Substitution Probabilities Research Articles

Substitution priority of Eu2+ in multi-cation compound Sr0.8Ca0.2Al2Si2O8 and energy transfer**Project supported by the National Natural Science Foundation of China (Grant Nos. 51672066 and 50902042), Funds for Distinguished Young Scientists of Hebei Province, China (Grant No. A2015201129), and Personnel Training Project of Hebei Province, China (Grant No. A2016002013).

A blue phosphor was obtained by doping Eu2+ into a multi-cation host Sr0.8Ca0.2Al2Si2O8 through high temperature solid state reaction. The emission spectra show a continuous red-shift behavior from 413 nm to 435 nm with Eu2+ concentration increasing. The substitution priority of Eu2+ in Sr0.8Ca0.2Al2Si2O8 was investigated via x-ray diffraction (XRD) and temperature properties in detail: the Ca2+ ions are preferentially substituted by Eu2+at lower doping, and with the Eu2+ concentration increasing, the probability of substitution for Sr2+ is greater than that of replacing Ca2+. Accordingly, we propose the underlying method of thermal property to determine the substitution of Eu2+ in the multi-cation hosts. Moreover, the abnormal increase of emission intensity with increasing temperature was studied by the thermoluminescence spectra. The energy transfer mechanism between the Eu2+ ions occupying different cation sites was studied by the lifetime decay curves. A series of warm white light emitting diodes were successfully fabricated using the blue phosphors Sr0.8Ca0.2Al2Si2O8: Eu2+ with commercial red phosphor (Ca Sr)SiAlN3: Eu2+ and green phosphor (Y Lu)3Al5O12: Ce3+, and the luminescent efficiency can reach 45 lm/W.

Demand estimation under multi-store multi-product substitution in high density traditional retail

In large cities in emerging economies, traditional retail is present in a very high density, with multiple independently owned small stores in each city block. Consequently, when faced with a stockout, consumers may not only substitute with a different product in the same store, but also switch to a neighboring store. Suppliers may take advantage of this behavior by strategically supplying these stores in a coherent manner. We study this problem using consumer choice models. We build two consumer choice models for this consumer behavior. First, we build a Nested Logit model for the consumer choice process, where the consumer chooses the store at the first level and selects the product at the second level. Then, we consider an Exogenous Substitution model. In both models, a consumer may substitute at either the store level or the product level. Furthermore, we estimate the parameters of the two models using a Markov chain Monte Carlo algorithm in a Bayesian manner. We numerically find that the Nested Logit model outperforms the Exogenous Substitution model in estimating substitution probabilities. Further, the information on consumers’ purchase records helps improve the estimation accuracies of both the first-choice probabilities and the substitution probabilities when the beginning inventory level is low. Finally, we show that explicitly including such substitution behavior in the inventory optimization process can significantly increase the expected profit.

Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms.

Fast genome sequencing offers invaluable opportunities for building updated and improved models of protein sequence evolution. We here show that Single Nucleotide Polymorphisms (SNPs) can be used to build a model capable of predicting the probability of substitution between amino acids in variants of the same protein in different species. The model is based on a substitution matrix inferred from the frequency of codon interchanges observed in a suitably selected subset of human SNPs, and predicts the substitution probabilities observed in alignments between Homo sapiens and related species at 85-100% of sequence identity better than any other approach we are aware of. The model gradually loses its predictive power at lower sequence identity. Our results suggest that SNPs can be employed, together with multiple sequence alignment data, to model protein sequence evolution. The SNP-based substitution matrix developed in this work can be exploited to better align protein sequences of related organisms, to refine the estimate of the evolutionary distance between protein variants from related species in phylogenetic trees and, in perspective, might become a useful tool for population analysis.

Mutational Signatures Are Critical for Proper Estimation of Purifying Selection Pressures in Cancer Somatic Mutation Data When Using the dN/dS Metric.

Large cancer genome sequencing initiatives have led to the identification of cancer driver genes based on signals of positive selection in somatic mutation data. Additionally, the identification of purifying (negative) selection has the potential to identify essential genes that may be of therapeutic interest. The most widely used way of quantifying selection pressures in protein-coding genes is the dN/dS metric, which compares non-synonymous to synonymous substitution rates. In this study, we examine whether and how this metric is influenced by the mutational processes that have been active during tumor evolution. We use exome sequencing data from six different cancer types from The Cancer Genome Atlas (TCGA) and demonstrate that dN/dS in its basic form, where uniform base substitution probabilities are assumed, is in fact strongly biased by these mutational processes. This is particularly true in malignant melanoma, where the mutational signature is characterized by a high amount of UV-induced cytosine to thymine mutations at dipyrimidine dinucleotides. This increases the likelihood of random synonymous mutations occurring in hydrophobic amino acid codons, leading to reduced dN/dS ratios in genes encoding membrane proteins and falsely suggesting purifying selection in these genes. When this effect is corrected for by taking mutational signature-derived substitution probabilities into account, purifying selection was found to be limited and similar in all cancer types studied. Our results demonstrate that it is crucial to take mutational signatures into account when applying the dN/dS metric to cancer somatic mutation data.

Hyperspectral and Multispectral Data Fusion: A comparative review of the recent literature

In recent years, enormous efforts have been made to design image-processing algorithms to enhance the spatial resolution of hyperspectral (HS) imagery. One of the most commonly addressed problems is the fusion of HS data with higher spatial resolution multispectral (MS) data. Various techniques have been proposed to solve this data-fusion problem based on different theories, including component substitution (CS), multiresolution analysis (MRA), spectral unmixing, and Bayesian probability. This article presents a comparative review of those HS-MS fusion techniques with extensive experiments. Ten state-of-the-art HS-MS fusion methods are compared by assessing their fusion performance both quantitatively and visually. Eight data sets featuring different geographical and sensor characteristics are used in the experiments to evaluate the generalizability and versatility of the fusion algorithms. To maximize the fairness and transparency of this comparison, publicly available source codes are used, and parameters are individually tuned for maximum performance.

Allies with Benefits: US Effect on European Demand for Military Expenditures

This paper examines the security relationship between the US and Europe, focusing on potential spillin effects of US military expenditures on European demand for military expenditures during the early twenty-first century. The goal is to test whether or not European states view US expenditures as a complement or as a substitute to their own military expenditures. Past work in this area has found mixed results concerning the effect of US military expenditures, but focus strictly on the spillins within a formal alliance, specifically NATO, and use a time series dominated by Cold War dynamics. This study differentiates itself by accounting for both US total military expenditures and its regional expenditures through incorporation of US military base and personnel deployments across Europe. Additionally, this paper uses government revenue in its estimation to mitigate potential endogeneity. Findings using Arellano–Bond dynamic panel analysis suggest that there is a strong probability of substitution among European states.

Allographs, graphic variants and iconic formulae in the kohau rongorongo script of Rapa Nui (Easter Island)

In a writing system with a large number of signs, in particular in the case of a pictorial script, some similarity of two graphic designs is an insufficient basis for considering them to have the same reading value. This paper seeks to apply concepts developed in the graphic analysis of other pictorial writing systems to the still undeciphered script of Rapa Nui (Easter Island). The following technical terms are adapted and defined from both theoretical and practical points of view: sign, reading value, graphic design, allograph, graphic variant, seeming graphic variant, iconic formula, and complete, incomplete and false substitution. A modified version of the substitution method (method of inverse sign substitution) is proposed for verifying equivalences and differences between readings values corresponding to the graphic designs analysed in this paper. This method is based on the assumption that two graphic designs that possess the same reading value are in free distribution, so the probability of sign substitution between them should be close to the probability obtained by multiplying the probabilities of their occurrences in texts. Application of these technical concepts to the parallel texts discovered by Boris Kudrjavtzev shows that many graphically similar signs with different reading values have not been previously recognised. This conservative graphic analysis also has permitted the identification of allographs in the strict sense of the word, i.e., signs that look different but possess the same reading value. However, technically speaking, “allograph” in the strict sense of the word is an antonym for “graphic variant”. It is suggested that the method of iconic formulae provides a useful foundation for future iconographic analysis of the highly pictorial signs of the Kohau Rongorongo script.

Optimal Issuing Policies for Substitutable Fresh Agricultural Products under Equal Ordering Policy

Small fresh agricultural products retailers often adopt equal ordering policy. Demand for the old fresh agricultural products and the new is described by consumer choice which is analyzed with price and freshness. Assuming that the market capacity is known and taking substitution of demand for the old and new fresh agricultural products into account, we establish LIFO and FIFO inventory models. To find the thresholds of freshness, price and the substitution probability, we give the suggestion about optimal issuing policy. This study helps small fresh agricultural products retailers to optimize their issuing policies.

Unrealistic phylogenetic trees may improve phylogenetic footprinting.

MotivationThe computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting requires phylogenetic trees with attached substitution probabilities for quantifying the evolution of binding sites, but these trees and substitution probabilities are typically not known and cannot be estimated easily.ResultsHere, we investigate the influence of phylogenetic trees with different substitution probabilities on the classification performance of phylogenetic footprinting using synthetic and real data. For synthetic data we find that the classification performance is highest when the substitution probability used for phylogenetic footprinting is similar to that used for data generation. For real data, however, we typically find that the classification performance of phylogenetic footprinting surprisingly increases with increasing substitution probabilities and is often highest for unrealistically high substitution probabilities close to one. This finding suggests that choosing realistic model assumptions might not always yield optimal predictions in general and that choosing unrealistically high substitution probabilities close to one might actually improve the classification performance of phylogenetic footprinting.Availability and ImplementationThe proposed PF is implemented in JAVA and can be downloaded from https://github.com/mgledi/PhyFooSupplementary information Supplementary data are available at Bioinformatics online.

Does the Use of Smartphone Influence Travel Outcome? An Investigation on the Determinants of the Impact of Smartphone Use on Vehicle Kilometres Travelled

Abstract This paper investigates the impact of smartphone on travel outcome that uses data from a web-based survey conducted in Halifax Regional Municipality, Nova Scotia in 2015. Following a Latent Class Modelling (LCM) Approach, the study analyses the change in vehicle kilometres travelled (VKT) as an influence of smartphone use and how this change differentiates among different socio-demographic groups, residential locations and life-style strata.Vehicle kilometres travelled has been examined on three choice contexts: smartphone use had i) reduced VKT ii) no impact on VKT and iii) increased VKT. The model identifies two classes based on socio-demographic characteristics where Class 1 can be characterized as student and young professionals, whose annual income is less than CAD 15K, female population with part-time or full-time employment and who are not full-time student. To facilitate the discussion, Class 1 has been branded as ‘Tech-Savvy’ and Class 2 of the model as ‘Non Tech-Savvy’. Results suggest that variation exists between Tech-Savvy and Non Tech-Savvy group. For example, in the Tech-Savvy group, the novice smartphone users have less probability of reduction in kilometres travelled compared to the other group, whereas in the Non Tech-Savvy group, the probability of substitution increases for the novice users. Determinants that can reduce VKT because of smartphone use are: higher use of smartphones for online shopping, active transportation as primary mode, home to work/school distance, pro-environment attitude, etc. This study offers important insights and could be useful for transport policy making.

Demand estimation and assortment planning in wireless communications

This paper provides an efficient and useful approach for demand estimation and assortment planning of cell phone cards in wireless communication industry. We use maximum likelihood estimation to estimate the primary demand and substitution probability of each cell phone card based on historical sales data. This estimation model is nonlinear, so we transform it to a mixed integer linear programming model by logarithmic transformations and piecewise linear approximation. On the basis of the estimation results, we can make assortment planning. Considering the resource of cell phone cards is limited, we jointly optimize the assortment and quantity planning of cell phone cards. In numerical study, we apply our approach to a large mobile service provider in China and find our approach can increase the revenue of this mobile service provider by 23.69%. Sensitivity analysis shows the mobile service provider should provide more assortments to increase revenue when the types of cell phone cards that can be assigned to each store are limited.

DNA barcoding reflects the diversity and variety of brooding traits of fish species in the family Syngnathidae along China’s coast

DNA barcoding offers a rapid and accurate assessment for species labelling and identification. Here, we investigated the performance of DNA barcodes in a sample of Syngnathidae, a unique group of fish with male pregnancy. A total of 1002 DNA barcodes using 649 base-pair fragments of the cytochrome c oxidase subunit I (COI) gene were generated. All species were associated with distinct DNA barcode and could be readily distinguished; seven of the COI barcode clusters represented the first species records submitted to the Barcode of Life Data Systems (BOLD) and GenBank databases. In the Neighbor-joining tree of COI sequences, two major clusters (Gastrophori and Urophori) were displayed, which could also be classified by their brood pouches. However, the tail-brooding Hippichthys cyanospilus and trunk-brooding Syngnathoides biaculeatus were reverse-clustered together with the Gastrophori and the Urophori, respectively. Both seahorse and pipefish sequences showed high frequencies of nucleotide substitutions. The probability of nucleotide substitutions, those in pipefish were higher than that of all seahorses. However, we identified no signal for positive selection based on the COI gene in any of the data sets. Our results supported DNA barcoding as an efficient molecular tool for achieving better monitoring, conservation, and management of fisheries.

Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts

Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences. Probability of all possible single-base substitutions for the C2 region predicted N:S values within 95% confidence limits of the corrected within-isolate N:S when the only constraint imposed was viral polymerase error bias for transitions over transversions. These results indicate that bottlenecks coupled with strong negative/purifying selection drive consensus sequences toward neutral sequence space, and that most polymorphism within single-insect isolates is composed of newly-minted mutations sampled prior to selection.

Study on the security of the authentication scheme with key recycling in QKD

In quantum key distribution (QKD), the information theoretically secure authentication is necessary to guarantee the integrity and authenticity of the exchanged information over the classical channel. In order to reduce the key consumption, the authentication scheme with key recycling (KR), in which a secret but fixed hash function is used for multiple messages while each tag is encrypted with a one-time pad (OTP), is preferred in QKD. Based on the assumption that the OTP key is perfect, the security of the authentication scheme has be proved. However, the OTP key of authentication in a practical QKD system is not perfect. How the imperfect OTP affects the security of authentication scheme with KR is analyzed thoroughly in this paper. In a practical QKD, the information of the OTP key resulting from QKD is partially leaked to the adversary. Although the information leakage is usually so little to be neglected, it will lead to the increasing degraded security of the authentication scheme as the system runs continuously. Both our theoretical analysis and simulation results demonstrate that the security level of authentication scheme with KR, mainly indicated by its substitution probability, degrades exponentially in the number of rounds and gradually diminishes to zero.

Low Genetic Quality Alters Key Dimensions of the Mutational Spectrum.

Mutations affect individual health, population persistence, adaptation, diversification, and genome evolution. There is evidence that the mutation rate varies among genotypes, but the causes of this variation are poorly understood. Here, we link differences in genetic quality with variation in spontaneous mutation in a Drosophila mutation accumulation experiment. We find that chromosomes maintained in low-quality genetic backgrounds experience a higher rate of indel mutation and a lower rate of gene conversion in a manner consistent with condition-based differences in the mechanisms used to repair DNA double strand breaks. These aspects of the mutational spectrum were also associated with body mass, suggesting that the effect of genetic quality on DNA repair was mediated by overall condition, and providing a mechanistic explanation for the differences in mutational fitness decline among these genotypes. The rate and spectrum of substitutions was unaffected by genetic quality, but we find variation in the probability of substitutions and indels with respect to several aspects of local sequence context, particularly GC content, with implications for models of molecular evolution and genome scans for signs of selection. Our finding that the chances of mutation depend on genetic context and overall condition has important implications for how sequences evolve, the risk of extinction, and human health.

ON PERFECT IMITATION RESISTANT CIPHERS BASED ON COMBINATORIAL OBJECTS

We study perfect imitation resistant ciphers, highlighting particularly the case in which the probabilities of successful imitation and substitution attain their lower limits. On the basis of A.Yu. Zubovs mathematical model of substitution cipher with unbounded key model of perfect and imitation resistant cipher based on combinatorial objects is constructed.

An expanded sequence context model broadly explains variability in polymorphism levels across the human genome.

The rate of single nucleotide polymorphism varies substantially across the human genome and fundamentally influences evolution and incidence of genetic disease. Previous studies have only considered the immediate flanking nucleotides around a polymorphic site –the site’s trinucleotide sequence context– to study polymorph levels across the genome. Moreover, the impact of larger sequence contexts has not been fully clarified, even though context substantially influences rates of polymorphism. Using a new statistical framework and data from the 1000 Genomes Project, we demonstrate that a heptanucleotide context explains >81% of variability in substitution probabilities, revealing new mutation-promoting motifs at ApT dinucleotide, CAAT, and TACG sequences. Our approach also identifies previously undocumented variability in C-to-T substitutions at CpG sites, which is not immediately explained by differential methylation intensity. Using our model, we present informative substitution intolerance scores for genes and a new intolerance score for amino acids, and we demonstrate clinical use of the model in neuropsychiatric diseases.

A Reference Point Logit Model for Estimating Substitution Probabilities Using Point of Sale Data

This paper presents a practical approach to estimate the substitution probabilities between products at a retail store by using the store’s point of sale data and prospect theory based structural restrictions on the consumer choice behavior. The prospect theory based reference dependent preference structure imposed on the consumer choice behavior (a) accounts for how consumers make their original choice as well as how they substitute, (b) eliminates the IIA and IPS assumptions that the standard utility theory based models impose on consumer choice, and (c) alleviates the need for inventory information for estimating the substitution probabilities. Simulations have been used to show that the estimates of the substitution probabilities are efficient and are robust to stock-out rates, and two empirical studies are presented to illustrate the estimation process.

Assortment Optimization with Product Level Demand and Substitution Information

This paper presents a mathematical model for jointly optimizing base stock levels for the multiple items subject to service level goals. The proposed model uses the expected demand and substitution probabilities between products as inputs and has been used to analyze the effects of demand variability on profitability under service level constraint. The results of the analysis demonstrate that neglecting customer-driven substitution or excluding the impacts of variability and correlations in demand leads to significantly inefficient assortments.

Bombarding Graphene with Oxygen Ions: Combining Effects of Incident Angle and Ion Energy To Control Defect Generation

Ion bombardment is a key physical process in the ion implantation and irradiation of graphene, with important implications for tuning graphene’s electronic properties and for understanding the material’s behavior in irradiative environment. Using molecular dynamics with a reactive force field, this work systematically investigates the influence of the incident angle on the generation of defects and vacancies during the bombardment process. It is found that larger incident angles (between the incident line and the surface of graphene) ranging from 70° to 90° are desired for substitution and single vacancy, whereas smaller incident angles ranging from 30° to 50° are favored for forming double vacancies, multiple vacancies, and in-plane disorder. Oxygen ions with the incident angle of 70° produce the highest probability of ion substitution, and the ions at 40–60 eV and 70° yield the highest quality of doping with minimum other defects. These results demonstrate that bombarding graphene along oblique directio...