Proof theory for lattice-ordered groups

Proof-theoretic methods are developed and exploited to establish properties of the variety of lattice-ordered groups. In particular, a hypersequent calculus with a cut rule is used to provide an alternative syntactic proof of the generation of the variety by the lattice-ordered group of automorphisms of the real number chain. Completeness is also established for an analytic (cut-free) hypersequent calculus using cut elimination and it is proved that the equational theory of the variety is co-NP complete.

Comparison of multiplex ligation-dependent probe amplification and real-time PCR accuracy for gene copy number quantification using the beta-defensin locus

The reliable quantification of gene copy number variations is a precondition for future investigations regarding their functional relevance. To date, there is no generally accepted gold standard method for copy number quantification, and methods in current use have given inconsistent results in selected cohorts. In this study, we compare two methods for copy number quantification. beta-defensin gene copy numbers were determined in parallel in 80 genomic DNA samples by real-time PCR and multiplex ligation-dependent probe amplification (MLPA). The pyrosequencing-based paralog ratio test (PPRT) was used as a standard of comparison in 79 out of 80 samples. Realtime PCR and MPLA results confirmed concordant DEFB4, DEFB103A, and DEFB104A copy numbers within samples. These two methods showed identical results in 32 out of 80 samples; 29 of these 32 samples comprised four or fewer copies. The coefficient of variation of MLPA is lower compared with PCR. In addition, the consistency between MLPA and PPRT is higher than either PCR/MLPA or PCR/PPRT consistency. In summary, these results suggest that MLPA is superior to real-time PCR in beta-defensin copy number quantification.

The word-length effect in acquired alexia, and real and virtual hemianopia

A word-length effect is often described in pure alexia, with reading time proportional to the number of letters in a word. Given the frequent association of right hemianopia with pure alexia, it is uncertain whether and how much of the word-length effect may be attributable to the hemifield loss. To isolate the contribution of the visual field defect, we simulated hemianopia in healthy subjects with a gaze-contingent paradigm during an eye-tracking experiment. We found a minimal word-length effect of 14 ms/letter for full-field viewing, which increased to 38 ms/letter in right hemianopia and to 31 ms/letter in left hemianopia. We found a correlation between mean reading time and the slope of the word-length effect in hemianopic conditions. The 95% upper prediction limits for the word-length effect were 51 ms/letter in subjects with full visual fields and 161 ms/letter with simulated right hemianopia. These limits, which can be considered diagnostic criteria for an alexic word-length effect, were consistent with the reading performance of six patients with diagnoses based independently on perimetric and imaging data: two patients with probable hemianopic dyslexia, and four with alexia and lesions of the left fusiform gyrus, two with and two without hemianopia. Two of these patients also showed reduction of the word-length effect over months, one with and one without a reading rehabilitation program. Our findings clarify the magnitude of the word-length effect that originates from hemianopia alone, and show that the criteria for a word-length effect indicative of alexia differ according to the degree of associated hemifield loss.

Learning real-world stimuli in a neural network with spike-driven synaptic dynamics

We present a model of spike-driven synaptic plasticity inspired by experimental observations and motivated by the desire to build an electronic hardware device that can learn to classify complex stimuli in a semisupervised fashion. During training, patterns of activity are sequentially imposed on the input neurons, and an additional instructor signal drives the output neurons toward the desired activity. The network is made of integrate-and-fire neurons with constant leak and a floor. The synapses are bistable, and they are modified by the arrival of presynaptic spikes. The sign of the change is determined by both the depolarization and the state of a variable that integrates the postsynaptic action potentials. Following the training phase, the instructor signal is removed, and the output neurons are driven purely by the activity of the input neurons weighted by the plastic synapses. In the absence of stimulation, the synapses preserve their internal state indefinitely. Memories are also very robust to the disruptive action of spontaneous activity. A network of 2000 input neurons is shown to be able to classify correctly a large number (thousands) of highly overlapping patterns (300 classes of preprocessed Latex characters, 30 patterns per class, and a subset of the NIST characters data set) and to generalize with performances that are better than or comparable to those of artificial neural networks. Finally we show that the synaptic dynamics is compatible with many of the experimental observations on the induction of long-term modifications (spike-timing-dependent plasticity and its dependence on both the postsynaptic depolarization and the frequency of pre- and postsynaptic neurons).

Reliable gene expression measurements from degraded RNA by quantitative real-time PCR depend on short amplicons and a proper normalization

Quantitative reverse transcriptase real-time PCR (QRT-PCR) is a robust method to quantitate RNA abundance. The procedure is highly sensitive and reproducible as long as the initial RNA is intact. However, breaks in the RNA due to chemical or enzymatic cleavage may reduce the number of RNA molecules that contain intact amplicons. As a consequence, the number of molecules available for amplification decreases. We determined the relation between RNA fragmentation and threshold values (Ct values) in subsequent QRT-PCR for four genes in an experimental model of intact and partially hydrolyzed RNA derived from a cell line and we describe the relation between RNA integrity, amplicon size and Ct values in this biologically homogenous system. We demonstrate that degradation-related shifts of Ct values can be compensated by calculating delta Ct values between test genes and the mean values of several control genes. These delta Ct values are less sensitive to fragmentation of the RNA and are unaffected by varying amounts of input RNA. The feasibility of the procedure was demonstrated by comparing Ct values from a larger panel of genes in intact and in partially degraded RNA. We compared Ct values from intact RNA derived from well-preserved tumor material and from fragmented RNA derived from formalin-fixed, paraffin-embedded (FFPE) samples of the same tumors. We demonstrate that the relative abundance of gene expression can be based on FFPE material even when the amount of RNA in the sample and the extent of fragmentation are not known.

Real-World Energy Measurements of a Wireless Mesh Network

Over the past several years the topics of energy consumption and energy harvesting have gained significant importance as a means for improved operation of wireless sensor and mesh networks. Energy-awareness of operation is especially relevant for application scenarios from the domain of environmental monitoring in hard to access areas. In this work we reflect upon our experiences with a real-world deployment of a wireless mesh network. In particular, a comprehensive study on energy measurements collected over several weeks during the summer and the winter period in a network deployment in the Swiss Alps is presented. Energy performance is monitored and analysed for three system components, namely, mesh node, battery and solar panel module. Our findings cover a number of aspects of energy consumption, including the amount of load consumed by a mesh node, the amount of load harvested by a solar panel module, and the dependencies between these two. With our work we aim to shed some light on energy-aware network operation and to help both users and developers in the planning and deployment of a new wireless (mesh) network for environmental research.

A Restriction-Centered Theory of Reasoning and Computation to materialize a Web 3.0

Researchers suggest that personalization on the Semantic Web adds up to a Web 3.0 eventually. In this Web, personalized agents process and thus generate the biggest share of information rather than humans. In the sense of emergent semantics, which supplements traditional formal semantics of the Semantic Web, this is well conceivable. An emergent Semantic Web underlying fuzzy grassroots ontology can be accomplished through inducing knowledge from users' common parlance in mutual Web 2.0 interactions [1]. These ontologies can also be matched against existing Semantic Web ontologies, to create comprehensive top-level ontologies. On the Web, if augmented with information in the form of restrictions andassociated reliability (Z-numbers) [2], this collection of fuzzy ontologies constitutes an important basis for an implementation of Zadeh's restriction-centered theory of reasoning and computation (RRC) [3]. By considering real world's fuzziness, RRC differs from traditional approaches because it can handle restrictions described in natural language. A restriction is an answer to a question of the value of a variable such as the duration of an appointment. In addition to mathematically well-defined answers, RRC can likewise deal with unprecisiated answers as "about one hour." Inspired by mental functions, it constitutes an important basis to leverage present-day Web efforts to a natural Web 3.0. Based on natural language information, RRC may be accomplished with Z-number calculation to achieve a personalized Web reasoning and computation. Finally, through Web agents' understanding of natural language, they can react to humans more intuitively and thus generate and process information.

Prometheus Framework for Fuzzy Information Retrieval in Semantic Spaces

This paper introduces a novel vision for further enhanced Internet of Things services. Based on a variety of data (such as location data, ontology-backed search queries, in- and outdoor conditions) the Prometheus framework is intended to support users with helpful recommendations and information preceding a search for context-aware data. Adapted from artificial intelligence concepts, Prometheus proposes user-readjusted answers on umpteen conditions. A number of potential Prometheus framework applications are illustrated. Added value and possible future studies are discussed in the conclusion.

Prometheus – Fuzzy Information Retrieval for Semantic Homes and Environments

This paper introduces a novel vision for further enhanced Internet of Things services. Based on a variety of data – such as location data, ontology-backed search queries, in- and outdoor conditions – the Prometheus framework is intended to support users with helpful recommendations and information preceding a search for context-aware data. Adapted from artificial intelligence concepts, Prometheus proposes user-readjusted answers on umpteen conditions. A number of potential Prometheus framework applications are illustrated. Added value and possible future studies are discussed in the conclusion.

Kubo relations and radiative corrections for lepton number washout

The rates for lepton number washout in extensions of the Standard Model containing right-handed neutrinos are key ingredients in scenarios for baryogenesis through leptogenesis. We relate these rates to real-time correlation functions at finite temperature, without making use of any particle approximations. The relations are valid to quadratic order in neutrino Yukawa couplings and to all orders in Standard Model couplings. They take into account all spectator processes, and apply both in the symmetric and in the Higgs phase of the electroweak theory. We use the relations to compute washout rates at next-to-leading order in g, where g denotes a Standard Model gauge or Yukawa coupling, both in the non-relativistic and in the relativistic regime. Even in the non-relativistic regime the parametrically dominant radiative corrections are only suppressed by a single power of g. In the non-relativistic regime radiative corrections increase the washout rate by a few percent at high temperatures, but they are of order unity around the weak scale and in the relativistic regime.

8p23 beta-defensin copy number determination by single-locus pseudogene-based paralog ratio tests risk bias due to low-frequency sequence variations.

BACKGROUND The copy number variation (CNV) in beta-defensin genes (DEFB) on human chromosome 8p23 has been proposed to contribute to the phenotypic differences in inflammatory diseases. However, determination of exact DEFB CN is a major challenge in association studies. Quantitative real-time PCR (qPCR), paralog ratio tests (PRT) and multiplex ligation-dependent probe amplification (MLPA) have been extensively used to determine DEFB CN in different laboratories, but inter-method inconsistencies were observed frequently. In this study we asked which one is superior among the three methods for DEFB CN determination. RESULTS We developed a clustering approach for MLPA and PRT to statistically correlate data from a single experiment. Then we compared qPCR, a newly designed PRT and MLPA for DEFB CN determination in 285 DNA samples. We found MLPA had the best convergence and clustering results of the raw data and the highest call rate. In addition, the concordance rates between MLPA or PRT and qPCR (32.12% and 37.99%, respectively) were unacceptably low with underestimated CN by qPCR. Concordance rate between MLPA and PRT (90.52%) was high but PRT systematically underestimated CN by one in a subset of samples. In these samples a sequence variant which caused complete PCR dropout of the respective DEFB cluster copies was found in one primer binding site of one of the targeted paralogous pseudogenes. CONCLUSION MLPA is superior to PRT and even more to qPCR for DEFB CN determination. Although the applied PRT provides in most cases reliable results, such a test is particularly sensitive to low-frequency sequence variations preferably accumulating in loci like pseudogenes which are most likely not under selective pressure. In the light of the superior performance of multiplex assays, the drawbacks of such single PRTs could be overcome by combining more test markers.

Verbalization of Dependencies Between Concepts Built Through Fuzzy Cognitive Maps

The new computing paradigm known as cognitive computing attempts to imitate the human capabilities of learning, problem solving, and considering things in context. To do so, an application (a cognitive system) must learn from its environment (e.g., by interacting with various interfaces). These interfaces can run the gamut from sensors to humans to databases. Accessing data through such interfaces allows the system to conduct cognitive tasks that can support humans in decision-making or problem-solving processes. Cognitive systems can be integrated into various domains (e.g., medicine or insurance). For example, a cognitive system in cities can collect data, can learn from various data sources and can then attempt to connect these sources to provide real time optimizations of subsystems within the city (e.g., the transportation system). In this study, we provide a methodology for integrating a cognitive system that allows data to be verbalized, making the causalities and hypotheses generated from the cognitive system more understandable to humans. We abstract a city subsystem—passenger flow for a taxi company—by applying fuzzy cognitive maps (FCMs). FCMs can be used as a mathematical tool for modeling complex systems built by directed graphs with concepts (e.g., policies, events, and/or domains) as nodes and causalities as edges. As a verbalization technique we introduce the restriction-centered theory of reasoning (RCT). RCT addresses the imprecision inherent in language by introducing restrictions. Using this underlying combinatorial design, our approach can handle large data sets from complex systems and make the output understandable to humans.

A certified plasmid reference material for the standardisation of BCR-ABL1 mRNA quantification by real-time quantitative PCR.

Serial quantification of BCR-ABL1 mRNA is an important therapeutic indicator in chronic myeloid leukaemia, but there is a substantial variation in results reported by different laboratories. To improve comparability, an internationally accepted plasmid certified reference material (CRM) was developed according to ISO Guide 34:2009. Fragments of BCR-ABL1 (e14a2 mRNA fusion), BCR and GUSB transcripts were amplified and cloned into pUC18 to yield plasmid pIRMM0099. Six different linearised plasmid solutions were produced with the following copy number concentrations, assigned by digital PCR, and expanded uncertainties: 1.08±0.13 × 10(6), 1.08±0.11 × 10(5), 1.03±0.10 × 10(4), 1.02±0.09 × 10(3), 1.04±0.10 × 10(2) and 10.0±1.5 copies/μl. The certification of the material for the number of specific DNA fragments per plasmid, copy number concentration of the plasmid solutions and the assessment of inter-unit heterogeneity and stability were performed according to ISO Guide 35:2006. Two suitability studies performed by 63 BCR-ABL1 testing laboratories demonstrated that this set of 6 plasmid CRMs can help to standardise a number of measured transcripts of e14a2 BCR-ABL1 and three control genes (ABL1, BCR and GUSB). The set of six plasmid CRMs is distributed worldwide by the Institute for Reference Materials and Measurements (Belgium) and its authorised distributors (https://ec.europa.eu/jrc/en/reference-materials/catalogue/; CRM code ERM-AD623a-f).