Miracle-dz/UniFAR-FTUs huggingface dataset:
Weak alternating automata are not that weak

Automata on infinite words are used for specification and verification of nonterminating programs. Different types of automata induce different levels of expressive power, of succinctness, and of complexity. Alternating automata have both existential and universal branching modes and are particularly suitable for specification of programs. In a weak alternating automaton, the state space is partitioned into partially ordered sets, and the automaton can proceed from a certain set only to smaller sets. Reasoning about weak alternating automata is easier than reasoning about alternating automata with no restricted structure. Known translations of alternating automata to weak alternating automata involve determinization, and therefore involve a double-exponential blow-up. In this paper we describe a quadratic translation, which circumvents the need for determinization, of Buchi (1962) and co-Buchi alternating automata to weak alternating automata. Beyond the independent interest of such a translation, it gives rise to a simple complementation algorithm for nondeterministic Buchi automata.
A Grammar-Based Modeling of Supply Chain Process

This paper proposed a modeling method applied to representation of the supply chain process which is prerequisite to supply chain process performance measurement and optimization. This method integrates the grammatical approach with some models that can represent dynamic supply chain process. The design of the modeling method includes four parts: the lexicon, the grammar elements, the graphical symbols and the connection rules of the grammar elements and their graphical symbols. Especially, modeling supply chain process in this way can make it possible to measure performance of supply chain process using standard performance metrics in SCOR (supply chain operations reference) model. An example is illustrated to verify the practicability of the proposed method
Internal Control System in Enterprise Management: Analysis and Interaction Matrices

Marina Viktorovna Romanova5, Alexei Valerievich Yumashev6 This study is aimed at the development of a guideline for analysis of the economic activity of an enterprise to control and ensure the interaction of tasks and functions of management in the current and strategic aspects in the conditions of innovative development. The proprietary methodology for enterprise management control system formation is developed. The concept of matrices of analysis and interaction between the functions of the enterprise management is introduced. The matrix of operational control and management, the matrix of strategic control and management, the matrix of integrated control and management are considered by the authors. The concept of enterprise management control is considered herein. The objectives of the management control system in the modern economy are also described. The key role of control in the implementation of the current and strategic objectives of the enterprise management is substantiated. The proposals are formulated to improve the control function at the enterprise with the help of new information technologies. Based on the proprietary methodology of matrix analysis and interaction of objectives and functions of the enterprise management system, the algorithm for the formation of a system of integrated flexible internal control is developed.
High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer

Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, with mutational inactivation of the remaining allele. We exploited the normal allele-specific differential methylation of the M6P/IGF2R intron 2 CpG island to rapidly evaluate potential LOH in ovarian cancers, since every normal individual is informative. To this end, we developed a method for bisulfite modification of genomic DNA in 96-well format that allows for rapid methylation profiling. We identified ovarian cancers with M6P/IGF2R LOH, but unexpectedly also found frequent abnormal acquisition of methylation on the paternally inherited allele at intron 2. These results demonstrate the utility of our high-throughput method of bisulfite modification for analysis of large sample numbers. They further show that the methylation status of the intron 2 CpG island may be a useful indicator of LOH and biomarker of disease.
The Street Network Evolution of Crowdsourced Maps: OpenStreetMap in Germany 2007-2011

The OpenStreetMap (OSM) project is a prime example in the field of Volunteered Geographic Information (VGI). Worldwide, several hundred thousand people are currently contributing information to the “free” geodatabase. However, the data contributions show a geographically heterogeneous pattern around the globe. Germany counts as one of the most active countries in OSM; thus, the German street network has undergone an extensive development in recent years. The question that remains is this: How does the street network perform in a relative comparison with a commercial dataset? By means of a variety of studies, we show that the difference between the OSM street network for car navigation in Germany and a comparable proprietary dataset was only 9% in June 2011. The results of our analysis regarding the entire street network showed that OSM even exceeds the information provided by the proprietary dataset by 27%. Further analyses show on what scale errors can be reckoned with in the topology of the street network, and the completeness of turn restrictions and street name information. In addition to the analyses conducted over the past few years, projections have additionally been made about the point in time by which the OSM dataset for Germany can be considered “complete” in relative comparison to a commercial dataset.
A Likelihood‐Based Trait‐Model‐Free Approach for Linkage Detection of Binary Trait

Summary Trait‐model‐free (or “allele‐sharing”) approach to linkage analysis is a popular tool in genetic mapping of complex traits, because of the absence of explicit assumptions about the underlying mode of inheritance of the trait. The likelihood framework introduced by Kong and Cox (1997, American Journal of Human Genetics 61, 1179–1188) allows calculation of accurate p‐values and LOD scores to test for linkage between a genomic region and a trait. Their method relies on the specification of a model for the trait‐dependent segregation of marker alleles at a genomic region linked to the trait. Here we propose a new such model that is motivated by the desire to extract as much information as possible from extended pedigrees containing data from individuals related over several generations. However, our model is also applicable to smaller pedigrees, and has some attractive features compared with existing models ( Kong and Cox, 1997 ), including the fact that it incorporates information on both affected and unaffected individuals. We illustrate the proposed model on simulated and real data, and compare its performance with the existing approach ( Kong and Cox, 1997 ). The proposed approach is implemented in the program lm_ibdtests within the framework of MORGAN 2.8 (http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml).
Higher-order rank analysis for web structure

In this paper, we propose a method for the structural analysis of Web sites.The Web has become one of the most widely used media for electronic information because of its great flexibility. However, this flexibility has led to complicated structures. A structure that differs from the typical structures in a Web site might confuse readers, thus reducing the effectiveness of the site. A method for detecting unusual structures would be useful for identifying such structures so that their impact can be studied and ways to improve Web site effectiveness developed.We viewed the Web as a directed graph, and introduced a higher-order rank based on the non-well-founded set theory. We then developed higher-order rank analysis for detecting irregularities, defined as structures which differ from the typical structure of a target site. To test the effectiveness of our method, we applied it to several Web sites in actual use, and succeeded in identifying irregular structures in the sites.
Discrete event system specification, synthesis, and optimization of low-power FPGA-based embedded systems

Discrete event system specification (DEVS) has been widely used within modeling and simulation to design, verify, and implement complex reactive systems. DEVS provides a robust formalism for designing systems using event-driven, state-based models in which timing information is explicitly defined. In this paper, we present an overview of a DEVS-based hardware design, synthesis, and optimization methodology. Within this approach, hardware DEVS (HDEVS) specifications can be synthesized to hardware, during which the event-driven model and explicit timing allow for an efficient hardware realization using globally asynchronous, locally synchronous design approach. Additionally, we present an optimization method for reducing power consumption through optimal frequency mapping and clock gating of individual components while ensuring system latency constraints are achieved. We further demonstrate the resulting power consumption savings for activity-driven forest fire and asthma health management applications targeting two low-power FPGA devices.
MHC-Peptide Complexes Conserved Hydrogen Bonds in Class II Mechanism That Does Not Require Specific Cutting Edge : HLA-DM Functions through a

HLA-DM catalyzes peptide dissociation and exchange in class II MHC molecules through a mechanism that has been proposed to involve the disruption of specific components of the conserved hydrogen bond network in MHC-peptide complexes. HLA-DR1 molecules with alanine substitutions at each of the six conserved H-bonding positions were expressed in cells, and susceptibility to DM catalytic activity was evaluated by measuring the release of CLIP. The mutants ␣N62A, ␣N69A, ␣R76A, and ␤H81A DR1 were fully susceptible to DM-mediated CLIP release, and ␤N82A resulted in spontaneous release of CLIP. Using recombinant soluble DR1 molecules, the amino acid ␤N82 was observed to contribute disproportionately in stabilizing peptide complexes. Remarkably, the catalytic potency of DM with each ␤-chain mutant was equal to or greater than that observed with wild-type DR1. Our results support the conclusion that no individual component of the conserved hydrogen bond network plays an essential role in the DM catalytic mechanism. C lass II MHC molecules initially assemble with the chaperone invariant chain (Ii) 4 followed by transport to endosomal compartments and proteolytic cleavage of Ii, leaving a fragment, CLIP, largely buried in the peptide-binding groove (1). HLA-DM catalyzes CLIP dissociation and peptide exchange reactions in class II molecules, accelerating the loading process for peptide Ags (2– 4) and editing the repertoire of peptides presented to CD4 ϩ T cells. DM is a non-polymorphic MHC class II protein that is structurally similar to other class II molecules (5). However, DM does not have the capacity to bind peptide Ags, and it functions as a chaperone-catalyst, stabilizing peptide-free (" empty ") class II molecules (6) and accelerating CLIP dissociation and peptide exchange through a mechanism that involves transient direct physical interaction with class II-peptide complexes. DM accelerates the rate of dissociation of all peptides (7), not just CLIP, but catalytic potency differs depending on the kinetic stability of the complex (7–10) and other less defined features of the complex (11–13). The capacity of DM to differentially " edit " peptide complexes has important biological implications through skew-ing of the repertoire of foreign and self-peptide complexes available for activation or tolerance induction in CD4 ϩ T cells. The structural basis for the DM catalytic mechanism remains poorly understood. The general orientation of the physical interaction between DM and substrate MHC class II molecules (i.e., HLA-DR) has been defined by using mutational and cross-linking approaches (14 –16). It is likely that DM preferentially …
Microevolution within a clonal population of pathogenic bacteria: recombination, gene duplication and horizontal genetic exchange in the opa gene family of Neisseria meningitidis

Opacity (Opa) proteins are a family of antigenically variable outer‐membrane proteins of Neisseria meningitidis. Even among clonally related epidemic meningococcal isolates, there is greater variation of Opa protein expression than can be accounted for by the opa gene repertoire of any individual strain. We characterized the opa genes of eight closely related Isolates of serogroup A N. meningitidis (subgroup IV‐1) from a recent meningitis epidemic in West Africa. DNA sequence analysis and Southern blot experiments indicated that changes occurred in the opa genes of these bacteria as they spread through the human population, over a relatively short period of time. Such changes in one or a few loci within a clonal population are referred to as microevolution. The distribution of sequences present in hypervariable (HV) regions of the opa genes suggests that duplication of all or part of opa genes into other opa loci changed the repertoire of Opa proteins that could be expressed. Additional variability in this gene family appears to have been introduced by horizontal exchange of opa sequences from other meningococcal strains and from Neisseria gonorrhoeae. These results indicate that processes of recombination and genetic exchange contributed to variability in major surface antigens of this clonal population of pathogenic bacteria.
The Effects of For-Profit Multihospital System Ownership on Hospital Financial and Operating Performance

The financial and operating performance of independent not-for-profit hospitals acquired by US for-profit multi-hospital systems in 10 Southern states between the years 1978 and 1982 was explored. The impact of system ownership on acquired hospitals was investigated by comparing the average financial performance of hospitals in the two years immediately prior to acquisition to the average for 1984 and 1985 and by comparing changes in the performance of acquired hospitals with changes in matched independent facilities. Findings suggest that for-profit multi-hospital systems were able to improve many of the financial and operating problems of acquired facilities. In comparison to independent not-for-profit hospitals, acquired hospitals were found to increase access to long-term debt, make improvements to plant and equipment, improve profitability, and increase efficiency to a greater extent. Prices in acquired hospitals rose more than those in independents and liquidity decreased to a greater extent.
A stochastic local volatility technique for TARN options

ABSTRACT Target Accumulation Redemption Notes (TARN) are financial derivatives which give their holders the right to receive periodic coupons until the accumulated sum of those ones reaches an agreed target. In this work, we solve a partial differential equations model for TARNs by a finite difference alternating directions method. We combine the numerical resolution with a stochastic local volatility technique and show the numerical results for a particular problem.
A Fusion of Multiple Classifiers Approach Based on Reliability function for Text Categorization

With the development of Internet and the rapid expansion of electronic resource, text classification technology is becoming an effective organization and management tool to deal with information. In this paper, a method for text categorization based on the fusion of multiple classifiers was presented, reliability function was introduction to select the text that hard to give determine by the main classifier, for these texts, multiple classifiers were used to give the determine which category the unlabeled documents belong to by voting. Experiments showed that the performance of text classification improved by the proposed method. Compared with single classifier, this method achieved better performance, only increasing a small amount of time than using single main classifier. Besides this, this method is more stable than using single classifier for text categorization task, especially when using different corpuses to check the performance of various methods.
Distributed algorithm for graph signal inpainting

We present a distributed and decentralized algorithm for graph signal inpainting. The previous work obtained a closed-form solution with matrix inversion. In this paper, we ease the computation by using a distributed algorithm, which solves graph signal inpainting by restricting each node to communicate only with its local nodes. We show that the solution of the distributed algorithm converges to the closed-form solution with the corresponding convergence speed. Experiments on online blog classification and temperature prediction suggest that the convergence speed of the proposed distributed algorithm is competitive with that of the centralized algorithm, especially when a graph tends to be regular. Since a distributed algorithm does not require to collect data to a center, it is more practical and efficient.
Transcriptome Analysis of the Intracellular Facultative Pathogen Piscirickettsia salmonis: Expression of Putative Groups of Genes Associated with Virulence and Iron Metabolism

The intracellular facultative bacteria Piscirickettsia salmonis is one of the most important pathogens of the Chilean aquaculture. However, there is a lack of information regarding the whole genomic transcriptional response according to different extracellular environments. We used next generation sequencing (NGS) of RNA (RNA-seq) to study the whole transcriptome of an isolate of P. salmonis (FAVET-INBIOGEN) using a cell line culture and a modified cell-free liquid medium, with or without iron supplementation. This was done in order to obtain information about the factors there are involved in virulence and iron acquisition. First, the isolate was grown in the Sf21 cell line; then, the bacteria were cultured into a cell-free liquid medium supplemented or not with iron. We identified in the transcriptome, genes associated with type IV secretion systems, genes related to flagellar structure assembly, several proteases and sigma factors, and genes related to the development of drug resistance. Additionally, we identified for the first time several iron-metabolism associated genes including at least two iron uptake pathways (ferrous iron and ferric iron uptake) that are actually expressed in the different conditions analyzed. We further describe putative genes that are related with the use and storage of iron in the bacteria, which have not been previously described. Several sets of genes related to virulence were expressed in both the cell line and cell-free culture media (for example those related to flagellar structure; such as basal body, MS-ring, C-ring, proximal and distal rod, and filament), which may play roles in other basic processes rather than been restricted to virulence.
Properties and Substrate Specificity of RppA, a Chalcone Synthase-related Polyketide Synthase in Streptomyces griseus *

RppA, a chalcone synthase-related polyketide synthase (type III polyketide synthase) in the bacteriumStreptomyces griseus, catalyzes the formation of 1,3,6,8-tetrahydroxynaphthalene (THN) from five molecules of malonyl-CoA. The K m value for malonyl-CoA and thek cat value for THN synthesis were determined to be 0.93 ± 0.1 μm and 0.77 ± 0.04 min−1, respectively. RppA accepted aliphatic acyl-CoAs with the carbon lengths from C4 to C8as starter substrates and catalyzed sequential condensation of malonyl-CoA to yield α-pyrones and phloroglucinols. In addition, RppA yielded a hexaketide, 4-hydroxy-6-(2′,4′,6′-trioxotridecyl)-2-pyrone, from octanoyl-CoA and five molecules of malonyl-CoA, suggesting that the size of the active site cavity of RppA is larger than any other chalcone synthase-related enzymes found so far in plants and bacteria. RppA was also found to synthesize a C-methylated pyrone, 3,6-dimethyl-4-hydroxy-2-pyrone, by using acetoacetyl-CoA as the starter and methylmalonyl-CoA as an extender. Thus, the broad substrate specificity of RppA yields a wide variety of products.
A Method of Bus Network Optimization Based on Complex Network and Beidou Vehicle Location

Aiming at the problems of poor time performance and accuracy in bus stops network optimization, this paper proposes an algorithm based on complex network and graph theory and Beidou Vehicle Location to measure the importance of bus stops. This method narrows the scope of points and edges to be optimized and is applied to the Jinan bus stop network. In this method, the bus driving efficiency, which can objectively reflect actual road conditions, is taken as the weight of the connecting edges in the network, and the network is optimized through the network efficiency. The experimental results show that, compared with the original network, the optimized network time performance is good and the optimized network bus driving efficiency is improved.
On the empirical distribution of eigenvalues of a class of large dimensional random matrices

A stronger result on the limiting distribution of the eigenvalues of random Hermitian matrices of the form A + XTX*, originally studied in Marcenko and Pastur, is presented. Here, X(N - n), T(n - n), and A(N - N) are independent, with X containing i.i. d. entries having finite second moments, T is diagonal with real (diagonal) entries, A is Hermitian, and n/N --> c > 0 as N --> [infinity]. Under additional assumptions on the eigenvalues of A and T, almost sure convergence of the empirical distribution function of the eigenvalues of A + XTX* is proven with the aid of Stieltjes transforms, taking a more direct approach than previous methods.
The streptomycin mouse model for Salmonella diarrhea: functional analysis of the microbiota, the pathogen’s virulence factors, and the host’s mucosal immune response

Summary: The mammalian intestine is colonized by a dense microbial community, the microbiota. Homeostatic and symbiotic interactions facilitate the peaceful co‐existence between the microbiota and the host, and inhibit colonization by most incoming pathogens (‘colonization resistance’). However, if pathogenic intruders overcome colonization resistance, a fierce, innate inflammatory defense can be mounted within hours, the adaptive arm of the immune system is initiated, and the pathogen is fought back. The molecular nature of the homeostatic interactions, the pathogen’s ability to overcome colonization resistance, and the triggering of native and adaptive mucosal immune responses are still poorly understood. To study these mechanisms, the streptomycin mouse model for Salmonella diarrhea is of great value. Here, we review how S. Typhimurium triggers mucosal immune responses by active (virulence factor elicited) and passive (MyD88‐dependent) mechanisms and introduce the S. Typhimurium mutants available for focusing on either response. Interestingly, mucosal defense turns out to be a double‐edged sword, limiting pathogen burdens in the gut tissue but enhancing pathogen growth in the gut lumen. This model allows not only studying the molecular pathogenesis of Salmonella diarrhea but also is ideally suited for analyzing innate defenses, microbe handling by mucosal phagocytes, adaptive secretory immunoglobulin A responses, probing microbiota function, and homeostatic microbiota–host interactions. Finally, we discuss the general need for defined assay conditions when using animal models for enteric infections and the central importance of littermate controls.