Combinatorial RNA Design: Designability and Structure-Approximating Algorithm

In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete characterizations for the structures that can be designed using restricted alphabets. Under a classic four-letter alphabet, we provide a complete characterization of designable structures without unpaired bases. When unpaired bases are allowed, we provide partial characterizations for classes of designable/undesignable structures, and show that the class of designable structures is closed under the stutter operation. Membership of a given structure to any of the classes can be tested in linear time and, for positive instances, a solution can be found in linear time. Finally, we consider a structure-approximating version of the problem that allows to extend bands (helices) and, assuming that the input structure avoids two motifs, we provide a linear-time algorithm that produces a designable structure with at most twice more base pairs than the input structure.Comment: CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy. LNCS, 201

Uncertainty Measurement for the Interval Type-2 Fuzzy Set

In this paper, two measures of uncertainty for interval type-2 fuzzy sets are presented, evaluated, compared and contrasted. Wu and Mendel regard the length of the type-reduced set as a measure of the uncertainty in an interval set. Green eld and John argue that the volume under the surface of the type-2 fuzzy set is a measure of the uncertainty relating to the set. For an interval type-2 fuzzy set, the volume measure is equivalent to the area of the footprint of uncertainty of the set. Experiments show that though the two measures give di erent results, there is considerable commonality between them. The concept of invariance under vertical translation is introduced; the uncertainty measure of a fuzzy set has the property of invariance under vertical translation if the value it generates remains constant under any vertical translation of the fuzzy set. It is left unresolved whether invariance under vertical translation is an essential property of a type-2 uncertainty measure

Fuzzy intelligence approach for modeling the migration of contaminants ina reservoir affected by AMD pollution

The Sancho Reservoir, located in the Huelva province (SW Spain), is supplied by the Meca River, which receives water contaminated by mining activities in Tharsis. This study focused on determining the relationship that temperature, pH, and electrical conductivity (EC) had with rainfall. The temperature, pH, and EC were simultaneously measured every 30 min by two probes suspended in the Sancho Reservoir. It was anticipated that the use of fuzzy logic and data mining would lead to a model that would show how the contaminant load evolved over space and time. Similar results were obtained for the two locations, except that the parameters had more outliers near the dam due to the greater distance from the contamination source. As expected, higher pH corresponded with lower EC, since, in the absence of chloride, sulphate was the principal anion. The dependency relationship of the variables as well as the cause–effect relationship with the rate of rainfall was more evident in the up-gradient sampling location than near the dam due to the different residence time and the transit time between the two points

Application of fuzzy logic to assess the quality of BPMN models

© Springer International Publishing AG, part of Springer Nature 2018. Modeling is the first stage in a Business Process’s (BP) lifecycle. A high-quality BP model is vital to the successful implementation, execution, and monitoring stages. Different works have evaluated BP models from a quality perspective. These works either used formal verification or a set of quality metrics. This paper adopts quality metric and targets models represented in Business Process Modeling and Notation (BPMN). It proposes an approach based on fuzzy logic along with a tool system developed under eclipse framework. The preliminary experimental evaluation of the proposed system shows encouraging results

Effects of habitat and land use on breeding season density of male Asian Houbara Chlamydotis macqueenii

Landscape-scale habitat and land-use influences on Asian Houbara Chlamydotis macqueenii (IUCN Vulnerable) remain unstudied, while estimating numbers of this cryptic, low-density, over-hunted species is challenging. In spring 2013, male houbara were recorded at 231 point counts, conducted twice, across a gradient of sheep density and shrub assemblages within 14,300 km² of the Kyzylkum Desert, Uzbekistan. Four sets of models related male abundance to: (1) vegetation structure (shrub height and substrate); (2) shrub assemblage; (3) shrub species composition (multidimensional scaling); (4) remote-sensed derived land-cover (GLOBCOVER, 4 variables). Each set also incorporated measures of landscape rugosity and sheep density. For each set, multi-model inference was applied to generalised linear mixed models of visit-specific counts that included important detectability covariates and point ID as a random effect. Vegetation structure received strongest support, followed by shrub species composition and shrub assemblage, with weakest support for the GLOBCOVER model set. Male houbara numbers were greater with lower mean shrub height, more gravel and flatter surfaces, but were unaffected by sheep density. Male density (mean 0.14 km-2, 95% CI, 0.12‒0.15) estimated by distance analysis differed substantially among shrub assemblages, being highest in vegetation dominated by Salsola rigida (0.22 [CI, 0.20‒0.25]), high in areas of S. arbuscula and Astragalus (0.14 [CI, 0.13‒0.16] and 0.15 [CI, 0.14‒0.17] respectively), lower (0.09 [CI, 0.08‒0.10]) in Artemisia and lowest (0.04 [CI, 0.04‒0.05]) in Calligonum. The study area was estimated to hold 1,824 males (CI: 1,645‒2,030). The spatial distribution of relative male houbara abundance, predicted from vegetation structure models, had the strongest correspondence with observed numbers in both model-calibration and the subsequent year’s data. We found no effect of pastoralism on male distribution but potential effects on nesting females are unknown. Density differences among shrub communities suggest extrapolation to estimate country- or range-wide population size must take account of vegetation composition

Alterations in the blood glucose, serum lipids and renal oxidative stress in diabetic rats by supplementation of onion (Allium cepa. Linn)

This study examined the anti-diabetic effect of onion (Allium cepa. Linn) in the streptozotocin (STZ)-induced diabetic rats. Male Sprague-Dawley rats were divided into normal rats fed control diet or supplemented with onion powder (7% w/w) and diabetic rats fed control diet or supplemented with onion powder. Diabetes was induced by a single injection of STZ (60 mg/kg, ip) in citrate buffer. The animals were fed each of the experimental diet for 5 weeks. Blood glucose levels of rats supplemented with onion were lower than those of rats fed control diet in the diabetic rats. Onion also decreased the total serum lipid, triglyceride, and atherogenic index and increased HDL-cholesterol/total cholesterol ratio in the diabetic rats. Glutathione peroxidase, glutathione reductase and glutathione S-transferase activities were high in the diabetic rats compared to normal rats and reverted to near-control values by onion. These results indicate that onion decreased blood glucose, serum lipid levels and reduced renal oxidative stress in STZ-induced diabetic rats and this effect might exert the anti-diabetic effect of onion

The logic of the future in quantum theory

According to quantum mechanics, statements about the future made by sentient beings like us are, in general, neither true nor false; they must satisfy a many-valued logic. I propose that the truth value of such a statement should be identified with the probability that the event it describes will occur. After reviewing the history of related ideas in logic, I argue that it gives an understanding of probability which is particularly satisfactory for use in quantum mechanics. I construct a lattice of future-tense propositions, with truth values in the interval $[0,1]$, and derive logical properties of these truth values given by the usual quantum-mechanical formula for the probability of a history

Quality of life and mortality from a nephrologist's view: a prospective observational study

<p>Abstract</p> <p>Background</p> <p>Although health-related quality of life (HRQOL) is a potential independent predictor of mortality, nephrologists have shown little interest in HRQOL with respect to mortality in chronic kidney disease (CKD). The aim of this article is to evaluate the impact of HRQOL on mortality in the elderly, who are likely to develop or already have CKD.</p> <p>Methods</p> <p>Among 1,000 randomly sampled participants aged more than 65 years (sourced from the Korean Longitudinal Study on Health and Ageing), 944 subjects were evaluated for HRQOL. HRQOL was assessed using a 36-item Short-Form health survey (SF36). A cumulative survival rate was calculated according to tertiles of SF36 scores and classified by the presence of CKD (estimated GFR <60 ml/min/1.73 m²).</p> <p>Results</p> <p>Among 944 subjects, 46.6% had CKD. CKD patients had lower total and physical component scores compared with subjects without CKD. The 3-year cumulative survival rate was 90.0% (non-CKD vs. CKD: 92.6% vs. 87.4%, <it>P </it>= 0.005 by log rank test). After adjusting for multiple variables, a reduced SF36 score (physical and mental components) was a strong predictor of all-cause mortality. Physical components were consistently able to predict mortality after CKD classification, but mental components were statistically significant only in the CKD group.</p> <p>Conclusion</p> <p>In addition to traditional risk factors of mortality, nephrologists should be aware of HRQOL as a predictor of mortality and should make efforts to improve HRQOL in CKD patients.</p

Interval type-2 fuzzy modelling and stochastic search for real-world inventory management

Real-world systems present a variety of challenges to the modeller, not least of which is the problem of uncertainty inherent in their operation. In this research, an interval type-2 fuzzy model is applied to a real-world problem, the goal being to discover a suitable optimisation configuration to enable a search for an inventory plan using the model. To this end, a series of simulated annealing configurations and the interval type-2 fuzzy model were used to search for appropriate inventory plans for a large-scale real-world problem. A further set of tests were conducted in which the performance of the interval type-2 fuzzy model was compared with a corresponding type-1 fuzzy model. In these tests the results were inconclusive, though, as will be discussed there are many ways in which type-2 fuzzy logic can be exploited to demonstrate its advantages over a type-1 approach. To conclude, in this research we have shown that a combination of interval type-2 fuzzy logic and simulated annealing is a logical choice for inventory management modelling and inventory plan search, and propose that the benefits that a type-2 model offers, can make it preferable to a corresponding type-1 system