement of tropical peat samples. The unconfined compressive strength (UCS) tests were performed after the time frame of 7, 21, and 30 days as curing time, respectively. Apart from the physicochemical characteristics of the stabilized peat, scanning electron microscopy and energy-dispersive X-ray spectroscopy tests were also carried out to study the ongoing microstructural changes. It is to be noted that the shear strength values for peat samples rose to 8, 6, 6, and 4 % of sodium silicate, calcium oxide, calcium chloride, and aluminum hydroxide, respectively. The highest observed UCS outcome is the one taken from the calcium oxide where the UCS of treated peat after 30-day curing time increased to 76 kPa. The strength changes resulted from the various cationic stabilizers can best be explained via the consideration within the mineralogical composition as well as those physicochemical changes happening in the peat

Future therapeutic targets in rheumatoid arthritis?

Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by persistent joint inflammation. Without adequate treatment, patients with RA will develop joint deformity and progressive functional impairment. With the implementation of treat-to-target strategies and availability of biologic therapies, the outcomes for patients with RA have significantly improved. However, the unmet need in the treatment of RA remains high as some patients do not respond sufficiently to the currently available agents, remission is not always achieved and refractory disease is not uncommon. With better understanding of the pathophysiology of RA, new therapeutic approaches are emerging. Apart from more selective Janus kinase inhibition, there is a great interest in the granulocyte macrophage-colony stimulating factor pathway, Bruton's tyrosine kinase pathway, phosphoinositide-3-kinase pathway, neural stimulation and dendritic cell-based therapeutics. In this review, we will discuss the therapeutic potential of these novel approaches

Mapping patterns of complementary and alternative medicine use in cancer: An explorative cross-sectional study of individuals with reported positive "exceptional" experiences

<p>Abstract</p> <p>Background</p> <p>While the use of complementary and alternative medicine (CAM) among cancer patients is common and widespread, levels of commitment to CAM vary. "Committed" CAM use is important to investigate, as it may be associated with elevated risks and benefits, and may affect use of biomedically-oriented health care (BHC). Multiple methodological approaches were used to explore and map patterns of CAM use among individuals postulated to be committed users, voluntarily reporting exceptional experiences associated with CAM use after cancer diagnosis.</p> <p>Method</p> <p>The verbatim transcripts of thirty-eight unstructured interviews were analyzed in two steps. First, manifest content analysis was used to elucidate and map participants' use of CAM, based on the National Center for Complementary Medicine (NCCAM)'s classification system. Second, patterns of CAM use were explored statistically using principal component analysis.</p> <p>Findings</p> <p>The 38 participants reported using a total of 274 specific CAM (median = 4) consisting of 148 different therapeutic modalities. Most reported therapies could be categorized using the NCCAM taxonomy (n = 224). However, a significant number of CAM therapies were not consistent with this categorization (n = 50); consequently, we introduced two additional categories: <it>Spiritual/health literature </it>and <it>Treatment centers</it>. The two factors explaining the largest proportion of variation in CAM usage patterns were a) number of CAM modalities used and b) a category preference for <it>Energy therapies </it>over the categories <it>Alternative Medical Systems </it>and <it>Treatment centers </it>or vice versa.</p> <p>Discussion</p> <p>We found considerable heterogeneity in patterns of CAM use. By analyzing users' own descriptions of CAM in relation to the most commonly used predefined professional taxonomy, this study highlights discrepancies between user and professional conceptualizations of CAM not previously addressed. Beyond variations in users' reports of CAM, our findings indicate some patterns in CAM usage related to number of therapies used and preference for different CAM categories.</p

Mathematical model of a telomerase transcriptional regulatory network developed by cell-based screening: analysis of inhibitor effects and telomerase expression mechanisms

Cancer cells depend on transcription of telomerase reverse transcriptase (TERT). Many transcription factors affect TERT, though regulation occurs in context of a broader network. Network effects on telomerase regulation have not been investigated, though deeper understanding of TERT transcription requires a systems view. However, control over individual interactions in complex networks is not easily achievable. Mathematical modelling provides an attractive approach for analysis of complex systems and some models may prove useful in systems pharmacology approaches to drug discovery. In this report, we used transfection screening to test interactions among 14 TERT regulatory transcription factors and their respective promoters in ovarian cancer cells. The results were used to generate a network model of TERT transcription and to implement a dynamic Boolean model whose steady states were analysed. Modelled effects of signal transduction inhibitors successfully predicted TERT repression by Src-family inhibitor SU6656 and lack of repression by ERK inhibitor FR180204, results confirmed by RT-QPCR analysis of endogenous TERT expression in treated cells. Modelled effects of GSK3 inhibitor 6-bromoindirubin-3′-oxime (BIO) predicted unstable TERT repression dependent on noise and expression of JUN, corresponding with observations from a previous study. MYC expression is critical in TERT activation in the model, consistent with its well known function in endogenous TERT regulation. Loss of MYC caused complete TERT suppression in our model, substantially rescued only by co-suppression of AR. Interestingly expression was easily rescued under modelled Ets-factor gain of function, as occurs in TERT promoter mutation. RNAi targeting AR, JUN, MXD1, SP3, or TP53, showed that AR suppression does rescue endogenous TERT expression following MYC knockdown in these cells and SP3 or TP53 siRNA also cause partial recovery. The model therefore successfully predicted several aspects of TERT regulation including previously unknown mechanisms. An extrapolation suggests that a dominant stimulatory system may programme TERT for transcriptional stability