Finite Automata for the Sub- and Superword Closure of CFLs: Descriptional and Computational Complexity

We answer two open questions by (Gruber, Holzer, Kutrib, 2009) on the state-complexity of representing sub- or superword closures of context-free grammars (CFGs): (1) We prove a (tight) upper bound of $2^{\mathcal{O}(n)}$ on the size of nondeterministic finite automata (NFAs) representing the subword closure of a CFG of size $n$. (2) We present a family of CFGs for which the minimal deterministic finite automata representing their subword closure matches the upper-bound of $2^{2^{\mathcal{O}(n)}}$ following from (1). Furthermore, we prove that the inequivalence problem for NFAs representing sub- or superword-closed languages is only NP-complete as opposed to PSPACE-complete for general NFAs. Finally, we extend our results into an approximation method to attack inequivalence problems for CFGs

A survey of task-oriented crowdsourcing

Since the advent of artificial intelligence, researchers have been trying to create machines that emulate human behaviour. Back in the 1960s however, Licklider (IRE Trans Hum Factors Electron 4-11, 1960) believed that machines and computers were just part of a scale in which computers were on one side and humans on the other (human computation). After almost a decade of active research into human computation and crowdsourcing, this paper presents a survey of crowdsourcing human computation systems, with the focus being on solving micro-tasks and complex tasks. An analysis of the current state of the art is performed from a technical standpoint, which includes a systematized description of the terminologies used by crowdsourcing platforms and the relationships between each term. Furthermore, the similarities between task-oriented crowdsourcing platforms are described and presented in a process diagram according to a proposed classification. Using this analysis as a stepping stone, this paper concludes with a discussion of challenges and possible future research directions.This work is part-funded by ERDF-European Regional Development Fund through the COMPETE Programme (Operational Programme for Competitiveness) and by National Funds through the FCT-Fundacao para a Ciencia e a Tecnologia (Portuguese Foundation for Science and Technology) within the Ph.D. Grant SFRH/BD/70302/2010 and by the Projects AAL4ALL (QREN11495), World Search (QREN 13852) and FCOMP-01-0124-FEDER-028980 (PTDC/EEI-SII/1386/2012). The authors also thank Jane Boardman for her assistance proof reading the document.info:eu-repo/semantics/publishedVersio

Rapid, sensitive, type specific PCR detection of the E7 region of human papillomavirus type 16 and 18 from paraffin embedded sections of cervical carcinoma

Human papillomavirus (HPV) infection, and in particularly infection with HPVs 16 and 18, is a central carcinogenic factor in the uterine cervix. We established and optimized a PCR assay for the detection and discrimination of HPV types 16 and 18 in archival formaldehyde fixed and paraffin embedded (FFPE) sections of cervical cancer

Relative adrenal insufficiency and hemodynamic status in cardiopulmonary bypass surgery patients. A prospective cohort study

<p>Abstract</p> <p>Background</p> <p>The objectives of this study were to determine the risk factors for relative adrenal insufficiency in cardiopulmonary bypass patients and the impact on postoperative vasopressor requirements.</p> <p>Methods</p> <p>Prospective cohort study on cardiopulmonary bypass patients who received etomidate or not during anesthetic induction. Relative adrenal insufficiency was defined as a rise in serum cortisol ≤ 9 μg/dl after the administration of 250 μg of consyntropin. Plasma cortisol levels were measured preoperatively, immediately before, 30, 60, and 90 minutes after the administration of cosyntropin, and at 24 hours after surgery.</p> <p>Results</p> <p>120 elective cardiopulmonary bypass patients were included. Relative adrenal insufficiency (Δcortisol ≤9 μg/dl) incidence was 77.5%. 78 patients received etomidate and 69 (88%) of them developed relative adrenal insufficiency, (<it>P </it>< 0.001). Controlling for clinical characteristics with a propensity analysis, etomidate was the only independent risk factor associated with relative adrenal insufficiency (OR 6.55, CI 95%: 2.47-17.4; <it>P </it>< 0.001). Relative adrenal insufficiency patients showed more vasopressor requirements just after surgery (<it>P </it>= 0.04), and at 4 hours after surgery (<it>P </it>= 0.01). Pre and post-test plasma cortisol levels were inversely associated with maximum norepinephrine dose (ρ = -0.22, <it>P </it>= 0.02; ρ = -0.18, <it>P </it>= 0.05; ρ = -0.21, <it>P </it>= 0.02; and ρ = -0.22, <it>P </it>= 0.02, respectively).</p> <p>Conclusions</p> <p>Relative adrenal insufficiency in elective cardiopulmonary bypass patients may induce postoperative vasopressor dependency. Use of etomidate in these patients is a modifiable risk factor for the development of relative adrenal insufficiency that should be avoided.</p

Potential climatic transitions with profound impact on Europe

We discuss potential transitions of six climatic subsystems with large-scale impact on Europe, sometimes denoted as tipping elements. These are the ice sheets on Greenland and West Antarctica, the Atlantic thermohaline circulation, Arctic sea ice, Alpine glaciers and northern hemisphere stratospheric ozone. Each system is represented by co-authors actively publishing in the corresponding field. For each subsystem we summarize the mechanism of a potential transition in a warmer climate along with its impact on Europe and assess the likelihood for such a transition based on published scientific literature. As a summary, the ‘tipping’ potential for each system is provided as a function of global mean temperature increase which required some subjective interpretation of scientific facts by the authors and should be considered as a snapshot of our current understanding. <br/

Thermodynamic State Ensemble Models of cis-Regulation

A major goal in computational biology is to develop models that accurately predict a gene's expression from its surrounding regulatory DNA. Here we present one class of such models, thermodynamic state ensemble models. We describe the biochemical derivation of the thermodynamic framework in simple terms, and lay out the mathematical components that comprise each model. These components include (1) the possible states of a promoter, where a state is defined as a particular arrangement of transcription factors bound to a DNA promoter, (2) the binding constants that describe the affinity of the protein–protein and protein–DNA interactions that occur in each state, and (3) whether each state is capable of transcribing. Using these components, we demonstrate how to compute a cis-regulatory function that encodes the probability of a promoter being active. Our intention is to provide enough detail so that readers with little background in thermodynamics can compose their own cis-regulatory functions. To facilitate this goal, we also describe a matrix form of the model that can be easily coded in any programming language. This formalism has great flexibility, which we show by illustrating how phenomena such as competition between transcription factors and cooperativity are readily incorporated into these models. Using this framework, we also demonstrate that Michaelis-like functions, another class of cis-regulatory models, are a subset of the thermodynamic framework with specific assumptions. By recasting Michaelis-like functions as thermodynamic functions, we emphasize the relationship between these models and delineate the specific circumstances representable by each approach. Application of thermodynamic state ensemble models is likely to be an important tool in unraveling the physical basis of combinatorial cis-regulation and in generating formalisms that accurately predict gene expression from DNA sequence