Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning regular languages by neural networks

In this paper, we introduce a new method for learning regular languages using neural networks. The method is based on two linear time algorithms and assume that the size of the alphabet is constant. The first algorithm constructs the initial neural network from the maximal length (i.e. M) of the words, belonging in a positive sample, and the site of the alphabet. The second algorithm (i.e. the learning algorithm) takes the sample, the value of M, and the initial neural network as inputs, and constructs by adjusting the weights of the final neural network.
Synaptic input sequence discrimination on behavioral timescales mediated by reaction-diffusion chemistry in dendrites

Sequences of events are ubiquitous in sensory, motor, and cognitive function. Key computational operations, including pattern recognition, event prediction, and plasticity, involve neural discrimination of spatio-temporal sequences. Here we show that synaptically-driven reaction-diffusion pathways on dendrites can perform sequence discrimination on behaviorally relevant time-scales. We used abstract signaling models to show that this selectivity arises when inputs at successive locations are aligned with, and amplified by, propagating chemical waves triggered by previous inputs. We incorporated biological detail using sequential synaptic input onto spines in morphologically, electrically, and chemically detailed pyramidal neuronal models. Again, sequences were recognized, and local channel modulation on the length-scale of sequence input could elicit changes in neuronal firing. We predict that dendritic sequence-recognition zones occupy 5 to 20 microns and recognize time-intervals of 0.2 to 5s. We suggest that this mechanism provides highly parallel and selective neural computation in a functionally important time range.
An alphabet of amino acid conformations in protein

An approach to the representation of individual amino acids using dihedral angle measurements, based on the maxi-min distance algorithm presented by J.T. Tou and R.C. Gonzalez (1974), is outlined. The methodology, based on maxi-min and data set partitions, generates 124 distinct cluster centers from 19121 total residues. While only 18 of the 124 capture 1% or more of the data set, the first cis-proline conformation is 49th in population and suggests that over fifty centers may be significant. Four applications of these centers are demonstrated: representation of individual proteins, tripeptide sequence dependency, analysis of neighboring centers, and a simple structure prediction algorithm. <<ETX>>
Ontology-based knowledge acquidition for knowledge systems

We present a prototype ontology-based knowledge system built with the Protege-2000 knowledge acquisition tool. Preliminary ideas about the role of ontologies in information systems (1) and its goal of reusing knowledge in information system development (2) are refined. A domain ontology in Protege and inference rules in Jess are combined into a knowledge system in which the elicitation and the validation of domain facts can be done at the same time. Ontology-based knowledge system development makes it possible to elicit domain facts after the implementation of the ontology-structured knowledge system.
Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations

Guanylate binding proteins (GBPs) belong to the dynamin-related superfamily and exhibit various functions in the fight against infections. The functions of the human guanylate binding protein 1 (hGBP1) are tightly coupled to GTP hydrolysis and dimerization. Despite known crystal structures of the hGBP1 monomer and GTPase domain dimer, little is known about the dynamics of hGBP1. To gain a mechanistic understanding of hGBP1, we performed sub-millisecond multi-resolution molecular dynamics simulations of both the hGBP1 monomer and dimer. We found that hGBP1 is a highly flexible protein that undergoes a hinge motion similar to the movements observed for other dynamin-like proteins. Another large-scale motion was observed for the C-terminal helix α13, providing a molecular view for the α13–α13 distances previously reported for the hGBP1 dimer. Most of the loops of the GTPase domain were found to be flexible, disclosing why GTP binding is needed for hGBP1 dimerization to occur. Author summary Gunaylate binding proteins are key fighters against microbial and viral pathogens. In the human body there are seven types of such proteins, among which is the guanylate binding protein 1 (hGBP1). This protein is able to perform its function only once it is activated by binding and converting guanosinetriphosphat (GTP) to guanosinediphosphat and guanosinemonophosphat via hydrolysis. In concert with the conversion of GTP the dimerization of hGBP1 occurs, which can further interact with the lipid membrane of the pathogen and disrupt it. While the crystal structure of the protein is known, the activation and dimerization steps are not well understood at molecular level as studying them experimentally is difficult. An alternative approach is given by molecular simulations, allowing us to elucidate the protein dynamics closely connected to these steps. From our simulations applied to both the hGBP1 monomer and dimer we identified large-scale motions taking place in hGBP1 that had not been reported before. We discuss the relevance of these motions in terms of their biological function, such as possible membrane damage caused by one of the motions or locking the protein in the dimer state.
SNP-based genetic diversity among few-branched-1 (Fbr1) maize lines and its relationship with heterosis, combining ability and grain yield of testcross hybrids

Single nucleotide polymorphism (SNP) markers are regarded as efficient,compared to other marker types in genetic characterization of maize (Zea mays L.) germplasm because of their vast coverage of the maize genome. The objectives of this study were to (a) genetically fingerprint few-branched-1’ (Fbr1) and normal tasselled CIMMYT elite lines using SNP markers, to assess their relatedness and level of homozygosity and (b) to determine SNP-based genetic distance among these maize lines and to find association of genetic distances with specific combining ability (SCA), mid-parent heterosis (MPH), high-parent heterosis (HPH) and mean grain yield of the hybrids. Twenty-six CIMMYT maize lines (12 with the Fbr1 gene, and 14 normal-tasselled) were genotyped using 1074 SNP marker loci. Fifteen of these lines were used in two separate diallel mating designs: a 9x9 and 6x6 crossing set-up, to make hybrids for yield evaluation. Average residual heterozygosity of SNP loci ranged from 0.2-36.1%, with an average of 8.2%, well above the expected ranges for residual heterozygosity found in maize inbred lines. The polymorphic information content (PIC) for the 1074 SNP loci ranged from 0.015-0.50, with an average of 0.25. Mean genetic distance for all pair wise comparisons of lines was lower (0.30) suggesting a high level of relatedness among lines. A number of elite CIMMYT lines were successfully converted to Fbr1, and were homozygous for the 1074 SNP loci, thus could be used in breeding programmes involving these new tassel mutants. The unweighted paired group method using arithmetic averages (UPGMA) cluster analysis revealed two discrete clusters for the inbred lines, reflecting heterotic groups used by CIMMYT. In the principal component (PC) analysis, PC1 and PC2 explained 10.87 and 9.08% respectively, of the molecular variance in tassel size for the 1074 SNPs. The results confirmed molecular markers as a powerful complement for use in genetic characterization, in assigning lines into defined heterotic groups and in examining the relationships among inbred lines at deoxyribonucleic acid (DNA) level. Marker-based genetic distances were positively correlated with hybrid performance, SCA and heterosis indicating that they could accurately predict hybrid performance in this set of germplasm. Grain yield for the hybrids ranged from 0.49-2.48 kg/plot, with an average of 1.80 kg/plot. Hybrids from closely related parental lines (according to SNP-based genetic distances) had the lowest mean grain yield, lowest SCA effects for grain yield, and had the lowest heterosis values. Thus, SNP-based genetic distance information would be useful for effective selection by avoiding genetically similar lines when selecting parents for breeding programmes that require genetically diverse lines as parents.
Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes

Ecologists have long studied the evolution of niche breadth, including how variability in environments can drive the evolution of specialism and generalism. This concept is of particular interest in viruses, where niche-breadth evolution may explain viral disease emergence, or underlie the potential for therapeutic measures like phage therapy. Despite the significance and potential applications of virus-host interactions, the genetic determinants of niche-breadth evolution remain unexplored in many bacteriophage. In this study, we present the results of an evolution experiment with a model bacteriophage system, Escherichia virus T4, in several host environments: exposure to E. coli C, exposure to E. coli K-12, and exposure to both E. coli C and E. coli K-12. This experimental framework allowed us to investigate the phenotypic and molecular manifestations of niche-breadth evolution. First, we show that selection on different hosts led to measurable changes in phage productivity in all experimental populations. Second, whole—genome sequencing of experimental populations revealed signatures of selection. Finally, clear and consistent patterns emerged across the host environments, especially the presence of new mutations in phage structural genes. A comparison of mutations found across functional gene categories revealed that structural genes acquired significantly more mutations than other categories. Our findings suggest that structural genes—those that provide morphological and biophysical integrity to a virus—are central determinants in bacteriophage niche breadth.
Modeling infectious diseases using a class of dynamical social networks

En este articulo estudiamos el modelo clasico epidemiologico susceptible-infeccioso-recuperado (SIR) utilizando lasredes dinamicas sociales, las cuales estan basadas en grafos dinamicos donde los nodos representan los individuos y lasconexiones entre nodos representan las interrelaciones sociales capaces de transmitir enfermedades. Las simulacionesdel modelo estocastico se realizan mediante el metodo de Monte Carlo y muestran como la dinamica de la red afecta laevolucion de las epidemias. Adicionalmente, tambien se estudia como el grado de conectividad social y la estructurainicial de la red, influyen sobre la propagacion de las enfermedades infecciosas. ABSTRACT In this article we study the classical susceptible-infectious-recovered (SIR) epidemiological model by means of socialdynamical networks which are based on dynamical graphs where the nodes represents the individuals and the linksbetween nodes representing the social relationships with potential to transmit a disease. The simulations of the proposedmodel are made using Monte Carlo method and show how the dynamics of the graph affects the epidemics evolution.Additionally, we study how the social connectivity degree and the initial structure of the network affect the propagationof the infectious diseases.Key words: Epidemics of communicable diseases, Dynamical networks, SIR mathematical models.
The Insect Societies

In his introduction to this detailed survey of knowledge of insect societies, the author points out that research on insect sociology has proceeded in three phases, the natural history phase, the physiological phase and the population-biology phase. Advances in the first two phases have permitted embarkation in the third phase on a more rigorous theory of social evolution based on population genetics and writing this book, the author wished to relate the three phases of research on insects and to express insect sociology as population biology. A glossary of terms, a considerable bibliography and a general index are included. Other CABI sites 
Fault Detection For AES Cryptographic Design

Cryptography is a method that has been developed to ensure the secrecy of messages and transfer data securely. Advanced Encryption Standard (AES) has been made as the first choice for many critical applications because of the high level of security and the fast hardware and software implementations, many of which are power and resource constrained and requires reliable and efficient hardware implementations. Naturally occurring and maliciously injected faults reduce the reliability of Advanced Encryption Standard (AES) and may leak confidential information. In this paper, a lightweight concurrent fault detection scheme for the AES is presented. In the proposed approach, the composite field S-box and inverse S-box are divided into blocks and the predicted parities of these blocks are obtained. For high speed applications, S-box implementation based on lookup tables is avoided. Instead, logic gate implementations based on composite fields are utilized. A compact architecture for the AES Mixcolumns operation and its inverse is also presented. This parity-based fault detection scheme reaches the maximum fault coverage when compared to other methods of fault detection. The proposed fault detection technique for AES encryption and decryption has the least area and power consumption compared to their counterparts with similar fault detection capabilities. Index terms — AES, composite fields, parity prediction, fault detection, S-box.
Classifying brain-computer interface features based on statistics and density of power spectrum

The use of Electroencephalography (EEG) signals as a vector of communication between men and machines represents one of the current challenges in signal theory research. The principal element of such a communication system, more known as 'brain-computer interface (BCI) ', is the interpretation of the EEG signals related to the characteristic parameters of brain electrical activity. In this paper, two feature extraction methods are applied: 'statistics method' and 'power spectral analysis (PSD)'. Then, two classification methods on a data set of BCI were compared: 'minimum distance classifier' and 'k-nearest neighbour classifier' to get the best results of discrimination between up and down movements. By applying the 'statistics method', it gives good results in both training data and test data. Also, the best classifier was the minimum distance for the training data and voting k-nearest neighbour for the test data.
Development of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) larvae feeding on the plant material contained in the water

Background: In this laboratory study we measured the trophic performances of Aedes aegypti and Aedes albopictus larvae (Diptera: Culicidae), both being vectors of the dengue fever, chikungunya and zika virus in the world. Methods: Depending on the quantities of plant material contained in the breeding sites, the bioassays enabled to assess the times it took for 50% of imaginal emergence to occur (IEt50). They also enabled to determine the amounts of plant material needed for 50% of adult emergence (IE50). Results: Water containing 3.3 g of plant material per liter allowed 50% of Ae. albopictus adults to emerge within 8 days (IEt50), against 60 days at 0.5g/liter. As for Ae. aegypti, the IEt50 took 8 days at 3.3g/l against 29 days at 1.7g/l. The IE50 also revealed that 0.61g of plant material were needed for a 50% of adult emergence of Ae. albopictus. To reach the same survival rate among Ae. aegypti, the larvae must grow in an environment twice as rich in food supply. Conclusion: This research work has revealed that the Ae. albopictus larvae can develop in water collections where the shortage of organic material hinders or compromises the development and survival of Ae. aegypti. The outstanding trophic performances of Ae. albopictus would thus partly account for the invasive character of Ae. albopictus, as well as the dying out of its competitor Ae. aegypti in the regions of the world shared by both species.
Development of Turkish Potato Varieties Tolerance to Potato Virus Y and Potato Virus X

Potato is one of the mos t important crops worldwide. The present s tudy was conducted in Yuksel Seed R&D Center, Antalya. Approximately 120.000 seeds from different genetic backgrounds were obtained and evaluated between 2008 and 2016 for developing new varieties. The aim of the research was to develop superior potato varieties tolerant to PVY and PVX with high agronomic, tuber and quality traits. Potato virus Y (PVY) and Potato virus X (PVX) are among the mos t important viruses, causing economic crop losses in potato crop in the world. The use of resis tance genes is the mos t effective method to control these viruses. Resis tance genes are transferred to new commercial varieties using molecular markers that are tightly linked to resis tance genes (Ryadg for PVY, Rx1 and Rx2 for PVX). Potato lines were tes ted in replicated trials in different potato regions of Turkey (Adana, Izmir, Afyonkarahisar, Nigde, Nevsehir and Kutahya) by 8 years to es timate the genotype x environment interaction and 85 superior lines were selected. At the end of the research 4 early season and 3 main season superior lines were submitted for regis tration as commercial varieties and 4 of 7 candidate commercial varieties were determined as suitable for French fries and were marketed.
Partial scan: what problem does it solve?

There has been considerable market activity about partial scan as a natural extension of full scan techniques. The authors present arguments for and against the partial scan. They argue that partial scan has little to offer compared to the two alternatives: no scan or full scan. For partial scan to replace full scan, it should combine the advantages of both no scan and full scan. It is suggested that with the one exception of critical timing, this is not the case. <<ETX>>
Findings Consistent with Nonselective Feeding in Tetrahymena pyriformis

In amoeboid cells, food particles are engulfed only after receptors on the phagocytic cell’s membrane bind to ligands on a particle’s surface. Ciliates also feed via phagocytosis but, instead of enveloping particles, some ciliates take them up through a complex, permanent, funnel-shaped, feeding apparatus. It is unclear whether receptor-ligand interactions are needed to trigger the process. If ciliates were shown to feed selectively on certain particles over others, based on the particles’ surface properties, then receptor-ligand interactions would likely play a role in phagocytosis. The literature includes few reports of such selectivity. To further investigate this issue, we chose to study feeding preference in the ciliate Tetrahymena pyriformis. We fed Tetrahymena mixtures of orange and green, fluorescent, 3 μm, polystyrene beads at two concentrations. One of the two types of beads was coated with bovine serum albumin. Authors were blinded to experimental conditions. We found no evidence of a preference for coated or uncoated beads at either concentration. We also found no trend toward the development of selective feeding as cells acquired more beads over time. Although we cannot rule out the possibility that Tetrahymena feeds selectively, we did not find convincing evidence of such selectivity when T. pyriformis is given a choice between uncoated beads and those coated with albumin. Our results failed to demonstrate a role for molecular recognition when Tetrahymena engages in phagocytosis.
UNIT 3.13 Ribonucleases

Ribonucleases (RNases) with different sequence or structural specificities are used for a variety of analytical purposes, including RNA sequencing, mapping, and quantitation. The development of RNase protection assays, structural determination assays, and the production of small interfering RNAs (siRNA) employed in RNA interference (RNAi) experiments has depended on the unique substrate specificities of commercially available RNases, including RNases A, I, T1, V1, HI, III, and Dicer. One very common application for high purity RNase A is also presented in this unit and involves hydrolyzing RNA that contaminates DNA preparations. RNase HII and the placental RNase inhibitor are also discussed. Curr. Protoc. Mol. Biol. 84:3.13. 1-3.13. 8. © 2008 by John Wiley & Sons, Inc. Keywords: RNase; RNase protection assay; RNA footprinting; RNAi; siRNA
Applying Customer Journey Methods in SST-based Service Design: A Proposed Methodology

This paper develops a methodology in how to apply customer journey methods in designing technology-mediated services. The focus is particularly on how to improve customer satisfaction and perceived value through introducing innovative services delivered through self-service technologies (SSTs). Action research is applied on a sub-program of a four-year-long government sponsored project in Taiwan. A methodology covering nine steps is proposed, which is believed valuable in bridging perspectives of service marketing, innovation design, and IT-enabled service (ITeS) development. The strategic roles and implications of customer journey methods in identifying current service gaps and diagnosing the potentials of SST-mediated services are also spotlighted.
PBS3 is the missing link in plant-specific isochorismate-derived salicylic acid biosynthesis

The phytohormone salicylic acid (SA) is a central regulator of plant immunity. Despite such functional importance, our knowledge of its biosynthesis is incomplete. Previous work showed that SA is synthesized from chorismic acid in plastids. The bulk of pathogen-induced SA derives from isochorismate generated by the catalytic activity of ISOCHORISMATE SYNTHASE1 (ICS1). How and in which cellular compartment isochorismate is converted to SA is unknown. Here we show that the pathway downstream of isochorismate requires only two additional proteins: the plastidial isochorismate exporter ENHANCED DISEASE SUSCEPTIBILITY5 (EDS5) and the cytosolic amido-transferase AvrPphB SUSCEPTIBLE3 (PBS3). PBS3 catalyzes the conjugation of glutamate to isochorismate. The reaction product isochorismate-9-glutamate spontaneously decomposes into enolpyruvyl-N-glutamate and SA. This previously unknown reaction mechanism appears to be conserved throughout the plant kingdom. One Sentence Summary Salicylic acid is synthesized via isochorismate-9-glutamate by PBS3.
Triseme decision trees in the continuous speech recognition system for a talking head

In this paper, we present a viseme (the basic speech units In the visual domain) based continuous speech recognition system, which segments speech into viseme sequences with timing boundaries to drive a talking head. In the viseme Hidden Markov Model (HMM) training, the instances of a viseme with different contexts are formulated as trisemes. Based on the mouth shape parameters Liprounding and the defined viseme similarity weight (VSW) from the 3D viseme facial models, 166 questions concerning the viseme contexts are designed to build triseme decision trees to tie the states of the trisemes with similar contexts, so that they can share the same parameters. To evaluate the system performance, the image related measurements are also taken to evaluate the resulting viseme sequences, with 'jerky instances' in Liprounding and VSW graphs evaluating their smoothness. Results show that compared to the phoneme based system, the tied-state triseme based speech recognition system gives talking head animation with smoother and more plausible mouth shapes.