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Robust k-mer frequency estimation using gapped k-mers.

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Ghandi, Mahmoud; Mohammad-Noori, Morteza; Beer, Michael A

2014-08-01

Oligomers of fixed length, k, commonly known as k-mers, are often used as fundamental elements in the description of DNA sequence features of diverse biological function, or as intermediate elements in the constuction of more complex descriptors of sequence features such as position weight matrices. k-mers are very useful as general sequence features because they constitute a complete and unbiased feature set, and do not require parameterization based on incomplete knowledge of biological mechanisms. However, a fundamental limitation in the use of k-mers as sequence features is that as k is increased, larger spatial correlations in DNA sequence elements can be described, but the frequency of observing any specific k-mer becomes very small, and rapidly approaches a sparse matrix of binary counts. Thus any statistical learning approach using k-mers will be susceptible to noisy estimation of k-mer frequencies once k becomes large. Because all molecular DNA interactions have limited spatial extent, gapped k-mers often carry the relevant biological signal. Here we use gapped k-mer counts to more robustly estimate the ungapped k-mer frequencies, by deriving an equation for the minimum norm estimate of k-mer frequencies given an observed set of gapped k-mer frequencies. We demonstrate that this approach provides a more accurate estimate of the k-mer frequencies in real biological sequences using a sample of CTCF binding sites in the human genome.
Statistically Consistent k-mer Methods for Phylogenetic Tree Reconstruction.

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Allman, Elizabeth S; Rhodes, John A; Sullivant, Seth

2017-02-01

Frequencies of k-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared Euclidean distance between k-mer vectors to approximate a tree metric can be statistically inconsistent. To remedy this, we derive model-based distance corrections for orthologous sequences without gaps, which lead to consistent tree inference. The identifiability of model parameters from k-mer frequencies is also studied. Finally, we report simulations showing that the corrected distance outperforms many other k-mer methods, even when sequences are generated with an insertion and deletion process. These results have implications for multiple sequence alignment as well since k-mer methods are usually the first step in constructing a guide tree for such algorithms.
Enhanced regulatory sequence prediction using gapped k-mer features.

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Ghandi, Mahmoud; Lee, Dongwon; Mohammad-Noori, Morteza; Beer, Michael A

2014-07-01

Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem.
Enhanced regulatory sequence prediction using gapped k-mer features.

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Mahmoud Ghandi

2014-07-01

Full Text Available Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem.
Implementation of hierarchical clustering using k-mer sparse matrix to analyze MERS-CoV genetic relationship

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Bustamam, A.; Ulul, E. D.; Hura, H. F. A.; Siswantining, T.

2017-07-01

Hierarchical clustering is one of effective methods in creating a phylogenetic tree based on the distance matrix between DNA (deoxyribonucleic acid) sequences. One of the well-known methods to calculate the distance matrix is k-mer method. Generally, k-mer is more efficient than some distance matrix calculation techniques. The steps of k-mer method are started from creating k-mer sparse matrix, and followed by creating k-mer singular value vectors. The last step is computing the distance amongst vectors. In this paper, we analyze the sequences of MERS-CoV (Middle East Respiratory Syndrome - Coronavirus) DNA by implementing hierarchical clustering using k-mer sparse matrix in order to perform the phylogenetic analysis. Our results show that the ancestor of our MERS-CoV is coming from Egypt. Moreover, we found that the MERS-CoV infection that occurs in one country may not necessarily come from the same country of origin. This suggests that the process of MERS-CoV mutation might not only be influenced by geographical factor.
K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

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Aaron Sievers

2017-04-01

Full Text Available In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4 on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs, which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST and the
Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding.

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Min, Xu; Zeng, Wanwen; Chen, Ning; Chen, Ting; Jiang, Rui

2017-07-15

Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k -mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k -mer co-occurrence information with recent advances in deep learning. We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k -mer embedding. We first split DNA sequences into k -mers and pre-train k -mer embedding vectors based on the co-occurrence matrix of k -mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k -mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility. The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm . tingchen@tsinghua.edu.cn or ruijiang@tsinghua.edu.cn. Supplementary materials are available at
Multiple comparative metagenomics using multiset k-mer counting

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Gaëtan Benoit

2016-11-01

Full Text Available Background Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results. Methods These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecological distances by replacing species counts by k-mer counts. Simka scales-up today’s metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Results Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecological distances on hundreds of metagenomic samples (690 samples, 32 billions of reads. We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy or which are based on taxonomic profiling.
Simrank: Rapid and sensitive general-purpose k-mer search tool

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DeSantis, T.Z.; Keller, K.; Karaoz, U.; Alekseyenko, A.V; Singh, N.N.S.; Brodie, E.L; Pei, Z.; Andersen, G.L; Larsen, N.

2011-04-01

Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project (http://nihroadmap.nih.gov/hmp). Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.
Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches.

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Almutairy, Meznah; Torng, Eric

2018-01-01

Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method.
Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches.

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Meznah Almutairy

Full Text Available Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method.
Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches

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Torng, Eric

2018-01-01

Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method. PMID:29389989
Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.

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Pan, Tony; Flick, Patrick; Jain, Chirag; Liu, Yongchao; Aluru, Srinivas

2017-10-09

Counting and indexing fixed length substrings, or k-mers, in biological sequences is a key step in many bioinformatics tasks including genome alignment and mapping, genome assembly, and error correction. While advances in next generation sequencing technologies have dramatically reduced the cost and improved latency and throughput, few bioinformatics tools can efficiently process the datasets at the current generation rate of 1.8 terabases every 3 days. We present Kmerind, a high performance parallel k-mer indexing library for distributed memory environments. The Kmerind library provides a set of simple and consistent APIs with sequential semantics and parallel implementations that are designed to be flexible and extensible. Kmerind's k-mer counter performs similarly or better than the best existing k-mer counting tools even on shared memory systems. In a distributed memory environment, Kmerind counts k-mers in a 120 GB sequence read dataset in less than 13 seconds on 1024 Xeon CPU cores, and fully indexes their positions in approximately 17 seconds. Querying for 1% of the k-mers in these indices can be completed in 0.23 seconds and 28 seconds, respectively. Kmerind is the first k-mer indexing library for distributed memory environments, and the first extensible library for general k-mer indexing and counting. Kmerind is available at https://github.com/ParBLiSS/kmerind.
Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

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Gruenheit Nicole

2012-03-01

Full Text Available Abstract Background Transcriptome analysis is increasingly being used to study the evolutionary origins and ecology of non-model plants. One issue for both transcriptome assembly and differential gene expression analyses is the common occurrence in plants of hybridisation and whole genome duplication (WGD and hybridization resulting in allopolyploidy. The divergence of duplicated genes following WGD creates near identical homeologues that can be problematic for de novo assembly and also reference based assembly protocols that use short reads (35 - 100 bp. Results Here we report a successful strategy for the assembly of two transcriptomes made using 75 bp Illumina reads from Pachycladon fastigiatum and Pachycladon cheesemanii. Both are allopolyploid plant species (2n = 20 that originated in the New Zealand Alps about 0.8 million years ago. In a systematic analysis of 19 different coverage cutoffs and 20 different k-mer sizes we showed that i none of the genes could be assembled across all of the parameter space ii assembly of each gene required an optimal set of parameter values and iii these parameter values could be explained in part by different gene expression levels and different degrees of similarity between genes. Conclusions To obtain optimal transcriptome assemblies for allopolyploid plants, k-mer size and k-mer coverage need to be considered simultaneously across a broad parameter space. This is important for assembling a maximum number of full length ESTs and for avoiding chimeric assemblies of homeologous and paralogous gene copies.
KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.

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Wang, Dapeng; Xu, Jiayue; Yu, Jun

2015-09-16

The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data.
The effects of sampling on the efficiency and accuracy of k-mer indexes: Theoretical and empirical comparisons using the human genome.

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Almutairy, Meznah; Torng, Eric

2017-01-01

One of the most common ways to search a sequence database for sequences that are similar to a query sequence is to use a k-mer index such as BLAST. A big problem with k-mer indexes is the space required to store the lists of all occurrences of all k-mers in the database. One method for reducing the space needed, and also query time, is sampling where only some k-mer occurrences are stored. Most previous work uses hard sampling, in which enough k-mer occurrences are retained so that all similar sequences are guaranteed to be found. In contrast, we study soft sampling, which further reduces the number of stored k-mer occurrences at a cost of decreasing query accuracy. We focus on finding highly similar local alignments (HSLA) over nucleotide sequences, an operation that is fundamental to biological applications such as cDNA sequence mapping. For our comparison, we use the NCBI BLAST tool with the human genome and human ESTs. When identifying HSLAs, we find that soft sampling significantly reduces both index size and query time with relatively small losses in query accuracy. For the human genome and HSLAs of length at least 100 bp, soft sampling reduces index size 4-10 times more than hard sampling and processes queries 2.3-6.8 times faster, while still achieving retention rates of at least 96.6%. When we apply soft sampling to the problem of mapping ESTs against the genome, we map more than 98% of ESTs perfectly while reducing the index size by a factor of 4 and query time by 23.3%. These results demonstrate that soft sampling is a simple but effective strategy for performing efficient searches for HSLAs. We also provide a new model for sampling with BLAST that predicts empirical retention rates with reasonable accuracy by modeling two key problem factors.
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.

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Murray, Kevin D; Webers, Christfried; Ong, Cheng Soon; Borevitz, Justin; Warthmann, Norman

2017-09-01

Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.
MicroRNA categorization using sequence motifs and k-mers.

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Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin; Allmer, Jens

2017-03-14

Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and they have been discovered in a variety of organisms ranging from viruses and microbes to eukaryotic organisms. The computational detection of pre-miRNAs is of great interest, and such approaches usually employ machine learning to discriminate between miRNAs and other sequences. Many features have been proposed describing pre-miRNAs, and we have previously introduced the use of sequence motifs and k-mers as useful ones. There have been reports of xeno-miRNAs detected via next generation sequencing. However, they may be contaminations and to aid that important decision-making process, we aimed to establish a means to differentiate pre-miRNAs from different species. To achieve distinction into species, we used one species' pre-miRNAs as the positive and another species' pre-miRNAs as the negative training and test data for the establishment of machine learned models based on sequence motifs and k-mers as features. This approach resulted in higher accuracy values between distantly related species while species with closer relation produced lower accuracy values. We were able to differentiate among species with increasing success when the evolutionary distance increases. This conclusion is supported by previous reports of fast evolutionary changes in miRNAs since even in relatively closely related species a fairly good discrimination was possible.
A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction.

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Guo, Yuchun; Tian, Kevin; Zeng, Haoyang; Guo, Xiaoyun; Gifford, David Kenneth

2018-04-13

The representation and discovery of transcription factor (TF) sequence binding specificities is critical for understanding gene regulatory networks and interpreting the impact of disease-associated noncoding genetic variants. We present a novel TF binding motif representation, the k -mer set memory (KSM), which consists of a set of aligned k -mers that are overrepresented at TF binding sites, and a new method called KMAC for de novo discovery of KSMs. We find that KSMs more accurately predict in vivo binding sites than position weight matrix (PWM) models and other more complex motif models across a large set of ChIP-seq experiments. Furthermore, KSMs outperform PWMs and more complex motif models in predicting in vitro binding sites. KMAC also identifies correct motifs in more experiments than five state-of-the-art motif discovery methods. In addition, KSM-derived features outperform both PWM and deep learning model derived sequence features in predicting differential regulatory activities of expression quantitative trait loci (eQTL) alleles. Finally, we have applied KMAC to 1600 ENCODE TF ChIP-seq data sets and created a public resource of KSM and PWM motifs. We expect that the KSM representation and KMAC method will be valuable in characterizing TF binding specificities and in interpreting the effects of noncoding genetic variations. © 2018 Guo et al.; Published by Cold Spring Harbor Laboratory Press.
Deterministic and stochastic models for middle east respiratory syndrome (MERS)

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Suryani, Dessy Rizki; Zevika, Mona; Nuraini, Nuning

2018-03-01

World Health Organization (WHO) data stated that since September 2012, there were 1,733 cases of Middle East Respiratory Syndrome (MERS) with 628 death cases that occurred in 27 countries. MERS was first identified in Saudi Arabia in 2012 and the largest cases of MERS outside Saudi Arabia occurred in South Korea in 2015. MERS is a disease that attacks the respiratory system caused by infection of MERS-CoV. MERS-CoV transmission occurs directly through direct contact between infected individual with non-infected individual or indirectly through contaminated object by the free virus. Suspected, MERS can spread quickly because of the free virus in environment. Mathematical modeling is used to illustrate the transmission of MERS disease using deterministic model and stochastic model. Deterministic model is used to investigate the temporal dynamic from the system to analyze the steady state condition. Stochastic model approach using Continuous Time Markov Chain (CTMC) is used to predict the future states by using random variables. From the models that were built, the threshold value for deterministic models and stochastic models obtained in the same form and the probability of disease extinction can be computed by stochastic model. Simulations for both models using several of different parameters are shown, and the probability of disease extinction will be compared with several initial conditions.

Renewed mer model of integral management

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Janko Belak

2015-12-01

Full Text Available Background: The research work on entrepreneurship, enterprise's policy and management, which started in 1992, successfully continued in the following years. Between 1992 and 2011, more than 400 academics and other researchers have participated in research work (MER research program whose main orientation has been the creation of their own model of integral management. Results: In past years, academics (researchers and authors of published papers from Austria, Belgium, Bosnia and Herzegovina, Bulgaria, Byelorussia, Canada, the Czech Republic, Croatia, Estonia, France, Germany, Hungary, Italy, Poland, Romania, Russia, the Slovak Republic, Slovenia, Switzerland, Ukraine, and the US have cooperated in MER programs, coming from more than fifty institutions. Thus, scientific doctrines of different universities influenced the development of the MER model which is based on both horizontal and vertical integration of the enterprises' governance and management processes, instruments and institutions into a consistently operating unit. Conclusions: The presented MER model is based on the multi-layer integration of governance and management with an enterprise and its environment, considering the fundamental desires for the enterprises' existence and, thus, their quantitative as well as qualitative changes. The process, instrumental, and institutional integrity of the governance and management is also the initial condition for the implementation of all other integration factors.
Forward Modeling of Reduced Power Spectra from Three-dimensional k-space

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von Papen, Michael; Saur, Joachim

2015-06-01

We present results from a numerical forward model to evaluate one-dimensional reduced power spectral densities (PSDs) from arbitrary energy distributions in {\\boldsymbol{k}} -space. In this model, we can separately calculate the diagonal elements of the spectral tensor for incompressible axisymmetric turbulence with vanishing helicity. Given a critically balanced turbulent cascade with {{k}\\parallel }∼ k\\bot α and α \\lt 1, we explore the implications on the reduced PSD as a function of frequency. The spectra are obtained under the assumption of Taylor’s hypothesis. We further investigate the functional dependence of the spectral index κ on the field-to-flow angle θ between plasma flow and background magnetic field from MHD to electron kinetic scales. We show that critically balanced turbulence asymptotically develops toward θ-independent spectra with a slope corresponding to the perpendicular cascade. This occurs at a transition frequency {{f}2D}(L,α ,θ ), which is analytically estimated and depends on outer scale L, critical balance exponent α, and field-to-flow angle θ. We discuss anisotropic damping terms acting on the {\\boldsymbol{k}} -space distribution of energy and their effects on the PSD. Further, we show that the spectral anisotropies κ (θ ) as found by Horbury et al. and Chen et al. in the solar wind are in accordance with a damped critically balanced cascade of kinetic Alfvén waves. We also model power spectra obtained by Papen et al. in Saturn’s plasma sheet and find that the change of spectral indices inside 9 {{R}s} can be explained by damping on electron scales.
Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.

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Yaron Orenstein

2017-10-01

Full Text Available With the rapidly increasing volume of deep sequencing data, more efficient algorithms and data structures are needed. Minimizers are a central recent paradigm that has improved various sequence analysis tasks, including hashing for faster read overlap detection, sparse suffix arrays for creating smaller indexes, and Bloom filters for speeding up sequence search. Here, we propose an alternative paradigm that can lead to substantial further improvement in these and other tasks. For integers k and L > k, we say that a set of k-mers is a universal hitting set (UHS if every possible L-long sequence must contain a k-mer from the set. We develop a heuristic called DOCKS to find a compact UHS, which works in two phases: The first phase is solved optimally, and for the second we propose several efficient heuristics, trading set size for speed and memory. The use of heuristics is motivated by showing the NP-hardness of a closely related problem. We show that DOCKS works well in practice and produces UHSs that are very close to a theoretical lower bound. We present results for various values of k and L and by applying them to real genomes show that UHSs indeed improve over minimizers. In particular, DOCKS uses less than 30% of the 10-mers needed to span the human genome compared to minimizers. The software and computed UHSs are freely available at github.com/Shamir-Lab/DOCKS/ and acgt.cs.tau.ac.il/docks/, respectively.
Influence of defects on the effective electrical conductivity of a monolayer produced by random sequential adsorption of linear k-mers onto a square lattice

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Tarasevich, Yuri Yu.; Laptev, Valeri V.; Goltseva, Valeria A.; Lebovka, Nikolai I.

2017-07-01

The effect of defects on the behaviour of electrical conductivity, σ, in a monolayer produced by the random sequential adsorption of linear k-mers (particles occupying k adjacent sites) onto a square lattice is studied by means of a Monte Carlo simulation. The k-mers are deposited on the substrate until a jamming state is reached. The presence of defects in the lattice (impurities) and of defects in the k-mers with concentrations of dl and dk, respectively, is assumed. The defects in the lattice are distributed randomly before deposition and these lattice sites are forbidden for the deposition of k-mers. The defects of the k-mers are distributed randomly on the deposited k-mers. The sites filled with k-mers have high electrical conductivity, σk, whereas the empty sites, and the sites filled by either types of defect have a low electrical conductivity, σl, i.e., a high-contrast, σk /σl ≫ 1, is assumed. We examined isotropic (both the possible x and y orientations of a particle are equiprobable) and anisotropic (all particles are aligned along one given direction, y) deposition. To calculate the effective electrical conductivity, the monolayer was presented as a random resistor network and the Frank-Lobb algorithm was used. The effects of the concentrations of defects dl and dk on the electrical conductivity for the values of k =2n, where n = 1 , 2 , … , 5, were studied. Increase of both the dl and dk parameters values resulted in decreases in the value of σ and the suppression of percolation. Moreover, for anisotropic deposition the electrical conductivity along the y direction was noticeably larger than in the perpendicular direction, x. Phase diagrams in the (dl ,dk)-plane for different values of k were obtained.
Recapitulating phylogenies using k-mers: from trees to networks.

Science.gov (United States)

Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.
GPI Spectra of HR8799 C, D, and E in H-K Bands with KLIP Forward Modeling

Science.gov (United States)

Greenbaum, Alexandra Z.; Pueyo, Laurent; Ruffio, Jean-Baptiste; Wang, Jason J.; De Rosa, Robert J.; Aguilar, Jonathan; Rameau, Julien; Barman, Travis; Marois, Christian; Marley, Mark S.;

2018-01-01

We demonstrate KLIP forward modeling spectral extraction on Gemini Planet Imager coronagraphic data of HR8799, using PyKLIP. We report new and re-reduced spectrophotometry of HR8799 c, d, and e from H-K bands. We discuss a strategy for choosing optimal KLIP PSF subtraction parameters by injecting fake sources and recovering them over a range of parameters. The K1/K2 spectra for planets c and d are similar to previously published results from the same dataset. We also present a K band spectrum of HR8799e for the first time and show that our H-band spectra agree well with previously published spectra from the VLT/SPHERE instrument. We compare planets c, d, and e with M, L, and T-type field objects. All objects are consistent with low gravity mid-to-late L dwarfs, however, a lack of standard spectra for low gravity late L-type objects lead to poor fit for gravity. We place our results in context of atmospheric models presented in previous publications and discuss differences in the spectra of the three planets.

A mouse model for MERS coronavirus-induced acute respiratory distress syndrome.

Science.gov (United States)

Cockrell, Adam S; Yount, Boyd L; Scobey, Trevor; Jensen, Kara; Douglas, Madeline; Beall, Anne; Tang, Xian-Chun; Marasco, Wayne A; Heise, Mark T; Baric, Ralph S

2016-11-28

Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel virus that emerged in 2012, causing acute respiratory distress syndrome (ARDS), severe pneumonia-like symptoms and multi-organ failure, with a case fatality rate of ∼36%. Limited clinical studies indicate that humans infected with MERS-CoV exhibit pathology consistent with the late stages of ARDS, which is reminiscent of the disease observed in patients infected with severe acute respiratory syndrome coronavirus. Models of MERS-CoV-induced severe respiratory disease have been difficult to achieve, and small-animal models traditionally used to investigate viral pathogenesis (mouse, hamster, guinea-pig and ferret) are naturally resistant to MERS-CoV. Therefore, we used CRISPR-Cas9 gene editing to modify the mouse genome to encode two amino acids (positions 288 and 330) that match the human sequence in the dipeptidyl peptidase 4 receptor, making mice susceptible to MERS-CoV infection and replication. Serial MERS-CoV passage in these engineered mice was then used to generate a mouse-adapted virus that replicated efficiently within the lungs and evoked symptoms indicative of severe ARDS, including decreased survival, extreme weight loss, decreased pulmonary function, pulmonary haemorrhage and pathological signs indicative of end-stage lung disease. Importantly, therapeutic countermeasures comprising MERS-CoV neutralizing antibody treatment or a MERS-CoV spike protein vaccine protected the engineered mice against MERS-CoV-induced ARDS.
A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach.

Science.gov (United States)

Melicher, Dacotah; Torson, Alex S; Dworkin, Ian; Bowsher, Julia H

2014-03-12

The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba. Our bioinformatics pipeline uses cloud computing services to assemble and analyze the transcriptome with off-site data management, processing, and backup. It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly. We used 454 sequencing to generate 1.48 million reads from cDNA generated from embryo, larva, and pupae of T. biloba and assembled a transcriptome consisting of 24,495 contigs. Annotation identified 16,705 transcripts, including those involved in embryogenesis and limb patterning. We assembled transcriptomes from an additional three non-model organisms to demonstrate that our pipeline assembled a higher-quality transcriptome than single k-mer approaches across multiple species. The pipeline we have developed for assembly and analysis increases contig length, recovers unique transcripts, and assembles more base pairs than other methods through the use of a meta-assembly. The T. biloba transcriptome is a critical resource for performing large-scale RNA-Seq investigations of gene expression patterns, and is the first transcriptome sequenced in this Dipteran family.
Push-pull effect on the geometrical, optical and charge transfer properties of disubstituted derivatives of mer-tris(4-hydroxy-1,5-naphthyridinato aluminum (mer-AlND3

Directory of Open Access Journals (Sweden)

Rao Joshi Laxmikanth

2016-01-01

Full Text Available To design innovative and novel optical materials with high mobility, two kinds of disubstituted derivatives for mer-tris(4-hydroxy-1,5-naphthyridinato aluminum (mer-AlND3 with push (EDG–pull (EWG substituents have been designed. The structures of mer-tris(8-EDG-2-EWG-4-hydroxy-1,5-naphthyridinato aluminum (type I and mer-tris(8-EWG-2-EDG-4-hydroxy-1,5-naphthyridinato aluminum (type II in the ground and first excited states have been optimized at the B3LYP/6-31G(D and CIS/6-31G(D level of theory, respectively. It can be seen from frontier molecular orbitals analysis, in all these complexes, the highest occupied molecular orbital (HOMO is localized on the pyridine-4-ol ring of A-ligand while lowest unoccupied molecular orbital (LUMO is on the pyridyl ring of B-ligand in ground state irrespective of electron donor/acceptor substitution present on the ligands similar to that of mer-tris(8-hydroxyquinoline aluminum (mer-Alq3 and parent mer-AlND3.The absorption and emission wavelengths have been evaluated at the TD-PBE0/6-31G(D level and it can be see that all the type I derivatives show blue shift while most of the type II derivatives show red shift compared to mer-AlND3. All the disubstituted complexes have showed hypsochromic shifts in both the absorption and emission spectra when compared with the calculated absorption and emission spectra respectively of mer-Alq3. It can be seen that the reorganization energies of some of the disubstituted derivatives are comparable with mer-Alq3 and these derivatives might be good candidates for emitting materials in OLED.
MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data

Energy Technology Data Exchange (ETDEWEB)

White, Richard A.; Panyala, Ajay R.; Glass, Kevin A.; Colby, Sean M.; Glaesemann, Kurt R.; Jansson, Georg C.; Jansson, Janet K.

2017-02-21

MerCat is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. MerCat inputs include assembled contigs and raw sequence reads from any platform resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST and/or DIAMOND for compositional analysis of whole community shotgun sequencing (e.g. metagenomes and metatranscriptomes).
A Novel Dynamic Model Describing the Spread of the MERS-CoV and the Expression of Dipeptidyl Peptidase 4

Directory of Open Access Journals (Sweden)

Siming Tang

2017-01-01

Full Text Available The Middle East respiratory syndrome (MERS coronavirus, a newly identified pathogen, causes severe pneumonia in humans. MERS is caused by a coronavirus known as MERS-CoV, which attacks the respiratory system. The recently defined receptor for MERS-CoV, dipeptidyl peptidase 4 (DPP4, is generally expressed in endothelial and epithelial cells and has been shown to be present on cultured human nonciliated bronchiolar epithelium cells. In this paper, a class of novel four-dimensional dynamic model describing the infection of MERS-CoV is given, and then global stability of the equilibria of the model is discussed. Our results show that the spread of MERS-CoV can also be controlled by decreasing the expression rate of DPP4.
Ionic conductivity and Raman spectra of Na--Li, K--Li, and K--Sn β-Al2O3

International Nuclear Information System (INIS)

Kaneda, T.; Bates, J.B.; Wang, J.C.; Engstrom, H.

1979-01-01

The ionic conductivity and Raman spectra of Na, Na--Li, K, K--Li, and K--Sn β-Al 2 O 3 were measured in order to understand the mechanisms of mixed-ion conduction. It was observed that at 300 0 K, for example, the conductivity of a crystal with composition Na 0 . 82 Li 0 . 18 β-Al 2 O 3 was about one-fifth that of pure Na cyrstals, while the conductivity of K 0 . 80 Li 0 . 20 β-Al 2 O 3 was more than three orders of magnitude lower than that of pure K compounds. The results of a model calculation indicated that the Li + ions are the main carrier species in the Na--Li and K--Li mixed compounds. Features observed in the Raman spectra were attributed to paired- and single-ion vibrations. It is concluded that the K + ions which contribute to a band at 69 cm -1 in K β-Al 2 O 3 are the effective carriers for conduction
MER SPICE Interface

Science.gov (United States)

Sayfi, Elias

2004-01-01

MER SPICE Interface is a software module for use in conjunction with the Mars Exploration Rover (MER) mission and the SPICE software system of the Navigation and Ancillary Information Facility (NAIF) at NASA's Jet Propulsion Laboratory. (SPICE is used to acquire, record, and disseminate engineering, navigational, and other ancillary data describing circumstances under which data were acquired by spaceborne scientific instruments.) Given a Spacecraft Clock value, MER SPICE Interface extracts MER-specific data from SPICE kernels (essentially, raw data files) and calculates values for Planet Day Number, Local Solar Longitude, Local Solar Elevation, Local Solar Azimuth, and Local Solar Time (UTC). MER SPICE Interface was adapted from a subroutine, denoted m98SpiceIF written by Payam Zamani, that was intended to calculate SPICE values for the Mars Polar Lander. The main difference between MER SPICE Interface and m98SpiceIf is that MER SPICE Interface does not explicitly call CHRONOS, a time-conversion program that is part of a library of utility subprograms within SPICE. Instead, MER SPICE Interface mimics some portions of the CHRONOS code, the advantage being that it executes much faster and can efficiently be called from a pipeline of events in a parallel processing environment.
Preliminary analysis of the MER magnetic properties experiment using a computational fluid dynamics model

DEFF Research Database (Denmark)

Kinch, K.M.; Merrison, J.P.; Gunnlaugsson, H.P.

2006-01-01

Motivated by questions raised by the magnetic properties experiments on the NASA Mars Pathfinder and Mars Exploration Rover (MER) missions, we have studied in detail the capture of airborne magnetic dust by permanent magnets using a computational fluid dynamics (CFD) model supported by laboratory...... simulations. The magnets studied are identical to the capture magnet and filter magnet on MER, though results are more generally applicable. The dust capture process is found to be dependent upon wind speed, dust magnetization, dust grain size and dust grain mass density. Here we develop an understanding...... of how these parameters affect dust capture rates and patterns on the magnets and set bounds for these parameters based on MER data and results from the numerical model. This results in a consistent picture of the dust as containing varying amounts of at least two separate components with different...
Generation of NSE-MerCreMer transgenic mice with tamoxifen inducible Cre activity in neurons.

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Mandy Ka Man Kam

Full Text Available To establish a genetic tool for conditional deletion or expression of gene in neurons in a temporally controlled manner, we generated a transgenic mouse (NSE-MerCreMer, which expressed a tamoxifen inducible type of Cre recombinase specifically in neurons. The tamoxifen inducible Cre recombinase (MerCreMer is a fusion protein containing Cre recombinase with two modified estrogen receptor ligand binding domains at both ends, and is driven by the neural-specific rat neural specific enolase (NSE promoter. A total of two transgenic lines were established, and expression of MerCreMer in neurons of the central and enteric nervous systems was confirmed. Transcript of MerCreMer was detected in several non-neural tissues such as heart, liver, and kidney in these lines. In the background of the Cre reporter mouse strain Rosa26R, Cre recombinase activity was inducible in neurons of adult NSE-MerCreMer mice treated with tamoxifen by intragastric gavage, but not in those fed with corn oil only. We conclude that NSE-MerCreMer lines will be useful for studying gene functions in neurons for the conditions that Cre-mediated recombination resulting in embryonic lethality, which precludes investigation of gene functions in neurons through later stages of development and in adult.
mer-Triammine trifluorido vanadium(III), mer-[VF{sub 3}(NH{sub 3}){sub 3}]. Synthesis and crystal structure

Energy Technology Data Exchange (ETDEWEB)

Woidy, Patrick [Technische Univ. Muenchen, Garching (Germany). Zentrale Technisch-Wissenschaftliche Betriebseinheit Radiochemie Muenchen RCM; Kraus, Florian [Marburg Univ. (Germany). Anorganische und Fluorchemie

2015-07-01

Vanadium trifluoride reacts with dry liquid ammonia under the formation of lilac plate-shaped crystals of mer-triammine trifluorido vanadium(III) (1), mer-[VF{sub 3}(NH{sub 3}){sub 3}]. Single-crystal X-ray analysis was carried out at low temperature to elucidate the structure. The compound crystallizes in the monoclinic space group P2{sup 1}/c with a = 5.7284(4), b = 9.2033(5), c = 10.5271(6) Aa, beta = 91.795(6)°, and V = 554.72(6) Aa{sup 3} at 123 K with Z = 4. The discrete [VF{sub 3}(NH{sub 3}){sub 3}] molecules are interconnected by hydrogen bonds.
The effects of downwelling radiance on MER surface spectra: the evil that atmospheres do

Science.gov (United States)

Wolff, M.; Ghosh, A.; Arvidson, R.; Christensen, P.; Guinness, E.; Ruff, S.; Seelos, F.; Smith, M.; Athena Science

2004-11-01

While it may not be surprising to some that downwelling radiation in the martian atmosphere may contribute a non-negligible fraction of the radiance for a given surface scene, others remain shocked and surprised (and often dismayed) to discover this fact; particularly with regard to mini-TES observations. Naturally, the relative amplitude of this sky ``contamination'' is often a complicated function of meteorological conditions, viewing geometry, surface properties, and (for the IR) surface temperature. Ideally, one would use a specialized observations to mimic the actual hemispherical-directional nature of the problem. Despite repeated attempts to obtain Pancam complete sky observations and mini-TES sky octants, such observations are not available in the MER observational database. As a result, one is left with the less-enviable, though certainly more computationally intensive, task of connecting point observations (radiance and derived meteorological parameters) to a hemispherical integral of downwelling radiance. Naturally, one must turn to a radiative transfer analysis, despite oft-repeated attempts to assert otherwise. In our presentation, we offer insight into the conditions under which one must worry about atmospheric removal, as well as semi-empirical approaches (based upon said radiative transfer efforts) for producing the correction factors from the available MER atmospheric observations. This work is proudly supported by the MER program through NASA/JPL Contract No. 1242889 (MJW), as well as the contracts for the co-authors.
An accurate method for computer-generating tungsten anode x-ray spectra from 30 to 140 kV.

Science.gov (United States)

Boone, J M; Seibert, J A

1997-11-01

A tungsten anode spectral model using interpolating polynomials (TASMIP) was used to compute x-ray spectra at 1 keV intervals over the range from 30 kV to 140 kV. The TASMIP is not semi-empirical and uses no physical assumptions regarding x-ray production, but rather interpolates measured constant potential x-ray spectra published by Fewell et al. [Handbook of Computed Tomography X-ray Spectra (U.S. Government Printing Office, Washington, D.C., 1981)]. X-ray output measurements (mR/mAs measured at 1 m) were made on a calibrated constant potential generator in our laboratory from 50 kV to 124 kV, and with 0-5 mm added aluminum filtration. The Fewell spectra were slightly modified (numerically hardened) and normalized based on the attenuation and output characteristics of a constant potential generator and metal-insert x-ray tube in our laboratory. Then, using the modified Fewell spectra of different kVs, the photon fluence phi at each 1 keV energy bin (E) over energies from 10 keV to 140 keV was characterized using polynomial functions of the form phi (E) = a0[E] + a1[E] kV + a2[E] kV2 + ... + a(n)[E] kVn. A total of 131 polynomial functions were used to calculate accurate x-ray spectra, each function requiring between two and four terms. The resulting TASMIP algorithm produced x-ray spectra that match both the quality and quantity characteristics of the x-ray system in our laboratory. For photon fluences above 10% of the peak fluence in the spectrum, the average percent difference (and standard deviation) between the modified Fewell spectra and the TASMIP photon fluence was -1.43% (3.8%) for the 50 kV spectrum, -0.89% (1.37%) for the 70 kV spectrum, and for the 80, 90, 100, 110, 120, 130 and 140 kV spectra, the mean differences between spectra were all less than 0.20% and the standard deviations were less than approximately 1.1%. The model was also extended to include the effects of generator-induced kV ripple. Finally, the x-ray photon fluence in the units of
Silicon K-edge XANES spectra of silicate minerals

Science.gov (United States)

Li, Dien; Bancroft, G. M.; Fleet, M. E.; Feng, X. H.

1995-03-01

Silicon K-edge x-ray absorption near-edge structure (XANES) spectra of a selection of silicate and aluminosilicate minerals have been measured using synchrotron radiation (SR). The spectra are qualitatively interpreted based on MO calculation of the tetrahedral SiO{4/4-}cluster. The Si K-edge generally shifts to higher energy with increased polymerization of silicates by about 1.3 eV, but with considerable overlap for silicates of different polymerization types. The substitution of Al for Si shifts the Si K-edge to lower energy. The chemical shift of Si K-edge is also sensitive to cations in more distant atom shells; for example, the Si K-edge shifts to lower energy with the substitution of Al for Mg in octahedral sites. The shifts of the Si K-edge show weak correlation with average Si-O bond distance (dSi-O), Si-O bond valence (sSi-O) and distortion of SiO4 tetrahedra, due to the crystal structure complexity of silicate minerals and multiple factors effecting the x-ray absorption processes.
Photoionization Modeling of Oxygen K Absorption in the Interstellar Medium: The Chandra Grating Spectra of XTE J1817-330

Science.gov (United States)

Gatuzz, E.; Garcia, J.; Menodza, C.; Kallman, T. R.; Witthoeft, M.; Lohfink, A.; Bautista, M. A.; Palmeri, P.; Quinet, P.

2013-01-01

We present detailed analyses of oxygen K absorption in the interstellar medium (ISM) using four high-resolution Chandra spectra towards the X-ray low-mass binary XTE J1817-330. The 11-25 A broadband is described with a simple absorption model that takes into account the pileup effect and results in an estimate of the hydrogen column density. The oxygen K-edge region (21-25 A) is fitted with the physical warmabs model, which is based on a photoionization model grid generated with the XSTAR code with the most up-to-date atomic database. This approach allows a benchmark of the atomic data which involves wavelength shifts of both the K lines and photoionization cross sections in order to fit the observed spectra accurately. As a result we obtain: a column density of N(sub H) = 1.38 +/- 0.01 x 10(exp 21) cm(exp -2); ionization parameter of log xi = .2.70 +/- 0.023; oxygen abundance of A(sub O) = 0.689(exp +0.015./-0.010); and ionization fractions of O I/O = 0.911, O II/O = 0.077, and O III/O = 0.012 that are in good agreement with previous studies. Since the oxygen abundance in warmabs is given relative to the solar standard of Grevesse and Sauval (1998), a rescaling with the revision by Asplund et al. (2009) yields A(sub O) = 0.952(exp +0.020/-0.013, a value close to solar that reinforces the new standard. We identify several atomic absorption lines.K-alpha , K-beta, and K-gamma in O I and O II; and K-alpha in O III, O VI, and O VII--last two probably residing in the neighborhood of the source rather than in the ISM. This is the first firm detection of oxygen K resonances with principal quantum numbers n greater than 2 associated to ISM cold absorption.

Photoionization Modeling of Oxygen K Absorption in the Interstellar Medium:. [The Chandra Grating Spectra of XTE J1817-330

Science.gov (United States)

Gatuzz, E.; Garcia, J.; Mendoza, C.; Kallman, T. R.; Witthoeft, M.; Lohfink, A.; Bautista, M. A.; Palmeri, P.; Quinet, P.

2013-01-01

We present detailed analyses of oxygen K absorption in the interstellar medium (ISM) using four high-resolution Chandra spectra toward the X-ray low-mass binary XTE J1817-330. The 11-25 Angstrom broadband is described with a simple absorption model that takes into account the pile-up effect and results in an estimate of the hydrogen column density. The oxygen K-edge region (21-25 Angstroms) is fitted with the physical warmabs model, which is based on a photoionization model grid generated with the xstar code with the most up-to-date atomic database. This approach allows a benchmark of the atomic data which involves wavelength shifts of both the K lines and photoionization cross sections in order to fit the observed spectra accurately. As a result we obtain a column density of N(sub H) = 1.38 +/- 0.01 × 10(exp 21) cm(exp -2); an ionization parameter of log xi = -2.70 +/- 0.023; an oxygen abundance of A(sub O) = 0.689 (+0.015/-0.010); and ionization fractions of O(sub I)/O = 0.911, O(sub II)/O = 0.077, and O(sub III)/O = 0.012 that are in good agreement with results from previous studies. Since the oxygen abundance in warmabs is given relative to the solar standard of Grevesse & Sauval, a rescaling with the revision by Asplund et al. yields A(sub O) = 0.952(+0.020/-0.013), a value close to solar that reinforces the new standard.We identify several atomic absorption lines-K(alpha), K(beta), and K(gamma) in O(sub I) and O(sub II) and K(alpha) in O(sub III), O(sub VI), and O(sub VII)-the last two probably residing in the neighborhood of the source rather than in the ISM. This is the first firm detection of oxygen K resonances with principal quantum numbers n greater than 2 associated with ISM cold absorption.
De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences

Directory of Open Access Journals (Sweden)

Shairul Izan

2017-08-01

Full Text Available Whole Genome Shotgun (WGS sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This re-sequencing approach may select against structural differences between the genomes especially in non-model species for which no close relatives have been sequenced before. The alternative approach is to de novo assemble the chloroplast genome from total genomic DNA sequences. In this study, we used k-mer frequency tables to identify and extract the chloroplast reads from the WGS reads and assemble these using a highly integrated and automated custom pipeline. Our strategy includes steps aimed at optimizing assemblies and filling gaps which are left due to coverage variation in the WGS dataset. We have successfully de novo assembled three complete chloroplast genomes from plant species with a range of nuclear genome sizes to demonstrate the universality of our approach: Solanum lycopersicum (0.9 Gb, Aegilops tauschii (4 Gb and Paphiopedilum henryanum (25 Gb. We also highlight the need to optimize the choice of k and the amount of data used. This new and cost-effective method for de novo short read assembly will facilitate the study of complete chloroplast genomes with more accurate analyses and inferences, especially in non-model plant genomes.
Progress in Noise Thermometry at 505 K and 693 K Using Quantized Voltage Noise Ratio Spectra

Science.gov (United States)

Tew, W. L.; Benz, S. P.; Dresselhaus, P. D.; Coakley, K. J.; Rogalla, H.; White, D. R.; Labenski, J. R.

2010-09-01

Technical advances and new results in noise thermometry at temperatures near the tin freezing point and the zinc freezing point using a quantized voltage noise source (QVNS) are reported. The temperatures are derived by comparing the power spectral density of QVNS synthesized noise with that of Johnson noise from a known resistance at both 505 K and 693 K. Reference noise is digitally synthesized so that the average power spectra of the QVNS match those of the thermal noise, resulting in ratios of power spectra close to unity in the low-frequency limit. Three-parameter models are used to account for differences in impedance-related time constants in the spectra. Direct comparison of noise temperatures to the International Temperature Scale of 1990 (ITS-90) is achieved in a comparison furnace with standard platinum resistance thermometers. The observed noise temperatures determined by operating the noise thermometer in both absolute and relative modes, and related statistics together with estimated uncertainties are reported. The relative noise thermometry results are combined with results from other thermodynamic determinations at temperatures near the tin freezing point to calculate a value of T - T 90 = +4(18) mK for temperatures near the zinc freezing point. These latest results achieve a lower uncertainty than that of our earlier efforts. The present value of T - T 90 is compared to other published determinations from noise thermometry and other methods.
Engineering MerR for Sequestration and MerA for Reduction of Toxic Metals and Radionuclides

International Nuclear Information System (INIS)

Summers, Anne O.

2008-01-01

The objectives of this project were (1) to alter a metalloregulatory protein (MerR) so that it would bind other toxic metals or radionuclides with similar affinity so that the engineered protein itself and/or bacteria expressing it could be deployed in the environment to specifically sequester such metals and (2) to alter the mercuric reductase, MerA, to reduce radionuclides and render them less mobile. Both projects had a basic science component. In the first case, such information about MerR illuminates how proteins discriminate very similar metals/elements. In the second case, information about MerA reveals the criteria for transmission of reducing equivalents from NADPH to redox-active metals. The work involved genetic engineering of all or parts of both proteins and examination of their resultant properties both in vivo and in vitro, the latter with biochemical and biophysical tools including equilibrium and non-equilibrium dialysis, XAFS, NMR, x-ray crystallography, and titration calorimetry. We defined the basis for metal specificity in MerR, devised a bacterial strain that sequesters Hg while growing, characterized gold reduction by MerA and the role of the metallochaperone domain of MerA, and determined the 3-D structure of MerB, the organomercurial lyase.
A k-mer-based barcode DNA classification methodology based on spectral representation and a neural gas network.

Science.gov (United States)

Fiannaca, Antonino; La Rosa, Massimo; Rizzo, Riccardo; Urso, Alfonso

2015-07-01

In this paper, an alignment-free method for DNA barcode classification that is based on both a spectral representation and a neural gas network for unsupervised clustering is proposed. In the proposed methodology, distinctive words are identified from a spectral representation of DNA sequences. A taxonomic classification of the DNA sequence is then performed using the sequence signature, i.e., the smallest set of k-mers that can assign a DNA sequence to its proper taxonomic category. Experiments were then performed to compare our method with other supervised machine learning classification algorithms, such as support vector machine, random forest, ripper, naïve Bayes, ridor, and classification tree, which also consider short DNA sequence fragments of 200 and 300 base pairs (bp). The experimental tests were conducted over 10 real barcode datasets belonging to different animal species, which were provided by the on-line resource "Barcode of Life Database". The experimental results showed that our k-mer-based approach is directly comparable, in terms of accuracy, recall and precision metrics, with the other classifiers when considering full-length sequences. In addition, we demonstrate the robustness of our method when a classification is performed task with a set of short DNA sequences that were randomly extracted from the original data. For example, the proposed method can reach the accuracy of 64.8% at the species level with 200-bp fragments. Under the same conditions, the best other classifier (random forest) reaches the accuracy of 20.9%. Our results indicate that we obtained a clear improvement over the other classifiers for the study of short DNA barcode sequence fragments. Copyright © 2015 Elsevier B.V. All rights reserved.
Surveillance of the Middle East respiratory syndrome (MERS) coronavirus (CoV) infection in healthcare workers after contact with confirmed MERS patients: incidence and risk factors of MERS-CoV seropositivity.

Science.gov (United States)

Kim, C-J; Choi, W S; Jung, Y; Kiem, S; Seol, H Y; Woo, H J; Choi, Y H; Son, J S; Kim, K-H; Kim, Y-S; Kim, E S; Park, S H; Yoon, J H; Choi, S-M; Lee, H; Oh, W S; Choi, S-Y; Kim, N-J; Choi, J-P; Park, S Y; Kim, J; Jeong, S J; Lee, K S; Jang, H C; Rhee, J Y; Kim, B-N; Bang, J H; Lee, J H; Park, S; Kim, H Y; Choi, J K; Wi, Y-M; Choi, H J

2016-10-01

Given the mode of transmission of Middle East respiratory syndrome (MERS), healthcare workers (HCWs) in contact with MERS patients are expected to be at risk of MERS infections. We evaluated the prevalence of MERS coronavirus (CoV) immunoglobulin (Ig) G in HCWs exposed to MERS patients and calculated the incidence of MERS-affected cases in HCWs. We enrolled HCWs from hospitals where confirmed MERS patients had visited. Serum was collected 4 to 6 weeks after the last contact with a confirmed MERS patient. We performed an enzyme-linked immunosorbent assay (ELISA) to screen for the presence of MERS-CoV IgG and an indirect immunofluorescence test (IIFT) to confirm MERS-CoV IgG. We used a questionnaire to collect information regarding the exposure. We calculated the incidence of MERS-affected cases by dividing the sum of PCR-confirmed and serology-confirmed cases by the number of exposed HCWs in participating hospitals. In total, 1169 HCWs in 31 hospitals had contact with 114 MERS patients, and among the HCWs, 15 were PCR-confirmed MERS cases in study hospitals. Serologic analysis was performed for 737 participants. ELISA was positive in five participants and borderline for seven. IIFT was positive for two (0.3%) of these 12 participants. Among the participants who did not use appropriate personal protective equipment (PPE), seropositivity was 0.7% (2/294) compared to 0% (0/443) in cases with appropriate PPE use. The incidence of MERS infection in HCWs was 1.5% (17/1169). The seroprevalence of MERS-CoV IgG among HCWs was higher among participants who did not use appropriate PPE. Copyright © 2016. Published by Elsevier Ltd.
Environmental Contamination and Viral Shedding in MERS Patients During MERS-CoV Outbreak in South Korea.

Science.gov (United States)

Bin, Seo Yu; Heo, Jung Yeon; Song, Min-Suk; Lee, Jacob; Kim, Eun-Ha; Park, Su-Jin; Kwon, Hyeok-Il; Kim, Se Mi; Kim, Young-Il; Si, Young-Jae; Lee, In-Won; Baek, Yun Hee; Choi, Won-Suk; Min, Jinsoo; Jeong, Hye Won; Choi, Young Ki

2016-03-15

Although Middle East Respiratory Syndrome coronavirus (MERS-CoV) is characterized by a risk of nosocomial transmission, the detailed mode of transmission and period of virus shedding from infected patients are poorly understood. The aims of this study were to investigate the potential role of environmental contamination by MERS-CoV in healthcare settings and to define the period of viable virus shedding from MERS patients. We investigated environmental contamination from 4 patients in MERS-CoV units of 2 hospitals. MERS-CoV was detected by reverse transcription polymerase chain reaction (PCR) and viable virus was isolated by cultures. Many environmental surfaces of MERS patient rooms, including points frequently touched by patients or healthcare workers, were contaminated by MERS-CoV. Viral RNA was detected up to five days from environmental surfaces following the last positive PCR from patients' respiratory specimens. MERS-CoV RNA was detected in samples from anterooms, medical devices, and air-ventilating equipment. In addition, MERS-CoV was isolated from environmental objects such as bed sheets, bedrails, IV fluid hangers, and X-ray devices. During the late clinical phase of MERS, viable virus could be isolated in 3 of the 4 enrolled patients on day 18 to day 25 after symptom onset. Most of touchable surfaces in MERS units were contaminated by patients and health care workers and the viable virus could shed through respiratory secretion from clinically fully recovered patients. These results emphasize the need for strict environmental surface hygiene practices, and sufficient isolation period based on laboratory results rather than solely on clinical symptoms. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.
Transcriptional switching by the MerR protein: Activation and repression mutants implicate distinct DNA and mercury(II) binding domains

International Nuclear Information System (INIS)

Shewchuk, L.M.; Helmann, J.D.; Ross, W.; Park, S.J.; Summers, A.O.; Walsh, C.T.

1989-01-01

Bacterial resistance to mercuric compounds is controlled by the MerR metalloregulatory protein. The MerR protein functions as both a transcriptional repressor and a mercuric ion dependent transcriptional activator. Chemical mutagenesis of the cloned merR structural gene has led to the identification of mutant proteins that are specifically deficient in transcriptional repression, activation, or both. Five mutant proteins have been overproduced, purified to homogeneity, and assayed for ability to dimerize, bind mer operator DNA, and bind mercuric ion. A mutation in the recognition helix of a proposed helix-turn-helix DNA binding motif (E22K) yields protein deficient in both activation and repression in vivo (a - r - ) and deficient in operator binding in vitro. In contrast, mutations in three of the four MerR cysteine residues are repression competent but activation deficient (a - r + ) in vivo. In vitro, the purified cysteine mutant proteins bind to the mer operator site with near wild-type affinity but are variable deficient in binding the in vivo inducer mercury(II) ion. A subset of the isolated proteins also appears compromised in their ability to form dimers at low protein concentrations. These data support a model in which DNA-bound MerR dimer binds one mercuric ion and transmits this occupancy information to a protein region involved in transcriptional activation
PHOTOIONIZATION MODELING OF OXYGEN K ABSORPTION IN THE INTERSTELLAR MEDIUM: THE CHANDRA GRATING SPECTRA OF XTE J1817-330

International Nuclear Information System (INIS)

Gatuzz, E.; Mendoza, C.; García, J.; Lohfink, A.; Kallman, T. R.; Witthoeft, M.; Bautista, M. A.; Palmeri, P.; Quinet, P.

2013-01-01

We present detailed analyses of oxygen K absorption in the interstellar medium (ISM) using four high-resolution Chandra spectra toward the X-ray low-mass binary XTE J1817-330. The 11-25 Å broadband is described with a simple absorption model that takes into account the pile-up effect and results in an estimate of the hydrogen column density. The oxygen K-edge region (21-25 Å) is fitted with the physical warmabs model, which is based on a photoionization model grid generated with the XSTAR code with the most up-to-date atomic database. This approach allows a benchmark of the atomic data which involves wavelength shifts of both the K lines and photoionization cross sections in order to fit the observed spectra accurately. As a result we obtain a column density of N H = 1.38 ± 0.01 × 10 21 cm –2 ; an ionization parameter of log ξ = –2.70 ± 0.023; an oxygen abundance of A O = 0.689 +0.015 -0.010 ; and ionization fractions of O I/O = 0.911, O II/O = 0.077, and O III/O = 0.012 that are in good agreement with results from previous studies. Since the oxygen abundance in warmabs is given relative to the solar standard of Grevesse and Sauval, a rescaling with the revision by Asplund et al. yields A O =0.952 +0.020 -0.013 , a value close to solar that reinforces the new standard. We identify several atomic absorption lines—Kα, Kβ, and Kγ in O I and O II and Kα in O III, O VI, and O VII—the last two probably residing in the neighborhood of the source rather than in the ISM. This is the first firm detection of oxygen K resonances with principal quantum numbers n > 2 associated with ISM cold absorption.
Carbon K-edge spectra of carbonate minerals.

Science.gov (United States)

Brandes, Jay A; Wirick, Sue; Jacobsen, Chris

2010-09-01

Carbon K-edge X-ray spectroscopy has been applied to the study of a wide range of organic samples, from polymers and coals to interstellar dust particles. Identification of carbonaceous materials within these samples is accomplished by the pattern of resonances in the 280-320 eV energy region. Carbonate minerals are often encountered in the study of natural samples, and have been identified by a distinctive resonance at 290.3 eV. Here C K-edge and Ca L-edge spectra from a range of carbonate minerals are presented. Although all carbonates exhibit a sharp 290 eV resonance, both the precise position of this resonance and the positions of other resonances vary among minerals. The relative strengths of the different carbonate resonances also vary with crystal orientation to the linearly polarized X-ray beam. Intriguingly, several carbonate minerals also exhibit a strong 288.6 eV resonance, consistent with the position of a carbonyl resonance rather than carbonate. Calcite and aragonite, although indistinguishable spectrally at the C K-edge, exhibited significantly different spectra at the Ca L-edge. The distinctive spectral fingerprints of carbonates provide an identification tool, allowing for the examination of such processes as carbon sequestration in minerals, Mn substitution in marine calcium carbonates (dolomitization) and serpentinization of basalts.
Carbon K-edge Spectra of Carbonate Minerals

Energy Technology Data Exchange (ETDEWEB)

Brandes, J.; Wirick, S; Jacobsen, C

2010-01-01

Carbon K-edge X-ray spectroscopy has been applied to the study of a wide range of organic samples, from polymers and coals to interstellar dust particles. Identification of carbonaceous materials within these samples is accomplished by the pattern of resonances in the 280-320 eV energy region. Carbonate minerals are often encountered in the study of natural samples, and have been identified by a distinctive resonance at 290.3 eV. Here C K-edge and Ca L-edge spectra from a range of carbonate minerals are presented. Although all carbonates exhibit a sharp 290 eV resonance, both the precise position of this resonance and the positions of other resonances vary among minerals. The relative strengths of the different carbonate resonances also vary with crystal orientation to the linearly polarized X-ray beam. Intriguingly, several carbonate minerals also exhibit a strong 288.6 eV resonance, consistent with the position of a carbonyl resonance rather than carbonate. Calcite and aragonite, although indistinguishable spectrally at the C K-edge, exhibited significantly different spectra at the Ca L-edge. The distinctive spectral fingerprints of carbonates provide an identification tool, allowing for the examination of such processes as carbon sequestration in minerals, Mn substitution in marine calcium carbonates (dolomitization) and serpentinization of basalts.
Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease

Energy Technology Data Exchange (ETDEWEB)

Johnson, Reed F., E-mail: johnsonreed@mail.nih.gov [Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD (United States); Via, Laura E. [Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD (United States); Kumar, Mia R.; Cornish, Joseph P. [Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD (United States); Yellayi, Srikanth; Huzella, Louis; Postnikova, Elena; Oberlander, Nicholas; Bartos, Christopher; Ork, Britini L.; Mazur, Steven; Allan, Cindy; Holbrook, Michael R. [Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD (United States); Solomon, Jeffrey [Center for Infectious Disease Imaging, Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD (United States); Johnson, Joshua C. [Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD (United States); Pickel, James [Transgenic Core Facility, National Institute of Mental Health, National Institutes of Health, Bethesda, MD (United States); Hensley, Lisa E. [Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD (United States); Jahrling, Peter B. [Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD (United States); Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD (United States)

2015-11-15

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) continues to be a threat to human health in the Middle East. Development of countermeasures is ongoing; however, an animal model that faithfully recapitulates human disease has yet to be defined. A recent study indicated that inoculation of common marmosets resulted in inconsistent lethality. Based on these data we sought to compare two isolates of MERS-CoV. We followed disease progression in common marmosets after intratracheal exposure with: MERS-CoV-EMC/2012, MERS-CoV-Jordan-n3/2012, media, or inactivated virus. Our data suggest that common marmosets developed a mild to moderate non-lethal respiratory disease, which was quantifiable by computed tomography (CT), with limited other clinical signs. Based on CT data, clinical data, and virological data, MERS-CoV inoculation of common marmosets results in mild to moderate clinical signs of disease that are likely due to manipulations of the marmoset rather than as a result of robust viral replication. - Highlights: • Common marmosets infected with MERS-EMC and MERS-JOR did not develop lethal disease. • Infected subjects developed transient signs of clinical disease. • CT indicated few differences between the infected and control groups. • Marmosets do not faithfully replicate human MERS pathogenesis.
Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease

International Nuclear Information System (INIS)

Johnson, Reed F.; Via, Laura E.; Kumar, Mia R.; Cornish, Joseph P.; Yellayi, Srikanth; Huzella, Louis; Postnikova, Elena; Oberlander, Nicholas; Bartos, Christopher; Ork, Britini L.; Mazur, Steven; Allan, Cindy; Holbrook, Michael R.; Solomon, Jeffrey; Johnson, Joshua C.; Pickel, James; Hensley, Lisa E.; Jahrling, Peter B.

2015-01-01

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) continues to be a threat to human health in the Middle East. Development of countermeasures is ongoing; however, an animal model that faithfully recapitulates human disease has yet to be defined. A recent study indicated that inoculation of common marmosets resulted in inconsistent lethality. Based on these data we sought to compare two isolates of MERS-CoV. We followed disease progression in common marmosets after intratracheal exposure with: MERS-CoV-EMC/2012, MERS-CoV-Jordan-n3/2012, media, or inactivated virus. Our data suggest that common marmosets developed a mild to moderate non-lethal respiratory disease, which was quantifiable by computed tomography (CT), with limited other clinical signs. Based on CT data, clinical data, and virological data, MERS-CoV inoculation of common marmosets results in mild to moderate clinical signs of disease that are likely due to manipulations of the marmoset rather than as a result of robust viral replication. - Highlights: • Common marmosets infected with MERS-EMC and MERS-JOR did not develop lethal disease. • Infected subjects developed transient signs of clinical disease. • CT indicated few differences between the infected and control groups. • Marmosets do not faithfully replicate human MERS pathogenesis.
Emission spectra of alkali-metal (K,Na,Li)-He exciplexes in cold helium gas

International Nuclear Information System (INIS)

Enomoto, K.; Hirano, K.; Kumakura, M.; Takahashi, Y.; Yabuzaki, T.

2004-01-01

We have observed emission spectra of excimers and exciplexes composed of a light alkali-metal atom in the first excited state and 4 He atoms [K*He n (n=1-6), Na * He n (n=1-4), and Li * He n (n=1,2)] in cryogenic He gas (the temperature 2 K -1 . Differently from exciplexes with heavier alkali-metal atoms, the spectra for the different number of He atoms were well separated, so that their assignment could be made experimentally. Comparing with the spectra of K * He n , we found that the infrared emission spectrum of the K atom excited in liquid He was from K*He 6 . To confirm the assignment, we have also carried out ab initio calculation of adiabatic potential curves and peak positions of the emission spectra of the exciplexes
Sur terre comme sur mer: organisations spatiales en mer du Nord et mer de Norvège

Directory of Open Access Journals (Sweden)

Maryvonne LE BERRE

1998-09-01

Full Text Available L'article montre, au moyen de représentations cartographiques et graphiques, les structures spatiales développées en mer pour l'exploitation des hydrocarbures. Malgré les différences de milieu, l'appropriation et l'occupation territoriales du domaine maritime s'effectuent selon les mêmes principes que sur le continent, à ceci près que ce qui s'étale en surface sur le continent se développe à la verticale en mer.
Extensive Viable Middle East Respiratory Syndrome (MERS) Coronavirus Contamination in Air and Surrounding Environment in MERS Isolation Wards.

Science.gov (United States)

Kim, Sung-Han; Chang, So Young; Sung, Minki; Park, Ji Hoon; Bin Kim, Hong; Lee, Heeyoung; Choi, Jae-Phil; Choi, Won Suk; Min, Ji-Young

2016-08-01

The largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) outside the Middle East occurred in South Korea in 2015 and resulted in 186 laboratory-confirmed infections, including 36 (19%) deaths. Some hospitals were considered epicenters of infection and voluntarily shut down most of their operations after nearly half of all transmissions occurred in hospital settings. However, the ways that MERS-CoV is transmitted in healthcare settings are not well defined. We explored the possible contribution of contaminated hospital air and surfaces to MERS transmission by collecting air and swabbing environmental surfaces in 2 hospitals treating MERS-CoV patients. The samples were tested by viral culture with reverse transcription polymerase chain reaction (RT-PCR) and immunofluorescence assay (IFA) using MERS-CoV Spike antibody, and electron microscopy (EM). The presence of MERS-CoV was confirmed by RT-PCR of viral cultures of 4 of 7 air samples from 2 patients' rooms, 1 patient's restroom, and 1 common corridor. In addition, MERS-CoV was detected in 15 of 68 surface swabs by viral cultures. IFA on the cultures of the air and swab samples revealed the presence of MERS-CoV. EM images also revealed intact particles of MERS-CoV in viral cultures of the air and swab samples. These data provide experimental evidence for extensive viable MERS-CoV contamination of the air and surrounding materials in MERS outbreak units. Thus, our findings call for epidemiologic investigation of the possible scenarios for contact and airborne transmission, and raise concern regarding the adequacy of current infection control procedures. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.
Computational modeling of the bat HKU4 coronavirus 3CLpro inhibitors as a tool for the development of antivirals against the emerging Middle East respiratory syndrome (MERS) coronavirus.

Science.gov (United States)

Abuhammad, Areej; Al-Aqtash, Rua'a A; Anson, Brandon J; Mesecar, Andrew D; Taha, Mutasem O

2017-11-01

The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus that poses a major challenge to clinical management. The 3C-like protease (3CL pro ) is essential for viral replication and thus represents a potential target for antiviral drug development. Presently, very few data are available on MERS-CoV 3CL pro inhibition by small molecules. We conducted extensive exploration of the pharmacophoric space of a recently identified set of peptidomimetic inhibitors of the bat HKU4-CoV 3CL pro . HKU4-CoV 3CL pro shares high sequence identity (81%) with the MERS-CoV enzyme and thus represents a potential surrogate model for anti-MERS drug discovery. We used 2 well-established methods: Quantitative structure-activity relationship (QSAR)-guided modeling and docking-based comparative intermolecular contacts analysis. The established pharmacophore models highlight structural features needed for ligand recognition and revealed important binding-pocket regions involved in 3CL pro -ligand interactions. The best models were used as 3D queries to screen the National Cancer Institute database for novel nonpeptidomimetic 3CL pro inhibitors. The identified hits were tested for HKU4-CoV and MERS-CoV 3CL pro inhibition. Two hits, which share the phenylsulfonamide fragment, showed moderate inhibitory activity against the MERS-CoV 3CL pro and represent a potential starting point for the development of novel anti-MERS agents. To the best of our knowledge, this is the first pharmacophore modeling study supported by in vitro validation on the MERS-CoV 3CL pro . MERS-CoV is an emerging virus that is closely related to the bat HKU4-CoV. 3CL pro is a potential drug target for coronavirus infection. HKU4-CoV 3CL pro is a useful surrogate model for the identification of MERS-CoV 3CL pro enzyme inhibitors. dbCICA is a very robust modeling method for hit identification. The phenylsulfonamide scaffold represents a potential starting point for MERS coronavirus 3CL pro inhibitors
Middle East Respiratory Syndrome (MERS)

Science.gov (United States)

Middle East Respiratory Syndrome Coronavirus; MERS-CoV; Novel coronavirus; nCoV ... for Disease Control and Prevention website. Middle East Respiratory Syndrome (MERS): Frequently asked questions and answers. www. ...
Simulations of the Fe K α Energy Spectra from Gravitationally Microlensed Quasars

Energy Technology Data Exchange (ETDEWEB)

Krawczynski, H. [Physics Department and McDonnell Center for the Space Sciences, Washington University in St. Louis, 1 Brookings Drive, CB 1105, St. Louis, MO 63130 (United States); Chartas, G., E-mail: krawcz@wustl.edu [Department of Physics and Astronomy, College of Charleston, Charleston, SC 29424 (United States)

2017-07-10

The analysis of the Chandra X-ray observations of the gravitationally lensed quasar RX J1131−1231 revealed the detection of multiple and energy-variable spectral peaks. The spectral variability is thought to result from the microlensing of the Fe K α emission, selectively amplifying the emission from certain regions of the accretion disk with certain effective frequency shifts of the Fe K α line emission. In this paper, we combine detailed simulations of the emission of Fe K α photons from the accretion disk of a Kerr black hole with calculations of the effect of gravitational microlensing on the observed energy spectra. The simulations show that microlensing can indeed produce multiply peaked energy spectra. We explore the dependence of the spectral characteristics on black hole spin, accretion disk inclination, corona height, and microlensing amplification factor and show that the measurements can be used to constrain these parameters. We find that the range of observed spectral peak energies of QSO RX J1131−1231 can only be reproduced for black hole inclinations exceeding 70° and for lamppost corona heights of less than 30 gravitational radii above the black hole. We conclude by emphasizing the scientific potential of studies of the microlensed Fe K α quasar emission and the need for more detailed modeling that explores how the results change for more realistic accretion disk and corona geometries and microlensing magnification patterns. A full analysis should furthermore model the signal-to-noise ratio of the observations and the resulting detection biases.
3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012

International Nuclear Information System (INIS)

Johnson, Reed F.; Bagci, Ulas; Keith, Lauren; Tang, Xianchun; Mollura, Daniel J.; Zeitlin, Larry; Qin, Jing; Huzella, Louis; Bartos, Christopher J.; Bohorova, Natasha; Bohorov, Ognian; Goodman, Charles; Kim, Do H.; Paulty, Michael H.; Velasco, Jesus; Whaley, Kevin J.; Johnson, Joshua C.; Pettitt, James; Ork, Britini L.; Solomon, Jeffrey

2016-01-01

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was identified in 2012 as the causative agent of a severe, lethal respiratory disease occurring across several countries in the Middle East. To date there have been over 1600 laboratory confirmed cases of MERS-CoV in 26 countries with a case fatality rate of 36%. Given the endemic region, it is possible that MERS-CoV could spread during the annual Hajj pilgrimage, necessitating countermeasure development. In this report, we describe the clinical and radiographic changes of rhesus monkeys following infection with 5×10"6 PFU MERS-CoV Jordan-n3/2012. Two groups of NHPs were treated with either a human anti-MERS monoclonal antibody 3B11-N or E410-N, an anti-HIV antibody. MERS-CoV Jordan-n3/2012 infection resulted in quantifiable changes by computed tomography, but limited other clinical signs of disease. 3B11-N treated subjects developed significantly reduced lung pathology when compared to infected, untreated subjects, indicating that this antibody may be a suitable MERS-CoV treatment. - Highlights: • MERS-CoV Jordan-n3/2012 challenge of rhesus monkeys results in a mild disease. • CT can be used to monitor disease progression to aid models of human disease. • Treatment with the human monoclonal antibody 3B11-N resulted in decreased disease.

3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012

Energy Technology Data Exchange (ETDEWEB)

Johnson, Reed F., E-mail: johnsonreed@mail.nih.gov [Emerging Viral Pathogens Section National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702 (United States); Bagci, Ulas [Center for Infectious Disease Imaging, National Institutes of Health Clinical Center, Bethesda MD 20892 (United States); Center for Research in Computer Vision (CRCV), Department of Electrics Electronics and Computer Science, University of Central Florida, Orlando, FL 32816, USA. (United States); Keith, Lauren [Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702 (United States); Tang, Xianchun [Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 (United States); Mollura, Daniel J. [Center for Infectious Disease Imaging, National Institutes of Health Clinical Center, Bethesda MD 20892 (United States); Zeitlin, Larry [Mapp Biopharmaceutical, Inc., San Diego CA 92121 (United States); Qin, Jing [Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 (United States); Huzella, Louis; Bartos, Christopher J. [Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702 (United States); Bohorova, Natasha; Bohorov, Ognian; Goodman, Charles; Kim, Do H.; Paulty, Michael H.; Velasco, Jesus; Whaley, Kevin J. [Mapp Biopharmaceutical, Inc., San Diego CA 92121 (United States); Johnson, Joshua C.; Pettitt, James; Ork, Britini L. [Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702 (United States); Solomon, Jeffrey [Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,Frederick, MD 21702-USA. (United States); and others

2016-03-15

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was identified in 2012 as the causative agent of a severe, lethal respiratory disease occurring across several countries in the Middle East. To date there have been over 1600 laboratory confirmed cases of MERS-CoV in 26 countries with a case fatality rate of 36%. Given the endemic region, it is possible that MERS-CoV could spread during the annual Hajj pilgrimage, necessitating countermeasure development. In this report, we describe the clinical and radiographic changes of rhesus monkeys following infection with 5×10{sup 6} PFU MERS-CoV Jordan-n3/2012. Two groups of NHPs were treated with either a human anti-MERS monoclonal antibody 3B11-N or E410-N, an anti-HIV antibody. MERS-CoV Jordan-n3/2012 infection resulted in quantifiable changes by computed tomography, but limited other clinical signs of disease. 3B11-N treated subjects developed significantly reduced lung pathology when compared to infected, untreated subjects, indicating that this antibody may be a suitable MERS-CoV treatment. - Highlights: • MERS-CoV Jordan-n3/2012 challenge of rhesus monkeys results in a mild disease. • CT can be used to monitor disease progression to aid models of human disease. • Treatment with the human monoclonal antibody 3B11-N resulted in decreased disease.
Ole Rømers mange talenter

DEFF Research Database (Denmark)

Pedersen, Kurt Møller

2005-01-01

Artiklen giver en oversigt over Ole Rømers videnskabelige liv som astronom, fysiker og matematiker samt hans betydning som kongelig embedsmand.......Artiklen giver en oversigt over Ole Rømers videnskabelige liv som astronom, fysiker og matematiker samt hans betydning som kongelig embedsmand....
Monoclonal Antibody Shows Promise as Potential Therapeutic for MERS | Poster

Science.gov (United States)

A monoclonal antibody has proven effective in preventing Middle Eastern Respiratory Syndrome (MERS) in lab animals, suggesting further development as a potential intervention for the deadly disease in humans, according to new research. MERS is a newly emerged coronavirus first detected in humans in 2012. Most cases have occurred in the Middle East, but the disease has appeared elsewhere. In all, MERS has infected more than 1,700 individuals and killed more than 600, according to the World Health Organization. No vaccines or antiviral therapies currently exist. Several candidate vaccines are being developed, and some have been tested in animal models, a prerequisite to human clinical trials.
Searching for animal models and potential target species for emerging pathogens: Experience gained from Middle East respiratory syndrome (MERS coronavirus

Directory of Open Access Journals (Sweden)

Júlia Vergara-Alert

2017-06-01

Full Text Available Emerging and re-emerging pathogens represent a substantial threat to public health, as demonstrated with numerous outbreaks over the past years, including the 2013–2016 outbreak of Ebola virus in western Africa. Coronaviruses are also a threat for humans, as evidenced in 2002/2003 with infection by the severe acute respiratory syndrome coronavirus (SARS-CoV, which caused more than 8000 human infections with 10% fatality rate in 37 countries. Ten years later, a novel human coronavirus (Middle East respiratory syndrome coronavirus, MERS-CoV, associated with severe pneumonia, arose in the Kingdom of Saudi Arabia. Until December 2016, MERS has accounted for more than 1800 cases and 35% fatality rate. Finding an animal model of disease is key to develop vaccines or antivirals against such emerging pathogens and to understand its pathogenesis. Knowledge of the potential role of domestic livestock and other animal species in the transmission of pathogens is of importance to understand the epidemiology of the disease. Little is known about MERS-CoV animal host range. In this paper, experimental data on potential hosts for MERS-CoV is reviewed. Advantages and limitations of different animal models are evaluated in relation to viral pathogenesis and transmission studies. Finally, the relevance of potential new target species is discussed.
A model for quasi parity-doublet spectra with strong coriolis mixing

International Nuclear Information System (INIS)

Minkov, N.; Drenska, S.; Strecker, M.

2013-01-01

The model of coherent quadrupole and octupole motion (CQOM) is combined with the reflection-asymmetric deformed shell model (DSM) in a way allowing fully microscopic description of the Coriolis decoupling and K-mixing effects in the quasi parity-doublet spectra of odd-mass nuclei. In this approach the even-even core is considered within the CQOM model, while the odd nucleon is described within DSM with pairing interaction. The Coriolis decoupling/mixing factors are calculated through a parity-projection of the single-particle wave function. Expressions for the Coriolis mixed quasi parity-doublet levels are obtained in the second order of perturbation theory, while the K-mixed core plus particle wave function is obtained in the first order. Expressions for the B(E1), B(E2) and B(E3) reduced probabilities for transitions within and between different quasi-doublets are obtained by using the total K-mixed wave function. The model scheme is elaborated in a form capable of describing the yrast and non-yrast quasi parity-doublet spectra in odd-mass nuclei. (author)
Energy spectra of odd nuclei in the generalized model

Directory of Open Access Journals (Sweden)

I. O. Korzh

2015-04-01

Full Text Available Based on the generalized nuclear model, energy spectra of the odd nuclei of such elements as 25Mg, 41K, and 65Cu are determined, and the structure of wave functions of these nuclei in the excited and normal states is studied. High quality in determining the energy spectra is possible due to the accurate calculations of all elements of the energy matrix. It is demonstrated that the structure of the wave functions so determined provides the possibility to more accurately select the nuclear model and the method for calculating the nucleon cross-sections of the inelastic scattering of nucleons by odd nuclei.
Molecular interaction study of commercial cyclic peptides and MERS-COV papain-like protease as novel drug candidate for MERS-COV

Science.gov (United States)

Nasution, M. A. F.; Azzuhdi, M. G.; Tambunan, U. S. F.

2017-07-01

Middle-east respiratory syndrome coronavirus (MERS-CoV) has become the current outbreak, MERS-CoV infection results in illness at the respiratory system, digestive, and even lead to death with an average mortality caused by MERS-CoV infection reaches 50 %. Until now, there is not any effective vaccine or drug to ward off MERS-CoV infection. Papain-like protease (PLpro) is responsible for cleavage of a nonstructural protein that is essential for viral maturation. Inhibition of PLpro with a ligand will block the cleavage process of nonstructural protein, thus reduce the infection of MERS-CoV. Through of bioinformatics study with molecular docking and binding interaction analysis of commercial cyclic peptides, aldosterone secretion inhibiting factor (1-35) (bovine) was obtained as an inhibitor for PLpro. Thus, aldosterone secretion inhibiting factor (1-35) (bovine) has a potential as a novel candidate drug for treating MERS-CoV.
Modelling air pollution transfers in the Fos-Sur-Mer area

International Nuclear Information System (INIS)

Dibi, Niagne Martin

1985-01-01

A 'puff' gaussian model with determined standard deviations based on transfer times of two classes of vertical stability of the atmosphere was developed in order to evaluate the atmospheric dispersion of industrial discharges in the Fos-sur-Mer area. This research was carried out within the framework of a large study for the processing of the data obtained during the measurement campaign organized by the European Communities. The model in its analytic form allows consideration of the main phenomena which modify the puff content during the transfer: reflectance, wet and dry deposition, physical-chemical transformation of the pollutant SO 2 . The model includes the site meteorological parameters measured in three dimensions (wind speed and direction at ground level and in altitude) and the characteristics of the different stacks. It can also calculate pollutions resulting from a short emission or from continuous emissions. Examples are presented. (author) [fr
Identification of species based on DNA barcode using k-mer feature vector and Random forest classifier.

Science.gov (United States)

Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Rao, A R

2016-11-05

DNA barcoding is a molecular diagnostic method that allows automated and accurate identification of species based on a short and standardized fragment of DNA. To this end, an attempt has been made in this study to develop a computational approach for identifying the species by comparing its barcode with the barcode sequence of known species present in the reference library. Each barcode sequence was first mapped onto a numeric feature vector based on k-mer frequencies and then Random forest methodology was employed on the transformed dataset for species identification. The proposed approach outperformed similarity-based, tree-based, diagnostic-based approaches and found comparable with existing supervised learning based approaches in terms of species identification success rate, while compared using real and simulated datasets. Based on the proposed approach, an online web interface SPIDBAR has also been developed and made freely available at http://cabgrid.res.in:8080/spidbar/ for species identification by the taxonomists. Copyright © 2016 Elsevier B.V. All rights reserved.
Isolation and Cloning of mercuric reductase gene (merA from mercury-resistant bacteria

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Parisa Khoshniyat

2018-03-01

Full Text Available Introduction: Some of the bacteria having merA gene coding mineral mercury reducing enzyme, has genetic potential of Hg removing via reduction of mineral mercury and transformation of that to gas form and finally bioremediation of polluted area. The aim of this study is the isolation of merA gene from resistance bacteria and cloning of that into suitable expression vector and then the environmental bioremediation by the transformation of bacteria with this vector. Materials and methods: A number of bacteria were collected in contaminated areas with mercury in order to isolate merA genes. Polymerase chain reaction had done on the four bacterial genomes including Klebsiella pneumoniae, Pseudomonas aeruginosa, Serratia marcescens and Escherichia coli using the specific primers in order to detect merA gene. For cloning, the primers containing restriction enzyme sites are used, merA gene was isolated and amplified. The amplified fragments were cloned in the expression vector pET21a+ and via heat shock method were transformed into E. coli TOP10 competent cell. For clustering of genes, Mega software version 4 was used and bioanformatic studies were achieved for predicted enzyme. Results: merA gene with 1686 bp in length was isolated from K pneumoniae and E. coli. Recombinant vectors in transgenic bacteria were confirmed by various methods and finally were confirmed by sequencing. The result of clustering these genes with existence genes in NCBI showed high similarity. Discussion and conclusion: The existence of merA gene in bacteria that adapted to Hg pollution area is because of resistance, so with cloning this gene into suitable expression vector and transformation of susceptible bacteria with this vector ability of resistance to Hg in bacteria for bioremediation could be given.
THE PERCEPTION OF OLD AND NEW VALUES IN THE TWO STORIES OF ÖMER SEYFETTİN “BAHAR VE KELEBEKLER” AND “AŞK DALGASI” ÖMER SEYFETTİN’İN “BAHAR VE KELEBEKLER” İLE “AŞK DALGASI” ADLI İKİ HİKÂYESİNDE ESKİ VE YENİ DEĞERLER ALGISI

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Gülten BULDUKER

2012-01-01

Full Text Available Ömer Seyfettin, a Pioneer within them ovement of Genç Kalemler, is a distinguished writer with his essay sand stories. He has aimed to write his work swith a pure language and national in an emotional way. The attitude, the post Tanzimat philosophers had taken, with the ideas towards the value judgements, more or less have defined the contents of his works. The writer is in search of new values to shape the society. In this article it has been the main goal toindicate Ömer Seyfettin’s ideas about the old and the modern way of life, and some sort of dilemmas he has been through in Bahar ve Kelebekler and Aşk Dalgası. It is seen that the writer, who believes that maro cilised society can be provided only by breaking hard fanaticism, supports equality of men and women, criticises arranged marriage style, is dreaming of a progressand development Ömer Seyfettin, öncüsü olduğu Genç Kalemler hareketi içerisinde hikâye ve makaleleriyle öne çıkan bir yazardır. Eserlerini sade bir dil ve millî bir duyuş-düşünüşle kaleme almayı amaçlamıştır. Tanzimat sonrası fikir adamlarının “Doğu ve Batı”ya ait değer yargıları karşısındaki düşünceleri ile almış oldukları tavır, az çok onun eserlerinin de muhtevasını belirlemiştir. Yazar, eski gelenek ve göreneklerin önemini yitirmesi durumunda, topluma şekil verecek yeni değerlerin arayışı içerisindedir. Bu makalede Ömer Seyfettin’in Bahar ve Kelebekler ile Aşk Dalgası adlı hikâyelerinde eski ve yeni yaşam tarzı konusundaki düşünceleri ile düştüğü bazı çelişkili durumlar sergilenmeye çalışılmıştır. Daha medenî bir toplum yapısının katı taassupların kırılmasıyla sağlanabileceğine inanan yazarın, kadın-erkek eşitliğini savunduğu, görücü usulünü eleştirdiği; ilim ve fen ışığında bir yükselme, ilerleme hayal ettiği görülmektedir.
MERS-coronavirus: From discovery to intervention

NARCIS (Netherlands)

W. Widagdo; N.M.A. Okba (Nisreen); V. Stalin Raj; B.L. Haagmans (Bart)

2017-01-01

textabstractMiddle East respiratory syndrome coronavirus (MERS-CoV) still causes outbreaks despite public awareness and implementation of health care measures, such as rapid viral diagnosis and patient quarantine. Here we describe the current epidemiological picture of MERS-CoV, focusing on humans
MERS transmission and risk factors: a systematic review.

Science.gov (United States)

Park, Ji-Eun; Jung, Soyoung; Kim, Aeran; Park, Ji-Eun

2018-05-02

Since Middle East respiratory syndrome (MERS) infection was first reported in 2012, many studies have analysed its transmissibility and severity. However, the methodology and results of these studies have varied, and there has been no systematic review of MERS. This study reviews the characteristics and associated risk factors of MERS. We searched international (PubMed, ScienceDirect, Cochrane) and Korean databases (DBpia, KISS) for English- or Korean-language articles using the terms "MERS" and "Middle East respiratory syndrome". Only human studies with > 20 participants were analysed to exclude studies with low representation. Epidemiologic studies with information on transmissibility and severity of MERS as well as studies containing MERS risk factors were included. A total of 59 studies were included. Most studies from Saudi Arabia reported higher mortality (22-69.2%) than those from South Korea (20.4%). While the R 0 value in Saudi Arabia was < 1 in all but one study, in South Korea, the R 0 value was 2.5-8.09 in the early stage and decreased to < 1 in the later stage. The incubation period was 4.5-5.2 days in Saudi Arabia and 6-7.8 days in South Korea. Duration from onset was 4-10 days to confirmation, 2.9-5.3 days to hospitalization, 11-17 days to death, and 14-20 days to discharge. Older age and concomitant disease were the most common factors related to MERS infection, severity, and mortality. The transmissibility and severity of MERS differed by outbreak region and patient characteristics. Further studies assessing the risk of MERS should consider these factors.
Novel Tc-99m labeled ELR-containing 6-mer peptides for tumor imaging in epidermoid carcinoma xenografts model. A pilot study

International Nuclear Information System (INIS)

Kim, Dae-Weung; Kim, Woo-Hyoung; Kim, Myoung-Hyoun; Kim, Chang-Guhn

2013-01-01

ELR-containing peptides targeting CXCR2 could be the excellent candidate for targeting ligand of molecular tumor imaging. In this study, we had developed two ELR-containing 6-mer peptides and evaluated the diagnostic performance of Tc-99m labeled 6-mer peptides as a molecular imaging agent in murine models bearing KB epidermoid carcinoma. Peptides were synthesized using Fmoc solid phase peptide synthesis. Radiolabeling efficiency with Tc-99m was evaluated using instant thin-layer chromatography. In KB epidermoid cancer-bearing mice, gamma images had acquired and tumor-to-muscle uptake ratio was calculated. Competition and biodistribution studies had performed. Two 6-mer peptides, ELR-ECG and ECG-ELR were successfully synthesized. After radiolabeling procedures with Tc-99m, the complex Tc-99m ELR-ECG and Tc-99m ECG-ELR were prepared in high yield. In the gamma camera imaging of murine model, Tc-99m ELR-ECG was substantially accumulated in the subcutaneously engrafted tumor and tumor uptake had been suppressed by the free ELR co-injection. However, Tc-99m ECG-ELR was minimally accumulated in the tumor. Two ELR-containing 6-mer peptides, ELR-ECG and ECG-ELR, were developed as a molecular imaging agent to target CXCR2 of epidermoid carcinoma. Tc-99m ELR-ECG had showed significant uptake in tumor and it was good candidate for a tumor imaging. (author)
The Synthesis and X-ray Structural Characterization of mer and fac isomers of the Technetium(I) Nitrosyl Complex [TcCl(2)(NO)(PNPpr)].

Science.gov (United States)

Nicholson, T L; Mahmood, A; Refosco, F; Tisato, F; Müller, P; Jones, A G

2009-08-01

The nitrosyl complex H[TcNOCl(4)] reacts with the tridentate ligand bis[(2-diphenylphosphino)propyl]amine (PNPpr) to yield a mixture of the mer or fac isomers of [TcCl(2)(NO)(PNPpr)]. In acetonitrile, where the ligand is freely soluble, reaction occurs at room temperature to yield mostly the mer isomer with the linear nitrosyl ligand cis to the amine ligand; and the phosphine ligands arranged in a mutually trans orientation. The reaction in methanol requires reflux to dissolve the lipophilic ligand and generates the fac isomer of [TcCl2(NO)(PNPpr)] as the major product, with the tridentate ligand in a facial arrangement, leaving the chlorides and nitrosyl ligand in the remaining facial sites. The steric bulk of the tridentate ligand's diphenylphophino- moieties results in a significant distortion from octahedral geometry, with the P-Tc-P bond angle expanded to 99.48(4)°. The infrared spectra display absorptions from these nitrosyl ligands in the 1700 and 1800 cm(-1) regions for the fac and mer isomers respectively. The ESI(+) mass spectra each display the parent ion at 647 m/z.
Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

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Haznedaroglu Berat Z

2012-07-01

Full Text Available Abstract Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG ortholog identifiers (KOIs, and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly. Results Analyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63. For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs in the assemblies of individual k-mers (k-19 to k-63 that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented. Conclusions This study demonstrated that different k-mer choices result in various quantities
The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2

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Jyoti K. Jha

2017-04-01

Full Text Available Replication of Vibrio cholerae chromosome 2 (Chr2 depends on molecular chaperone DnaK to facilitate binding of the initiator (RctB to the replication origin. The binding occurs at two kinds of site, 12-mers and 39-mers, which promote and inhibit replication, respectively. Here we show that DnaK employs different mechanisms to enhance the two kinds of binding. We found that mutations in rctB that reduce DnaK binding also reduce 12-mer binding and initiation. The initiation defect is suppressed by second-site mutations that increase 12-mer binding only marginally. Instead, they reduce replication inhibitory mechanisms: RctB dimerization and 39-mer binding. One suppressing change was in a dimerization domain which is folded similarly to the initiator of an iteron plasmid—the presumed progenitor of Chr2. In plasmids, DnaK promotes initiation by reducing dimerization. A different mutation was in the 39-mer binding domain of RctB and inactivated it, indicating an alternative suppression mechanism. Paradoxically, although DnaK increases 39-mer binding, the increase was also achieved by inactivating the DnaK binding site of RctB. This result suggests that the site inhibits the 39-mer binding domain (via autoinhibition when prevented from binding DnaK. Taken together, our results reveal an important feature of the transition from plasmid to chromosome: the Chr2 initiator retains the plasmid-like dimerization domain and its control by chaperones but uses the chaperones in an unprecedented way to control the inhibitory 39-mer binding.
Human Centered Design and Development for NASA's MerBoard

Science.gov (United States)

Trimble, Jay

2003-01-01

This viewgraph presentation provides an overview of the design and development process for NASA's MerBoard. These devices are large interactive display screens which can be shown on the user's computer, which will allow scientists in many locations to interpret and evaluate mission data in real-time. These tools are scheduled to be used during the 2003 Mars Exploration Rover (MER) expeditions. Topics covered include: mission overview, Mer Human Centered Computers, FIDO 2001 observations and MerBoard prototypes.
Actinide L-line ED-XRF and Hybrid K-edge Densitometer Spectra Processing

International Nuclear Information System (INIS)

Esbelin, E.

2015-01-01

The analysis laboratory in the CEA Atalante complex at Marcoule (France) performs numerous R and D studies carried out in glove-boxes or in hot cells. Most of the samples are measured in liquid phase, aqueous or organic. The concentration of the main actinides of interest (U, Np, Pu, Am and Cm) are determined by XRF in a hot cell via their L-line X-ray between 13 and 15 keV. In order to limit the counting rate of many radioactive emitters (X-ray and gamma emitters) in the analysis solution and the continuous spectrum, a graphite monochromator is placed between the sample and detector. Commercial or free, the software packages available for processing X-ray spectra are designed and dedicated to a specific instrument and/or do not take into account the specific feature of our system, in other words, the presence of a monochromator. Therefore, a new X-ray analysis software programme was developed for this particular system which takes into account matrix effects corrections. For sample with U and/or Pu in high concentrations, the hybrid K-edge densitometer is used. A new software programme was also developed. For K-edge densitometry spectra processing, no calibration process is used. Spectra processing is based on theoretical equation and uses XCOM database for mass attenuation coefficients. Measured spectra on K-edge densitometer of Rokkasho Safeguards Analytical Laboratory were processed with this software and a very good agreement was found with IDTIMS results. The new graphical user interface allows to manually correct the defined edge. For the XRF spectra processing, new algorithms are used to define the base line and to find/integrate peaks. With these two analytical devices in laboratory, U and Pu concentrations can be measured from 0.5 mg/l to several hundred of g/l. (author)
MERS and SARS

Science.gov (United States)

... primary antibody and Goat anti-Rabbit 10 nm gold particles. Middle East Respiratory Syndrome (MERS-CoV) is ... standard mice or hamsters, scientists at NIAID Rocky Mountain Laboratories (RML) took the unusual step of moving ...

Krypton K-shell X-ray spectra recorded by the HENEX spectrometer

Energy Technology Data Exchange (ETDEWEB)

Seely, J.F. [Naval Research Laboratory, Space Science Division, Washington DC 20375 (United States)]. E-mail: john.seely@nrl.navy.mil; Back, C.A. [Lawrence Livermore National Laboratory, Livermore CA 94550 (United States); Constantin, C. [Lawrence Livermore National Laboratory, Livermore CA 94550 (United States); Lee, R.W. [Lawrence Livermore National Laboratory, Livermore CA 94550 (United States); Chung, H.-K. [Lawrence Livermore National Laboratory, Livermore CA 94550 (United States); Hudson, L.T. [National Institute of Standards and Technology, Gaithersburg MD 20899 (United States); Szabo, C.I. [National Institute of Standards and Technology, Gaithersburg MD 20899 (United States); Henins, A. [National Institute of Standards and Technology, Gaithersburg MD 20899 (United States); Holland, G.E. [SFA Inc., 9315 Largo Drive West Suite 200, Largo MD 20774 (United States); Atkin, R. [Tiger Innovations, L.L.C., 3610 Vacation Lane, Arlington VA 22207 (United States); Marlin, L. [Naval Research Laboratory, Space Science Division, Washington DC 20375 (United States)

2006-05-15

High-resolution X-ray spectra were recorded by the High-Energy Electronic X-ray (HENEX) spectrometer from a variety of targets irradiated by the Omega laser at the Laboratory for Laser Energetics. The HENEX spectrometer utilizes four reflection crystals covering the 1-20keV energy range and one quartz(10-11) transmission crystal (Laue geometry) covering the 11-40keV range. The time-integrated spectral images were recorded on five CMOS X-ray detectors. In the spectra recorded from krypton-filled gasbag and hohlraum targets, the helium-like K-shell transitions n=1-2, 1-3, and 1-4 appeared in the 13-17keV energy range. A number of additional spectral features were observed at energies lower than the helium-like n=1-3 and n=1-4 transitions. Based on computational simulations of the spectra using the FLYCHK/FLYSPEC codes, which included opacity effects, these additional features are identified to be inner-shell transitions from the Li-like through N-like krypton charge states. The comparisons of the calculated and observed spectra indicate that these transitions are characteristic of the plasma conditions immediately after the laser pulse when the krypton density is 2x10{sup 18}cm{sup -3} and the electron temperature is in the range 2.8-3.2keV. These spectral features represent a new diagnostic for the charge state distribution, the density and electron temperature, and the plasma opacity. Laboratory experiments indicate that it is feasible to record K-shell spectra from gold and higher Z targets in the >60keV energy range using a Ge(220) transmission crystal.
Assessment of modern spectral analysis methods to improve wavenumber resolution of F-K spectra

International Nuclear Information System (INIS)

Shirley, T.E.; Laster, S.J.; Meek, R.A.

1987-01-01

The improvement in wavenumber spectra obtained by using high resolution spectral estimators is examined. Three modern spectral estimators were tested, namely the Autoregressive/Maximum Entropy (AR/ME) method, the Extended Prony method, and an eigenstructure method. They were combined with the conventional Fourier method by first transforming each trace with a Fast Fourier Transform (FFT). A high resolution spectral estimator was applied to the resulting complex spatial sequence for each frequency. The collection of wavenumber spectra thus computed comprises a hybrid f-k spectrum with high wavenumber resolution and less spectral ringing. Synthetic and real data records containing 25 traces were analyzed by using the hybrid f-k method. The results show an FFT-AR/ME f-k spectrum has noticeably better wavenumber resolution and more spectral dynamic range than conventional spectra when the number of channels is small. The observed improvement suggests the hybrid technique is potentially valuable in seismic data analysis
Calculation of optical and K pre-edge absorption spectra for ferrous iron of distorted sites in oxide crystals

Science.gov (United States)

Vercamer, Vincent; Hunault, Myrtille O. J. Y.; Lelong, Gérald; Haverkort, Maurits W.; Calas, Georges; Arai, Yusuke; Hijiya, Hiroyuki; Paulatto, Lorenzo; Brouder, Christian; Arrio, Marie-Anne; Juhin, Amélie

2016-12-01

Advanced semiempirical calculations have been performed to compute simultaneously optical absorption and K pre-edge x-ray absorption spectra of Fe2 + in four distinct site symmetries found in minerals. The four symmetries, i.e., a distorted octahedron, a distorted tetrahedron, a square planar site, and a trigonal bipyramidal site, are representative of the Fe2 + sites found in crystals and glasses. A particular attention has been paid to the definition of the p -d hybridization Hamiltonian which occurs for noncentrosymmetric symmetries in order to account for electric dipole transitions. For the different sites under study, an excellent agreement between calculations and experiments was found for both optical and x-ray absorption spectra, in particular in terms of relative intensities and energy positions of electronic transitions. To our knowledge, these are the first calculations of optical absorption spectra on Fe2 + placed in such diverse site symmetries, including centrosymmetric sites. The proposed theoretical model should help to interpret the features of both the optical absorption and the K pre-edge absorption spectra of 3 d transition metal ions and to go beyond the usual fingerprint interpretation.
Complete Genome Sequence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) from the First Imported MERS-CoV Case in China.

Science.gov (United States)

Lu, Roujian; Wang, Yanqun; Wang, Wenling; Nie, Kai; Zhao, Yanjie; Su, Juan; Deng, Yao; Zhou, Weimin; Li, Yang; Wang, Huijuan; Wang, Wen; Ke, Changwen; Ma, Xuejun; Wu, Guizhen; Tan, Wenjie

2015-08-13

On 26 May 2015, an imported Middle East respiratory syndrome coronavirus (MERS-CoV) was identified in Guangdong Province, China, and found to be closely related to the MERS-CoV strain prevalent in South Korea. The full genome of the ChinaGD01 strain was sequenced and analyzed to investigate the epidemiology and evolution of MERS-CoV circulating in South Korea and China. Copyright © 2015 Lu et al.
Rapid detection of MERS coronavirus-like viruses in bats: pote1ntial for tracking MERS coronavirus transmission and animal origin.

Science.gov (United States)

Woo, Patrick C Y; Lau, Susanna K P; Chen, Yixin; Wong, Emily Y M; Chan, Kwok-Hung; Chen, Honglin; Zhang, Libiao; Xia, Ningshao; Yuen, Kwok-Yung

2018-03-07

Recently, we developed a monoclonal antibody-based rapid nucleocapsid protein detection assay for diagnosis of MERS coronavirus (MERS-CoV) in humans and dromedary camels. In this study, we examined the usefulness of this assay to detect other lineage C betacoronaviruses closely related to MERS-CoV in bats. The rapid MERS-CoV nucleocapsid protein detection assay was tested positive in 24 (88.9%) of 27 Tylonycteris bat CoV HKU4 (Ty-BatCoV-HKU4) RNA-positive alimentary samples of Tylonycteris pachypus and 4 (19.0%) of 21 Pipistrellus bat CoV HKU5 (Pi-BatCoV-HKU5) RNA-positive alimentary samples of Pipistrellus abramus. There was significantly more Ty-BatCoV-HKU4 RNA-positive alimentary samples than Pi-BatCoV-HKU5 RNA-positive alimentary samples that were tested positive by the rapid MERS-CoV nucleocapsid protein detection assay (P < 0.001 by Chi-square test). The rapid assay was tested negative in all 51 alimentary samples RNA-positive for alphacoronaviruses (Rhinolophus bat CoV HKU2, Myotis bat CoV HKU6, Miniopterus bat CoV HKU8 and Hipposideros batCoV HKU10) and 32 alimentary samples positive for lineage B (SARS-related Rhinolophus bat CoV HKU3) and lineage D (Rousettus bat CoV HKU9) betacoronaviruses. No significant difference was observed between the viral loads of Ty-BatCoV-HKU4/Pi-BatCoV-HKU5 RNA-positive alimentary samples that were tested positive and negative by the rapid test (Mann-Witney U test). The rapid MERS-CoV nucleocapsid protein detection assay is able to rapidly detect lineage C betacoronaviruses in bats. It detected significantly more Ty-BatCoV-HKU4 than Pi-BatCoV-HKU5 because MERS-CoV is more closely related to Ty-BatCoV-HKU4 than Pi-BatCoV-HKU5. This assay will facilitate rapid on-site mass screening of animal samples for ancestors of MERS-CoV and tracking transmission in the related bat species.
Modeling Li I and K I sensitivity to Pleiades activity

NARCIS (Netherlands)

Stuik, R.; Bruls, J.H.M.J.; Rutten, R.J.

1996-01-01

We compare schematic modeling of spots and plage on the surface of cool dwarfs with Pleiades data to assess effects of magnetic activity on the strengths of the L II and K I resonance lines in Pleiades spectra. Comprehensive L II and K I NLTE line formation computation is combined with comparatively
Factors affecting antimicrobial activity of MUC7 12-mer, a human salivary mucin-derived peptide

Directory of Open Access Journals (Sweden)

Bobek Libuse A

2007-11-01

Full Text Available Abstract Background MUC7 12-mer (RKSYKCLHKRCR, a cationic antimicrobial peptide derived from the human low-molecular-weight salivary mucin MUC7, possesses potent antimicrobial activity in vitro. In order to evaluate the potential therapeutic application of the MUC7 12-mer, we examined the effects of mono- and divalent cations, EDTA, pH, and temperature on its antimicrobial activity. Methods Minimal Inhibitory Concentrations (MICs were determined using a liquid growth inhibition assay in 96-well microtiter plates. MUC7 12-mer was added at concentrations of 1.56–50 μM. MICs were determined at three endpoints: MIC-0, MIC-1, and MIC-2 (the lowest drug concentration showing 10%, 25% and 50% of growth, respectively. To examine the effect of salts or EDTA, a checkerboard microdilution technique was used. Fractional inhibitory concentration index (FICi was calculated on the basis of MIC-0. The viability of microbial cells treated with MUC7 12-mer in the presence of sodium or potassium was also determined by killing assay or flow cytometry. Results The MICs of MUC7 12-mer against organisms tested ranged from 6.25–50 μM. For C. albicans, antagonism (FICi 4.5 was observed for the combination of MUC7 12-mer and calcium; however, there was synergism (FICi 0.22 between MUC7 12-mer and EDTA, and the synergism was retained in the presence of calcium at its physiological concentration (1–2 mM. No antagonism but additivity or indifference (FICi 0.55–2.5 was observed for the combination of MUC7 12-mer and each K+, Na+, Mg2+, or Zn2+. MUC7 12-mer peptide (at 25 μM also exerted killing activity in the presence of NaCl, (up to 25 mM for C. albicans and up to 150 mM for E. coli, a physiological concentration of sodium in the oral cavity and serum, respectively and retained candidacidal activity in the presence of KCl (up to 40 mM. The peptide exhibited higher inhibitory activity against C. albicans at pH 7, 8, and 9 than at pH 5 and 6, and temperature up to
Multiple Scattering Approach to Polarization Dependence of F K-Edge XANES Spectra for Highly Oriented Polytetrafluoroethylene (PTFE) Thin Film

International Nuclear Information System (INIS)

Nagamatsu, S.; Ono, M.; Kera, S.; Okudaira, K. K.; Fujikawa, T.; Ueno, N.

2007-01-01

The polarization dependence of F K-edge X-ray absorption near edge structure (XANES) spectra of highly-oriented thin-film of polytetrafluoroethylene (PTFE) has been analyzed by using multiple scattering theory. The spectra show clear polarization dependence due to the highly-oriented structure. The multiple scattering calculations reflects a local structure around an absorbing atom. The calculated results obtained by considering intermolecular-interactions are in good agreement with the observed polarization-dependence. We have also analyzed structural models of the radiation damaged PTFE films
A Library of ATMO Forward Model Transmission Spectra for Hot Jupiter Exoplanets

Science.gov (United States)

Goyal, Jayesh M.; Mayne, Nathan; Sing, David K.; Drummond, Benjamin; Tremblin, Pascal; Amundsen, David S.; Evans, Thomas; Carter, Aarynn L.; Spake, Jessica; Baraffe, Isabelle;

2017-01-01

We present a grid of forward model transmission spectra, adopting an isothermal temperature-pressure profile, alongside corresponding equilibrium chemical abundances for 117 observationally significant hot exoplanets (equilibrium temperatures of 547-2710 K). This model grid has been developed using a 1D radiative-convective-chemical equilibrium model termed ATMO, with up-to-date high-temperature opacities. We present an interpretation of observations of 10 exoplanets, including best-fitting parameters and X(exp 2) maps. In agreement with previous works, we find a continuum from clear to hazy/cloudy atmospheres for this sample of hot Jupiters. The data for all the 10 planets are consistent with subsolar to solar C/O ratio, 0.005 to 10 times solar metallicity and water rather than methane-dominated infrared spectra. We then explore the range of simulated atmospheric spectra for different exoplanets, based on characteristics such as temperature, metallicity, C/O ratio, haziness and cloudiness. We find a transition value for the metallicity between 10 and 50 times solar, which leads to substantial changes in the transmission spectra. We also find a transition value of C/O ratio, from water to carbon species dominated infrared spectra, as found by previous works, revealing a temperature dependence of this transition point ranging from approximately 0.56 to approximately 1-1.3 for equilibrium temperatures from approximately 900 to approximately 2600 K. We highlight the potential of the spectral features of HCN and C2H2 to constrain the metallicities and C/O ratios of planets, using James Webb Space Telescope (JWST) observations. Finally, our entire grid (approximately 460 000 simulations) is publicly available and can be used directly with the JWST simulator PandExo for planning observations.

A library of ATMO forward model transmission spectra for hot Jupiter exoplanets

Science.gov (United States)

Goyal, Jayesh M.; Mayne, Nathan; Sing, David K.; Drummond, Benjamin; Tremblin, Pascal; Amundsen, David S.; Evans, Thomas; Carter, Aarynn L.; Spake, Jessica; Baraffe, Isabelle; Nikolov, Nikolay; Manners, James; Chabrier, Gilles; Hebrard, Eric

2018-03-01

We present a grid of forward model transmission spectra, adopting an isothermal temperature-pressure profile, alongside corresponding equilibrium chemical abundances for 117 observationally significant hot exoplanets (equilibrium temperatures of 547-2710 K). This model grid has been developed using a 1D radiative-convective-chemical equilibrium model termed ATMO, with up-to-date high-temperature opacities. We present an interpretation of observations of 10 exoplanets, including best-fitting parameters and χ2 maps. In agreement with previous works, we find a continuum from clear to hazy/cloudy atmospheres for this sample of hot Jupiters. The data for all the 10 planets are consistent with subsolar to solar C/O ratio, 0.005 to 10 times solar metallicity and water rather than methane-dominated infrared spectra. We then explore the range of simulated atmospheric spectra for different exoplanets, based on characteristics such as temperature, metallicity, C/O ratio, haziness and cloudiness. We find a transition value for the metallicity between 10 and 50 times solar, which leads to substantial changes in the transmission spectra. We also find a transition value of C/O ratio, from water to carbon species dominated infrared spectra, as found by previous works, revealing a temperature dependence of this transition point ranging from ˜0.56 to ˜1-1.3 for equilibrium temperatures from ˜900 to ˜2600 K. We highlight the potential of the spectral features of HCN and C2H2 to constrain the metallicities and C/O ratios of planets, using James Webb Space Telescope (JWST) observations. Finally, our entire grid (˜460 000 simulations) is publicly available and can be used directly with the JWST simulator PandExo for planning observations.
Nucleation and Growth Kinetics from LaMer Burst Data.

Science.gov (United States)

Chu, Daniel B K; Owen, Jonathan S; Peters, Baron

2017-10-12

In LaMer burst nucleation, the individual nucleation events happen en masse, quasi-simultaneously, and at nearly identical homogeneous conditions. These properties make LaMer burst nucleation important for applications that require monodispersed particles and also for theoretical analyses. Sugimoto and co-workers predicted that the number of nuclei generated during a LaMer burst depends only on the solute supply rate and the growth rate, independent of the nucleation kinetics. Some experiments confirm that solute supply kinetics control the number of nuclei, but flaws in the original theoretical analysis raise questions about the predicted roles of growth and nucleation kinetics. We provide a rigorous analysis of the coupled equations that govern concentrations of nuclei and solutes. Our analysis confirms that the number of nuclei is largely determined by the solute supply and growth rates, but our predicted relationship differs from that of Sugimoto et al. Moreover, we find that additional nucleus size dependent corrections should emerge in systems with slow growth kinetics. Finally, we show how the nucleation kinetics determine the particle size distribution. We suggest that measured particle size distributions might therefore provide ways to test theoretical models of homogeneous nucleation kinetics.
Environmental Conditions Constrain the Distribution and Diversity of Archaeal merA in Yellowstone National Park, Wyoming, U.S.A.

Science.gov (United States)

Wang, Y.; Boyd, E.; Crane, S.; Lu-Irving, P.; Krabbenhoft, D.; King, S.; Dighton, J.; Geesey, G.; Barkay, T.

2011-01-01

The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient. ?? 2011 Springer Science+Business Media, LLC.
Environmental conditions constrain the distribution and diversity of archaeal merA in Yellowstone National Park, Wyoming, U.S.A.

Science.gov (United States)

Wang, Yanping; Boyd, Eric; Crane, Sharron; Lu-Irving, Patricia; Krabbenhoft, David; King, Susan; Dighton, John; Geesey, Gill; Barkay, Tamar

2011-11-01

The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient.
MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

Energy Technology Data Exchange (ETDEWEB)

Menachery, Vineet D.; Mitchell, Hugh D.; Cockrell, Adam S.; Gralinski, Lisa E.; Yount, Boyd L.; Graham, Rachel L.; McAnarney, Eileen T.; Douglas, Madeline G.; Scobey, Trevor; Beall, Anne; Dinnon, Kenneth; Kocher, Jacob F.; Hale, Andrew E.; Stratton, Kelly G.; Waters, Katrina M.; Baric, Ralph S.; Racaniello, Vincent R.

2017-08-22

ABSTRACT
While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation.In vitroreplication attenuation also extends toin vivomodels, allowing use of dORF3-5 as a live attenuated vaccine platform. Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward.

IMPORTANCEThe initial emergence and periodic outbreaks of MERS-CoV highlight a continuing threat posed by zoonotic pathogens to global public health. In these studies, mutant virus generation demonstrates the necessity of accessory ORFs in regard to MERS-CoV infection and pathogenesis. With this in mind, accessory ORF functions can be targeted for both therapeutic and vaccine treatments in response to MERS-CoV and related group 2C coronaviruses. In addition, disruption of accessory ORFs in parallel may offer a rapid response platform to attenuation of future emergent strains based on both SARS- and MERS-CoV accessory ORF mutants.
A truncated receptor-binding domain of MERS-CoV spike protein potently inhibits MERS-CoV infection and induces strong neutralizing antibody responses: implication for developing therapeutics and vaccines.

Directory of Open Access Journals (Sweden)

Lanying Du

Full Text Available An emerging respiratory infectious disease with high mortality, Middle East respiratory syndrome (MERS, is caused by a novel coronavirus (MERS-CoV. It was first reported in 2012 in Saudi Arabia and has now spread to eight countries. Development of effective therapeutics and vaccines is crucial to save lives and halt the spread of MERS-CoV. Here, we show that a recombinant protein containing a 212-amino acid fragment (residues 377-588 in the truncated receptor-binding domain (RBD: residues 367-606 of MERS-CoV spike (S protein fused with human IgG Fc fragment (S377-588-Fc is highly expressed in the culture supernatant of transfected 293T cells. The purified S377-588-Fc protein efficiently binds to dipeptidyl peptidase 4 (DPP4, the receptor of MERS-CoV, and potently inhibited MERS-CoV infection, suggesting its potential to be further developed as a therapeutic modality for treating MERS-CoV infection and saving the patients' lives. The recombinant S377-588-Fc is able to induce in the vaccinated mice strong MERS-CoV S-specific antibodies, which blocks the binding of RBD to DPP4 receptor and effectively neutralizes MERS-CoV infection. These findings indicate that this truncated RBD protein shows promise for further development as an effective and safe vaccine for the prevention of MERS-CoV infection.
Mer tyrosine kinase promotes the survival of t(1;19)-positive acute lymphoblastic leukemia (ALL) in the central nervous system (CNS).

Science.gov (United States)

Krause, Sarah; Pfeiffer, Christian; Strube, Susanne; Alsadeq, Ameera; Fedders, Henning; Vokuhl, Christian; Loges, Sonja; Waizenegger, Jonas; Ben-Batalla, Isabel; Cario, Gunnar; Möricke, Anja; Stanulla, Martin; Schrappe, Martin; Schewe, Denis M

2015-01-29

Patients with t(1;19)-positive acute lymphoblastic leukemia (ALL) are prone to central nervous system (CNS) relapses, and expression of the TAM (Tyro3, Axl, and Mer) receptor Mer is upregulated in these leukemias. We examined the functional role of Mer in the CNS in preclinical models and performed correlative studies in 64 t(1;19)-positive and 93 control pediatric ALL patients. ALL cells were analyzed in coculture with human glioma cells and normal rat astrocytes: CNS coculture caused quiescence and protection from methotrexate toxicity in Mer(high) ALL cell lines, which was antagonized by short hairpin RNA-mediated knockdown of Mer. Mer expression was upregulated, prosurvival Akt and mitogen-activated protein kinase signaling were activated, and secretion of the Mer ligand Galectin-3 was stimulated. Mer(high) t(1;19) primary cells caused CNS involvement to a larger extent in murine xenografts than in their Mer(low) counterparts. Leukemic cells from Mer(high) xenografts showed enhanced survival in coculture. Treatment of Mer(high) patient cells with the Mer-specific inhibitor UNC-569 in vivo delayed leukemia onset, reduced CNS infiltration, and prolonged survival of mice. Finally, a correlation between high Mer expression and CNS positivity upon initial diagnosis was observed in t(1;19) patients. Our data provide evidence that Mer is associated with survival in the CNS in t(1;19)-positive ALL, suggesting a role as a diagnostic marker and therapeutic target. © 2015 by The American Society of Hematology.
Optimization of tungsten x-ray spectra for digital mammography: a comparison of model to experiment

Science.gov (United States)

Andre, Michael P.; Spivey, Brett A.

1997-05-01

Tungsten (W) target x-rays tubes are being studied for use in digital mammography to improve x-ray flux, reduce noise and increase tube heat capacity. A parametric model was developed for digital mammography to evaluate optimization of x-ray spectra for a particular sensor. The model computes spectra and mean glandular doses (MGD) for combinations of W target, beam filters, kVp, breast type and thickness. Two figures of merit were defined: (signal/noise)2/MGD and spectral quantum efficiency; these were computed as a means to approach optimization of object contrast. The model is derived from a combination of classic equations, XCOM from NBS, and published data. X-ray spectra were calculated and measured for filters of Al, Sn, Rh, Mo and Ag on a Eureka tube. (Signal/noise)2/MGD was measured for a filtered W target tube and a digital camera employing CsI scintillator optically coupled to a CCD for which the detective quantum efficiency (DQE) was known. A 3-mm thick acrylic disk was imaged on thickness of 3-8 cm of acrylic and the results were compared to the predictions of the model. The relative error between predicted and measured spectra was +/- 2 percent from 24 to 34 kVp. Calculated MGD as a function of breast thickness, half-value layer and beam filter compares very well to published data. Best performance was found for the following combinations: Mo filter with 30 mm breast, Ag filter with 45 mm, Sn filter for 60 mm, and Al filter for 75 mm thick breast. The parametric model agrees well with measurement and provides a means to explore optimum combinations of kVp and beam filter. For a particular detector, this data may be used with the DQE to estimate total system signal-to-noise ratio for a particular imaging task.
PEPSI deep spectra. II. Gaia benchmark stars and other M-K standards

Science.gov (United States)

Strassmeier, K. G.; Ilyin, I.; Weber, M.

2018-04-01

Context. High-resolution échelle spectra confine many essential stellar parameters once the data reach a quality appropriate to constrain the various physical processes that form these spectra. Aim. We provide a homogeneous library of high-resolution, high-S/N spectra for 48 bright AFGKM stars, some of them approaching the quality of solar-flux spectra. Our sample includes the northern Gaia benchmark stars, some solar analogs, and some other bright Morgan-Keenan (M-K) spectral standards. Methods: Well-exposed deep spectra were created by average-combining individual exposures. The data-reduction process relies on adaptive selection of parameters by using statistical inference and robust estimators. We employed spectrum synthesis techniques and statistics tools in order to characterize the spectra and give a first quick look at some of the science cases possible. Results: With an average spectral resolution of R ≈ 220 000 (1.36 km s-1), a continuous wavelength coverage from 383 nm to 912 nm, and S/N of between 70:1 for the faintest star in the extreme blue and 6000:1 for the brightest star in the red, these spectra are now made public for further data mining and analysis. Preliminary results include new stellar parameters for 70 Vir and α Tau, the detection of the rare-earth element dysprosium and the heavy elements uranium, thorium and neodymium in several RGB stars, and the use of the 12C to 13C isotope ratio for age-related determinations. We also found Arcturus to exhibit few-percent Ca II H&K and Hα residual profile changes with respect to the KPNO atlas taken in 1999. Based on data acquired with PEPSI using the Large Binocular Telescope (LBT) and the Vatican Advanced Technology Telescope (VATT). The LBT is an international collaboration among institutions in the United States, Italy, and Germany. LBT Corporation partners are the University of Arizona on behalf of the Arizona university system; Istituto Nazionale di Astrofisica, Italy; LBT
Analyzing MER Uplink Reports

Science.gov (United States)

Savin, Stephen C.

2005-01-01

The MER project includes two rovers working simultaneously on opposite sides of Mars each receiving commands only once a day. Creating this uplink is critical, since a failed uplink means a lost day and a waste of money. Examining the process of creating this uplink, I tracked the use of the system developed for requesting observations as well as the development, from stage to stage, in forming an activity plan. I found the system for requesting observations was commonly misused, if used at all. There are half a dozen reports to document the creation of the uplink plan and often there are discrepancies among them. Despite this, the uplink process worked very well and MER has been one of the most successful missions for NASA in recent memory. Still it is clear there is room for improvement.
Evaluation of Reduced Power Spectra from Three-Dimensional k-Space

Science.gov (United States)

Saur, J.; von Papen, M.

2014-12-01

We present a new tool to evaluate one dimensional reduced power spectral densities (PSD) from arbitrary energy distributions in kk-space. This enables us to calculate the power spectra as they are measured in spacecraft frame for any given measurement geometry assuming Taylor's frozen-in approximation. It is possible to seperately calculate the diagonal elements of the spectral tensor and also to insert additional, non-turbulent energy in kk-space (e.g. mirror mode waves). Given a critically balanced turbulent cascade with k∥˜kα⊥k_\\|sim k_perp^alpha, we explore the implications on the spectral form of the PSD and the functional dependence of the spectral index κkappa on the field-to-flow angle θtheta between plasma flow and background magnetic field. We show that critically balanced turbulence develops a θtheta-independent cascade with the spectral slope of the perpendicular cascade κ(θ=90∘)kappa(theta{=}90^circ). This happens at frequencies f>fmaxf>f_mathrm{max}, where fmax(L,α,θ)f_mathrm{max}(L,alpha,theta) is a function of outer scale LL, critical balance exponent αalpha and field-to-flow angle θtheta. We also discuss potential damping terms acting on the kk-space distribution of energy and their effect on the PSD. Further, we show that the functional dependence κ(θ)kappa(theta) as found by textit{Horbury et al.} (2008) and textit{Chen et al.} (2010) can be explained with a damped critically balanced turbulence model.

Fac–mer equilibria of coordinated iminodiacetate (ida ) in ternary Cu ...

Indian Academy of Sciences (India)

Unknown

Keywords. Fac–mer equilibria; CuII-iminodiacetate-imidazole/benzimidazole ternary complexes; stability constants. 1. Introduction. Mixed ligand complexes of transition metal ions with amino acids, peptides or their derivatives or analogues, and heterocyclic N-bases can serve as model compounds of bioinorganic interests ...
Ole Rømer som enevældens administrator

DEFF Research Database (Denmark)

Olden-Jørgensen, Sebastian

2002-01-01

En gennemgang af Ole Rømers liv med vægt på hans rolle som embedsmand og hans deltagelse eller mangel på samme i det politiske spil.......En gennemgang af Ole Rømers liv med vægt på hans rolle som embedsmand og hans deltagelse eller mangel på samme i det politiske spil....
A Novel Role of MerC in Methylmercury Transport and Phytoremediation of Methylmercury Contamination.

Science.gov (United States)

Sone, Yuka; Uraguchi, Shimpei; Takanezawa, Yasukazu; Nakamura, Ryosuke; Pan-Hou, Hidemitsu; Kiyono, Masako

2017-01-01

MerC, encoded by merC in the transposon Tn21 mer operon, is a heavy metal transporter with potential applications for phytoremediation of heavy metals such as mercuric ion and cadmium. In this study, we demonstrate that MerC also acts as a transporter for methylmercury. When MerC was expressed in Escherichia coli XL1-Blue, cells became hypersensitive to CH 3 Hg(I) and the uptake of CH 3 Hg(I) by these cells was higher than that by cells of the isogenic strain. Moreover, transgenic Arabidopsis plants expressing bacterial MerC or MerC fused to plant soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) accumulated CH 3 Hg(I) effectively and their growth was comparable to the wild-type plants. These results demonstrate that when the bacterium-derived merC gene is ectopically introduced in genetically modified plants, MerC expression in the transgenic plants promotes the transport and sequestration of methylmercury. Thus, our results show that the expression of merC in Arabidopsis results in transgenic plants that could be used for the phytoremediation and elimination of toxic methylmercury from the environment.
K-shell spectra from hot dense aluminum layers buried in carbon and heated by ultrashort laser pulses

International Nuclear Information System (INIS)

Eidmann, K.; Andiel, U.; Pisani, F.; Hakel, P.; Mancini, R.C.; Junkel-Vives, G.C.; Abdallah, J.; Witte, K.

2003-01-01

Ultrashort laser pulses allow for the generation of hot plasmas near solid state densities. For this purpose a Ti:Sapphire laser was used, which delivers after frequency doubling, pulses of high contrast with an energy of about 60 mJ and a duration of 150 fs at 395 nm. The typical intensity on the target was a few 10 17 W/cm 2 . To achieve a high degree of uniformity we used targets consisting of a 25 nm thin Al tracer layer buried at different depths up to 400 nm in solid carbon. Time-integrated Al K-shell spectra are presented. Characteristic features of the spectra are significant high-order satellite line emission, strong line broadening and a center-of-mass line shift to the red, which was observed in transitions from principal quantum number n=2 or 3 to 1. Accurate measurement of the shift was made possible by using the cold Si K α line as an absolute wavelength calibration. In addition to time-integrated measurements, we used an ultrafast X-ray streak camera to obtain time and spectrally resolved spectra. Typical durations of the Ly α and He α lines are in the range 2-4 ps. The experimental results are compared with a time-dependent model, which combines hydrodynamic simulations, time-dependent atomic kinetics, detailed spectral line shapes including line shifts, and radiation transport
A pandemic risk assessment of middle east respiratory syndrome coronavirus (MERS-CoV in Saudi Arabia

Directory of Open Access Journals (Sweden)

Saleh A. Eifan

2017-11-01

Full Text Available Since the initial emergence of Middle East respiratory syndrome coronavirus (MERS-CoV in 2012, a high incidence rate has been observed in Saudi Arabia. This suggests that the country is at continuous risk. The epidemic level of MERS-CoV infection was examined in Saudi Arabia by the Susceptible-Infectious-Recovered (SIR model using a Bayesian approach for estimation of time dependent reproduction number (R across a two-year interval (May, 2013-May, 2015 in five defined clusters, followed by sensitivity analysis of the most significant clusters. Significant MERS-CoV peaks were detected in the period between March and May of each year. Moreover, MERS-CoV infection was highlighted in western (40.8% and central (31.9% regions, followed by eastern region (20%. The temporal-based Bayesian approach indicated a sub-critical epidemic in all regions in the baseline scenario (R: 0.85–0.97. However, R potential limit was exceeded in the sensitivity analysis scenario in only central and western regions (R: 1.08–1.12 that denoted epidemic level in those regions. The impact of sporadic cases was found relatively insignificant and pinpointed to the lack of zoonotic influence on MERS-CoV transmission dynamics. The results of current study would be helpful for evaluation of future progression of MERS-CoV infections, better understanding and control interventions.
Estimation of basic reproduction number of the Middle East respiratory syndrome coronavirus (MERS-CoV) during the outbreak in South Korea, 2015.

Science.gov (United States)

Chang, Hyuk-Jun

2017-06-13

In South Korea, an outbreak of Middle East respiratory syndrome (MERS) occurred in 2015. It was the second largest MERS outbreak. As a result of the outbreak in South Korea, 186 infections were reported, and 36 patients died. At least 16,693 people were isolated with suspicious symptoms. This paper estimates the basic reproduction number of the MERS coronavirus (CoV), using data on the spread of MERS in South Korea. The basic reproduction number of an epidemic is defined as the average number of secondary cases that an infected subject produces over its infectious period in a susceptible and uninfected population. To estimate the basic reproduction number of the MERS-CoV, we employ data from the 2015 South Korea MERS outbreak and the susceptible-infected-removed (SIR) model, a mathematical model that uses a set of ordinary differential equations (ODEs). We fit the model to the epidemic data of the South Korea outbreak minimizing the sum of the squared errors to identify model parameters. Also we derive the basic reproductive number as the terms of the parameters of the SIR model. Then we determine the basic reproduction number of the MERS-CoV in South Korea in 2015 as 8.0977. It is worth comparing with the basic reproductive number of the 2014 Ebola outbreak in West Africa including Guinea, Sierra Leone, and Liberia, which had values of 1.5-2.5. There was no intervention to control the infection in the early phase of the outbreak, thus the data used here provide the best conditions to evaluate the epidemic characteristics of MERS, such as the basic reproduction number. An evaluation of basic reproduction number using epidemic data could be problematic if there are stochastic fluctuations in the early phase of the outbreak, or if the report is not accurate and there is bias in the data. Such problems are not relevant to this study because the data used here were precisely reported and verified by Korea Hospital Association.
High-resolution K-shell spectra from laser excited molybdenum plasmas

Directory of Open Access Journals (Sweden)

Szabo C.I.

2013-11-01

Full Text Available X-ray spectra from Molybdenum plasmas were recorded by a Cauchois-type cylindrically bent Transmission Crystal Spectrometer (TCS. The absolutely calibrated spectrometer provides an unprecedented resolution of inner shell transitions (K x-ray radiation. This tool allows us to resolve individual lines from different charge states existing inside the laser-produced plasma. The inner shell transitions from highly charged Molybdenum shown in this report have never been resolved before in such detail in a laser-produced plasma.
Tissue Distribution of the MERS-Coronavirus Receptor in Bats

NARCIS (Netherlands)

W. Widagdo; L. Begeman (Lineke); D. Schipper (Debby); P.R.W.A. van Run (Peter); Cunningham, A.A. (Andrew A); Kley, N. (Nils); C.B.E.M. Reusken (Chantal); B.L. Haagmans (Bart); J.M.A. van den Brand (Judith)

2017-01-01

textabstractMiddle East respiratory syndrome coronavirus (MERS-CoV) has been shown to infect both humans and dromedary camels using dipeptidyl peptidase-4 (DPP4) as its receptor.The distribution of DPP4 in the respiratory tract tissues of humans and camels reflects MERS-CoV tropism.Apart from
Tissue Distribution of the MERS-Coronavirus Receptor in Bats

NARCIS (Netherlands)

Widagdo, W; Begeman, Lineke; Schipper, Debby; van Run, Peter R; Cunningham, Andrew A; Kley, Nils; Reusken, Chantal B E M; Haagmans, Bart L; van den Brand, Judith M A

2017-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) has been shown to infect both humans and dromedary camels using dipeptidyl peptidase-4 (DPP4) as its receptor. The distribution of DPP4 in the respiratory tract tissues of humans and camels reflects MERS-CoV tropism. Apart from dromedary
A novel method of providing a library of n-mers or biopolymers

DEFF Research Database (Denmark)

2012-01-01

The present invention relates to a method of providing a library of n-mer sequences, wherein the library is composed of an n-mer sequence. Also the invention concerns a method of providing a library of biopolymer sequences having one or more n-mers in common. Further provided are specific primers...
Edge profiles in K shell photoabsorption spectra of gaseous hydrides of 3p elements and homologues

Science.gov (United States)

Hauko, R.; Gomilšek, J. Padežnik; Kodre, A.; Arčon, I.; Aquilanti, G.

2017-10-01

Photoabsorption spectra of gaseous hydrides of 3p elements (PH3, H2S, HCl) are measured in the energy region of photoexcitations pertaining to K edge. The analysis of the edge profile is extended to hydrides of 4p series (GeH4, AsH3, H2Se, HBr) from an earlier experiment, and to published spectra of 2p hydrides (CH4, NH3, H2O, HF) and noble gases Ar, Kr and Ne and SiH4. The edge profiles are modelled with a linear combination of lorentzian components, describing excitations to individual bound states and to continuum. Transition energies and probabilities are also calculated in the non-relativistic molecular model of the ORCA code, in good agreement with the experiment. Edge profiles in the heavier homologues are closely similar, the symmetry of the molecule governs the transitions to the lowest unoccupied orbitals. In 2p series the effect of the strong nuclear potential prevails. Transitions to higher, atomic-like levels remain very much the same as in free atoms.
AUTOMATED UNSUPERVISED CLASSIFICATION OF THE SLOAN DIGITAL SKY SURVEY STELLAR SPECTRA USING k-MEANS CLUSTERING

Energy Technology Data Exchange (ETDEWEB)

Sanchez Almeida, J.; Allende Prieto, C., E-mail: jos@iac.es, E-mail: callende@iac.es [Instituto de Astrofisica de Canarias, E-38205 La Laguna, Tenerife (Spain)

2013-01-20

Large spectroscopic surveys require automated methods of analysis. This paper explores the use of k-means clustering as a tool for automated unsupervised classification of massive stellar spectral catalogs. The classification criteria are defined by the data and the algorithm, with no prior physical framework. We work with a representative set of stellar spectra associated with the Sloan Digital Sky Survey (SDSS) SEGUE and SEGUE-2 programs, which consists of 173,390 spectra from 3800 to 9200 A sampled on 3849 wavelengths. We classify the original spectra as well as the spectra with the continuum removed. The second set only contains spectral lines, and it is less dependent on uncertainties of the flux calibration. The classification of the spectra with continuum renders 16 major classes. Roughly speaking, stars are split according to their colors, with enough finesse to distinguish dwarfs from giants of the same effective temperature, but with difficulties to separate stars with different metallicities. There are classes corresponding to particular MK types, intrinsically blue stars, dust-reddened, stellar systems, and also classes collecting faulty spectra. Overall, there is no one-to-one correspondence between the classes we derive and the MK types. The classification of spectra without continuum renders 13 classes, the color separation is not so sharp, but it distinguishes stars of the same effective temperature and different metallicities. Some classes thus obtained present a fairly small range of physical parameters (200 K in effective temperature, 0.25 dex in surface gravity, and 0.35 dex in metallicity), so that the classification can be used to estimate the main physical parameters of some stars at a minimum computational cost. We also analyze the outliers of the classification. Most of them turn out to be failures of the reduction pipeline, but there are also high redshift QSOs, multiple stellar systems, dust-reddened stars, galaxies, and, finally, odd
Nitrogen K-edge X-ray absorption near edge structure (XANES) spectra of purine-containing nucleotides in aqueous solution

Energy Technology Data Exchange (ETDEWEB)

Shimada, Hiroyuki; Fukao, Taishi; Minami, Hirotake; Ukai, Masatoshi [Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588 (Japan); Fujii, Kentaro; Yokoya, Akinari [Advanced Science Research Center, Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki 319-1195 (Japan); Fukuda, Yoshihiro; Saitoh, Yuji [Synchrotron Radiation Research Center, Japan Atomic Energy Agency, Sayo-gun, Hyougo 679-5148 (Japan)

2014-08-07

The N K-edge X-ray absorption near edge structure (XANES) spectra of the purine-containing nucleotide, guanosine 5{sup ′}-monophosphate (GMP), in aqueous solution are measured under various pH conditions. The spectra show characteristic peaks, which originate from resonant excitations of N 1s electrons to π* orbitals inside the guanine moiety of GMP. The relative intensities of these peaks depend on the pH values of the solution. The pH dependence is explained by the core-level shift of N atoms at specific sites caused by protonation and deprotonation. The experimental spectra are compared with theoretical spectra calculated by using density functional theory for GMP and the other purine-containing nucleotides, adenosine 5{sup ′}-monophosphate, and adenosine 5{sup ′}-triphosphate. The N K-edge XANES spectra for all of these nucleotides are classified by the numbers of N atoms with particular chemical bonding characteristics in the purine moiety.
A 7-mer knowledge-based potential for detecting native protein structures from decoys

DEFF Research Database (Denmark)

Røgen, Peter

for faster sampling methods. Background: The C-alpha atoms define a polygonal curve in 3-space which is smoothened by the method presented in [1] and is illustrated below. The geometry of a 7-mer is described by two numbers that describe how stretched and curved the smoothening of the 7-mer is. These two...... numbers are called length and distance excess, c.f. [2], and give one point in the length - distance excess - plane, LDE-plane. Method: Given a sequence of amino acids, we break it down to all its 7-mers and search a database of known 3d-structures for similar 7-mer sequences. For the query 7-mer we...... define an energy function in the LDE-plane. This energy is given by the 7-mer found and depends linearly on some design parameters. The energy function of the full query sequence, F, is then a sum over all 7-mers. For a protein P and a decoy D we ideally want F(D)-F(P)=constant.RMSD( D , P ), where 0...
The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2

Energy Technology Data Exchange (ETDEWEB)

Jha, Jyoti K.; Li, Mi; Ghirlando, Rodolfo; Miller Jenkins, Lisa M.; Wlodawer, Alexander; Chattoraj, Dhruba; Dunny, Gary M.

2017-04-18

Replication of Vibrio cholerae chromosome 2 (Chr2) depends on molecular chaperone DnaK to facilitate binding of the initiator (RctB) to the replication origin. The binding occurs at two kinds of site, 12-mers and 39-mers, which promote and inhibit replication, respectively. Here we show that DnaK employs different mechanisms to enhance the two kinds of binding. We found that mutations inrctBthat reduce DnaK binding also reduce 12-mer binding and initiation. The initiation defect is suppressed by second-site mutations that increase 12-mer binding only marginally. Instead, they reduce replication inhibitory mechanisms: RctB dimerization and 39-mer binding. One suppressing change was in a dimerization domain which is folded similarly to the initiator of an iteron plasmid—the presumed progenitor of Chr2. In plasmids, DnaK promotes initiation by reducing dimerization. A different mutation was in the 39-mer binding domain of RctB and inactivated it, indicating an alternative suppression mechanism. Paradoxically, although DnaK increases 39-mer binding, the increase was also achieved by inactivating the DnaK binding site of RctB. This result suggests that the site inhibits the 39-mer binding domain (via autoinhibition) when prevented from binding DnaK. Taken together, our results reveal an important feature of the transition from plasmid to chromosome: the Chr2 initiator retains the plasmid-like dimerization domain and its control by chaperones but uses the chaperones in an unprecedented way to control the inhibitory 39-mer binding. IMPORTANCE The capacity of proteins to undergo remodeling provides opportunities to control their function. However, remodeling remains a poorly understood aspect of the structure-function paradigm due to its dynamic nature. Here we have studied remodeling of the initiator of replication ofVibrio choleraeChr2 by the molecular chaperone, DnaK. We show that DnaK binds to a site on the Chr2 initiator (RctB) that
Velocity Models of the Upper Mantle Beneath the MER, Somali Platform, and Ethiopian Highlands from Body Wave Tomography

Science.gov (United States)

Hariharan, A.; Keranen, K. M.; Alemayehu, S.; Ayele, A.; Bastow, I. D.; Eilon, Z.

2016-12-01

The Main Ethiopian Rift (MER) presents a unique opportunity to improve our understanding of an active continental rift. Here we use body wave tomography to generate compressional and shear wave velocity models of the region beneath the rift. The models help us understand the rifting process over the broader region around the MER, extending the geographic region beyond that captured in past studies. We use differential arrival times of body waves from teleseismic earthquakes and multi-channel cross correlation to generate travel time residuals relative to the global IASP91 1-d velocity model. The events used for the tomographic velocity model include 200 teleseismic earthquakes with moment magnitudes greater than 5.5 from our recent 2014-2016 deployment in combination with 200 earthquakes from the earlier EBSE and EAGLE deployments (Bastow et al. 2008). We use the finite-frequency tomography analysis of Schmandt et al. (2010), which uses a first Fresnel zone paraxial approximation to the Born theoretical kernel with spatial smoothing and model norm damping in an iterative LSQR algorithm. Results show a broad, slow region beneath the rift with a distinct low-velocity anomaly beneath the northwest shoulder. This robust and well-resolved low-velocity anomaly is visible at a range of depths beneath the Ethiopian plateau, within the footprint of Oligocene flood basalts, and near surface expressions of diking. We interpret this anomaly as a possible plume conduit, or a low-velocity finger rising from a deeper, larger plume. Within the rift, results are consistent with previous work, exhibiting rift segmentation and low-velocities beneath the rift valley.
Preventing cleavage of Mer promotes efferocytosis and suppresses acute lung injury in bleomycin treated mice

International Nuclear Information System (INIS)

Lee, Ye-Ji; Lee, Seung-Hae; Youn, Young-So; Choi, Ji-Yeon; Song, Keung-Sub; Cho, Min-Sun; Kang, Jihee Lee

2012-01-01

Mer receptor tyrosine kinase (Mer) regulates macrophage activation and promotes apoptotic cell clearance. Mer activation is regulated through proteolytic cleavage of the extracellular domain. To determine if membrane-bound Mer is cleaved during bleomycin-induced lung injury, and, if so, how preventing the cleavage of Mer enhances apoptotic cell uptake and down-regulates pulmonary immune responses. During bleomycin-induced acute lung injury in mice, membrane-bound Mer expression decreased, but production of soluble Mer and activity as well as expression of disintegrin and metalloproteinase 17 (ADAM17) were enhanced . Treatment with the ADAM inhibitor TAPI-0 restored Mer expression and diminished soluble Mer production. Furthermore, TAPI-0 increased Mer activation in alveolar macrophages and lung tissue resulting in enhanced apoptotic cell clearance in vivo and ex vivo by alveolar macrophages. Suppression of bleomycin-induced pro-inflammatory mediators, but enhancement of hepatocyte growth factor induction were seen after TAPI-0 treatment. Additional bleomycin-induced inflammatory responses reduced by TAPI-0 treatment included inflammatory cell recruitment into the lungs, levels of total protein and lactate dehydrogenase activity in bronchoalveolar lavage fluid, as well as caspase-3 and caspase-9 activity and alveolar epithelial cell apoptosis in lung tissue. Importantly, the effects of TAPI-0 on bleomycin-induced inflammation and apoptosis were reversed by coadministration of specific Mer-neutralizing antibodies. These findings suggest that restored membrane-bound Mer expression by TAPI-0 treatment may help resolve lung inflammation and apoptosis after bleomycin treatment. -- Highlights: ►Mer expression is restored by TAPI-0 treatment in bleomycin-stimulated lung. ►Mer signaling is enhanced by TAPI-0 treatment in bleomycin-stimulated lung. ►TAPI-0 enhances efferocytosis and promotes resolution of lung injury.
Photoabsorption spectra of potassium and rubidium near the K-edge

International Nuclear Information System (INIS)

Azuma, Y.; Berry, H.G.; Cowan, P.L.

1995-01-01

We have used a high-temperature circulating heat-pipe absorption cell together with monochromatized X-ray beams at the X24A and X23A2 beam lines at the NSLS to obtain photoabsorption spectra of potassium and rubidium at their K- and KM-edges. The photon-energy ranges lay near 3600 eV and 15200 eV, respectively. We have also obtained first measurements of the LII and LIII edges in cesium. Although the K-edge photoabsorptions of the rare gases have been studied, there is little previous work on other atomic vapors. Most of the edges and resonance peaks that we observed have now been identified using Dirac Hartree-Fock calculations. As a check, we have compared these results with those obtained previously in closed-shell rare-gas absorption spectra. The absolute energies were obtained through a calibration of the X24A systems using measurements of several metal L-edges in the 3200-5000 eV energy range. We found that the 4p resonance in potassium is significantly enhanced compared with the corresponding situation in argon. Likewise, the 5p resonance in krypton is unresolved from the background ionization cross section, whereas it is well resolved in rubidium. As suggested by Amusia, these enhancements may be due to the enhanced potential seen in the excited state of the alkali systems as a result of the presence of an s-electron which reduces the nuclear shielding
Constitutive synthesis of a transport function encoded by the Thiobacillus ferrooxidans merC gene cloned in Escherichia coli

International Nuclear Information System (INIS)

Kusano, Tomonobu; Ji, Guangyong; Silver, S.; Inoue, Chihiro

1990-01-01

Mercuric reductase activity determined by the Thiobacillus ferrooxidans merA gene (cloned and expressed constitutively in Escherichia coli) was measured by volatilization of 203 Hg 2+ . (The absence of a merR regulatory gene in the cloned Thiobacillus mer determinant provides a basis for the constitutive synthesis of this system.) In the absence of the Thiobacillus merC transport gene, the mercury volatilization activity was cryptic and was not seen with whole cells but only with sonication-disrupted cells. The Thiobacillus merC transport function was compared with transport via the merT-merP system of plasmid pDU1358. Both systems, cloned and expressed in E. coli, governed enhanced uptake of 203 Hg 2+ in a temperature- and concentration-dependent fashion. Uptake via MerT-MerP was greater and conferred greater hypersensitivity to Hg 2+ than did uptake with MerC. Mercury uptake was inhibited by N-ethylmaleimide but not by EDTA. Ag + salts inhibited mercury uptake by the MerT-MerP system but did not inhibit uptake via MerC. Radioactive mercury accumulated by the MerT-MerP and by the MerC systems was exchangeable with nonradioactive Hg 2+
MERS-CoV infection: Mind the public knowledge gap.

Science.gov (United States)

Bawazir, Amen; Al-Mazroo, Eman; Jradi, Hoda; Ahmed, Anwar; Badri, Motasim

In August 2015, the Corona outbreak caused by Middle East respiratory syndrome coronavirus (MERS-CoV) was the 9th episode since June 2012 in Saudi Arabia. Little is known about the public awareness toward the nature or prevention of the disease. The aim of this work was to assess the knowledge of the adult population in Riyadh toward the MERS-CoV. In this cross-sectional survey, a self-administrated questionnaire was distributed to randomly selected participants visiting malls in Riyadh. The questionnaire contained measurable epidemiological and clinical MERS-CoV knowledge level variables and relevant source of information. The study included 676 participants. Mean age was 32.5 (±SD 8.6) years and 353 (47.8%) were males. Almost all participants heard about the corona disease and causative agent. The study showed a fair overall knowledge (66.0%), less knowledge on epidemiological features of the disease (58.3%), and good knowledge (90.7%) on the clinical manifestation of the MERS-CoV. Internet was the major (89.0%) source of disease information, and other sources including health care providers, SMS, television, magazines and books were low rated (all knowledge. This study concludes that there was inadequate epidemiological knowledge received by the public and the reliance mostly on the clinical manifestations to recognizing the MERS-CoV disease. Comprehensive public health education programs is important to increase awareness of simple epidemiological determinants of the disease is warranted. Copyright © 2017. Published by Elsevier Ltd.

Antibodies against MERS coronavirus in dromedary camels, United Arab Emirates, 2003 and 2013.

Science.gov (United States)

Meyer, Benjamin; Müller, Marcel A; Corman, Victor M; Reusken, Chantal B E M; Ritz, Daniel; Godeke, Gert-Jan; Lattwein, Erik; Kallies, Stephan; Siemens, Artem; van Beek, Janko; Drexler, Jan F; Muth, Doreen; Bosch, Berend-Jan; Wernery, Ulrich; Koopmans, Marion P G; Wernery, Renate; Drosten, Christian

2014-04-01

Middle East respiratory syndrome coronavirus (MERS-CoV) has caused an ongoing outbreak of severe acute respiratory tract infection in humans in the Arabian Peninsula since 2012. Dromedary camels have been implicated as possible viral reservoirs. We used serologic assays to analyze 651 dromedary camel serum samples from the United Arab Emirates; 151 of 651 samples were obtained in 2003, well before onset of the current epidemic, and 500 serum samples were obtained in 2013. Recombinant spike protein-specific immunofluorescence and virus neutralization tests enabled clear discrimination between MERS-CoV and bovine CoV infections. Most (632/651, 97.1%) camels had antibodies against MERS-CoV. This result included all 151 serum samples obtained in 2003. Most (389/651, 59.8%) serum samples had MERS-CoV-neutralizing antibody titers >1,280. Dromedary camels from the United Arab Emirates were infected at high rates with MERS-CoV or a closely related, probably conspecific, virus long before the first human MERS cases.
Determination of the Light Element Fraction in MSL APXS Spectra

Science.gov (United States)

Perrett, G. M.; Pradler, I.; Campbell, J. L.; Gellert, R.; Leshin, L. A.; Schmidt, M. E.; Team, M.

2013-12-01

Additional light invisible components (ALICs), measured using the alpha particle X-ray spectrometer (APXS), represent all light elements (e.g. CO3, OH, H2O) present in a sample below Na, excluding bound oxygen. The method for quantifying ALICs was originally developed for the Mars Exploration Rover (MER) APXS (Mallet et al, 2006; Campbell et al, 2008). This method has been applied to data collected by the Mars Science Laboratory (MSL) APXS up to sol 269 using a new terrestrial calibration. ALICs are investigated using the intensity ratio of Pu L-alpha Compton and Rayleigh scatter peaks (C/R). Peak areas of the scattered X-rays are determined by the GUAPX fitting program. This experimental C/R is compared to a Monte Carlo simulated C/R. The ratio of simulated and experimental C/R values is called the K-value. ALIC concentrations are calculated by comparing the K-value to the fraction of all invisibles present; the invisible fraction is produced from the spectrum fit by GUAPX. This method is applied to MSL spectra with long integration duration (greater than 3 hours) and with energy resolution less than 180 eV at 5.9 keV. These overnight spectra encompass a variety of geologic materials examined by the Curiosity Rover, including volcanic and sedimentary lithologies. Transfer of the K-value calibration produced in the lab to the flight APXS has been completed and temperature, geometry and spectrum duration effects have been thoroughly examined. A typical limit of detection of ALICs is around 5 wt% with uncertainties of approximately 5 wt%. Accurate elemental concentrations are required as input to the Monte Carlo program (Mallet et al, 2006; Lee, 2010). Elemental concentrations are obtained from the GUAPX code using the same long duration, good resolution spectra used for determining the experimental C/R ratios (Campbell et al. 2012). Special attention was given to the assessment of Rb, Sr, and Y as these element peaks overlap the scatter peaks. Mineral effects
MERS Coronavirus Neutralizing Antibodies in Camels, Eastern Africa, 1983-1997

NARCIS (Netherlands)

Müller, Marcel A; Corman, Victor Max; Jores, Joerg; Meyer, Benjamin; Younan, Mario; Liljander, Anne; Bosch, Berend-Jan; Lattwein, Erik; Hilali, Mosaad; Musa, Bakri E; Bornstein, Set; Drosten, Christian

2014-01-01

To analyze the distribution of Middle East respiratory syndrome coronavirus (MERS-CoV)-seropositive dromedary camels in eastern Africa, we tested 189 archived serum samples accumulated during the past 30 years. We identified MERS-CoV neutralizing antibodies in 81.0% of samples from the main
MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity.

Science.gov (United States)

Chu, Daniel K W; Hui, Kenrie P Y; Perera, Ranawaka A P M; Miguel, Eve; Niemeyer, Daniela; Zhao, Jincun; Channappanavar, Rudragouda; Dudas, Gytis; Oladipo, Jamiu O; Traoré, Amadou; Fassi-Fihri, Ouafaa; Ali, Abraham; Demissié, Getnet F; Muth, Doreen; Chan, Michael C W; Nicholls, John M; Meyerholz, David K; Kuranga, Sulyman A; Mamo, Gezahegne; Zhou, Ziqi; So, Ray T Y; Hemida, Maged G; Webby, Richard J; Roger, Francois; Rambaut, Andrew; Poon, Leo L M; Perlman, Stanley; Drosten, Christian; Chevalier, Veronique; Peiris, Malik

2018-03-20

Middle East respiratory syndrome coronavirus (MERS-CoV) causes a zoonotic respiratory disease of global public health concern, and dromedary camels are the only proven source of zoonotic infection. Although MERS-CoV infection is ubiquitous in dromedaries across Africa as well as in the Arabian Peninsula, zoonotic disease appears confined to the Arabian Peninsula. MERS-CoVs from Africa have hitherto been poorly studied. We genetically and phenotypically characterized MERS-CoV from dromedaries sampled in Morocco, Burkina Faso, Nigeria, and Ethiopia. Viruses from Africa (clade C) are phylogenetically distinct from contemporary viruses from the Arabian Peninsula (clades A and B) but remain antigenically similar in microneutralization tests. Viruses from West (Nigeria, Burkina Faso) and North (Morocco) Africa form a subclade, C1, that shares clade-defining genetic signatures including deletions in the accessory gene ORF4b Compared with human and camel MERS-CoV from Saudi Arabia, virus isolates from Burkina Faso (BF785) and Nigeria (Nig1657) had lower virus replication competence in Calu-3 cells and in ex vivo cultures of human bronchus and lung. BF785 replicated to lower titer in lungs of human DPP4-transduced mice. A reverse genetics-derived recombinant MERS-CoV (EMC) lacking ORF4b elicited higher type I and III IFN responses than the isogenic EMC virus in Calu-3 cells. However, ORF4b deletions may not be the major determinant of the reduced replication competence of BF785 and Nig1657. Genetic and phenotypic differences in West African viruses may be relevant to zoonotic potential. There is an urgent need for studies of MERS-CoV at the animal-human interface. Copyright © 2018 the Author(s). Published by PNAS.
Enzymatic Mercury Detoxification: The Regulatory Protein MerR

CERN Multimedia

Ctortecka, B; Walsh, C T; Comess, K M

2002-01-01

Mercury ions and organomercurial reagents are extremely toxic due to their affinity for thiol groups. Many bacteria contain an elaborate detoxification system for a metabolic conversion of toxic Hg$^{2+}$ or organomercurials to less toxic elemental Hg$^0$. The main components of the enzymatic mercury detoxification (see Fig. 1) are the regulatory protein MerR (mercury responsive genetic switch), the organomercurial lyase MerB (cleavage of carbon mercury bonds), and the mercuric ion reductase MerA (reduction of mercuric ions). In these proteins Hg$^{2+}$ is usually coordinated by the thiol groups of cysteines. We utilize the nuclear quadrupole interaction (NQI) of ${\\rm^{199m}}$Hg detected by time differential perturbed angular correlation (TDPAC) to identify the Hg metal site geometries in these proteins in order to elucidate the molecular origin of the ultrasensitivity, selectivity and reaction mechanism of this detoxification system. The short lived TDPAC probe ${\\rm^{199m}}$Hg ($\\tau_{1/2} =$ 43 min) is su...
Discovery of novel bat coronaviruses in south China that use the same receptor as MERS coronavirus.

Science.gov (United States)

Luo, Chu-Ming; Wang, Ning; Yang, Xing-Lou; Liu, Hai-Zhou; Zhang, Wei; Li, Bei; Hu, Ben; Peng, Cheng; Geng, Qi-Bin; Zhu, Guang-Jian; Li, Fang; Shi, Zheng-Li

2018-04-18

Middle East respiratory syndrome coronavirus (MERS-CoV) has represented a human health threat since 2012. Although several MERS-related CoVs, which belong to the same species as MERS-CoV, have been identified from bats, they do not use the MERS-CoV receptor, dipeptidyl peptidase 4 (DPP4). Here, we screened 1059 bat samples from at least 30 bat species collected in different regions in south China and identified 89 strains of lineage C betacoronaviruses, including Tylonycteris pachypus HKU4 , Pipistrellus pipistrellus HKU5, and MERS-related CoVs. We sequenced the full-length genomes of two positive samples collected from the great evening bat, Ia io , from Guangdong Province. The two genomes were highly similar and exhibited genomic structures identical to those of other lineage C betacoronaviruses. While they exhibited genome-wide nucleotide identities of only 75.3 to 81.2% with other MERS-related CoVs, their gene-coding regions were highly similar to their counterparts, except in the case of the spike proteins. Further protein--protein interaction assays demonstrated that the spike proteins of these MERS-related CoVs bind to the receptor DPP4. Recombination analysis suggested that the newly discovered MERS-related CoVs might have acquired their spike genes from a DPP4-recognizing bat HKU4. Our study provides further evidence that bats represent the evolutionary origins of MERS-CoV. IMPORTANCE Previous studies suggested that the Middle East respiratory syndrome coronavirus (MERS-CoV) may have originated in bats. However, its evolutionary path from bats to humans remains unclear. In this study, we discovered 89 novel lineage C betacoronaviruses (BetaCoVs) in eight bat species. We provide the evidence of a MERS-related CoV derived from the great evening bat that uses the same host receptor as human MERS-CoV. This virus also provides evidence for a natural recombination event between the bat MERS-related CoV and another bat coronavirus HKU4. Our study expands the host
Application of State Analysis and Goal-based Operations to a MER Mission Scenario

Science.gov (United States)

Morris, John Richard; Ingham, Michel D.; Mishkin, Andrew H.; Rasmussen, Robert D.; Starbird, Thomas W.

2006-01-01

State Analysis is a model-based systems engineering methodology employing a rigorous discovery process which articulates operations concepts and operability needs as an integrated part of system design. The process produces requirements on system and software design in the form of explicit models which describe the system behavior in terms of state variables and the relationships among them. By applying State Analysis to an actual MER flight mission scenario, this study addresses the specific real world challenges of complex space operations and explores technologies that can be brought to bear on future missions. The paper first describes the tools currently used on a daily basis for MER operations planning and provides an in-depth description of the planning process, in the context of a Martian day's worth of rover engineering activities, resource modeling, flight rules, science observations, and more. It then describes how State Analysis allows for the specification of a corresponding goal-based sequence that accomplishes the same objectives, with several important additional benefits.
Mild encephalitis/encephalopathy with reversible splenial lesion (MERS) in adults-a case report and literature review.

Science.gov (United States)

Yuan, Junliang; Yang, Shuna; Wang, Shuangkun; Qin, Wei; Yang, Lei; Hu, Wenli

2017-05-25

Mild encephalitis/encephalopathy with reversible splenial lesion (MERS) is a rare clinico-radiological entity characterized by the magnetic resonance imaging (MRI) finding of a reversible lesion in the corpus callosum, sometimes involved the symmetrical white matters. Many cases of child-onset MERS with various causes have been reported. However, adult-onset MERS is relatively rare. The clinical characteristics and pathophysiologiccal mechanisms of adult-onset MERS are not well understood. We reviewed the literature on adult-onset MERS in order to describe the characteristics of MERS in adults and to provide experiences for clinician. We reported a case of adult-onset MERS with acute urinary retension and performed literature search from PubMed and web of science databases to identify other adult-onset MERS reports from Januarary 2004 to March 2016. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was followed on selection process. And then we summarized the clinico-radiological features of adult-onset MERS. Twenty-nine adult-onset MERS cases were reviewed from available literature including the case we have. 86.2% of the cases (25/29) were reported in Asia, especially in Japan. Ages varied between 18 and 59 years old with a 12:17 female-to-male ratio. The major cause was infection by virus or bacteria. Fever and headache were the most common clinical manifestation, and acute urinary retention was observed in 6 patients. All patients recovered completely within a month. Adult-onset MERS is an entity with a broad clinico-radiological spectrum because of the various diseases and conditions. There are similar characteristics between MERS in adults and children, also some differences.
A QUANTUM BAND MODEL OF THE ν3 FUNDAMENTAL OF METHANOL (CH3OH) AND ITS APPLICATION TO FLUORESCENCE SPECTRA OF COMETS

International Nuclear Information System (INIS)

Villanueva, G. L.; DiSanti, M. A.; Mumma, M. J.; Xu, L.-H.

2012-01-01

Methanol (CH 3 OH) radiates efficiently at infrared wavelengths, dominating the C-H stretching region in comets, yet inadequate quantum-mechanical models have imposed limits on the practical use of its emission spectra. Accordingly, we constructed a new line-by-line model for the ν 3 fundamental band of methanol at 2844 cm –1 (3.52 μm) and applied it to interpret cometary fluorescence spectra. The new model permits accurate synthesis of line-by-line spectra for a wide range of rotational temperatures, ranging from 10 K to more than 400 K. We validated the model by comparing simulations of CH 3 OH fluorescent emission with measured spectra of three comets (C/2001 A2 LINEAR, C/2004 Q2 Machholz and 8P/Tuttle) acquired with high-resolution infrared spectrometers at high-altitude sites. The new model accurately describes the complex emission spectrum of the ν 3 band, providing distinct rotational temperatures and production rates at greatly improved confidence levels compared with results derived from earlier fluorescence models. The new model reconciles production rates measured at infrared and radio wavelengths in C/2001 A2 (LINEAR). Methanol can now be quantified with unprecedented precision and accuracy in astrophysical sources through high-dispersion spectroscopy at infrared wavelengths.
A Quantum Band Model of the nu3 Fundamental of Methanol (CH3OH) and Its Application to Fluorcescence Spectra of Comets

Science.gov (United States)

Villanueva, Geronimo L.; DiSanti, M. A.; Mumma, M. J.; Xu, L.-H.

2012-01-01

Methanol (CH3OH) radiates efficiently at infrared wavelengths, dominating the C-H stretching region in comets, yet inadequate quantum-mechanical models have imposed limits on the practical use of its emission spectra. Accordingly, we constructed a new line-by-line model for the 3 fundamental band of methanol at 2844 / cm (3.52 micron) and applied it to interpret cometary fluorescence spectra. The new model permits accurate synthesis of line-by-line spectra for a wide range of rotational temperatures, ranging from 10 K to more than 400 K.We validated the model by comparing simulations of CH3OH fluorescent emission with measured spectra of three comets (C/2001 A2 LINEAR, C/2004 Q2 Machholz and 8P/Tuttle) acquired with high-resolution infrared spectrometers at high-altitude sites. The new model accurately describes the complex emission spectrum of the nu3 band, providing distinct rotational temperatures and production rates at greatly improved confidence levels compared with results derived from earlier fluorescence models. The new model reconciles production rates measured at infrared and radio wavelengths in C/2001 A2 (LINEAR). Methanol can now be quantified with unprecedented precision and accuracy in astrophysical sources through high-dispersion spectroscopy at infrared wavelengths
Ole Rømer som enevældens administrator

DEFF Research Database (Denmark)

Olden-Jørgensen, Sebastian

2004-01-01

En biografisk skitse af Ole Rømers virke med vægt på hans rolle som embedsmand og rådgiver for Christian V. Hans virke analyseres på baggrund af en ny forståelse for den tidlige enevældes politiske kultur.......En biografisk skitse af Ole Rømers virke med vægt på hans rolle som embedsmand og rådgiver for Christian V. Hans virke analyseres på baggrund af en ny forståelse for den tidlige enevældes politiske kultur....
Sn-L3 EDGE and Fe K edge XANES spectra of the surface layer of ancient Chinese black mirror Heiqigu

International Nuclear Information System (INIS)

Gaowei Mengjia; Liu Yuzhen; Chu Wangsheng; Wu Ziyu; Wang Changsui

2009-01-01

The Chinese ancient black mirror known as Heiqigu was studied by x-ray-absorption near-edge structure spectroscopy and results were reported. The Sn-L 3 edge and Fe K edge spectra further confirmed the Schottky-type defect model in the Heiqigu surface system. And it was suggested that the surface layer of the mirror was a combined structure of oxidation of Sn(IV) and Sn(II). (authors)
Effect of disorder correlation in random mers

International Nuclear Information System (INIS)

Brezini, A.; Sebbani, M.; Depollier, C.; Belbachir, M.

1995-12-01

A widely held view in solid-state physics is that disorder precludes the presence of long-range transport in one-dimension. Recently a series of models has been proposed that do not conform to this view such as the well known Random Dimer Model (RDM). In the following paper, we must present a generalization of the RDM. In particular, the nature of the eigenstates of a non-interacting electron is investigated by means of a popular one-dimensional Kronig-Penney Hamiltonian in which n-mers have been placed at random on a regular lattice. Mainly in each allowed energy band of the spectrum, it is found that n-mers exhibits n - 1 resonances associated to extended states. Moreover these resonances appear to be narrower if the potential is attractive against repulsive, i.e. constituted of wells instead barriers, which discriminates the ability in localizing the eigenstates. Attention has been paid to the energy transition as one approaches the two resonances of the random trimer within the first allowed band. The transition exhibits a smooth behaviour for the lower energy when compared to the higher one with respect to the first resonance and shows quite a similar behaviour for both sides close to the second resonance. The discrepancy is attributed to the typical nature of the eigenstates for each resonance. Correspondingly, the wave functions associated to the first resonance are not like Bloch-waves while for the second one they look like the crystal wave functions displaying only minor distortions. (author). 44 refs, 6 figs
Adaptive evolution influences the infectious dose of MERS-CoV necessary to achieve severe respiratory disease.

Science.gov (United States)

Douglas, Madeline G; Kocher, Jacob F; Scobey, Trevor; Baric, Ralph S; Cockrell, Adam S

2018-04-01

We recently established a mouse model (288-330 +/+ ) that developed acute respiratory disease resembling human pathology following infection with a high dose (5 × 10 6 PFU) of mouse-adapted MERS-CoV (icMERSma1). Although this high dose conferred fatal respiratory disease in mice, achieving similar pathology at lower viral doses may more closely reflect naturally acquired infections. Through continued adaptive evolution of icMERSma1 we generated a novel mouse-adapted MERS-CoV (maM35c4) capable of achieving severe respiratory disease at doses between 10 3 and 10 5 PFU. Novel mutations were identified in the maM35c4 genome that may be responsible for eliciting etiologies of acute respiratory distress syndrome at 10-1000 fold lower viral doses. Importantly, comparative genetics of the two mouse-adapted MERS strains allowed us to identify specific mutations that remained fixed through an additional 20 cycles of adaptive evolution. Our data indicate that the extent of MERS-CoV adaptation determines the minimal infectious dose required to achieve severe respiratory disease. Copyright © 2017 Elsevier Inc. All rights reserved.
Model uncertainties of local-thermodynamic-equilibrium K-shell spectroscopy

Science.gov (United States)

Nagayama, T.; Bailey, J. E.; Mancini, R. C.; Iglesias, C. A.; Hansen, S. B.; Blancard, C.; Chung, H. K.; Colgan, J.; Cosse, Ph.; Faussurier, G.; Florido, R.; Fontes, C. J.; Gilleron, F.; Golovkin, I. E.; Kilcrease, D. P.; Loisel, G.; MacFarlane, J. J.; Pain, J.-C.; Rochau, G. A.; Sherrill, M. E.; Lee, R. W.

2016-09-01

Local-thermodynamic-equilibrium (LTE) K-shell spectroscopy is a common tool to diagnose electron density, ne, and electron temperature, Te, of high-energy-density (HED) plasmas. Knowing the accuracy of such diagnostics is important to provide quantitative conclusions of many HED-plasma research efforts. For example, Fe opacities were recently measured at multiple conditions at the Sandia National Laboratories Z machine (Bailey et al., 2015), showing significant disagreement with modeled opacities. Since the plasma conditions were measured using K-shell spectroscopy of tracer Mg (Nagayama et al., 2014), one concern is the accuracy of the inferred Fe conditions. In this article, we investigate the K-shell spectroscopy model uncertainties by analyzing the Mg spectra computed with 11 different models at the same conditions. We find that the inferred conditions differ by ±20-30% in ne and ±2-4% in Te depending on the choice of spectral model. Also, we find that half of the Te uncertainty comes from ne uncertainty. To refine the accuracy of the K-shell spectroscopy, it is important to scrutinize and experimentally validate line-shape theory. We investigate the impact of the inferred ne and Te model uncertainty on the Fe opacity measurements. Its impact is small and does not explain the reported discrepancies.
ASHIQ OMER IN THE MODERN CRIMEAN TATAR LITERATURE MODERN KIRIM-TATAR EDEBİYATINDA ÂŞIK ÖMER

Directory of Open Access Journals (Sweden)

Emek ÜŞENMEZ

2012-01-01

Full Text Available Ashiq Omer is a bard of the 17th century. Researches that have been made lately new perspectives about his origin and the literary circle he is a member of most of the works produced in Turkey claim that he is from Gozleve (Qorualan, a small town in Qonya whereas works produced abroad claim him to be from Kezlev (Gezleve in Crimea. Therefore two different literary circles Turkey anda Crimea emerge.This article aims to compare and contrast the works on Ashiq Omer. Works produced about Ashiq Omer the contemporary Crimean Tatar literatüre and his influence on the so-called literary tradition are discussed Âşık Ömer 17. Yüzyıl saz şairlerindendir. Son zamanlarda yapılan çalışmalarda Âşık Ömer’in nereli ve hangi edebî muhite dâhil olduğu konusunda farklı görüşler ortaya konulmuştur. Türkiye’de yapılan çalışmaların çoğunda Âşık Ömer’in Konya’nın Hadim ilçesine bağlı Gözleve (Korualan kasabasından olduğu kesin bir dille ifade edilirken yurtdışında yapılan çalışmalarda ise onun Kırım’ın Kezlev (Gezleve şehrinden olduğu söylenmektedir. Bu durumda Kırım ve Türkiye olmak üzere iki farklı edebî muhit ortaya çıkmaktadır.Bu çalışmada öncelikle Âşık Ömer hakkında söylenilenler ve yapılan çalışmalar mukayeseli olarak ortaya konulmuştur. Çağdaş Kırım Tatar edebiyatında Âşık Ömer üzerine yapılan çalışmalar ele alınıp onun modern Kırım Tatar edebiyatına olan etkisi üzerinde durulmuştur.
Enhanced inflammation in New Zealand white rabbits when MERS-CoV reinfection occurs in the absence of neutralizing antibody.

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Katherine V Houser

2017-08-01

Full Text Available The Middle East respiratory syndrome coronavirus (MERS-CoV is a zoonotic betacoronavirus that was first detected in humans in 2012 as a cause of severe acute respiratory disease. As of July 28, 2017, there have been 2,040 confirmed cases with 712 reported deaths. While many infections have been fatal, there have also been a large number of mild or asymptomatic cases discovered through monitoring and contact tracing. New Zealand white rabbits are a possible model for asymptomatic infection with MERS-CoV. In order to discover more about non-lethal infections and to learn whether a single infection with MERS-CoV would protect against reinfection, we inoculated rabbits with MERS-CoV and monitored the antibody and inflammatory response. Following intranasal infection, rabbits developed a transient dose-dependent pulmonary infection with moderately high levels of viral RNA, viral antigen, and perivascular inflammation in multiple lung lobes that was not associated with clinical signs. The rabbits developed antibodies against viral proteins that lacked neutralizing activity and the animals were not protected from reinfection. In fact, reinfection resulted in enhanced pulmonary inflammation, without an associated increase in viral RNA titers. Interestingly, passive transfer of serum from previously infected rabbits to naïve rabbits was associated with enhanced inflammation upon infection. We further found this inflammation was accompanied by increased recruitment of complement proteins compared to primary infection. However, reinfection elicited neutralizing antibodies that protected rabbits from subsequent viral challenge. Our data from the rabbit model suggests that people exposed to MERS-CoV who fail to develop a neutralizing antibody response, or persons whose neutralizing antibody titers have waned, may be at risk for severe lung disease on re-exposure to MERS-CoV.
PCA: Principal Component Analysis for spectra modeling

Science.gov (United States)

Hurley, Peter D.; Oliver, Seb; Farrah, Duncan; Wang, Lingyu; Efstathiou, Andreas

2012-07-01

The mid-infrared spectra of ultraluminous infrared galaxies (ULIRGs) contain a variety of spectral features that can be used as diagnostics to characterize the spectra. However, such diagnostics are biased by our prior prejudices on the origin of the features. Moreover, by using only part of the spectrum they do not utilize the full information content of the spectra. Blind statistical techniques such as principal component analysis (PCA) consider the whole spectrum, find correlated features and separate them out into distinct components. This code, written in IDL, classifies principal components of IRS spectra to define a new classification scheme using 5D Gaussian mixtures modelling. The five PCs and average spectra for the four classifications to classify objects are made available with the code.
Public response to MERS-CoV in the Middle East: iPhone survey in six countries.

Science.gov (United States)

Alqahtani, Amani S; Rashid, Harunor; Basyouni, Mada H; Alhawassi, Tariq M; BinDhim, Nasser F

Gulf Cooperation Council (GCC) countries bear the heaviest brunt of MERS-CoV. This study aims to compare public awareness and practice around MERS-CoV across GCC countries. A cross-sectional survey was conducted using the Gulf Indicators (GI) smartphone app among people in the six GCC countries, namely Saudi Arabia, Kuwait, the United Arab Emirates, Qatar, Bahrain, and Oman. A total of 1812 participants recruited. All were aware of MERS-CoV, yet the perception and practice around MERS-CoV varied widely between countries. Over two thirds were either "not concerned" or "slightly concerned" about contracting MERS-CoV; believing that they were under Allah's (God's) protection (40%) was the most cited reason. While 79% were aware that the disease can transmit through droplet from infected person, only 12% stated that MERS-CoV transmits via camels; people in Saudi Arabia were better aware of the transmission. Nevertheless, only 22% of respondents believed that camels are the zoonotic reservoir of MERS-CoV. Those who were concerned about contracting MERS-CoV (aOR: 1.6, 95% CI: 1.2-2.1, pAuthors. Published by Elsevier Ltd.. All rights reserved.
Worry experienced during the 2015 Middle East Respiratory Syndrome (MERS pandemic in Korea.

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Jun-Soo Ro

Full Text Available Korea failed in its risk communication during the early stage of the Middle East Respiratory Syndrome (MERS outbreak; consequently, it faced difficulties in managing MERS, while disease-related worry increased. Disease-related worry can help disease prevention and management, but can also have a detrimental effect. This study measured the overall level of disease-related worry during the MERS outbreak period in Korea and the influencing factors and levels of disease-related worry during key outbreak periods.The cross-sectional survey included 1,000 adults who resided in Korea. An ordinal logistic regression was performed for the overall level of MERS-related worry, and influencing factors of worry were analyzed. A reliability test was performed on the levels of MERS-related worry during key outbreak periods.The overall level of MERS-related worry was 2.44. Multivariate analysis revealed that women and respondents w very poor subjective health status had higher levels of worry. Respondents with very high stress in daily life had higher levels of worry than those who reported having little stress. The reliability test results on MERS-related worry scores during key outbreak periods showed consistent scores during each period.Level of worry increased in cases having higher perceived susceptibility and greater trust in informal information, while initial stage of outbreak was closely associated with that at later stages. These findings suggest the importance of managing the level of worry by providing timely and accurate disease-related information during the initial stage of disease outbreak.

Asy2/Mer2: an evolutionarily conserved mediator of meiotic recombination, pairing, and global chromosome compaction.

Science.gov (United States)

Tessé, Sophie; Bourbon, Henri-Marc; Debuchy, Robert; Budin, Karine; Dubois, Emeline; Liangran, Zhang; Antoine, Romain; Piolot, Tristan; Kleckner, Nancy; Zickler, Denise; Espagne, Eric

2017-09-15

Meiosis is the cellular program by which a diploid cell gives rise to haploid gametes for sexual reproduction. Meiotic progression depends on tight physical and functional coupling of recombination steps at the DNA level with specific organizational features of meiotic-prophase chromosomes. The present study reveals that every step of this coupling is mediated by a single molecule: Asy2/Mer2. We show that Mer2, identified so far only in budding and fission yeasts, is in fact evolutionarily conserved from fungi (Mer2/Rec15/Asy2/Bad42) to plants (PRD3/PAIR1) and mammals (IHO1). In yeasts, Mer2 mediates assembly of recombination-initiation complexes and double-strand breaks (DSBs). This role is conserved in the fungus Sordaria However, functional analysis of 13 mer2 mutants and successive localization of Mer2 to axis, synaptonemal complex (SC), and chromatin revealed, in addition, three further important functions. First, after DSB formation, Mer2 is required for pairing by mediating homolog spatial juxtaposition, with implications for crossover (CO) patterning/interference. Second, Mer2 participates in the transfer/maintenance and release of recombination complexes to/from the SC central region. Third, after completion of recombination, potentially dependent on SUMOylation, Mer2 mediates global chromosome compaction and post-recombination chiasma development. Thus, beyond its role as a recombinosome-axis/SC linker molecule, Mer2 has important functions in relation to basic chromosome structure. © 2017 Tessé et al.; Published by Cold Spring Harbor Laboratory Press.
Middle East Respiratory Syndrome (MERS) coronavirus seroprevalence in domestic livestock in Saudi Arabia, 2010 to 2013.

Science.gov (United States)

Hemida, M G; Perera, R A; Wang, P; Alhammadi, M A; Siu, L Y; Li, M; Poon, L L; Saif, L; Alnaeem, A; Peiris, M

2013-12-12

In Saudi Arabia, including regions of Riyadh and Al Ahsa, pseudoparticle neutralisation (ppNT) and microneutralisation (MNT) tests detected no antibodies to Middle East Respiratory Syndrome coronavirus (MERS-CoV) in sheep (n= 100), goats (n= 45), cattle (n= 50) and chickens (n= 240). Dromedary camels however, had a high prevalence of MERS-CoV antibodies. Bovine coronavirus (BCoV) infected sera from cattle had no cross-reactivity in MERS-CoV ppNT or MNT, while many dromedary camels’ sera reacted to both BCoV and MERS-CoV. Some nevertheless displayed specific serologic reaction profiles to MERS-CoV.
The Middle East respiratory syndrome coronavirus (MERS-CoV does not replicate in Syrian hamsters.

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Emmie de Wit

Full Text Available In 2012 a novel coronavirus, MERS-CoV, associated with severe respiratory disease emerged in the Arabian Peninsula. To date, 55 human cases have been reported, including 31 fatal cases. Several of the cases were likely a result of human-to-human transmission. The emergence of this novel coronavirus prompts the need for a small animal model to study the pathogenesis of this virus and to test the efficacy of potential intervention strategies. In this study we explored the use of Syrian hamsters as a small animal disease model, using intratracheal inoculation and inoculation via aerosol. Clinical signs of disease, virus replication, histological lesions, cytokine upregulation nor seroconversion were observed in any of the inoculated animals, indicating that MERS-CoV does not replicate in Syrian hamsters.
Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.

Science.gov (United States)

Pettengill, James B; Pightling, Arthur W; Baugher, Joseph D; Rand, Hugh; Strain, Errol

2016-01-01

The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). When analyzing empirical data (whole-genome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.
Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.

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James B Pettengill

Full Text Available The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis. In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples and computational (petabytes of sequence data issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST scheme. When analyzing empirical data (whole-genome sequence data from 18,997 Salmonella isolates there are features (e.g., genomic, assembly, and contamination that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.
Biomolecular Mechanisms of Mercury Transfers and Transformations by Proteins of the Mer Operon

Science.gov (United States)

Miller, S. M.; Hong, B.; Nauss, R.; Momany, C.; Summers, A. O.; Feng, X.; Harwood, I.; Stroud, R.

2008-12-01

Aerobic bacteria exhibiting resistance to the toxic effects of Hg(II) and organomercurials [RHg(I), e.g. MeHg(I)] and are widely found in both pristine and mercury contaminated environments. Resistance, afforded by a plasmid- or transposon-associated mer operon, involves an unusual pathway where Hg(II) and organomercurials [RHg(I)] undergo facilitated entry into the bacterial cytoplasm via an integral membrane transport protein (MerT) and are then "detoxified" by the concerted effort of two enzymes, organomercurial lyase (MerB), which catalyzes dealkylation (i.e., demethylation) of RHg(I) to Hg(II) and a hydrocarbon, and mercuric ion reductase (MerA), which catalyzes reduction of Hg(II) to Hg(0) as the ultimate detoxification for the organism. With a widespread distribution, these bacterial transformations play a significant role in the fate of mercury in the environment. Our focus is on elucidation of the molecular mechanisms for the transport and catalytic transformations of RHg(I) and Hg(II) by these proteins and the factors that influence the overall efficiency of the process. Current efforts are focused primarily on elucidating details of RHg(I) binding and dealkylation by MerB as well as the mechanism for transfer of the Hg(II) product to MerA. Key findings include the demonstration of a non-cysteine residue as essential for the catalytic activity and demonstration that direct transfer of Hg(II) to MerA proceeds more rapidly and more completely than transfer to small MW thiols such as cysteines or glutathione. Reuslts of these studies as well as an overview of our current understanding of the whole system will be presented.
Modeling of XANES-spectra with the FEFF-program

Energy Technology Data Exchange (ETDEWEB)

Bosman, E; Thieme, J, E-mail: e.bosman@gmx.d, E-mail: jthieme@gwdg.d [Institute for X-Ray Physics, Georg-August-University Gottingen, Friedrich-Hund-Platz 1, 37077 Gottingen (Germany)

2009-09-01

The aim of this project is the calculation of the absorption coefficient {mu} of x-ray absorption spectra as a function of energy and a comparison with experimental data. A characteristic fine structure can be found in x-ray absorption spectra (XAS) consisting of the XANES (X-Ray Absorption Near Edge Structure) and the EXAFS (Extended X-Ray Absorption Fine Structure) region. XANES is characterized by multiple scattering and provides information about coordination chemistry and bonding angles of the irradiated sample. The program FEFF 8.4 was used for the calculations of the absorption K-edge spectra. FEFF was generated for ab initio multiple scattering calculations of X-ray Absorption Fine Structure (XAFS) of atom-clusters. The code yields scattering amplitudes, phases and other quantities. We computed {mu} at the K-edge of several elements like Ti, S and Fe. For this purpose, clusters of Na{sub 2}SO{sub 4}, Ba{sub 2}TiO{sub 4}, FeS{sub 2}, CaSO{sub 2} 2(H {sub 2}O) were used, working with several space groups. Some of the calculations are consistent with the results of the experiments, but others show energy shifts in the range of some eV. In summary, the FEFF calculations and the experimental data exhibit similarities as well as deviations. By using trimming parameters, deviations could be eliminated to a certain extent, which will be presented.
METALLICITY AND TEMPERATURE INDICATORS IN M DWARF K-BAND SPECTRA: TESTING NEW AND UPDATED CALIBRATIONS WITH OBSERVATIONS OF 133 SOLAR NEIGHBORHOOD M DWARFS

Energy Technology Data Exchange (ETDEWEB)

Rojas-Ayala, Barbara [Department of Astrophysics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 (United States); Covey, Kevin R.; Lloyd, James P. [Department of Astronomy, Cornell University, 122 Sciences Drive, Ithaca, NY 14853 (United States); Muirhead, Philip S., E-mail: babs@amnh.org [Department of Astronomy, California Institute of Technology, 1200 East California Boulevard, MC 249-17, Pasadena, CA 91125 (United States)

2012-04-01

We present K-band spectra for 133 nearby (d < 33 ps) M dwarfs, including 18 M dwarfs with reliable metallicity estimates (as inferred from an FGK type companion), 11 M dwarf planet hosts, more than 2/3 of the M dwarfs in the northern 8 pc sample, and several M dwarfs from the LSPM catalog. From these spectra, we measure equivalent widths of the Ca and Na lines, and a spectral index quantifying the absorption due to H{sub 2}O opacity (the H{sub 2}O-K2 index). Using empirical spectral type standards and synthetic models, we calibrate the H{sub 2}O-K2 index as an indicator of an M dwarf's spectral type and effective temperature. We also present a revised relationship that estimates the [Fe/H] and [M/H] metallicities of M dwarfs from their Na I, Ca I, and H{sub 2}O-K2 measurements. Comparisons to model atmosphere provide a qualitative validation of our approach, but also reveal an overall offset between the atomic line strengths predicted by models as compared to actual observations. Our metallicity estimates also reproduce expected correlations with Galactic space motions and H{alpha} emission line strengths, and return statistically identical metallicities for M dwarfs within a common multiple system. Finally, we find systematic residuals between our H{sub 2}O-based spectral types and those derived from optical spectral features with previously known sensitivity to stellar metallicity, such as TiO, and identify the CaH1 index as a promising optical index for diagnosing the metallicities of near-solar M dwarfs.
Intégration régionale et politique des outre-mers

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Didier Benjamin

1999-06-01

Full Text Available Grâce à ses outre-mers, qui lui apportent 96% de sa zone économique exclusive, la France dispose du troisième domaine maritime du monde et assure une présence sur tous les océans. Cependant, les outre-mers ne jouent plus qu'un rôle mineur dans la politique des océans. Ce paradoxe s'explique en partie par les difficultés qu'ils rencontrent à s'insérer dans les échanges internationaux et à s'intégrer aux organisations régionales. Les différences de niveaux de développement socioéconomique avec les pays voisins contribuent à isoler les outre-mers dans leur environnement immédiat.
Comparison between SARS CoV and MERS CoV Using Apriori Algorithm, Decision Tree, SVM

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Jang Seongpil

2016-01-01

Full Text Available MERS (Middle East Respiratory Syndrome is a worldwide disease these days. The number of infected people is 1038(08/03/2015 in Saudi Arabia and 186(08/03/2015 in South Korea. MERS is all over the world including Europe and the fatality rate is 38.8%, East Asia and the Middle East. The MERS is also known as a cousin of SARS (Severe Acute Respiratory Syndrome because both diseases show similar symptoms such as high fever and difficulty in breathing. This is why we compared MERS with SARS. We used data of the spike glycoprotein from NCBI. As a way of analyzing the protein, apriori algorithm, decision tree, SVM were used, and particularly SVM was iterated by normal, polynomial, and sigmoid. The result came out that the MERS and the SARS are alike but also different in some way.
Ole Rømer-Observatoriet

DEFF Research Database (Denmark)

Buhl, Hans; Knudsen, Ole J.; Nielsen, Axel V.

Siden 1911 har der ligget et astronomisk observatorium i Århus. Ole Rømer-Observatoriet blev efter en turbulent start drevet af kommunen, indtil Aarhus Universitet i 1956 overtog det. Der har fra tid til anden været både kontroverser og trusler om lukning, men arbejdet på observatoriet har også...... fortæller museumsinspektør Hans Buhl og planetarieleder Ole J. Knudsen, begge Steno Museet, de næste 95 år af observatoriets brogede historie....
Temperature Dependence of Polarized Low Wavenumber Raman Spectra of Aminopropylsilanetriol Polymer

International Nuclear Information System (INIS)

V, Volovsek; L, Bistrcic; K, Furic; V, Daanic; I, Movre Sapic

2006-01-01

Low wavenumber polarized Raman spectra of aminopropylsilanetriol (APST) polymer deposited on PVC substrate were measured in the temperature range from 300 K to 78 K. In the low wavenumber Raman spectra of these samples a very strong Bose band was observed. The best results in modeling the low wavenumber Raman spectra were achieved with the exponential correlation function of disorder G dis (ν) = exp(-r/R c )using three contributions: transversal and longitudinal acoustic phonons and molecular vibration. Results suggest medium range ordered ladder structure, stacked in layers with different orientations of ladders
‘Postage-stamp PIV’: small velocity fields at 400 kHz for turbulence spectra measurements

Science.gov (United States)

Beresh, Steven J.; Henfling, John F.; Spillers, Russell W.; Spitzer, Seth M.

2018-03-01

Time-resolved particle image velocimetry recently has been demonstrated in high-speed flows using a pulse-burst laser at repetition rates reaching 50 kHz. Turbulent behavior can be measured at still higher frequencies if the field of view is greatly reduced and lower laser pulse energy is accepted. Current technology allows image acquisition at 400 kHz for sequences exceeding 4000 frames but for an array of only 128 × 120 pixels, giving the moniker of ‘postage-stamp PIV’. The technique has been tested far downstream of a supersonic jet exhausting into a transonic crossflow. Two-component measurements appear valid until 120 kHz, at which point a noise floor emerges whose magnitude is dependent on the reduction of peak locking. Stereoscopic measurement offers three-component data for turbulent kinetic energy spectra, but exhibits a reduced signal bandwidth and higher noise in the out-of-plane component due to the oblique camera images. The resulting spectra reveal two regions exhibiting power-law dependence describing the turbulent decay. The frequency response of the present measurement configuration exceeds nearly all previous velocimetry measurements in high speed flow.
Nordic Winter and Cold: Their Correspondence with Tomas Tranströmer's Poetry

Science.gov (United States)

Hosian, Mohammad Akbar

2015-01-01

The Nobel Prize winning poet Tomas Tranströmer was born and bred in Sweden, a remarkably Scandinavian country. Topographically, Scandinavian countries are locations of extreme cold and snowing. This distinguishing climatic condition has had a dominant influence and impact on almost all Scandinavian art and literature, including Tomas Tranströmer's…
High resolution spectroscopy over 8500-8750 Å for GAIA library of synthetic spectra for T_eff <= 7500 K

Science.gov (United States)

Munari, U.; Castelli, F.

2000-01-01

We present a library of synthetic spectra characterized by -2.5 7500 K will be given later on in this series. The 254 synthetic spectra presented here are based on Kurucz's codes and line data and have been computed over a more extended wavelength interval (7650-8750 Ä) than that currently baselined for implementation on GAIA, i.e. the 8500-8750 Ä. This last range is dominated by the near-IR Ca II triplet and the head of the Paschen series. The more extended wavelength range allows us to investigate the behaviour of other strong near-IR spectral features (severely contaminated by telluric absorptions in ground-based observed spectra) as the K I doublet (7664, 7699 Ä), the Na I doublet (8183, 8194 Ä) and the lines of Fe I multiplet N.60 at 8327 and 8388 Ä. The synthetic spectra support our previous conclusions about the superior performance of the Paschen/Ca II 8500-8750 Ä region in meeting the GAIA requirements when compared to other near-IR intervals of similar bigtriangleup lambda = 250 Ä. Table 2 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/Abstract.html Figures 5-93 are only available in electronic form at the http://www.edpsciences.org The spectra are also available in electronic form at the CDS or via the personal HomePage http://ulisse.pd.astro.it/Astro/Atlases/
Comparative Modelling of the Spectra of Cool Giants

Science.gov (United States)

Lebzelter, T.; Heiter, U.; Abia, C.; Eriksson, K.; Ireland, M.; Neilson, H.; Nowotny, W; Maldonado, J; Merle, T.; Peterson, R.;

2012-01-01

Our ability to extract information from the spectra of stars depends on reliable models of stellar atmospheres and appropriate techniques for spectral synthesis. Various model codes and strategies for the analysis of stellar spectra are available today. Aims. We aim to compare the results of deriving stellar parameters using different atmosphere models and different analysis strategies. The focus is set on high-resolution spectroscopy of cool giant stars. Methods. Spectra representing four cool giant stars were made available to various groups and individuals working in the area of spectral synthesis, asking them to derive stellar parameters from the data provided. The results were discussed at a workshop in Vienna in 2010. Most of the major codes currently used in the astronomical community for analyses of stellar spectra were included in this experiment. Results. We present the results from the different groups, as well as an additional experiment comparing the synthetic spectra produced by various codes for a given set of stellar parameters. Similarities and differences of the results are discussed. Conclusions. Several valid approaches to analyze a given spectrum of a star result in quite a wide range of solutions. The main causes for the differences in parameters derived by different groups seem to lie in the physical input data and in the details of the analysis method. This clearly shows how far from a definitive abundance analysis we still are.

OPTIMAL REPRESENTATION OF MER SIGNALS APPLIED TO THE IDENTIFICATION OF BRAIN STRUCTURES DURING DEEP BRAIN STIMULATION

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Hernán Darío Vargas Cardona

2015-07-01

Full Text Available Identification of brain signals from microelectrode recordings (MER is a key procedure during deep brain stimulation (DBS applied in Parkinson’s disease patients. The main purpose of this research work is to identify with high accuracy a brain structure called subthalamic nucleus (STN, since it is the target structure where the DBS achieves the best therapeutic results. To do this, we present an approach for optimal representation of MER signals through method of frames. We obtain coefficients that minimize the Euclidean norm of order two. From optimal coefficients, we extract some features from signals combining the wavelet packet and cosine dictionaries. For a comparison frame with the state of the art, we also process the signals using the discrete wavelet transform (DWT with several mother functions. We validate the proposed methodology in a real data base. We employ simple supervised machine learning algorithms, as the K-Nearest Neighbors classifier (K-NN, a linear Bayesian classifier (LDC and a quadratic Bayesian classifier (QDC. Classification results obtained with the proposed method improves significantly the performance of the DWT. We achieve a positive identification of the STN superior to 97,6%. Identification outcomes achieved by the MOF are highly accurate, as we can potentially get a false positive rate of less than 2% during the DBS.
28-mer Fragment Derived from Enterocin CRL35 Displays an Unexpected Bactericidal Effect on Listeria Cells.

Science.gov (United States)

Masias, Emilse; Sanches, Paulo R S; Dupuy, Fernando G; Acuna, Leonardo; Bellomio, Augusto; Cilli, Eduardo; Saavedra, Lucila; Minahk, Carlos

2015-01-01

Two shorter peptides derived from enterocin CRL35, a 43-mer bacteriocin, were synthesized i.e. the N-terminal fragment spanning from residues 1 to 15, and a 28-mer fragment that represents the C-terminal of enterocin CRL35, the residues 16 to 43. The separate peptides showed no activity when combined. On one hand, the 28-mer peptide displayed an unpredicted antimicrobial activity. On the other, 15- mer peptide had no consistent anti-Listeria effect. The dissociation constants calculated from experimental data indicated that all peptides could bind at similar extent to the sensitive cells. However, transmembrane electrical potential was not dissipated to the same level by the different peptides; whereas the full-length and the C-terminal 28-mer fragment induced almost full dissipation, 15-mer fragment produced only a slow and incomplete effect. Furthermore, a different interaction of each peptide with membranes was demonstrated based on studies carried out with liposomes, which led us to conclude that activity was related to structure rather than to net positive charges. These results open up the possibility of designing new peptides based on the 28-mer fragment with enhanced activity, which would represent a promising approach for combating Listeria and other pathogens.
MCNP modelling of scintillation-detector gamma-ray spectra from natural radionuclides.

Science.gov (United States)

Hendriks, P H G M; Maucec, M; de Meijer, R J

2002-09-01

gamma-ray spectra of natural radionuclides are simulated for a BGO detector in a borehole geometry using the Monte Carlo code MCNP. All gamma-ray emissions of the decay of 40K and the series of 232Th and 238U are used to describe the source. A procedure is proposed which excludes the time-consuming electron tracking in less relevant areas of the geometry. The simulated gamma-ray spectra are benchmarked against laboratory data.
Mercuric ion reduction and resistance in transgenic Arabidopsis thaliana plants expressing a modified bacterial merA gene.

Science.gov (United States)

Rugh, C L; Wilde, H D; Stack, N M; Thompson, D M; Summers, A O; Meagher, R B

1996-01-01

With global heavy metal contamination increasing, plants that can process heavy metals might provide efficient and ecologically sound approaches to sequestration and removal. Mercuric ion reductase, MerA, converts toxic Hg2+ to the less toxic, relatively inert metallic mercury (Hg0) The bacterial merA sequence is rich in CpG dinucleotides and has a highly skewed codon usage, both of which are particularly unfavorable to efficient expression in plants. We constructed a mutagenized merA sequence, merApe9, modifying the flanking region and 9% of the coding region and placing this sequence under control of plant regulatory elements. Transgenic Arabidopsis thaliana seeds expressing merApe9 germinated, and these seedlings grew, flowered, and set seed on medium containing HgCl2 concentrations of 25-100 microM (5-20 ppm), levels toxic to several controls. Transgenic merApe9 seedlings evolved considerable amounts of Hg0 relative to control plants. The rate of mercury evolution and the level of resistance were proportional to the steady-state mRNA level, confirming that resistance was due to expression of the MerApe9 enzyme. Plants and bacteria expressing merApe9 were also resistant to toxic levels of Au3+. These and other data suggest that there are potentially viable molecular genetic approaches to the phytoremediation of metal ion pollution. Images Fig. 2 Fig. 3 Fig. 4 PMID:8622910

The P K-near edge absorption spectra of phosphates

Science.gov (United States)

Franke, R.; Hormes, J.

1995-12-01

The X-ray absorption near edge structure (XANES) at the P K-edge in several orthophosphates with various cations, in condensed, and in substituted sodium phosphates have been measured using synchrotron radiation from the ELSA storage ring at the University of Bonn. The measured spectra demonstrate that chemical changes beyond the PO 4- tetrahedra are reflected by energy shifts of the pre-edge and continuum resonances, by the presence of characteristic shoulders and new peaks and by differences in the intensity of the white line. We discuss the energy differences between the white line positions and the corresponding P ls binding energies as a measure of half of the energy gap. The corresponding values correlate with the valence of the cations and the intensity of the white lines. The energy positions of the continuum resonances are discussed on the basis of an empirical bond-length correlation supporting a 1/ r2 - dependence.
The effect of multiple external representations (MERs) worksheets toward complex system reasoning achievement

Science.gov (United States)

Sumarno; Ibrahim, M.; Supardi, Z. A. I.

2018-03-01

The application of a systems approach to assessing biological systems provides hope for a coherent understanding of cell dynamics patterns and their relationship to plant life. This action required the reasoning about complex systems. In other sides, there were a lot of researchers who provided the proof about the instructional successions. They involved the multiple external representations which improved the biological learning. The researcher conducted an investigation using one shoot case study design which involved 30 students in proving that the MERs worksheets could affect the student's achievement of reasoning about complex system. The data had been collected based on test of reasoning about complex system and student's identification result who worked through MERs. The result showed that only partially students could achieve reasoning about system complex, but their MERs skill could support their reasoning ability of complex system. This study could bring a new hope to develop the MERs worksheet as a tool to facilitate the reasoning about complex system.
Feasibility of Using Convalescent Plasma Immunotherapy for MERS-CoV Infection, Saudi Arabia

Science.gov (United States)

Hajeer, Ali H.; Luke, Thomas; Raviprakash, Kanakatte; Balkhy, Hanan; Johani, Sameera; Al-Dawood, Abdulaziz; Al-Qahtani, Saad; Al-Omari, Awad; Al-Hameed, Fahad; Hayden, Frederick G.; Fowler, Robert; Bouchama, Abderrezak; Shindo, Nahoko; Al-Khairy, Khalid; Carson, Gail; Taha, Yusri; Sadat, Musharaf; Alahmadi, Mashail

2016-01-01

We explored the feasibility of collecting convalescent plasma for passive immunotherapy of Middle East respiratory syndrome coronavirus (MERS-CoV) infection by using ELISA to screen serum samples from 443 potential plasma donors: 196 patients with suspected or laboratory-confirmed MERS-CoV infection, 230 healthcare workers, and 17 household contacts exposed to MERS-CoV. ELISA-reactive samples were further tested by indirect fluorescent antibody and microneutralization assays. Of the 443 tested samples, 12 (2.7%) had a reactive ELISA result, and 9 of the 12 had reactive indirect fluorescent antibody and microneutralization assay titers. Undertaking clinical trials of convalescent plasma for passive immunotherapy of MERS-CoV infection may be feasible, but such trials would be challenging because of the small pool of potential donors with sufficiently high antibody titers. Alternative strategies to identify convalescent plasma donors with adequate antibody titers should be explored, including the sampling of serum from patients with more severe disease and sampling at earlier points during illness. PMID:27532807
Transmission of MERS-coronavirus in household contacts

NARCIS (Netherlands)

Drosten, Christian; Meyer, Benjamin; Müller, Marcel A; Corman, Victor M; Al-Masri, Malak; Hossain, Raheela; Madani, Hosam; Sieberg, Andrea; Bosch, Berend Jan|info:eu-repo/dai/nl/273306049; Lattwein, Erik; Alhakeem, Raafat F; Assiri, Abdullah M; Hajomar, Waleed; Albarrak, Ali M; Al-Tawfiq, Jaffar A; Zumla, Alimuddin I; Memish, Ziad A

2014-01-01

BACKGROUND: Strategies to contain the Middle East respiratory syndrome coronavirus (MERS-CoV) depend on knowledge of the rate of human-to-human transmission, including subclinical infections. A lack of serologic tools has hindered targeted studies of transmission. METHODS: We studied 26 index
The impact of multichannel microelectrode recording (MER) in deep brain stimulation of the basal ganglia.

Science.gov (United States)

Kinfe, Thomas M; Vesper, Jan

2013-01-01

Deep brain stimulation (DBS) of the basal ganglia (Ncl. subthalamicus, Ncl. ventralis intermedius thalami, globus pallidus internus) has become an evidence-based and well-established treatment option in otherwise refractory movement disorders. The Ncl. subthalamicus (STN) is the target of choice in Parkinson's disease.However, a considerable discussion is currently ongoing with regard to the necessity for micro-electrode recording (MER) in DBS surgery.The present review provides an overview on deep brain stimulation and (MER) of the STN in patients with Parkinson's disease. Detailed description is given concerning the multichannel MER systems nowadays available for DBS of the basal ganglia, especially of the STN, as a useful tool for target refinement. Furthermore, an overview is given of the historical aspects, spatial mapping of the STN by MER, and its impact for accuracy and precision in current functional stereotactic neurosurgery.The pros concerning target refinement by MER means on the one hand, and cons including increased bleeding risk, increased operation time, local or general anesthesia, and single versus multichannel microelectrode recording are discussed in detail. Finally, the authors favor the use of MER with intraoperative testing combined with imaging to achieve a more precise electrode placement, aiming to ameliorate clinical outcome in therapy-resistant movement disorders.
Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis.

Science.gov (United States)

Sharmin, Refat; Islam, Abul B M M K

2016-01-01

MERS-CoV is a newly emerged human coronavirus reported closely related with HKU4 and HKU5 Bat coronaviruses. Bat and MERS corona-viruses are structurally related. Therefore, it is of interest to estimate the degree of conserved antigenic sites among them. It is of importance to elucidate the shared antigenic-sites and extent of conservation between them to understand the evolutionary dynamics of MERS-CoV. Multiple sequence alignment of the spike (S), membrane (M), enveloped (E) and nucleocapsid (N) proteins was employed to identify the sequence conservation among MERS and Bat (HKU4, HKU5) coronaviruses. We used various in silico tools to predict the conserved antigenic sites. We found that MERS-CoV shared 30 % of its S protein antigenic sites with HKU4 and 70 % with HKU5 bat-CoV. Whereas 100 % of its E, M and N protein's antigenic sites are found to be conserved with those in HKU4 and HKU5. This sharing suggests that in case of pathogenicity MERS-CoV is more closely related to HKU5 bat-CoV than HKU4 bat-CoV. The conserved epitopes indicates their evolutionary relationship and ancestry of pathogenicity.
Design of Chemical Literacy Assessment by Using Model of Educational Reconstruction (MER) on Solubility Topic

Science.gov (United States)

Yusmaita, E.; Nasra, Edi

2018-04-01

This research aims to produce instrument for measuring chemical literacy assessment in basic chemistry courses with solubility topic. The construction of this measuring instrument is adapted to the PISA (Programme for International Student Assessment) problem’s characteristics and the Syllaby of Basic Chemistry in KKNI-IndonesianNational Qualification Framework. The PISA is a cross-country study conducted periodically to monitor the outcomes of learners' achievement in each participating country. So far, studies conducted by PISA include reading literacy, mathematic literacy and scientific literacy. Refered to the scientific competence of the PISA study on science literacy, an assessment designed to measure the chemical literacy of the chemistry department’s students in UNP. The research model used is MER (Model of Educational Reconstruction). The validity and reliability values of discourse questions is measured using the software ANATES. Based on the acquisition of these values is obtained a valid and reliable chemical literacy questions.There are seven question items limited response on the topic of solubility with valid category, the acquisition value of test reliability is 0,86, and has a difficulty index and distinguishing good
A Parameter Study for Modeling Mg ii h and k Emission during Solar Flares

Energy Technology Data Exchange (ETDEWEB)

Rubio da Costa, Fatima [Department of Physics, Stanford University, Stanford, CA 94305 (United States); Kleint, Lucia, E-mail: frubio@stanford.edu [University of Applied Sciences and Arts Northwestern Switzerland, 5210, Windisch (Switzerland)

2017-06-20

Solar flares show highly unusual spectra in which the thermodynamic conditions of the solar atmosphere are encoded. Current models are unable to fully reproduce the spectroscopic flare observations, especially the single-peaked spectral profiles of the Mg ii h and k lines. We aim to understand the formation of the chromospheric and optically thick Mg ii h and k lines in flares through radiative transfer calculations. We take a flare atmosphere obtained from a simulation with the radiative hydrodynamic code RADYN as input for a radiative transfer modeling with the RH code. By iteratively changing this model atmosphere and varying thermodynamic parameters such as temperature, electron density, and velocity, we study their effects on the emergent intensity spectra. We reproduce the typical single-peaked Mg ii h and k flare spectral shape and approximate the intensity ratios to the subordinate Mg ii lines by increasing either densities, temperatures, or velocities at the line core formation height range. Additionally, by combining unresolved upflows and downflows up to ∼250 km s{sup −1} within one resolution element, we reproduce the widely broadened line wings. While we cannot unambiguously determine which mechanism dominates in flares, future modeling efforts should investigate unresolved components, additional heat dissipation, larger velocities, and higher densities and combine the analysis of multiple spectral lines.
Non-equilibrium effects evidenced by vibrational spectra during the coil-to-globule transition in poly(N-isopropylacrylamide) subjected to an ultrafast heating-cooling cycle.

Science.gov (United States)

Deshmukh, Sanket A; Kamath, Ganesh; Suthar, Kamlesh J; Mancini, Derrick C; Sankaranarayanan, Subramanian K R S

2014-03-14

Molecular dynamics simulations in conjunction with finite element calculations are used to explore the conformational dynamics of a thermo-sensitive oligomer, namely poly(N-isopropylacrylamide) (PNIPAM), subjected to an ultra-fast heating-cooling cycle. Finite element (FE) calculations were used to predict the temperature profile resulting from laser-induced heating of the polymer-aqueous system. The heating rate (∼0.6 K ps(-1)) deduced from FE calculations was used to heat an aqueous solution of PNIPAM consisting of 30 monomeric units (30-mer) from 285 K to 315 K. Non-equilibrium effects arising from the ultra-fast heating-cooling cycle results in a hysteresis during the coil-to-globule transition. The corresponding atomic scale conformations were characterized by monitoring the changes in the vibrational spectra, which provided a reliable metric to study the coil-to-globule transition in PNIPAM and vice-versa across the LCST. The vibrational spectra of bonds involving atoms from the oligomer backbone and the various side-groups (amide I, amide II, and the isopropyl group of PNIPAM) of the oligomers were analyzed to study the conformational changes in the oligomer corresponding to the observed hysteresis. The differences in the vibrational spectra calculated at various temperatures during heating and cooling cycles were used to understand the coil-to-globule and globule-to-coil transitions in the PNIPAM oligomer and identify the changes in the relative interactions between various atoms in the backbone and in the side groups of the oligomer with water. The shifts in the computed vibrational spectral peaks and the changes in the intensity of peaks for the different regions of PNIPAM, seen across the LCST during the heating cycle, are in good agreement with previous experimental studies. The changes in the radius of gyration (Rg) and vibrational spectra for amide I and amide II regions of PNIPAM suggest a clear coil-to-globule transition at ∼301 K during the
Laboratory-based grain-shape models for simulating dust infrared spectra

NARCIS (Netherlands)

Mutschke, H.; Min, M.; Tamanai, A.

2009-01-01

Context. Analysis of thermal dust emission spectra for dust mineralogy and physical grain properties depends on comparison spectra, which are either laboratory-measured infrared extinction spectra or calculated extinction cross sections based on certain grain models. Often, the agreement between
Logarithmic divergences in the k-inflationary power spectra computed through the uniform approximation

Energy Technology Data Exchange (ETDEWEB)

Alinea, Allan L.; Kubota, Takahiro; Naylor, Wade, E-mail: alinea@het.phys.sci.osaka-u.ac.jp, E-mail: kubota@celas.osaka-u.ac.jp, E-mail: naylor@phys.sci.osaka-u.ac.jp [Department of Physics, Osaka University, Toyonaka, Osaka 560-0043 (Japan)

2016-02-01

We investigate a calculation method for solving the Mukhanov-Sasaki equation in slow-roll k-inflation based on the uniform approximation (UA) in conjunction with an expansion scheme for slow-roll parameters with respect to the number of e-folds about the so-called turning point. Earlier works on this method have so far gained some promising results derived from the approximating expressions for the power spectra among others, up to second order with respect to the Hubble and sound flow parameters, when compared to other semi-analytical approaches (e.g., Green's function and WKB methods). However, a closer inspection is suggestive that there is a problem when higher-order parts of the power spectra are considered; residual logarithmic divergences may come out that can render the prediction physically inconsistent. Looking at this possibility, we map out up to what order with respect to the mentioned parameters several physical quantities can be calculated before hitting a logarithmically divergent result. It turns out that the power spectra are limited up to second order, the tensor-to-scalar ratio up to third order, and the spectral indices and running converge to all orders. This indicates that the expansion scheme is incompatible with the working equations derived from UA for the power spectra but compatible with that of the spectral indices. For those quantities that involve logarithmically divergent terms in the higher-order parts, existing results in the literature for the convergent lower-order parts calculated in the equivalent fashion should be viewed with some caution; they do not rest on solid mathematical ground.
Dromedary camels and the transmission of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

Science.gov (United States)

Hemida, Maged G; Elmoslemany, Ahmed; Al-Hizab, Fahad; Alnaeem, Abdulmohsen; Almathen, Faisal; Faye, Bernard; Chu, Daniel KW; Perera, Ranawaka A; Peiris, Malik

2015-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is an existential threat to global public health. The virus has been repeatedly detected in dromedary camels (Camelus dromedarius). Adult animals in many countries in the Middle East as well as in North and East Africa showed high (>90%) sero-prevalence to the virus. MERS-CoV isolated from dromedaries is genetically and phenotypically similar to viruses from humans. We summarise current understanding of the ecology of MERS-CoV in animals and transmission at the animal-human interface. We review aspects of husbandry, animal movements and trade and the use and consumption of camel dairy and meat products in the Middle East that may be relevant to the epidemiology of MERS. We also highlight the gaps in understanding the transmission of this virus in animals and from animals to humans. PMID:26256102
Modeling a gamma spectroscopy system and predicting spectra with Geant-4

International Nuclear Information System (INIS)

Sahin, D.; Uenlue, K.

2009-01-01

An activity predictor software was previously developed to foresee activities, exposure rates and gamma spectra of activated samples for Radiation Science and Engineering Center (RSEC), Penn State Breazeale Reactor (PSBR), Neutron Activation Analysis (NAA) measurements. With Activity Predictor it has been demonstrated that the predicted spectra were less than satisfactory. In order to obtain better predicted spectra, a new detailed model for the RSEC NAA spectroscopy system with High Purity Germanium (HPGe) detector is developed using Geant-4. The model was validated with a National Bureau of Standards certified 60 Co source and tree activated high purity samples at PSBR. The predicted spectra agreed well with measured spectra. Error in net photo peak area values were 8.6-33.6%. Along with the previously developed activity predictor software, this new model in Geant-4 provided realistic spectra prediction for NAA experiments at RSEC PSBR. (author)
Nonlinear permittivity spectra of supercooled ionic liquids: Observation of a "hump" in the third-order permittivity spectra and comparison to double-well potential models.

Science.gov (United States)

Patro, L N; Burghaus, O; Roling, B

2017-04-21

We have measured the third-order permittivity spectra ε 3 3 of a monocationic and of a dicationic liquid close to the glass transition temperature by applying ac electric fields with large amplitudes up to 180 kV/cm. A peak ("hump") in the modulus of ε 3 3 is observed for a mono-cationic liquid after subtraction of the dc contribution from the imaginary part of ε 3 3 . We show that the origin of this experimental "hump" is a peak in the imaginary part of ε 3 3 , with the peak height strongly increasing with decreasing temperature. Overall, the spectral shape of the third-order permittivity of both ionic liquids is similar to the predictions of a symmetric double well potential model, although this model does not predict a "hump" in the modulus. In contrast, an asymmetric double well potential model predicts a "hump," but the spectral shape of both the real and imaginary part of ε 3 3 deviates significantly from the experimental spectra. These results show that not only the modulus of ε 3 3 but also its phase is an important quantity when comparing experimental results with theoretical predictions.
A Computational Approach for Predicting Role of Human MicroRNAs in MERS-CoV Genome

Directory of Open Access Journals (Sweden)

Md Mahmudul Hasan

2014-01-01

Full Text Available The new epidemic Middle East Respiratory Syndrome (MERS is caused by a type of human coronavirus called MERS-CoV which has global fatality rate of about 30%. We are investigating potential antiviral therapeutics against MERS-CoV by using host microRNAs (miRNAs which may downregulate viral gene expression to quell viral replication. We computationally predicted potential 13 cellular miRNAs from 11 potential hairpin sequences of MERS-CoV genome. Our study provided an interesting hypothesis that those miRNAs, that is, hsa-miR-628-5p, hsa-miR-6804-3p, hsa-miR-4289, hsa-miR-208a-3p, hsa-miR-510-3p, hsa-miR-18a-3p, hsa-miR-329-3p, hsa-miR-548ax, hsa-miR-3934-5p, hsa-miR-4474-5p, hsa-miR-7974, hsa-miR-6865-5p, and hsa-miR-342-3p, would be antiviral therapeutics against MERS-CoV infection.
Histopathology of Middle East respiratory syndrome coronovirus (MERS-CoV) infection - clinicopathological and ultrastructural study.

Science.gov (United States)

Alsaad, Khaled O; Hajeer, Ali H; Al Balwi, Mohammed; Al Moaiqel, Mohammed; Al Oudah, Nourah; Al Ajlan, Abdulaziz; AlJohani, Sameera; Alsolamy, Sami; Gmati, Giamal E; Balkhy, Hanan; Al-Jahdali, Hamdan H; Baharoon, Salim A; Arabi, Yaseen M

2018-02-01

The pathogenesis, viral localization and histopathological features of Middle East respiratory syndrome - coronavirus (MERS-CoV) in humans are not described sufficiently. The aims of this study were to explore and define the spectrum of histological and ultrastructural pathological changes affecting various organs in a patient with MERS-CoV infection and represent a base of MERS-CoV histopathology. We analysed the post-mortem histopathological findings and investigated localisation of viral particles in the pulmonary and extrapulmonary tissue by transmission electron microscopic examination in a 33-year-old male patient of T cell lymphoma, who acquired MERS-CoV infection. Tissue needle biopsies were obtained from brain, heart, lung, liver, kidney and skeletal muscle. All samples were collected within 45 min from death to reduce tissue decomposition and artefact. Histopathological examination showed necrotising pneumonia, pulmonary diffuse alveolar damage, acute kidney injury, portal and lobular hepatitis and myositis with muscle atrophic changes. The brain and heart were histologically unremarkable. Ultrastructurally, viral particles were localised in the pneumocytes, pulmonary macrophages, renal proximal tubular epithelial cells and macrophages infiltrating the skeletal muscles. The results highlight the pulmonary and extrapulmonary pathological changes of MERS-CoV infection and provide the first evidence of the viral presence in human renal tissue, which suggests tissue trophism for MERS-CoV in kidney. © 2017 John Wiley & Sons Ltd.
Application of a mer-lux biosensor for estimating bioavailable mercury in soil

DEFF Research Database (Denmark)

Rasmussen, Lasse Dam; Sørensen, S. J.; Turner, R. R.

2000-01-01

A previously described bioassay using a mer-lux gene fusion for detection of bioavailable mercury was applied for the estimation of the bioavailable fraction of mercury in soil. The bioavailable fraction is defined here as being part of the water leachable fraction. Due to masking of light emission...... responses. The utility of the mer-lux biosensor assay was tested by relating measurements of bioavailable and total mercury to the response of the soil microbial community to mercury exposure. Two different soil types (an agricultural and a beech forest soil) were spiked with 2.5 µg Hg(II) g-1 in microcosms...... in resistance or diversity. This study showed that the bioassay using the mer-lux biosensor is a useful and sensitive tool for estimation of bioavailable mercury in soil....
Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia.

Science.gov (United States)

Sabir, Jamal S M; Lam, Tommy T-Y; Ahmed, Mohamed M M; Li, Lifeng; Shen, Yongyi; Abo-Aba, Salah E M; Qureshi, Muhammd I; Abu-Zeid, Mohamed; Zhang, Yu; Khiyami, Mohammad A; Alharbi, Njud S; Hajrah, Nahid H; Sabir, Meshaal J; Mutwakil, Mohammed H Z; Kabli, Saleh A; Alsulaimany, Faten A S; Obaid, Abdullah Y; Zhou, Boping; Smith, David K; Holmes, Edward C; Zhu, Huachen; Guan, Yi

2016-01-01

Outbreaks of Middle East respiratory syndrome (MERS) raise questions about the prevalence and evolution of the MERS coronavirus (CoV) in its animal reservoir. Our surveillance in Saudi Arabia in 2014 and 2015 showed that viruses of the MERS-CoV species and a human CoV 229E-related lineage co-circulated at high prevalence, with frequent co-infections in the upper respiratory tract of dromedary camels. viruses of the betacoronavirus 1 species, we found that dromedary camels share three CoV species with humans. Several MERS-CoV lineages were present in camels, including a recombinant lineage that has been dominant since December 2014 and that subsequently led to the human outbreaks in 2015. Camels therefore serve as an important reservoir for the maintenance and diversification of the MERS-CoVs and are the source of human infections with this virus. Copyright © 2016, American Association for the Advancement of Science.
Mer partagée, part maudite. La fabrique rituelle d’un horizon maritime : mer et sacré chez les pêcheurs Imrâgen (Mauritanie

Directory of Open Access Journals (Sweden)

Hélène Artaud

2012-02-01

Full Text Available La mer a longtemps été perçue pour la société maure comme un monde en marge, étranger et étrange. Seule exception notable : la relation liant les communautés imrâgen à l’espace maritime. Dans la perception imrâgen de la mer se présentent d’emblée comme enchevêtrés les mondes naturels et surnaturels. Les modalités de leur articulation procèdent toutefois de logiques que seuls distinguent et maîtrisent certains initiés, dépositaires du « secret de la mer ». Quelques familles, issues des groupes maraboutiques Bârikalla et Buhubbayni, ont ainsi réussi à asseoir leur légitimité sur la côte par l’exercice de pouvoirs supposés influencer le cours des phénomènes naturels (vents, intensité des courants, cycle de la lune ou le comportement d’espèces marines (dauphins et tortues, dont ils ont fait leurs principaux émissaires. Quelles sont la nature, l’efficacité et les limites de ce pouvoir sur la mer? Comment inscrit-il le marabout au cœur de l’écologie imrâgen, le sacré au principe de l’équilibre naturel ? C’est à ces questionnements que nous nous proposons d’apporter quelques éléments d’analyse.
Composite Risers for Deepwater Applications Risers composites pour applications en mer profonde

Directory of Open Access Journals (Sweden)

Metivaud G.

2006-11-01

Full Text Available This paper is devoted to the high performance composite tubes developed by the Institut Français du Pétrole (IFP and Aerospatiale for deepwater risers applications. The design principles of the tubes are first presented, along with results of preliminary work carried out as part of the initial feasibility study. Applications of composite tubes to drilling riser Kill and Choke lines and to TLP production risers, both of which have been studied in detail, are then described. Technical and operational advantages obtained from such applications are discussed. Cet article présente les travaux réalisés par l'Institut Français du Pétrole et l'Aerospatiale dans le domaine des tubes composites haute performance pour les applications aux liaisons fond-surface de forage et de production en mer profonde. Les matériaux composites avancés sont une classe de matériaux très particulière, présentant à la fois des caractéristiques mécaniques élevées et une densité spécifique faible. Ils sont utilisés principalement par les industries de l'aéronautique et de l'espace, mais l'industrie pétrolière en mer profonde est un secteur où ils peuvent trouver dans l'avenir des applications très intéressantes, notamment les tubes de risers. Les tubes de risers pétroliers en mer présentent en effet une gamme de spécifications élevées (diamètres, pression, traction, fatigue dans un environnement sévère et leur poids suspendu peut pénaliser fortement les systèmes de forage ou de production par grande profondeur d'eau. Un premier concept de tube composite haute performance a été développé par IFP et Aerospatiale au début des années 1980 ; sa partie courante, réalisée par enroulement filamentaire de fibres de verre R ou de fibres de carbone, et son système d'embout ont été soumis à une série d'essais mécaniques (pression interne jusqu'à 105 MPa, traction supérieure à 1 000 kN pour un diamètre nominal de 0,1 m, millions de

Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs

Directory of Open Access Journals (Sweden)

Fereshteh Shiri

2016-03-01

Full Text Available Mer receptor tyrosine kinase is a promising novel cancer therapeutic target in many human cancers, because abnormal activation of Mer has been implicated in survival signaling and chemoresistance. 3D-QSAR analyses based on alignment independent descriptors were performed on a series of 81 Mer specific tyrosine kinase inhibitors. The fractional factorial design (FFD and the enhanced replacement method (ERM were applied and tested as variable selection algorithms for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. The data set was split into 65 molecules as the training set and 16 compounds as the test set. All descriptors were generated by using the GRid INdependent descriptors (GRIND approach. After variable selection, GRIND were correlated with activity values (pIC50 by PLS regression. Of the two applied variable selection methods, ERM had a noticeable improvement on the statistical parameters of PLS model, and yielded a q2 value of 0.77, an rpred2 of 0.94, and a low RMSEP value of 0.25. The GRIND information contents influencing the affinity on Mer specific tyrosine kinase were also confirmed by docking studies. In a quantum calculation study, the energy difference between HOMO and LUMO (gap implied the high interaction of the most active molecule in the active site of the protein. In addition, the molecular electrostatic potential energy at DFT level confirmed results obtained from the molecular docking. The identified key features obtained from the molecular modeling, enabled us to design novel kinase inhibitors.
Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs.

Science.gov (United States)

Shiri, Fereshteh; Pirhadi, Somayeh; Ghasemi, Jahan B

2016-03-01

Mer receptor tyrosine kinase is a promising novel cancer therapeutic target in many human cancers, because abnormal activation of Mer has been implicated in survival signaling and chemoresistance. 3D-QSAR analyses based on alignment independent descriptors were performed on a series of 81 Mer specific tyrosine kinase inhibitors. The fractional factorial design (FFD) and the enhanced replacement method (ERM) were applied and tested as variable selection algorithms for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. The data set was split into 65 molecules as the training set and 16 compounds as the test set. All descriptors were generated by using the GRid INdependent descriptors (GRIND) approach. After variable selection, GRIND were correlated with activity values (pIC50) by PLS regression. Of the two applied variable selection methods, ERM had a noticeable improvement on the statistical parameters of PLS model, and yielded a q (2) value of 0.77, an [Formula: see text] of 0.94, and a low RMSEP value of 0.25. The GRIND information contents influencing the affinity on Mer specific tyrosine kinase were also confirmed by docking studies. In a quantum calculation study, the energy difference between HOMO and LUMO (gap) implied the high interaction of the most active molecule in the active site of the protein. In addition, the molecular electrostatic potential energy at DFT level confirmed results obtained from the molecular docking. The identified key features obtained from the molecular modeling, enabled us to design novel kinase inhibitors.
Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers

KAUST Repository

Kandeel, Mahmoud; Al-Taher, Abdulla; Li, Huifang; Schwingenschlö gl, Udo; Alnazawi, Mohamed

2018-01-01

Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulation was carried out to unravel changes in the MERS CoV heptad repeat domains (HRs
Identifying Monoclonal Antibodies that Potently Inhibit MERS-CoV | Center for Cancer Research

Science.gov (United States)

The Middle East respiratory syndrome coronavirus (MERS-CoV), first isolated in September 2012, infects cells lining the human airway, causing severe flu-like symptoms that, in some cases, lead to death. As of July 2, 2014, 824 confirmed cases of MERS-CoV infection, including at least 286 related deaths, have been reported to the World Health Organization. While there are currently no effective therapies against the virus, monoclonal antibodies (MAbs) may be a promising candidate. Having previously developed MAbs against other viruses, including the related severe acute respiratory syndrome coronavirus or SARS-CoV, Dimiter Dimitrov, Ph.D., of CCR’s Laboratory of Experimental Immunology (LEI), and his colleagues decided to pan a library of antigen binding fragments (Fab) for activity against MERS-CoV.
Effects of operational decisions on the diffusion of epidemic disease: A system dynamics modeling of the MERS-CoV outbreak in South Korea.

Science.gov (United States)

Shin, Nina; Kwag, Taewoo; Park, Sangwook; Kim, Yon Hui

2017-05-21

We evaluated the nosocomial outbreak of Middle East Respiratory Syndrome (MERS) Coronavirus (CoV) in the Republic of Korea, 2015, from a healthcare operations management perspective. Establishment of healthcare policy in South Korea provides patients' freedom to select and visit multiple hospitals. Current policy enforces hospitals preference for multi-patient rooms to single-patient rooms, to lower financial burden. Existing healthcare systems tragically contributed to 186 MERS outbreak cases, starting from single "index patient" into three generations of secondary infections. By developing a macro-level health system dynamics model, we provide empirical knowledge to examining the case from both operational and financial perspectives. In our simulation, under base infectivity scenario, high emergency room occupancy circumstance contributed to an estimated average of 101 (917%) more infected patients, compared to when in low occupancy circumstance. Economic patient room design showed an estimated 702% increase in the number of infected patients, despite the overall 98% savings in total expected costs compared to optimal room design. This study provides first time, system dynamics model, performance measurements from an operational perspective. Importantly, the intent of this study was to provide evidence to motivate public, private, and government healthcare administrators' recognition of current shortcomings, to optimize performance as a whole system, rather than mere individual aspects. Copyright © 2017 Elsevier Ltd. All rights reserved.
Inclusive zero-angle neutron spectra at the ISR and OPER-model

International Nuclear Information System (INIS)

Grigoryan, A.A.

1977-01-01

The invlusive zero-angle neutron spectra in pp-collisions measured at the ISR are compared with the OPER-model predictions. OPER-model rather well describes the experimental data. Some features of the spectra behaviour at fixed transverse momentum and large x are considered
Healthcare Workers Emotions, Perceived Stressors and Coping Strategies During a MERS-CoV Outbreak.

Science.gov (United States)

Khalid, Imran; Khalid, Tabindeh J; Qabajah, Mohammed R; Barnard, Aletta G; Qushmaq, Ismael A

2016-03-01

Healthcare workers (HCWs) are at high risk of contracting Middle East respiratory syndrome coronavirus (MERS-CoV) during an epidemic. We explored the emotions, perceived stressors, and coping strategies of healthcare workers who worked during a MERS-CoV outbreak in our hospital. A cross-sectional descriptive survey design. A tertiary care hospital. HCWs (150) who worked in high risk areas during the April-May 2014 MERS-CoV outbreak that occurred in Jeddah, Saudi Arabia. We developed and administered a "MERS-CoV staff questionnaire" to study participants. The questionnaire consisted of 5 sections with 72 questions. The sections evaluated hospital staffs emotions, perceived stressors, factors that reduced their stress, coping strategies, and motivators to work during future outbreaks. Responses were scored on a scale from 0-3. The varying levels of stress or effectiveness of measures were reported as mean and standard deviation, as appropriate. Completed questionnaires were returned by 117 (78%) of the participants. The results had many unique elements. HCWs ethical obligation to their profession pushed them to continue with their jobs. The main sentiments centered upon fear of personal safety and well-being of colleagues and family. Positive attitudes in the workplace, clinical improvement of infected colleagues, and stoppage of disease transmission among HCWs after adopting strict protective measures alleviated their fear and drove them through the epidemic. They appreciated recognition of their efforts by hospital management and expected similar acknowledgment, infection control guidance, and equipment would entice them to work during future epidemics. The MERS-CoV outbreak was a distressing time for our staff. Hospitals can enhance HCWs experiences during any future MERS-CoV outbreak by focusing on the above mentioned aspects. © 2016 Marshfield Clinic.
Value, market preferences and trade of Beche-de-mer from Pacific Island sea cucumbers.

Directory of Open Access Journals (Sweden)

Steven W Purcell

Full Text Available Market preferences of natural resources contribute to shape their exploitation and production. Beche-de-mer, the product after gutting, cooking, salting and drying sea cucumbers, is exported worldwide to Asian dried seafood markets. A better understanding of the trade, value and market preferences of Pacific island beche-de-mer could identify critical postharvest processing techniques and management strategies for fisheries and aquaculture. Data were collected on export prices and trade of beche-de-mer from Kiribati, Fiji, Tonga and New Caledonia, and the selling prices, respective sizes and organoleptic properties of the products in stores in China. Export prices varied considerably within and among the four countries and low-value species were the most exported by volume. Most of the beche-de-mer from the four Pacific islands is exported to Hong Kong, where quality products are sold and others are distributed to mainland China. Prices of the beche-de-mer in Chinese stores varied up to ten-fold and were mostly influenced by species, body size and, to a lesser extent, physical damage to the products. Market prices across species (averaging US$15-385 kg-1 appear to have mostly increased six- to twelve-fold over the past decade. The data allude that fisheries for Holothuria scabra, H. lessoni, H. fuscogilva, H. whitmaei and Thelenota ananas should be most carefully managed because they were the highest-value species and under greatest demand. The relationships between size of beche-de-mer and sale price were species specific and highly varied. This study also highlights the need for better regulations and/or enforcement of minimum size limits in sea cucumber fisheries, which can help to maximise economic benefits of wild stocks.
X-ray Reflected Spectra from Accretion Disk Models. III. A Complete Grid of Ionized Reflection Calculations

Science.gov (United States)

Garcia, J.; Dauser, T.; Reynolds, C. S.; Kallman, T. R.; McClintock, J. E.; Wilms, J.; Ekmann, W.

2013-01-01

We present a new and complete library of synthetic spectra for modeling the component of emission that is reflected from an illuminated accretion disk. The spectra were computed using an updated version of our code xillver that incorporates new routines and a richer atomic data base. We offer in the form of a table model an extensive grid of reflection models that cover a wide range of parameters. Each individual model is characterized by the photon index Gamma of the illuminating radiation, the ionization parameter zeta at the surface of the disk (i.e., the ratio of the X-ray flux to the gas density), and the iron abundance A(sub Fe) relative to the solar value. The ranges of the parameters covered are: 1.2 <= Gamma <= 3.4, 1 <= zeta <= 104, and 0.5 <= A(sub Fe) <= 10. These ranges capture the physical conditions typically inferred from observations of active galactic nuclei, and also stellar-mass black holes in the hard state. This library is intended for use when the thermal disk flux is faint compared to the incident power-law flux. The models are expected to provide an accurate description of the Fe K emission line, which is the crucial spectral feature used to measure black hole spin. A total of 720 reflection spectra are provided in a single FITS file suitable for the analysis of X-ray observations via the atable model in xspec. Detailed comparisons with previous reflection models illustrate the improvements incorporated in this version of xillver.
Gigahertz-peaked Spectra Pulsars and Thermal Absorption Model

Energy Technology Data Exchange (ETDEWEB)

Kijak, J.; Basu, R.; Lewandowski, W.; Rożko, K. [Janusz Gil Institute of Astronomy, University of Zielona Góra, ul. Z. Szafrana 2, PL-65-516 Zielona Góra (Poland); Dembska, M., E-mail: jkijak@astro.ia.uz.zgora.pl [DLR Institute of Space Systems, Robert-Hooke-Str. 7 D-28359 Bremen (Germany)

2017-05-10

We present the results of our radio interferometric observations of pulsars at 325 and 610 MHz using the Giant Metrewave Radio Telescope. We used the imaging method to estimate the flux densities of several pulsars at these radio frequencies. The analysis of the shapes of the pulsar spectra allowed us to identify five new gigahertz-peaked spectra (GPS) pulsars. Using the hypothesis that the spectral turnovers are caused by thermal free–free absorption in the interstellar medium, we modeled the spectra of all known objects of this kind. Using the model, we were able to put some observational constraints on the physical parameters of the absorbing matter, which allows us to distinguish between the possible sources of absorption. We also discuss the possible effects of the existence of GPS pulsars on future search surveys, showing that the optimal frequency range for finding such objects would be from a few GHz (for regular GPS sources) to possibly 10 GHz for pulsars and radio magnetars exhibiting very strong absorption.
A conservative region of the mercuric reductase gene (merA as a molecular marker of bacterial mercury resistance Região conservada do gene da mercúrio redutase (merA como marcador molecular da resistência bacteriana ao mercúrio

Directory of Open Access Journals (Sweden)

Adriana Sotero-Martins

2008-06-01

Full Text Available The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II to Hg0, which is dependent of the mercuric reductase enzyme (MerA activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains.O mecanismo de resistência bacteriana ao mercúrio mais comum é baseada na redução do Hg(II a Hg0, através da atividade da enzima mercúrio redutase (MerA. O uso do fragmento de 431 pb amplificado de uma região conservada do gene merA, que codifica a enzima MerA,foi utilizado como marcador molecular deste mecanismo, permitindo a identificação de bactérias resistentes ao mercúrio.
Modelling Velocity Spectra in the Lower Part of the Planetary Boundary Layer

DEFF Research Database (Denmark)

Olesen, H.R.; Larsen, Søren Ejling; Højstrup, Jørgen

1984-01-01

of the planetary boundary layer. Knowledge of the variation with stability of the (reduced) frequency f, for the spectral maximum is utilized in this modelling. Stable spectra may be normalized so that they adhere to one curve only, irrespective of stability, and unstable w-spectra may also be normalized to fit...... one curve. The problem of using filtered velocity variances when modelling spectra is discussed. A simplified procedure to provide a first estimate of the filter effect is given. In stable, horizontal velocity spectra, there is often a ‘gap’ at low frequencies. Using dimensional considerations...... and the spectral model previously derived, an expression for the gap frequency is found....
Spectra of late type dwarf stars of known abundance for stellar population models

Science.gov (United States)

Oconnell, R. W.

1990-01-01

The project consisted of two parts. The first was to obtain new low-dispersion, long-wavelength, high S/N IUE spectra of F-G-K dwarf stars with previously determined abundances, temperatures, and gravities. To insure high quality, the spectra are either trailed, or multiple exposures are taken within the large aperture. Second, the spectra are assembled into a library which combines the new data with existing IUE Archive data to yield mean spectral energy distributions for each important type of star. My principal responsibility is the construction and maintenance of this UV spectral library. It covers the spectral range 1200-3200A and is maintained in two parts: a version including complete wavelength coverage at the full spectral resolution of the Low Resolution cameras; and a selected bandpass version, consisting of the mean flux in pre-selected 20A bands. These bands are centered on spectral features or continuum regions of special utility - e.g. the C IV lambda 1550 or Mg II lambda 2800 feature. In the middle-UV region, special emphasis is given to those features (including continuum 'breaks') which are most useful in the study of F-G-K star spectra in the integrated light of old stellar populations.
The prevalence of Middle East respiratory Syndrome coronavirus (MERS-CoV) infection in livestock and temporal relation to locations and seasons.

Science.gov (United States)

Kasem, Samy; Qasim, Ibrahim; Al-Doweriej, Ali; Hashim, Osman; Alkarar, Ali; Abu-Obeida, Ali; Saleh, Mohamed; Al-Hofufi, Ali; Al-Ghadier, Hussein; Hussien, Raed; Al-Sahaf, Ali; Bayoumi, Faisal; Magouz, Asmaa

2018-01-29

The Middle East respiratory syndrome (MERS) has been reported for the first time infecting a human being since 2012. The WHO was notified of 27 countries have reported cases of MERS, the majority of these cases occur in the Arabian Peninsula, particularly in Saudi Arabia. Dromedary camels are likely to be the main source of Middle East respiratory syndrome virus (MERS-CoV) infection in humans. MERS-CoV infection rates among camels in livestock markets and slaughterhouses were investigated in Saudi Arabia. A total of 698 nasal swabs were collected and examined with Rapid assay and rtRT-PCR. Ten MERS-CoV positive samples were subjected to full genomic sequencing. In addition, the sensitivity and specificity of the Rapid immunochromatographic assay (BioNote, South Korea) was evaluated as a diagnostic tool for MERS-CoV compared to rtRT-PCR. The results showed a high percentage of dromedaries (56.4%) had evidence for nasal MERS-CoV infection. Phylogenetic analysis of the ten MERS-CoV isolates showed that the sequences were closely related to the other MERS-CoV strains recovered from camels and human cases. Moreover, the results showed that 195 samples were positive for MERS-CoV by rapid assay compared to 394 positive samples of rtRT-PCR, which showed low rapid assay sensitivity (49.49%) while, the specificity were found to be 100%. These findings indicate that these sites are a highly-hazardous to zoonotic diseases. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.
Prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels in Abu Dhabi Emirate, United Arab Emirates.

Science.gov (United States)

Yusof, Mohammed F; Eltahir, Yassir M; Serhan, Wissam S; Hashem, Farouk M; Elsayed, Elsaeid A; Marzoug, Bahaaeldin A; Abdelazim, Assem Si; Bensalah, Oum Keltoum A; Al Muhairi, Salama S

2015-06-01

High seroprevalence of Middle East respiratory syndrome corona virus (MERS-CoV) in dromedary camels has been previously reported in United Arab Emirates (UAE). However, the molecular detection of the virus has never been reported before in UAE. Of the 7,803 nasal swabs tested in the epidemiological survey, MERS-CoV nucleic acid was detected by real-time PCR in a total of 126 (1.6 %) camels. Positive camels were detected at the borders with Saudi Arabia and Oman and in camels' slaughter houses. MERS-CoV partial sequences obtained from UAE camels were clustering with human- and camel-derived MERS-CoV sequences in the same geographic area. Results provide further evidence of MERS-CoV zoonosis.
The receptor binding domain of MERS-CoV: The dawn of vaccine and treatment development

Directory of Open Access Journals (Sweden)

Nan Zhou

2014-03-01

Full Text Available The newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV is becoming another “SARS-like” threat to the world. It has an extremely high death rate (∼50% as there is no vaccine or efficient therapeutics. The identification of the structures of both the MERS-CoV receptor binding domain (RBD and its complex with dipeptidyl peptidase 4 (DPP4, raises the hope of alleviating this currently severe situation. In this review, we examined the molecular basis of the RBD-receptor interaction to outline why/how could we use MERS-CoV RBD to develop vaccines and antiviral drugs.
Measurement of characteristic to total spectrum ratio of tungsten X-ray spectra for the validation of the modified Tbc model

International Nuclear Information System (INIS)

Lopez G, A. H.; Costa, P. R.; Tomal, A.

2014-08-01

Primary X-ray spectra were measured in the range of 80 to 150 kV in order to validate a computer program based on a semiempirical model for X-ray spectra evaluation(tbc and mod). The ratio between the characteristic lines and total spectrum was considered for comparing the simulated results and experimental data. The raw spectra measured by the Cd Te detector were corrected by the detector efficiency, Compton effects and characteristic Cd and Te X-rays escape peaks, using a software specifically developed. The software Origin 8.5.1 was used to calculate the spectra and characteristic peaks areas. The obtained result shows that the experimental spectra have higher effective energy than the simulated spectra computed with tbc and mod software. The behavior of the ratio between the characteristic lines and total spectrum for simulated data presents discrepancy with the experimental result. Computed results are in good agreement with theoretical data published by Green, for spectra obtained with 3.04 mm of additional aluminum filtration. The difference of characteristic to total spectrum ratio between experimental and simulated data increases with the tube voltage. (Author)
Measurement of characteristic to total spectrum ratio of tungsten X-ray spectra for the validation of the modified Tbc model

Energy Technology Data Exchange (ETDEWEB)

Lopez G, A. H.; Costa, P. R. [University of Sao Paulo, Institute of Physics, Laboratory of Radiation Dosimetry and Medical Physics, Matao Street, alley R, 187, 66318 Sao Paulo (Brazil); Tomal, A., E-mail: ahlopezg@usp.br [Universidade Federal de Goias, Physics Institute, Campus Samambaia, 131 Goiania, Goias (Brazil)

2014-08-15

Primary X-ray spectra were measured in the range of 80 to 150 kV in order to validate a computer program based on a semiempirical model for X-ray spectra evaluation(tbc and mod). The ratio between the characteristic lines and total spectrum was considered for comparing the simulated results and experimental data. The raw spectra measured by the Cd Te detector were corrected by the detector efficiency, Compton effects and characteristic Cd and Te X-rays escape peaks, using a software specifically developed. The software Origin 8.5.1 was used to calculate the spectra and characteristic peaks areas. The obtained result shows that the experimental spectra have higher effective energy than the simulated spectra computed with tbc and mod software. The behavior of the ratio between the characteristic lines and total spectrum for simulated data presents discrepancy with the experimental result. Computed results are in good agreement with theoretical data published by Green, for spectra obtained with 3.04 mm of additional aluminum filtration. The difference of characteristic to total spectrum ratio between experimental and simulated data increases with the tube voltage. (Author)
Universal scaling of strange particle pT spectra in pp collisions

Science.gov (United States)

Yang, Liwen; Wang, Yanyun; Hao, Wenhui; Liu, Na; Du, Xiaoling; Zhang, Wenchao

2018-04-01

As a complementary study to that performed on the transverse momentum (pT) spectra of charged pions, kaons and protons in proton-proton (pp) collisions at LHC energies 0.9, 2.76 and 7TeV, we present a scaling behaviour in the pT spectra of strange particles (KS0, Λ, Ξ and φ) at these three energies. This scaling behaviour is exhibited when the spectra are expressed in a suitable scaling variable z=pT/K, where the scaling parameter K is determined by the quality factor method and increases with the center of mass energy (√{s}). The rates at which K increases with ln √{s} for these strange particles are found to be identical within errors. In the framework of the colour string percolation model, we argue that these strange particles are produced through the decay of clusters that are formed by the colour strings overlapping. We observe that the strange mesons and baryons are produced from clusters with different size distributions, while the strange mesons (baryons) KS0 and φ ( Λ and Ξ) originate from clusters with the same size distributions. The cluster's size distributions for strange mesons are more dispersed than those for strange baryons. The scaling behaviour of the pT spectra for these strange particles can be explained by the colour string percolation model in a quantitative way.
A correlated-k model of radiative transfer in the near-infrared windows of Venus

International Nuclear Information System (INIS)

Tsang, C.C.C.; Irwin, P.G.J.; Taylor, F.W.; Wilson, C.F.

2008-01-01

We present a correlated-k-based model for generating synthetic spectra in the near-infrared window regions, from 1.0 to 2.5 μm, emitted from the deep atmosphere of Venus on the nightside. This approach is applicable for use with any near-infrared instrument, ground-based and space-borne, for analysis of the thermal emissions in this spectral range. We also approach this work with the view of using the model, in conjunction with a retrieval algorithm, to retrieve minor species from the Venus Express/VIRTIS instrument. An existing radiative-transfer model was adapted for Venusian conditions to deal with the prevailing high pressures and temperatures and other conditions. A comprehensive four-modal cloud structure model based on Pollack et al. [Near-infrared light from venus' nightside: a spectroscopic analysis. Icarus 1993;103:1-42], using refractive indices for a 75% H 2 SO 4 25% H 2 O mixture from Palmer and Williams [Optical constants of sulfuric acid; application to the clouds of Venus? Appl Opt 1975;14(1):208-19], was also implemented. We then utilized a Mie scattering algorithm to account for the multiple scattering effect between cloud and haze layers that occur in the Venusian atmosphere. The correlated-k model is shown to produce good agreement with ground-based spectra of Venus in the near infrared, and to match the output from a line-by-line radiative-transfer model to better than 10%

Distinct immune response in two MERS-CoV-infected patients: can we go from bench to bedside?

Directory of Open Access Journals (Sweden)

Emmanuel Faure

Full Text Available One year after the occurrence of the first case of infection by the Middle East Respiratory Syndrome coronavirus (MERS-CoV there is no clear consensus on the best treatment to propose. The World Health Organization, as well as several other national agencies, are still working on different clinical approaches to implement the most relevant treatment in MERS-CoV infection. We compared innate and adaptive immune responses of two patients infected with MERS-CoV to understand the underlying mechanisms involved in the response and propose potential therapeutic approaches. Broncho-alveolar lavage (BAL of the first week and sera of the first month from the two patients were used in this study. Quantitative polymerase chain reaction (qRTPCR was performed after extraction of RNA from BAL cells of MERS-CoV infected patients and control patients. BAL supernatants and sera were used to assess cytokines and chemokines secretion by enzyme-linked immunosorbent assay. The first patient died rapidly after 3 weeks in the intensive care unit, the second patient still recovers from infection. The patient with a poor outcome (patient 1, compared to patient 2, did not promote type-1 Interferon (IFN, and particularly IFNα, in response to double stranded RNA (dsRNA from MERS-CoV. The absence of IFNα, known to promote antigen presentation in response to viruses, impairs the development of a robust antiviral adaptive Th-1 immune response. This response is mediated by IL-12 and IFNγ that decreases viral clearance; levels of both of these mediators were decreased in patient 1. Finally, we confirm previous in vitro findings that MERS-CoV can drive IL-17 production in humans. Host recognition of viral dsRNA determines outcome in the early stage of MERS-CoV infection. We highlight the critical role of IFNα in this initial stage to orchestrate a robust immune response and bring substantial arguments for the indication of early IFNα treatment during MERS-CoV infection.
Exciton spectra and energy band structure of Cu{sub 2}ZnSiSe{sub 4}

Energy Technology Data Exchange (ETDEWEB)

Guc, M., E-mail: gmax@phys.asm.md [Institute of Applied Physics, Academy of Sciences of Moldova, Academiei Str. 5, Chisinau MD 2028, Republic of Moldova (Moldova, Republic of); Levcenko, S. [Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, D-14109 Berlin (Germany); Dermenji, L. [Institute of Applied Physics, Academy of Sciences of Moldova, Academiei Str. 5, Chisinau MD 2028, Republic of Moldova (Moldova, Republic of); Gurieva, G. [Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, D-14109 Berlin (Germany); Schorr, S. [Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, D-14109 Berlin (Germany); Free University Berlin, Institute of Geological Sciences, Malteserstr. 74-100, Berlin (Germany); Syrbu, N.N. [Technical University of Moldova, Chisinau MD-2004, Republic of Moldova (Moldova, Republic of); Arushanov, E. [Institute of Applied Physics, Academy of Sciences of Moldova, Academiei Str. 5, Chisinau MD 2028, Republic of Moldova (Moldova, Republic of)

2014-02-25

Highlights: • Reflection spectra of Cu{sub 2}ZnSiSe{sub 4} were studied for E ⊥ c and E || c light polarizations. • Four excitonic series are revealed in the reflection spectra at 10 K. • Model of exciton dispersion and the presence of a dead-layer. • Exciton Rydberg energies and free carriers effective masses were calculated. • Reflectivity for E ⊥ c and E || c were analyzed in the region 3–6 eV at 300 K. -- Abstract: Exciton spectra are studied in Cu{sub 2}ZnSiSe{sub 4} single crystals at 10 and 300 K by means of reflection spectroscopy. The exciton parameters, dielectric constant and free carriers effective masses are deduced from experimental spectra by calculations in the framework of a model taking into account the spatial dispersion and the presence of a dead-layer. The structure found in the reflectivity was analyzed and related to the theoretical electronic band structure of close related Cu{sub 2}ZnSiS{sub 4} semiconductor.
Spectra of conformal sigma models

International Nuclear Information System (INIS)

Tlapak, Vaclav

2015-04-01

In this thesis the spectra of conformal sigma models defined on (generalized) symmetric spaces are analysed. The spaces where sigma models are conformal without the addition of a Wess-Zumino term are supermanifolds, in other words spaces that include fermionic directions. After a brief review of the general construction of vertex operators and the background field expansion, we compute the diagonal terms of the one-loop anomalous dimensions of sigma models on semi-symmetric spaces. We find that the results are formally identical to the symmetric case. However, unlike for sigma models on symmetric spaces, off diagonal terms that lead to operator mixing are also present. These are not computed here. We then present a detailed analysis of the one-loop spectrum of the supersphere S 3 vertical stroke 2 sigma model as one of the simplest examples. The analysis illustrates the power and simplicity of the construction. We use this data to revisit a duality with the OSP(4 vertical stroke 2) Gross-Neveu model that was proposed by Candu and Saleur. With the help of a recent all-loop result for the anomalous dimension of (1)/(2)BPS operators of Gross-Neveu models, we are able to recover the entire zero-mode spectrum of the supersphere model. We also argue that the sigma model constraints and its equations of motion are implemented correctly in the Gross-Neveu model, including the one-loop data. The duality is further supported by a new all-loop result for the anomalous dimension of the ground states of the sigma model. However, higher-gradient operators cannot be completely recovered. It is possible that this discrepancy is related to a known instability of the sigma model. The instability of sigma models is due to symmetry preserving high-gradient operators that become relevant at arbitrarily small values of the coupling. This feature has been observed long ago in one-loop calculations of the O(N)-vector model and soon been realized to be a generic property of sigma models
Occurrence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) across the Gulf Corporation Council countries: Four years update.

Science.gov (United States)

Aly, Mahmoud; Elrobh, Mohamed; Alzayer, Maha; Aljuhani, Sameera; Balkhy, Hanan

2017-01-01

The emergence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections has become a global issue of dire concerns. MERS-CoV infections have been identified in many countries all over the world whereas high level occurrences have been documented in the Middle East and Korea. MERS-CoV is mainly spreading across the geographical region of the Middle East, especially in the Arabian Peninsula, while some imported sporadic cases were reported from the Europe, North America, Africa, and lately Asia. The prevalence of MERS-CoV infections across the Gulf Corporation Council (GCC) countries still remains unclear. Therefore, the objective of the current study was to report the prevalence of MERS-CoV in the GCC countries and to also elucidate on its demographics in the Arabian Peninsula. To date, the World Health Organization (WHO) has reported 1,797 laboratory-confirmed cases of MERS-CoV infection since June 2012, involving 687 deaths in 27 different countries worldwide. Within a time span of 4 years from June 2012 to July 2016, we collect samples form MERS-CoV infected individuals from National Guard Hospital, Riyadh, and Ministry of health Saudi Arabia and other GCC countries. Our data comprise a total of 1550 cases (67.1% male and 32.9% female). The age-specific prevalence and distribution of MERS-CoV was as follow: countries was as follows: Saudi Arabia (1441 cases: 93%), Kuwait (4 cases: 0.3%), Bahrain (1 case: 0.1%), Oman (8 cases: 0.5%), Qatar (16 cases: 1.0%), and United Arab Emirates (80 cases: 5.2%). Thus, MERS-CoV was found to be more prevalent in Saudi Arabia especially in Riyadh, where 756 cases (52.4%) were the worst hit area of the country identified, followed by the western region Makkah where 298 cases (20.6%) were recorded. This prevalence update indicates that the Arabian Peninsula, particularly Saudi Arabia, is the hardest hit region regarding the emerging MERS-CoV infections worldwide. GCC countries including Saudi Arabia now have the
Electronic Raman spectra in iron-based superconductors with two-orbital model

International Nuclear Information System (INIS)

Lu Hongyan; Wang Da; Chen San; Wang Wei; Gong Pifeng

2011-01-01

Electronic Raman spectra were calculated in orbital space in a microscopic theory. Both Raman spectra and spectra weight were presented. Raman spectra for the gap symmetries are different from each other. The results can help decide the gap symmetry by comparing with experiments. Electronic Raman spectra in iron-based superconductors with two-orbital model is discussed. In the orbital space, some possible pairing symmetries of the gap are selected. To further discriminate them, electronic Raman spectra and spectra weight at Fermi surface (FS) which helps understand the Raman spectra are calculated in each case. From the low energy threshold, the number of Raman peaks, and the low frequency power law behavior, we can judge whether it is full gap or nodal gap, and even one gap or multi-gaps. The results provide useful predictions for comparison with experiments.
A Comparative Study of Clinical Presentation and Risk Factors for Adverse Outcome in Patients Hospitalised with Acute Respiratory Disease Due to MERS Coronavirus or Other Causes.

Directory of Open Access Journals (Sweden)

Musa A Garbati

Full Text Available Middle East Respiratory syndrome (MERS first emerged in Saudi Arabia in 2012 and remains a global health concern. The objective of this study was to compare the clinical features and risk factors for adverse outcome in patients with RT-PCR confirmed MERS and in those with acute respiratory disease who were MERS-CoV negative, presenting to the King Fahad Medical City (KFMC in Riyadh between October 2012 and May 2014. The demographics, clinical and laboratory characteristics and clinical outcomes of patients with RT-PCR confirmed MERS-CoV infection was compared with those testing negative MERS-CoV PCR. Health care workers (HCW with MERS were compared with MERS patients who were not health care workers. One hundred and fifty nine patients were eligible for inclusion. Forty eight tested positive for MERS CoV, 44 (92% being hospital acquired infections and 23 were HCW. There were 111 MERS-CoV negative patients with acute respiratory illnesses included in this study as "negative controls". Patient with confirmed MERS-CoV infection were not clinically distinguishable from those with negative MERS-CoV RT-PCR results although diarrhoea was commoner in MERS patients. A high level of suspicion in initiating laboratory tests for MERS-CoV is therefore indicated. Variables associated with adverse outcome were older age and diabetes as a co-morbid illness. Interestingly, co-morbid illnesses other than diabetes were not significantly associated with poor outcome. Health care workers with MERS had a markedly better clinical outcome compared to non HCW MERS patients.
Meson and baryon production in K/sup +/ and. pi. /sup +/ beam jets and quark-diquark cascade model

Energy Technology Data Exchange (ETDEWEB)

Kinoshita, Kisei [Kagoshima Univ. (Japan). Faculty of Education; Noda, Hujio; Tashiro, Tsutomu

1982-11-01

A quark-diquark cascade model which includes flavor dependence and resonance effect is studied. The inclusive distributions of vector and pseudoscalar mesons and octet baryons and antibaryons in K/sup +/ and ..pi../sup +/ beam jets are analyzed. The contribution of decuplet baryons to the octet baryon spectra is very important in meson beam jet. The effects of the asymmetric u- and anti s-quark distributions in K/sup +/ and the SU(6)-symmetry breaking for the produced octet baryon are discussed in connection with the ..pi../sup +//K/sup +/ beam ratio and other data.
Serological evidence of MERS-CoV antibodies in dromedary camels (camelus dromedaries) in laikipia county, Kenya

NARCIS (Netherlands)

S.L. Deem (Sharon L.); E.M. Fèvre (Eric); M. Kinnaird (Margaret); A.S. Browne (A. Springer); D. Muloi (Dishon); G-J. Godeke (Gert-Jan); M.P.G. Koopmans D.V.M. (Marion); C.B.E.M. Reusken (Chantal)

2015-01-01

textabstractMiddle East respiratory syndrome coronavirus (MERS-CoV) is a recently identified virus causing severe viral respiratory illness in people. Little is known about the reservoir in the Horn of Africa. In Kenya, where no human MERS cases have been reported, our survey of 335 dromedary
Pattern recognition in spectra

International Nuclear Information System (INIS)

Gebran, M; Paletou, F

2017-01-01

We present a new automated procedure that simultaneously derives the effective temperature T eff , surface gravity log g , metallicity [ Fe/H ], and equatorial projected rotational velocity v e sin i for stars. The procedure is inspired by the well-known PCA-based inversion of spectropolarimetric full-Stokes solar data, which was used both for Zeeman and Hanle effects. The efficiency and accuracy of this procedure have been proven for FGK, A, and late type dwarf stars of K and M spectral types. Learning databases are generated from the Elodie stellar spectra library using observed spectra for which fundamental parameters were already evaluated or with synthetic data. The synthetic spectra are calculated using ATLAS9 model atmospheres. This technique helped us to detect many peculiar stars such as Am, Ap, HgMn, SiEuCr and binaries. This fast and efficient technique could be used every time a pattern recognition is needed. One important application is the understanding of the physical properties of planetary surfaces by comparing aboard instrument data to synthetic ones. (paper)
MCNP modelling of scintillation-detector gamma-ray spectra from natural radionuclides

NARCIS (Netherlands)

Hendriks, Peter; Maucec, M; de Meijer, RJ

gamma-ray spectra of natural radionuclides are simulated for a BGO detector in a borehole geometry using the Monte Carlo code MCNP. All gamma-ray emissions of the decay of K-40 and the series of Th-232 and U-238 are used to describe the source. A procedure is proposed which excludes the
Cultivation of hard-to-culture subsurface mercury-resistant bacteria and discovery of new merA gene sequences

DEFF Research Database (Denmark)

Rasmussen, L D; Zawadsky, C; Binnerup, S J

2008-01-01

different 16S rRNA gene sequences were observed, including Alpha-, Beta-, and Gammaproteobacteria; Actinobacteria; Firmicutes; and Bacteroidetes. The diversity of isolates obtained by direct plating included eight different 16S rRNA gene sequences (Alpha- and Betaproteobacteria and Actinobacteria). Partial...... sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One...
Improvement of an enzyme-linked immunosorbent assay for equine herpesvirus type 4 by using a synthetic-peptide 24-mer repeat sequence of glycoprotein G as an antigen.

Science.gov (United States)

Bannai, Hiroshi; Nemoto, Manabu; Tsujimura, Koji; Yamanaka, Takashi; Maeda, Ken; Kondo, Takashi

2016-02-01

To increase the sensitivity of an enzyme-linked immunosorbent assay (ELISA) for equine herpesvirus type 4 (EHV-4) that uses a 12-mer peptide of glycoprotein G (gG4-12-mer: MKNNPIYSEGSL) [4], we used a longer peptide consisting of a 24-mer repeat sequence (gG4-24-mer: MKNNPIYSEGSLMLNVQHDDSIHT) as an antigen. Sera of horses experimentally infected with EHV-4 reacted much more strongly to the gG4-24-mer peptide than to the gG4-12-mer peptide. We used peptide ELISAs to test paired sera from horses naturally infected with EHV-4 (n=40). gG4-24-mer ELISA detected 37 positive samples (92.5%), whereas gG4-12-mer ELISA detected only 28 (70.0%). gG4-24-mer ELISA was much more sensitive than gG4-12-mer ELISA.
Spectroscopic modeling for tungsten EUV spectra

International Nuclear Information System (INIS)

Murakami, Izumi; Kato, Daiji; Sakaue, Hiroyuki A.; Suzuki, Chihiro; Morita, Shigeru; Goto, Motoshi; Sasaki, Akira; Nakamura, Nobuyuki; Yamamoto, Norimasa; Koike, Fumihiro

2014-01-01

We have constructed an atomic model for tungsten extreme ultraviolet (EUV) spectra to reconstruct characteristic spectral feature of unresolved transition array (UTA) observed at 4-7 nm for tungsten ions. In the tungsten atomic modeling, we considered fine-structure levels with the quantum principal number n up to 6 as the atomic structure and calculated the electron-impact collision cross sections by relativistic distorted-wave method, using HULLAC atomic code. We measured tungsten EUV spectra in Large Helical Device (LHD) and Compact Electron Beam Ion Trap device (CoBIT) and compared them with the model calculation. The model successfully explain series of emission peaks at 1.5-3.5 nm as n=5-4 and 6-4 transitions of W"2"4"+ - W"3"2"+ measured in CoBIT and LHD and the charge state distributions were estimated for LHD plasma. The UTA feature observed at 4-7 nm was also successfully reconstructed with our model. The peak at ∼5 nm is produced mainly by many 4f-4d transition of W"2"2"+ - W"3"5"+ ions, and the second peak at ∼6 nm is produced by 4f-4d transition of W"2"5"+ - W"2"8"+ ions, and 4d-4p inner-shell transitions, 4p"54d"n"+"1 - 4p"64d"n, of W"2"9"+ - W"3"5"+ ions. These 4d-4p inner-shell transitions become strong since we included higher excited states such as 4p"54d"n4f state, which ADAS atomic data set does not include for spectroscopic modeling with fine structure levels. (author)
Modeling and interpretation of electrical impedance spectra of dye solar cells operated under open-circuit conditions

International Nuclear Information System (INIS)

Kern, R.; Sastrawan, R.; Ferber, J.; Stangl, R.; Luther, J.

2002-01-01

Electrical impedance spectroscopy (EIS) was applied in order to investigate electrochemical nanocrystalline TiO 2 dye solar cells (DSC). Typically, three characteristic frequency peaks were observed in the spectra. These frequency peaks could be explained by variations of cell parameters and by comparison with intensity-modulated photovoltage spectroscopy (IMVS). It was shown that the low-frequency peak (in the mHz range) corresponds to the Nernstian diffusion within the electrolyte, while the middle-frequency peak (in the 10-100 Hz range) reflects the properties of the photoinjected electrons within the TiO 2 . The high-frequency peak (in the kHz range) corresponds to the charge-transfer at the platinum counter electrode. For a detailed analysis of the spectra, a model was developed which allows the evaluation of EIS spectra, measured under bias illumination and under open-circuit conditions. The influence of cell parameters such as the TiO 2 layer thickness, cell thickness, charge-transfer resistance of the platinum counter electrode, and the lifetime of the photoinjected electrons, on the impedance spectra was studied both experimentally and theoretically. Finally, it is shown that EIS is a measurement method suited well for the investigation of the long-term stability of DSC, as changes of the inner cell parameters can be revealed
DIE RECHTSPOSITION DER EHRLICHEN UND UNEHRLICHEN BESITZER IN BEZUG AUF EIGENTÜMER

Directory of Open Access Journals (Sweden)

Jadranko Jug

2017-01-01

Full Text Available Diese Arbeit beschäftigt sich mit den Problemen, die mit der rechtlichen Stellung ehrlicher und unehrlicher Besitzer im Verhältnis zum Eigentümer verbunden sind, d.h. sie analysiert die Rechte des Besitzers und die Forderungen, welche der Besitzer vom Eigentümer verlangen kann, damit der Besitzer sein Besitz abgibt. Im Gegensatz dazu werden die Rechte und Anforderungen des Eigentümers in Bezug auf ehrliche und unehrliche Besitzer analysiert. In der Praxis entstehen Dilemmas, wie die wesentlichen und vorteilhaften Ausgaben des ehrlichen Besitzers bestimmt werden, welche Voraussetzungen es sind und bis zu welchen Zeitpunkt das Zurückbehaltungsrecht für die Vergütung dieser Ausgaben ausgeübt werden kann, wann die Verjährungsfrist anfängt und von welcher Bedeutung die Bestimmungen des Zivilverfahrensgesetzes in Bezug auf die ungerechte Anreicherung, die Geschäftsführung ohne Anordnung oder das Zurückbehaltungsrecht sind und welche Bestimmungen diese und ähnliche Fragen regeln. Die Antworten auf einige von diesen Dilemmas sind in der Rechtsprechung vorgelegt, weshalb die Analyse und Forschung der Rechtsprechung, insbesondere Entscheidungen des Obersten Gerichtshofs der Republik Kroatien, die grundlegende Methode dieser Arbeit ist. In der Einführung bietet diese Artikel die grundlegenden Merkmale des Begriffs des Besitzens und des Eigentumsbesitzes und die Art und Qualität des Besitzes an, um eine Grundlage für die anschließende Analyse der Rechtsposition des Eigentumsbesitzers in Bezug auf den Eigentümer zu schaffen.
Cross host transmission in the emergence of MERS coronavirus

NARCIS (Netherlands)

C.B.E.M. Reusken (Chantal); V.S. Raj (Stalin); M.P.G. Koopmans D.V.M. (Marion); B.L. Haagmans (Bart)

2016-01-01

textabstractCoronaviruses (CoVs) able to infect humans emerge through cross-host transmission from animals. There is substantial evidence that the recent Middle East respiratory syndrome (MERS)-CoV outbreak is fueled by zoonotic transmission from dromedary camels. This is largely based on the fact
Improvement of an enzyme-linked immunosorbent assay for equine herpesvirus type 4 by using a synthetic-peptide 24-mer repeat sequence of glycoprotein G as an antigen

Science.gov (United States)

BANNAI, Hiroshi; NEMOTO, Manabu; TSUJIMURA, Koji; YAMANAKA, Takashi; MAEDA, Ken; KONDO, Takashi

2015-01-01

To increase the sensitivity of an enzyme-linked immunosorbent assay (ELISA) for equine herpesvirus type 4 (EHV-4) that uses a 12-mer peptide of glycoprotein G (gG4-12-mer: MKNNPIYSEGSL) [4], we used a longer peptide consisting of a 24-mer repeat sequence (gG4-24-mer: MKNNPIYSEGSLMLNVQHDDSIHT) as an antigen. Sera of horses experimentally infected with EHV-4 reacted much more strongly to the gG4-24-mer peptide than to the gG4-12-mer peptide. We used peptide ELISAs to test paired sera from horses naturally infected with EHV-4 (n=40). gG4-24-mer ELISA detected 37 positive samples (92.5%), whereas gG4-12-mer ELISA detected only 28 (70.0%). gG4-24-mer ELISA was much more sensitive than gG4-12-mer ELISA. PMID:26424485
21 CFR 177.1040 - Acrylonitrile/styrene copoly-mer.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Acrylonitrile/styrene copoly-mer. 177.1040 Section 177.1040 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) INDIRECT FOOD ADDITIVES: POLYMERS Substances for Use as Basic Components of Single and Repeated Use Food...
Transverse Momentum Spectra of KS0 and K*0 at Midrapidity in d + Au, Cu + Cu, and p+p Collisions at √(sNN)=200 GeV

International Nuclear Information System (INIS)

Zhang, Guo-Xing; Li, Bao-Chun; Guo, Yuan-Yuan

2015-01-01

We analyze transverse momentum spectra of K S 0 and K *0 at midrapidity in d + Au, Cu + Cu, and p+p collisions at √(s NN )=200 GeV in the formworks of Tsallis statistics and Boltzmann statistics, respectively. Both of them can describe the transverse momentum spectra and extract the thermodynamics parameters of matter evolution in the collisions. The parameters are helpful for us to understand the thermodynamics factors of the particle production
Influenza not MERS CoV among returning Hajj and Umrah pilgrims with respiratory illness, Kashmir, north India, 2014-15.

Science.gov (United States)

Koul, Parvaiz A; Mir, Hyder; Saha, Siddhartha; Chadha, Mandeep S; Potdar, Varsha; Widdowson, Marc-Alain; Lal, Renu B; Krishnan, Anand

The increasing reports of Middle East Respiratory Syndrome (MERS) caused by MERS coronavirus (MERS-CoV) from many countries emphasize its importance for international travel. Muslim pilgrimages of Hajj and Umrah involve mass gatherings of international travellers. We set out to assess the presence of influenza and MERS-CoV in Hajj/Umrah returnees with acute respiratory infection. . Disembarking passengers (n = 8753) from Saudi Arabia (October 2014 to April 2015) were interviewed for the presence of respiratory symptoms; 977 (11%) reported symptoms and 300 (age 26-90, median 60 years; 140 male) consented to participate in the study. After recording clinical and demographic data, twin swabs (nasopharyngeal and throat) were collected from each participant, pooled in viral transport media and tested by real-time RT PCR for MERS-CoV and influenza A and B viruses and their subtypes. The participants had symptoms of 1-15 days (median 5d); cough (90%) and nasal discharge (86%) being the commonest. None of the 300 participants tested positive for MERS-CoV; however, 33 (11%) tested positive for influenza viruses (A/H3N2 = 13, A/H1N1pdm09 = 9 and B/Yamagata = 11). Eighteen patients received oseltamivir. No hospitalizations were needed and all had uneventful recovery. Despite a high prevalence of acute respiratory symptoms, MERS coV was not seen in returning pilgrims from Hajj and Umrah. However detection of flu emphasises preventive strategies like vaccination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of residues on human receptor DPP4 critical for MERS-CoV binding and entry

Energy Technology Data Exchange (ETDEWEB)

Song, Wenfei [Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084 (China); Wang, Ying [Comprehensive AIDS Research Center, Research Center for Public Health, School of Medicine, Tsinghua University, Beijing 100084 (China); Wang, Nianshuang; Wang, Dongli [Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084 (China); Guo, Jianying; Fu, Lili [Comprehensive AIDS Research Center, Research Center for Public Health, School of Medicine, Tsinghua University, Beijing 100084 (China); Shi, Xuanling, E-mail: shixuanlingsk@tsinghua.edu.cn [Comprehensive AIDS Research Center, Research Center for Public Health, School of Medicine, Tsinghua University, Beijing 100084 (China)

2014-12-15

Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Here, we report identification of critical residues on hDPP4 for RBD binding and virus entry through analysis of a panel of hDPP4 mutants. Based on the RBD–hDPP4 crystal structure we reported, the mutated residues were located at the interface between RBD and hDPP4, which potentially changed the polarity, hydrophobic or hydrophilic properties of hDPP4, thereby interfering or disrupting their interaction with RBD. Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay, we showed that several residues in hDPP4–RBD binding interface were important on hDPP4–RBD binding and viral entry. These results provide atomic insights into the features of interactions between hDPP4 and MERS-CoV RBD, and also provide potential explanation for cellular and species tropism of MERS-CoV infection. - Highlights: • It has been demonstrated that MERS-CoV infects host cells through binding its envelope spike (S) glycoprotein to the host cellular receptor dipeptidyl peptidase 4 (DPP4). • To identify the critical residues on hDPP4 for RBD binding and virus entry, we constructed a panel of hDPP4 mutants based on structure-guided mutagenesis. • Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay, we showed that several residues on hDPP4 had significant impacts on virus/receptor interactions and viral entry. • Our study has provided new insights into the features of interactions between hDPP4 and MERS-CoV RBD, and provides potential explanation for cellular and species tropism of MERS-CoV infection.
Characterization of novel monoclonal antibodies against the MERS-coronavirus spike protein and their application in species-independent antibody detection by competitive ELISA.

Science.gov (United States)

Fukushi, Shuetsu; Fukuma, Aiko; Kurosu, Takeshi; Watanabe, Shumpei; Shimojima, Masayuki; Shirato, Kazuya; Iwata-Yoshikawa, Naoko; Nagata, Noriyo; Ohnishi, Kazuo; Ato, Manabu; Melaku, Simenew Keskes; Sentsui, Hiroshi; Saijo, Masayuki

2018-01-01

Since discovering the Middle East respiratory syndrome coronavirus (MERS-CoV) as a causative agent of severe respiratory illness in the Middle East in 2012, serological testing has been conducted to assess antibody responses in patients and to investigate the zoonotic reservoir of the virus. Although the virus neutralization test is the gold standard assay for MERS diagnosis and for investigating the zoonotic reservoir, it uses live virus and so must be performed in high containment laboratories. Competitive ELISA (cELISA), in which a labeled monoclonal antibody (MAb) competes with test serum antibodies for target epitopes, may be a suitable alternative because it detects antibodies in a species-independent manner. In this study, novel MAbs against the spike protein of MERS-CoV were produced and characterized. One of these MAbs was used to develop a cELISA. The cELISA detected MERS-CoV-specific antibodies in sera from MERS-CoV-infected rats and rabbits immunized with the spike protein of MERS-CoV. The MAb-based cELISA was validated using sera from Ethiopian dromedary camels. Relative to the neutralization test, the cELISA detected MERS-CoV-specific antibodies in 66 Ethiopian dromedary camels with a sensitivity and specificity of 98% and 100%, respectively. The cELISA and neutralization test results correlated well (Pearson's correlation coefficients=0.71-0.76, depending on the cELISA serum dilution). This cELISA may be useful for MERS epidemiological investigations on MERS-CoV infection. Copyright © 2017 Elsevier B.V. All rights reserved.
H-Ras and K-Ras Oncoproteins Induce Different Tumor Spectra When Driven by the Same Regulatory Sequences.

Science.gov (United States)

Drosten, Matthias; Simón-Carrasco, Lucía; Hernández-Porras, Isabel; Lechuga, Carmen G; Blasco, María T; Jacob, Harrys K C; Fabbiano, Salvatore; Potenza, Nicoletta; Bustelo, Xosé R; Guerra, Carmen; Barbacid, Mariano

2017-02-01

Genetic studies in mice have provided evidence that H-Ras and K-Ras proteins are bioequivalent. However, human tumors display marked differences in the association of RAS oncogenes with tumor type. Thus, to further assess the bioequivalence of oncogenic H-Ras and K-Ras, we replaced the coding region of the murine K-Ras locus with H-Ras G12V oncogene sequences. Germline expression of H-Ras G12V or K-Ras G12V from the K-Ras locus resulted in embryonic lethality. However, expression of these genes in adult mice led to different tumor phenotypes. Whereas H-Ras G12V elicited papillomas and hematopoietic tumors, K-Ras G12V induced lung tumors and gastric lesions. Pulmonary expression of H-Ras G12V created a senescence-like state caused by excessive MAPK signaling. Likewise, H-Ras G12V but not K-Ras G12V induced senescence in mouse embryonic fibroblasts. Label-free quantitative analysis revealed that minor differences in H-Ras G12V expression levels led to drastically different biological outputs, suggesting that subtle differences in MAPK signaling confer nonequivalent functions that influence tumor spectra induced by RAS oncoproteins. Cancer Res; 77(3); 707-18. ©2016 AACR. ©2016 American Association for Cancer Research.
Occurrence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV across the Gulf Corporation Council countries: Four years update.

Directory of Open Access Journals (Sweden)

Mahmoud Aly

Full Text Available The emergence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV infections has become a global issue of dire concerns. MERS-CoV infections have been identified in many countries all over the world whereas high level occurrences have been documented in the Middle East and Korea. MERS-CoV is mainly spreading across the geographical region of the Middle East, especially in the Arabian Peninsula, while some imported sporadic cases were reported from the Europe, North America, Africa, and lately Asia. The prevalence of MERS-CoV infections across the Gulf Corporation Council (GCC countries still remains unclear. Therefore, the objective of the current study was to report the prevalence of MERS-CoV in the GCC countries and to also elucidate on its demographics in the Arabian Peninsula. To date, the World Health Organization (WHO has reported 1,797 laboratory-confirmed cases of MERS-CoV infection since June 2012, involving 687 deaths in 27 different countries worldwide. Within a time span of 4 years from June 2012 to July 2016, we collect samples form MERS-CoV infected individuals from National Guard Hospital, Riyadh, and Ministry of health Saudi Arabia and other GCC countries. Our data comprise a total of 1550 cases (67.1% male and 32.9% female. The age-specific prevalence and distribution of MERS-CoV was as follow: <20 yrs (36 cases: 3.28%, 20-39 yrs (331 cases: 30.15%, 40-59 yrs (314 cases: 28.60%, and the highest-risk elderly group aged ≥60 yrs (417 cases: 37.98%. The case distribution among GCC countries was as follows: Saudi Arabia (1441 cases: 93%, Kuwait (4 cases: 0.3%, Bahrain (1 case: 0.1%, Oman (8 cases: 0.5%, Qatar (16 cases: 1.0%, and United Arab Emirates (80 cases: 5.2%. Thus, MERS-CoV was found to be more prevalent in Saudi Arabia especially in Riyadh, where 756 cases (52.4% were the worst hit area of the country identified, followed by the western region Makkah where 298 cases (20.6% were recorded. This prevalence update
Dalitz plot analysis of the $D^+ \\rightarrow K^- K^+ K^+$ decay with the isobar model

CERN Document Server

The LHCb Collaboration

2016-01-01

This note presents a study of the $K^-K^+$ S-wave amplitude in doubly Cabibbo-suppressed ${D^+ \\rightarrow K^- K^+ K^+}$ decays performed using $2 \\text{fb}^{-1}$ of data collected by the LHCb detector in $pp$ collisions at $8~\\text{TeV}$ centre-of-mass energy. The Dalitz plot is studied under the assumption of the isobar model for resonance scattering. Models with combinations of resonant states are tested. Fits of comparable quality are obtained for different $K^-K^+$ S-wave parameterizations. The results obtained indicate that a variation of the S-wave phase at both ends of $K^-K^+$ spectrum is needed to describe the data. Further studies beyond the näive isobar model are foreseen to understand the $K^-K^+$ S-wave.
TRANSMISSION SPECTRA OF THREE-DIMENSIONAL HOT JUPITER MODEL ATMOSPHERES

International Nuclear Information System (INIS)

Fortney, J. J.; Shabram, M.; Showman, A. P.; Lian, Y.; Lewis, N. K.; Freedman, R. S.; Marley, M. S.

2010-01-01

We compute models of the transmission spectra of planets HD 209458b, HD 189733b, and generic hot Jupiters. We examine the effects of temperature, surface gravity, and metallicity for the generic planets as a guide to understanding transmission spectra in general. We find that carbon dioxide absorption at 4.4 and 15 μm is prominent at high metallicity, and is a clear metallicity indicator. For HD 209458b and HD 189733b, we compute spectra for both one-dimensional and three-dimensional model atmospheres and examine the differences between them. The differences are usually small, but can be large if atmospheric temperatures are near important chemical abundance boundaries. The calculations for the three-dimensional atmospheres, and their comparison with data, serve as constraints on these dynamical models that complement the secondary eclipse and light curve data sets. For HD 209458b, even if TiO and VO gases are abundant on the dayside, their abundances can be considerably reduced on the cooler planetary limb. However, given the predicted limb temperatures and TiO abundances, the model's optical opacity is too high. For HD 189733b we find a good match with some infrared data sets and constrain the altitude of a postulated haze layer. For this planet, substantial differences can exist between the transmission spectra of the leading and trailing hemispheres, which are an excellent probe of carbon chemistry. In thermochemical equilibrium, the cooler leading hemisphere is methane-dominated, and the hotter trailing hemisphere is CO-dominated, but these differences may be eliminated by non-equilibrium chemistry due to vertical mixing. It may be possible to constrain the carbon chemistry of this planet, and its spatial variation, with James Webb Space Telescope.
Differential expression of the MERS-coronavirus receptor in the upper respiratory tract of humans and dromedary camels

NARCIS (Netherlands)

Widagdo, W; Raj, V Stalin; Schipper, Debby; Kolijn, Kimberley; van Leenders, Geert J L H; Bosch, Berend J; Bensaid, Albert; Segalés, Joaquim; Baumgärtner, Wolfgang; Osterhaus, Albert D M E; Koopmans, Marion P; van den Brand, Judith M A; Haagmans, Bart L

Middle East respiratory syndrome coronavirus (MERS-CoV) is not efficiently transmitted between humans, but it is highly prevalent in dromedary camels. Here we report that the MERS-CoV receptor - dipeptidyl peptidase 4 (DPP4) - is expressed in the upper respiratory tract epithelium of camels but not
Discovery of Carbonate-Rich Outcrops in the Gusev Crater Columbia Hills by the MER Rover Spirit

Science.gov (United States)

Morris, Richard V.; Ruff, Steven W.; Gellert, Ralf; Ming, Douglas W.; Arvidson, Raymond E.; Clark, Benton C.; Golden, Dadi C.; Siebach, Kirsten L.; Klingelhoefer, Goestar; Schroeder, Christian;

2010-01-01

The chemical composition, global abundance, distribution, and formation pathways of carbonates are central to understanding aqueous processes, climate, and habitability of early Mars. The Mars Exploration Rover (MER) Spirit analyzed a series of olivine-rich outcrops while descending from the summit region of Husband Hill into the Inner Basin of the Columbia Hills of Gusev Crater to the eastern edge of the El Dorado ripple field in late 2005. Reanalysis of Spirit s mineralogical data from the Moessbauer Spectrometer (MB) and the Miniature Thermal Emission Spectrometer (Mini-TES) and chemical data from the Alpha Particle X-Ray Spectrometer (APXS) in 2010, coupled with new laboratory data for carbonate-bearing samples, lead to identification of carbonate in one of the outcrops (Comanche) [Morris, R.V., et al., Science, 329, 421-424]. The carbonate is rich in magnesium and iron (Mc62Sd25Cc11Rh2, assuming all Ca and Mn is associated with the carbonate) and is a major component of the Comanche outcrops (16 to 34 wt.%). The mineralogical, chemical, and abundance data are constrained in multiple, mutually consistent ways by the MER analyses. For example, a low-Ca carbonate is required by the MB and APXS data and is consistent with Mini-TES data. Three spectral features attributable to fundamental infrared vibrational modes of low-Ca carbonate are present in the Mini-TES spectra of Comanche outcrops. The average composition of Comanche carbonate approximates the average composition of the carbonate globules in Martian meteorite ALH 84001. Analogy with ALH 84001, terrestrial, and synthetic carbonate globules suggests that Comanche carbonate precipitated from aqueous solutions under hydrothermal conditions at near neutral pH in association with volcanic activity during the Noachian era. Comanche outcrop morphology suggests they are remnants of a larger carbonate-bearing formation that evolved in ultramafic rock and then preferentially eroded by a combination of aeolian

Correlation-Induced Changes of Spectra

Science.gov (United States)

1989-12-01

tances has been one of the central have been observed etperimental- other end of the frequency spec- issues of debate among astrono - ly could be...limited consideration by astrono - I mers. in the updated theory, described in the Nov. 13 PHYSICAL REVIEw LETTERS, Wolf outlines a more general - and...billions of light-years apart. Many astrono - mers-ncluding Christopher L. Carilli of Harvard University, who with two colleagues found the most recent
Measurement of X-ray spectra by PIN photodiode: comparative study

International Nuclear Information System (INIS)

Costa, Paulo R.; Furquim, Tania A.C.; Herdade, Silvio B.

1996-01-01

Two different approaches for the evaluation of diagnostic X-ray spectra are presented : one based on a semiempirical model and other based on measurements using a silicon PIN photodiode. Measured and calculated values using typical kVp and filter combinations are compared
MER 1 MARS NAVCAM 3 RADIOMETRIC RDR SCI V1.0

Data.gov (United States)

National Aeronautics and Space Administration — This data set contains radiometrically calibrated MER-1 Navcam data. The calibration has removed bias, dark current, and flatfield effects from the raw Navcam data,...
MERS-CoV at the Animal-Human interface: inputs on exposure pathways from an Expert-Opinion elicitation

Directory of Open Access Journals (Sweden)

Anna Funk

2016-10-01

Full Text Available Nearly four years after the first report of the emergence of Middle-East respiratory syndrome Coronavirus (MERS-CoV and nearly 1800 human cases later, the ecology of MERS-CoV, its epidemiology, and risk factors of MERS-CoV transmission between camels are poorly understood. Knowledge about the pathways and mechanisms of transmission from animals to humans is limited; as of yet, transmission risks have not been quantified. Moreover the divergent sanitary situations and exposures to animals among populations in the Arabian Peninsula, where human primary cases appear to dominate, vs. other regions in the Middle East and Africa, with no reported human clinical cases and where the virus has been detected only in dromedaries, represents huge scientific and health challenges. Here, we have used expert opinion elicitation in order to obtain ideas on relative importance of MERS-CoV risk factors and estimates of transmission risks from various types of contact between humans and dromedaries. Fourteen (14 experts with diverse and extensive experience in MERS-CoV relevant fields were enrolled and completed an online questionnaire that examined pathways based on several scenarios e.g. camels-camels, camels-human, bats/other species to camels/humans and the role of diverse biological substances (milk, urine etc. and potential fomites.Experts believed that dromedary camels play the largest role in MERS-CoV infection of other dromedaries; however, they also indicated a significant influence of the season (i.e. calving or weaning periods on transmission risk. All experts thought that MERS-CoV infected dromedaries and asymptomatic humans play the most important role in infection of humans, with bats and other species presenting a possible, but yet undefined, risk. Direct and indirect contact of humans with dromedary camels were identified as the most risky types of contact, when compared to consumption of various camel products, with estimated 'most
Endogenous GAS6 and Mer receptor signaling regulate prostate cancer stem cells in bone marrow.

Science.gov (United States)

Jung, Younghun; Decker, Ann M; Wang, Jingcheng; Lee, Eunsohl; Kana, Lulia A; Yumoto, Kenji; Cackowski, Frank C; Rhee, James; Carmeliet, Peter; Buttitta, Laura; Morgan, Todd M; Taichman, Russell S

2016-05-03

GAS6 and its receptors (Tryo 3, Axl, Mer or "TAM") are known to play a role in regulating tumor progression in a number of settings. Previously we have demonstrated that GAS6 signaling regulates invasion, proliferation, chemotherapy-induced apoptosis of prostate cancer (PCa) cells. We have also demonstrated that GAS6 secreted from osteoblasts in the bone marrow environment plays a critical role in establishing prostate tumor cell dormancy. Here we investigated the role that endogenous GAS6 and Mer receptor signaling plays in establishing prostate cancer stem cells in the bone marrow microenvironment.We first observed that high levels of endogenous GAS6 are expressed by disseminated tumor cells (DTCs) in the bone marrow, whereas relatively low levels of endogenous GAS6 are expressed in PCa tumors grown in a s.c. Interestingly, elevated levels of endogenous GAS6 were identified in putative cancer stem cells (CSCs, CD133+/CD44+) compared to non-CSCs (CD133-/CD44-) isolated from PCa/osteoblast cocultures in vitro and in DTCs isolated from the bone marrow 24 hours after intracardiac injection. Moreover, we found that endogenous GAS6 expression is associated with Mer receptor expression in growth arrested (G1) PCa cells, which correlates with the increase of the CSC populations. Importantly, we found that overexpression of GAS6 activates phosphorylation of Mer receptor signaling and subsequent induction of the CSC phenotype in vitro and in vivo.Together these data suggest that endogenous GAS6 and Mer receptor signaling contribute to the establishment of PCa CSCs in the bone marrow microenvironment, which may have important implications for targeting metastatic disease.
Construction of a catalog of X-ray spectra for mammography simulations

International Nuclear Information System (INIS)

Santos, L.C.S.; Vieira, J.W.

2017-01-01

Computational Exposure Models (MCEs) allow the simulation of the interaction of radiation with matter by means of Monte Carlo (MC) techniques. Generally, MCEs are composed of phantom, simulator algorithms of radioactive sources and an MC code to simulate the transport, interaction of the radiation with matter and to evaluate the energy deposited in regions of interest. To compose an MCE for simulations in mammography, the construction of a catalog of X-ray spectra was started, based on the catalog model constructed and using until then in MCEs by the Group of Research in Numerical Dosimetry and by the Group of Research in Computational Dosimetry & Embedded Systems (both referenced in this work as GDN). Potential of 25 kV and 35 kV and used target / filter were applied to the tube: Mo / Mo. The file containing the spectra was read correctly by EGSnrc
Knowledge, Attitudes and Behaviours of Healthcare Workers in the Kingdom of Saudi Arabia to MERS Coronavirus and Other Emerging Infectious Diseases

Directory of Open Access Journals (Sweden)

Abdullah J. Alsahafi

2016-12-01

Full Text Available Background: The Kingdom of Saudi Arabia has experienced a prolonged outbreak of Middle East Respiratory Syndrome (MERS coronavirus since 2012. Healthcare workers (HCWs form a significant risk group for infection. Objectives: The aim of this survey was to assess the knowledge, attitudes, infection control practices and educational needs of HCWs in the Kingdom of Saudi Arabia to MERS coronavirus and other emerging infectious diseases. Methods: 1500 of HCWs from Saudi Ministry of Health were invited to fill a questionnaire developed to cover the survey objectives from 9 September 2015 to 8 November 2015. The response rate was about 81%. Descriptive statistics was used to summarise the responses. Results: 1216 HCWs were included in this survey. A total of 56.5% were nurses and 22% were physicians. The most common sources of MERS-coronavirus (MERS-CoV information were the Ministry of Health (MOH memo (74.3%. Only (47.6% of the physicians, (30.4% of the nurses and (29.9% of the other HCWs were aware that asymptomatic MERS-CoV was described. Around half of respondents who having been investigated for MERS-CoV reported that their work performance decreased while they have suspicion of having MERS-CoV and almost two thirds reported having psychological problems during this period. Almost two thirds of the HCWs (61.2% reported anxiety about contracting MERS-CoV from patients. Conclusions: The knowledge about emerging infectious diseases was poor and there is need for further education and training programs particularly in the use of personal protective equipment, isolation and infection control measures. The self-reported infection control practices were sub-optimal and seem to be overestimated.
Etude de la performance des radars hautes-frequences CODAR et WERA pour la mesure des courants marins en presence partielle de glace de mer

Science.gov (United States)

Kamli, Emna

Les radars hautes-frequences (RHF) mesurent les courants marins de surface avec une portee pouvant atteindre 200 kilometres et une resolution de l'ordre du kilometre. Cette etude a pour but de caracteriser la performance des RHF, en terme de couverture spatiale, pour la mesure des courants de surface en presence partielle de glace de mer. Pour ce faire, les mesures des courants de deux radars de type CODAR sur la rive sud de l'estuaire maritime du Saint-Laurent, et d'un radar de type WERA sur la rive nord, prises pendant l'hiver 2013, ont ete utilisees. Dans un premier temps, l'aire moyenne journaliere de la zone ou les courants sont mesures par chaque radar a ete comparee a l'energie des vagues de Bragg calculee a partir des donnees brutes d'acceleration fournies par une bouee mouillee dans la zone couverte par les radars. La couverture des CODARs est dependante de la densite d'energie de Bragg, alors que la couverture du WERA y est pratiquement insensible. Un modele de fetch appele GENER a ete force par la vitesse du vent predite par le modele GEM d'Environnement Canada pour estimer la hauteur significative ainsi que la periode modale des vagues. A partir de ces parametres, la densite d'energie des vagues de Bragg a ete evaluee pendant l'hiver a l'aide du spectre theorique de Bretschneider. Ces resultats permettent d'etablir la couverture normale de chaque radar en absence de glace de mer. La concentration de glace de mer, predite par le systeme canadien operationnel de prevision glace-ocean, a ete moyennee sur les differents fetchs du vent selon la direction moyenne journaliere des vagues predites par GENER. Dans un deuxieme temps, la relation entre le ratio des couvertures journalieres obtenues pendant l'hiver 2013 et des couvertures normales de chaque radar d'une part, et la concentration moyenne journaliere de glace de mer d'autre part, a ete etablie. Le ratio des couvertures decroit avec l'augmentation de la concentration de glace de mer pour les deux types
MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

Energy Technology Data Exchange (ETDEWEB)

Menachery, Vineet D.; Schafer, Alexandra; Burnum-Johnson, Kristin E.; Mitchell, Hugh D.; Eisfeld-Fenney, Amie J.; Walters, Kevin B.; Nicora, Carrie D.; Purvine, Samuel O.; Casey, Cameron P.; Monroe, Matthew E.; Weitz, Karl K.; Stratton, Kelly G.; Webb-Robertson, Bobbie-Jo M.; Gralinski, Lisa; Metz, Thomas O.; Smith, Richard D.; Waters, Katrina M.; Sims, Amy C.; Kawaoka, Yoshihiro; Baric, Ralph

2018-01-16

Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways in order to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems based approach, we examined differential regulation of IFNγ dependent genes following infection with highly pathogenic viruses including influenza (H5N1-VN1203, H1N1-CA04) and coronaviruses (SARS-CoV, MERS-CoV). Categorizing by function, we observed down regulation of genes associated with antigen presentation following both H5N1-VN1203 and MERS-CoV infection. Further examination revealed global down regulation of antigen presentation genes and was confirmed by proteomics for both H5N1-VN1203 and MERS-CoV infection. Importantly, epigenetic analysis suggested that DNA methylation rather than histone modification plays a crucial role in MERS-CoV mediated antagonism of antigen presentation genes; in contrast, H5N1-VN1203 likely utilizes a combination of epigenetic mechanisms to target antigen presentation. Together, the results indicate a common approach utilized by H5N1-VN1203 and MERS-CoV to modulate antigen presentation and the host adaptive immune response.
Vaccines for emerging infectious diseases: Lessons from MERS coronavirus and Zika virus.

Science.gov (United States)

Maslow, Joel N

2017-12-02

The past decade and a half has been characterized by numerous emerging infectious diseases. With each new threat, there has been a call for rapid vaccine development. Pathogens such as the Middle East Respiratory Syndrome coronavirus (MERS-CoV) and the Zika virus represent either new viral entities or viruses emergent in new geographic locales and characterized by novel complications. Both serve as paradigms for the global spread that can accompany new pathogens. In this paper, we review the epidemiology and pathogenesis of MERS-CoV and Zika virus with respect to vaccine development. The challenges in vaccine development and the approach to clinical trial design to test vaccine candidates for disease entities with a changing epidemiology are discussed.
The trans influence in mer-trichloronitridobis(triphenylarsine)ruthenium(VI)

DEFF Research Database (Denmark)

Magnussen, Magnus; Bendix, Jesper

2003-01-01

The title compound, mer-[RuCl(3)N(C(18)H(15)As)(2)], is the first structurally characterized example of a nitride complex in which ruthenium is six-coordinated to monodentate ligands only. The Ru[triple-bond]N bond length [1.6161 (15) A] is relatively long, and the trans influence of the nitride...
Passivity Based Nonlinear Attitude Control of the Rømer Satellite

DEFF Research Database (Denmark)

Quottrup, Michael Melholt; Krogh-Sørensen, J.; Wisniewski, Rafal

2001-01-01

This paper suggests nonlinear attitude control of the Danish satellite Rømer. This satellite will be designed to fulfil two scientific objectives: The observation of stellar oscillations and the detection and localisation of gamma-ray bursts. The satellite will be equipped with a tetrahedron...

Quantifying K, U and Th contents of marine sediments using shipboard natural gamma radiation spectra measured on DV JOIDES Resolution

Science.gov (United States)

De Vleeschouwer, David; Dunlea, Ann G.; Auer, Gerald; Anderson, Chloe H.; Brumsack, Hans; de Loach, Aaron; Gurnis, Michael C.; Huh, Youngsook; Ishiwa, Takeshige; Jang, Kwangchul; Kominz, Michelle A.; März, Christian; Schnetger, Bernhard; Murray, Richard W.; Pälike, Heiko; Expedition 356 shipboard scientists, IODP

2017-04-01

During International Ocean Discovery Program (IODP) expeditions, shipboard-generated data provide the first insights into the cored sequences. The natural gamma radiation (NGR) of the recovered material, for example, is routinely measured on the ocean drilling research vessel DV JOIDES Resolution. At present, only total NGR counts are readily available as shipboard data, although full NGR spectra (counts as a function of gamma-ray energy level) are produced and archived. These spectra contain unexploited information, as one can estimate the sedimentary contents of potassium (K), thorium (Th), and uranium (U) from the characteristic gamma-ray energies of isotopes in the 40K, 232Th, and 238U radioactive decay series. Dunlea et al. [2013] quantified K, Th and U contents in sediment from the South Pacific Gyre by integrating counts over specific energy levels of the NGR spectrum. However, the algorithm used in their study is unavailable to the wider scientific community due to commercial proprietary reasons. Here, we present a new MATLAB algorithm for the quantification of NGR spectra that is transparent and accessible to future NGR users. We demonstrate the algorithm's performance by comparing its results to shore-based inductively coupled plasma-mass spectrometry (ICP-MS), inductively coupled plasma-emission spectrometry (ICP-ES), and quantitative wavelength-dispersive X-ray fluorescence (XRF) analyses. Samples for these comparisons come from eleven sites (U1341, U1343, U1366-U1369, U1414, U1428-U1430, U1463) cored in two oceans during five expeditions. In short, our algorithm rapidly produces detailed high-quality information on sediment properties during IODP expeditions at no extra cost. Dunlea, A. G., R. W. Murray, R. N. Harris, M. A. Vasiliev, H. Evans, A. J. Spivack, and S. D'Hondt (2013), Assessment and use of NGR instrumentation on the JOIDES Resolution to quantify U, Th, and K concentrations in marine sediment, Scientific Drilling, 15, 57-63.
Detection of specific IgA antibodies against a novel deamidated 8-Mer gliadin peptide in blood plasma samples from celiac patients.

Directory of Open Access Journals (Sweden)

Sara Vallejo-Diez

Full Text Available We studied whether celiac disease (CD patients produce antibodies against a novel gliadin peptide specifically generated in the duodenum of CD patients by a previously described pattern of CD-specific duodenal proteases. Fingerprinting and ion-trap mass spectrometry of CD-specific duodenal gliadin-degrading protease pattern revealed a new 8-mer gliadin-derived peptide. An ELISA against synthetic deamidated 8-mer peptides (DGP 8-mer was used to study the presence of IgA anti-DGP 8-mer antibodies in plasma samples from 81 children (31 active CD patients (aCD, 17 CD patients on a gluten-free diet (GFD, 10 healthy controls (C and 23 patients with other gastrointestinal pathology (GP and 101 adults (16 aCD, 12 GFD, 27 C and 46 GP-patients. Deamidation of the 8-mer peptide significantly increased the reactivity of the IgA antibodies from CD patients against the peptide. Significant IgA anti-DGP 8-mer antibodies levels were detected in 93.5% of aCD-, 11.8% of GFD- and 4.3% of GP-patients in children. In adults, antibodies were detected in 81.3% of aCD-patients and 8.3% of GFD-patients while were absent in 100% of C- and GP-patients. Duodenal CD-specific gliadin degrading proteases release an 8-mer gliadin peptide that once deamidated is an antigen for specific IgA antibodies in CD patients which may provide a new accurate diagnostic tool in CD.
Comparison between simplified load spectra in accordance with Germanische Lloyd guidelines, and load spectra derived from time domain simulations

Energy Technology Data Exchange (ETDEWEB)

Rees, M [Aerodyn Energiesysteme gmbH, Rendsburg (Germany)

1996-09-01

The Germanische Lloyd guideline allows calculations of load spectra in two fundamentally different ways. In the case of the so-called `simplified load spectra` the maximum amplitude of fluctuation of a load component is formed as {+-}75% of the average value of the purely aerodynamic loads of this component at rated wind conditions, together with an overlay of mass-related loads. The second method allowed in the GL guideline is the calculation of load spectra from simulation results in the time domain. For a number of average wind speeds the time-dependent characteristics of the load components are calculated taking account of the natural spatial turbulence of the wind. These are converted into load spectra using the rainflow method. In a parametric study the load spectra are calculated according to both methods and compared. The calculations are performed for turbines with rated powers of 100 kW to 2000 kW, with two and three blades, and also for stall-controlled and pitch-controlled turbines. The calculated load spectra are compared with each by means of 1 P fatigue equivalent load spectra. The influence of individual parameters is presented, as is the validity of the simplified load spectra. (au)
Isolation, identification and PCR amplification of merA gene from ...

African Journals Online (AJOL)

Mercury resistant Escherichia coli strains have been isolated from different mercury polluted sites of India and their minimum inhibitory concentration (MIC) levels were determined. The zone of inhibition was measured to find the antibiotic sensitivity level. The location of mer operon was determined by transforming the ...
Modeling of A-DLTS Spectra of MOS Structures

Directory of Open Access Journals (Sweden)

Peter Hockicko

2008-01-01

Full Text Available Acquisition of basic characteristic of defects has become possible through a wide class of measurement techniqueswhich probe the interface, the near interface, as well as the bulk of semiconductor. Results presented here are basedessentially on the acoustic version of Deep Level Transient Spectroscopy (A-DLTS measurements. This method is based onthe acoustoelectric response effect observed at the interface. The A-DLTS uses the acoustoelectric response signal (ARSproduced by MOS structure interface when a longitudal acoustic wave propagates through a structure. The ARS is extremelysensitive to external conditions of the structure and reflects any changes in the charge distribution connected with chargedtraps. The temperature dependence of ARS after bias voltage step application is investigated and the activation energies andsome other parameters of traps at the insulator – semiconductor interface are determined. The results obtained formArrhenius plots of A-DLTS spectra of selected MOS structures are compared with results obtained from modeling of ADLTS spectra using theoretical model.
Thermophysical properties of the MER and Beagle II landing site regions on Mars

Science.gov (United States)

Jakosky, Bruce M.; Hynek, Brian M.; Pelkey, Shannon M.; Mellon, Michael T.; Martínez-Alonso, Sara; Putzig, Nathaniel E.; Murphy, Nate; Christensen, Philip R.

2006-08-01

We analyzed remote-sensing observations of the Isidis Basin, Gusev Crater, and Meridiani Planum landing sites for Beagle II, MER-A Spirit, and MER-B Opportunity spacecraft, respectively. We emphasized the thermophysical properties using daytime and nighttime radiance measurements from the Mars Global Surveyor (MGS) Thermal Emission Spectrometer and Mars Odyssey Thermal Emission Imaging System (THEMIS) and thermal inertias derived from nighttime data sets. THEMIS visible images, MGS Mars Orbiter Camera (MOC) narrow-angle images, and MGS Mars Orbiter Laser Altimeter (MOLA) data are incorporated as well. Additionally, the remote-sensing data were compared with ground-truth at the MER sites. The Isidis Basin surface layer has been shaped by aeolian processes and erosion by slope winds coming off of the southern highlands and funneling through notches between massifs. In the Gusev region, surface materials of contrasting thermophysical properties have been interpreted as rocks or bedrock, duricrust, and dust deposits; these are consistent with a complex geological history dominated by volcanic and aeolian processes. At Meridiani Planum the many layers having different thermophysical and erosional properties suggest periodic deposition of differing sedimentological facies possibly related to clast size, grain orientation and packing, or mineralogy.
Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers

KAUST Repository

Kandeel, Mahmoud

2018-05-17

Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulation was carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lowest root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HR, monomers were also discovered in both of viral and cellular membranes. In order to find the differences between S2 monomer and trimer molecular dynamics, S2 monomer were modelled and subjected to MD simulation. In contrast to S2 trimer, S2 monomer was unstable, having high RMSDs with major drifts above 8 Å. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer. Hydrophobic residues at the “a” and “d” positions of HR helices stabilize the whole system, having minimal changes in RMSD. The global distance test and contact area difference scores support instability of MERS CoV S2 monomer. Analysis of HR1-HR2 inter-residue contacts and interaction energy revealed three different energy scales along HR helices. Two strong interaction energies were identified at the start of the HR2 helix and at the C-terminal of HR2. The identified critical residues by MD simulation and residues at a and d position of HR helix were strong stabilizers of HRs recognition.
Modeling midwave infrared muzzle flash spectra from unsuppressed and flash-suppressed large caliber munitions

Science.gov (United States)

Steward, Bryan J.; Perram, Glen P.; Gross, Kevin C.

2012-07-01

Time-resolved infrared spectra of firings from a 152 mm howitzer were acquired over an 1800-6000 cm-1 spectral range using a Fourier-transform spectrometer. The instrument collected primarily at 32 cm-1 spectral and 100 Hz temporal resolutions. Munitions included unsuppressed and chemically flash suppressed propellants. Secondary combustion occurred with unsuppressed propellants resulting in flash emissions lasting ˜100 ms and dominated by H2O and CO2 spectral structure. Non-combusting plume emissions were one-tenth as intense and approached background levels within 20-40 ms. A low-dimensional phenomenological model was used to reduce the data to temperatures, soot absorbances, and column densities of H2O, CO2, CH4, and CO. The combusting plumes exhibit peak temperatures of ˜1400 K, areas of greater than 32 m2, low soot emissivity of ˜0.04, with nearly all the CO converted to CO2. The non-combusting plumes exhibit lower temperatures of ˜1000 K, areas of ˜5 m2, soot emissivity of greater than 0.38 and CO as the primary product. Maximum fit residual relative to peak intensity are 14% and 8.9% for combusting and non-combusting plumes, respectively. The model was generalized to account for turbulence-induced variations in the muzzle plumes. Distributions of temperature and concentration in 1-2 spatial regions demonstrate a reduction in maximum residuals by 40%. A two-region model of combusting plumes provides a plausible interpretation as a ˜1550 K, optically thick plume core and ˜2550 K, thin, surface-layer flame-front. Temperature rate of change was used to characterize timescales and energy release for plume emissions. Heat of combustion was estimated to be ˜5 MJ/kg.
Boundary spectra in superspace σ-models

International Nuclear Information System (INIS)

Quella, T.; Schomerus, V.; Creutzig, T.

2007-12-01

In this note we compute exact boundary spectra for D-instantons in σ-models on the supergroup PSL(22). Our results are obtained through an explicit summation of the perturbative expansion for conformal dimensions to all orders in the curvature radius. The analysis exploits several remarkable properties of the perturbation series that arises from rescalings of the metric on PSL(22) relative to a fixed Wess- Zumino term. According to Berkovits, Vafa and Witten, the models are relevant in the context of string theory on AdS 3 with non-vanishing RR-flux. The note concludes with a number of comments on various possible generalizations to other supergroups and higher dimensional supercoset theories. (orig.)
Fitting PAC spectra with stochastic models: PolyPacFit

Energy Technology Data Exchange (ETDEWEB)

Zacate, M. O., E-mail: zacatem1@nku.edu [Northern Kentucky University, Department of Physics and Geology (United States); Evenson, W. E. [Utah Valley University, College of Science and Health (United States); Newhouse, R.; Collins, G. S. [Washington State University, Department of Physics and Astronomy (United States)

2010-04-15

PolyPacFit is an advanced fitting program for time-differential perturbed angular correlation (PAC) spectroscopy. It incorporates stochastic models and provides robust options for customization of fits. Notable features of the program include platform independence and support for (1) fits to stochastic models of hyperfine interactions, (2) user-defined constraints among model parameters, (3) fits to multiple spectra simultaneously, and (4) any spin nuclear probe.
Vaccines for emerging infectious diseases: Lessons from MERS coronavirus and Zika virus

Science.gov (United States)

Maslow, Joel N.

2017-01-01

ABSTRACT The past decade and a half has been characterized by numerous emerging infectious diseases. With each new threat, there has been a call for rapid vaccine development. Pathogens such as the Middle East Respiratory Syndrome coronavirus (MERS-CoV) and the Zika virus represent either new viral entities or viruses emergent in new geographic locales and characterized by novel complications. Both serve as paradigms for the global spread that can accompany new pathogens. In this paper, we review the epidemiology and pathogenesis of MERS-CoV and Zika virus with respect to vaccine development. The challenges in vaccine development and the approach to clinical trial design to test vaccine candidates for disease entities with a changing epidemiology are discussed. PMID:28846484
A multi-faceted approach of a nursing led education in response to MERS-CoV infection

Directory of Open Access Journals (Sweden)

Jaffar A. Al-Tawfiq

2018-03-01

Full Text Available Background: The emergence of the Middle East respiratory syndrome-coronavirus (MERS-CoV resulted in multiple healthcare associated outbreaks. In response, we developed a nurse-led program to screen and triage patients with MERS-CoV infection. Methods: A formal educational program was implemented to ensure a standardized approach to care planning and delivery. The essential skills that were included were the use of Personal Protective Equipment (PPE including gown, gloves, head cover and N95 mask, hand hygiene, the practice of donning and doffing and the collection of MERS-CoV nasopharyngeal specimens. Results: A core group of nurses were identified from high-risk units. The education program consisted of four skill-days. Nurses were assigned a pre-course work from Mosby’s Nursing Skills, an online skill module, donning and doffing of PPE, and the process for obtaining a nasopharyngeal swab. The skill lab incorporated multiple methods such group discussion, watching an on-line video, and a simulated demonstration and practice on a mannequin. In total, 450 nurses attended the Nasopharyngeal Skills Day and 1000 nurses received training. Donning and doffing PPE and N95 mask fit testing has become an annual mandatory competency requirement for staff in nursing and clinical services. Conclusion: The application of specified protocols minimizes the risks of cross infection, placing emphasis on patient and staff safety as well as expediting the patient to definitive treatment. Nurse educators have an instrumental role in training nurses and other healthcare providers on the specifics needed to identify, contain and manage patient presenting with MERS-CoV. Keywords: Coronavirus, Education, MERS-CoV, Middle East respiratory syndrome, Saudi Arabia, Outbreak preparedness, Hospital care
Inclusive spectra of mesons with large transverse momenta in proton-nuclear collisions at high energies

International Nuclear Information System (INIS)

Lykasov, G.I.; Sherkhonov, B.Kh.

1982-01-01

Basing on the proposed earlier quark model of hadron-nucleus processes with large transverse momenta psub(perpendicular) the spectra of π +- , K +- meson production with large psub(perpendicular) in proton-nucleus collisions at high energies are calculated. The performed comparison of their dependence of the nucleus-target atomic number A with experimental data shows a good agreement. Theoretical and experimental ratios of inclusive spectra of K +- and π +- mesons in the are compared. Results of calculations show a rather good description of experimental data on large psub(perpendicular) meson production at high energies
Renewable energies in the French DOM-TOM : a study of the costs and benefits of transitioning from fossil fuels to renewable energies in the French Départements d’Outre Mer et Territoires d’Outre Mer

OpenAIRE

Stanley-Smith, Adam P.

2010-01-01

The French Départements d’Outre Mer et Territoires d’Outre Mer (DOM-TOM) are not the most populous region of France. Nor are they the most prosperous, the most important, or even centers of industrial production. Rather, the DOM-TOM possessions have a unique value in French culture: they represent the past glory of the state and its people, and the courage that lead French explorers and settlers to roam the world. Unfortunately, the DOM-TOM represents an ever growing burden upon...
Transverse momentum spectra of hadrons in p + p collisions at CERN SPS energies from the UrQMD transport model

Science.gov (United States)

Ozvenchuk, V.; Rybicki, A.

2018-05-01

The UrQMD transport model, version 3.4, is used to study the new experimental data on transverse momentum spectra of π±, K±, p and p bar produced in inelastic p + p interactions at SPS energies, recently published by the NA61/SHINE Collaboration. The comparison of model predictions to these new measurements is presented as a function of collision energy for central and forward particle rapidity intervals. In addition, the inverse slope parameters characterizing the transverse momentum distributions are extracted from the predicted spectra and compared to the corresponding values obtained from NA61/SHINE distributions, as a function of particle rapidity and collision energy. A complex pattern of deviations between the experimental data and the UrQMD model emerges. For charged pions, the fair agreement visible at top SPS energies deteriorates with the decreasing energy. For charged K mesons, UrQMD significantly underpredicts positive kaon production at lower beam momenta. It also underpredicts the central rapidity proton yield at top collision energy and overpredicts antiproton production at all considered energies. We conclude that the new experimental data analyzed in this paper still constitute a challenge for the present version of the model.
Studies of the X-ray absorption spectra of some methylcyano esters

International Nuclear Information System (INIS)

Takahashi, Osamu; Saito, Ko; Mitani, Masaki; Yoshida, Hiroaki; Tahara, Fumitaka; Sunami, Tetsuji; Waki, Keiichiro; Senba, Yasunori; Hiraya, Atsunari; Pettersson, Lars G.M.

2005-01-01

Density functional theory (DFT) has been applied to simulate core-excited photoabsorption spectra for some methylcyano esters within a transition potential (TP) framework. Our calculations for methylcyano formate at the N and O K-edges are consistent with previous experimental spectra. For methylcyano acetate the photoabsorption spectra at the N and O K-edges were reinvestigated experimentally. Contrary to the previous experiment, only one main peak was observed at the N K-edge and this peak was assigned to N(1s) ->π* excitation. This result was supported by our theoretical calculations. The general trends in the X-ray absorption spectra and the site-specific bond scission of methylcyano esters at the N and O K-edges are also discussed
Healthcare worker exposure to Middle East respiratory syndrome coronavirus (MERS-CoV: Revision of screening strategies urgently needed

Directory of Open Access Journals (Sweden)

Hala Amer

2018-06-01

Conclusions: The data obtained in this study support the widespread testing of all close contacts of MERS-CoV cases, regardless of the significance of the contact or presence or absence of symptoms. In addition, urgent careful review of guidance regarding the return of asymptomatic MERS-CoV-positive HCWs under investigation to active duty is needed.
Compressed shell conditions extracted from spectroscopic analysis of Ti K-shell absorption spectra with evaluation of line self-emission

Energy Technology Data Exchange (ETDEWEB)

Johns, H. M.; Mancini, R. C.; Hakel, P.; Nagayama, T. [Physics Department, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557 (United States); Smalyuk, V. A.; Regan, S. P.; Delettrez, J. [Laboratory for Laser Energetics, University of Rochester, 250 E. River Road, Rochester, New York 14623 (United States)

2014-08-15

Ti-doped tracer layers embedded in the shell at varying distances from the fuel-shell interface serve as a spectroscopic diagnostic for direct-drive experiments conducted at OMEGA. Detailed modeling of Ti K-shell absorption spectra produced in the tracer layer considers n = 1–2 transitions in F- through Li-like Ti ions in the 4400–4800 eV range, both including and excluding line self-emission. Testing the model on synthetic spectra generated from 1-D LILAC hydrodynamic simulations reveals that the model including self-emission best reproduces the simulation, while the model excluding self-emission overestimates electron temperature T{sub e} and density N{sub e} to a higher degree for layers closer to the core. The prediction of the simulation that the magnitude of T{sub e} and duration of Ti absorption will be strongly tied to the distance of the layer from the core is consistent with the idea that regions of the shell close to the core are more significantly heated by thermal transport out of the hot dense core, but more distant regions are less affected by it. The simulation predicts more time variation in the observed T{sub e}, N{sub e} conditions in the compressed shell than is observed in the experiment, analysis of which reveals conditions remain in the range T{sub e} = 400–600 eV and N{sub e} = 3.0–10.0 × 10{sup 24} cm{sup −3} for all but the most distant Ti-doped layer, with error bars ∼5% T{sub e} value and ∼10% N{sub e} on average. The T{sub e}, N{sub e} conditions of the simulation lead to a greater degree of ionization for zones close to the core than occurs experimentally, and less ionization for zones far from the core.
INTRIGOSS: A new Library of High Resolution Synthetic Spectra

Science.gov (United States)

Franchini, Mariagrazia; Morossi, Carlo; Di Marcancantonio, Paolo; Chavez, Miguel; GES-Builders

2018-01-01

INTRIGOSS (INaf Trieste Grid Of Synthetic Spectra) is a new High Resolution (HiRes) synthetic spectral library designed for studying F, G, and K stars. The library is based on atmosphere models computed with specified individual element abundances via ATLAS12 code. Normalized SPectra (NSP) and surface Flux SPectra (FSP), in the 4800-5400 Å wavelength range, were computed by means of the SPECTRUM code. The synthetic spectra are computed with an atomic and bi-atomic molecular line list including "bona fide" Predicted Lines (PLs) built by tuning loggf to reproduce very high SNR Solar spectrum and the UVES-U580 spectra of five cool giants extracted from the Gaia-ESO survey (GES). The astrophysical gf-values were then assessed by using more than 2000 stars with homogenous and accurate atmosphere parameters and detailed chemical composition from GES. The validity and greater accuracy of INTRIGOSS NSPs and FSPs with respect to other available spectral libraries is discussed. INTRIGOSS will be available on the web and will be a valuable tool for both stellar atmospheric parameters and stellar population studies.
VizieR Online Data Catalog: A library of high-S/N optical spectra of FGKM stars (Yee+, 2017)

Science.gov (United States)

Yee, S. W.; Petigura, E. A.; von Braun, K.

2017-09-01

Classification of stars, by comparing their optical spectra to a few dozen spectral standards, has been a workhorse of observational astronomy for more than a century. Here, we extend this technique by compiling a library of optical spectra of 404 touchstone stars observed with Keck/HIRES by the California Planet Search. The spectra have high resolution (R~60000), high signal-to-noise ratio (S/N~150/pixel), and are registered onto a common wavelength scale. The library stars have properties derived from interferometry, asteroseismology, LTE spectral synthesis, and spectrophotometry. To address a lack of well-characterized late-K dwarfs in the literature, we measure stellar radii and temperatures for 23 nearby K dwarfs, using modeling of the spectral energy distribution and Gaia parallaxes. This library represents a uniform data set spanning the spectral types ~M5-F1 (Teff~3000-7000K, R*~0.1-16R{Sun}). We also present "Empirical SpecMatch" (SpecMatch-Emp), a tool for parameterizing unknown spectra by comparing them against our spectral library. For FGKM stars, SpecMatch-Emp achieves accuracies of 100K in effective temperature (Teff), 15% in stellar radius (R*), and 0.09dex in metallicity ([Fe/H]). Because the code relies on empirical spectra it performs particularly well for stars ~K4 and later, which are challenging to model with existing spectral synthesizers, reaching accuracies of 70K in Teff, 10% in R*, and 0.12dex in [Fe/H]. We also validate the performance of SpecMatch-Emp, finding it to be robust at lower spectral resolution and S/N, enabling the characterization of faint late-type stars. Both the library and stellar characterization code are publicly available. (2 data files).

Merónimos de la gastronomía costarricense: Limón y Valle Central

OpenAIRE

Leoni de León, Jorge Antonio; Barahona Gamboa, Hazel

2016-01-01

Resumen La definición de un platillo culinario implica la descripción de sus partes, dentro de las cuales podemos incluir los ingredientes; por ejemplo, la carne es parte de un estofado. En este sentido, los ingredientes son merónimos y, además, pueden ser objeto de una clasificación según el proceso al que están sometidos en la receta; es decir, si son mezclados, hervidos, horneados, polvoreados, cortados, etc. Así, nos avocamos a establecer y clasificar los merónimos, según estos criterios,...
No MERS-CoV but positive influenza viruses in returning Hajj pilgrims, China, 2013–2015

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Xuezheng Ma

2017-11-01

Full Text Available Abstract Background There is global health concern that the mass movement of pilgrims to and from Mecca annually could contribute to the international spread of Middle East Respiratory Syndrome Coronavirus (MERS-CoV. In China, about 11,000 Muslim pilgrims participate in the Hajj gathering in Mecca annually. This is the first report of MERS-CoV and respiratory virus molecular screening of returning pilgrims at points of entry in China from 2013 to 2015. Methods and results A total of 847 returning Hajj pilgrims participated in this study. The test results indicated that of the travelers, 34 tested positive for influenza A virus, 14 for influenza B virus, 4 for metapneumo virus, 2 for respiratory syncytial virus, and 3 for human coronavirus. There was a significant difference in the rates of positive and negative influenza virus tests between Hajj pilgrims with symptoms and those without. The detection rates of influenza virus were not significantly different among the three years studied, at 5.3, 6.0 and 6.3% for 2013, 2014 and 2015, respectively. Discussion and conclusion The MERS-CoV and respiratory viruses detection results at points of entry in China from 2013 to 2015 indicated that there were no MERS-CoV infection but a 5.7% positive influenza viruses in returning Chinese pilgrims.
Temperature dependent analysis of three classes of fluorescence spectra from p-6P nanofiber films

DEFF Research Database (Denmark)

Balzer, F.; Pogantsch, Alexander; Rubahn, Horst-Günter

2009-01-01

devices, given that the spectra are reproducible for varying surface temperatures. A detailed investigation as a function of surface temperature variation from 300 to 30 K reveals three classes of spectra: (a) spectra with well resolved excitonic peaks, which shift 35meV to the blue with decreasing...... temperature, (b) similar spectra with an additional intermediate broadening around 150 K, and (c) excitonic spectra similar to (b), but with a green defect emission band. Quantitative fitting of type (a) spectra results in an exciton–phonon coupling factor of 80 ± 10meV and an average phonon temperature of Θ...... = 670 ± 70 K. The Huang–Rhys factor decreases linearly from 1.2 at 300 K to 1.0 at 30 K. Fitting of type (b) spectra reveals that the apparent intermediate temperature broadening is due to additional fluorescence peaks, the relative importance of which increasing with decreasing temperature....
Observing the Spectra of MEarth and TRAPPIST Planets with JWST

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Morley, Caroline; Kreidberg, Laura; Rustamkulov, Zafar; Robinson, Tyler D.; Fortney, Jonathan J.

2017-10-01

During the past two years, nine planets close to Earth in radius have been discovered around nearby M dwarfs cooler than 3300 K. These planets include the 7 planets in the TRAPPIST-1 system and two planets discovered by the MEarth survey, GJ 1132b and LHS 1140b (Dittmann et al. 2017; Berta-Thompson et al. 2015; Gillon et al. 2017). These planets are the smallest planets discovered to date that will be amenable to atmospheric characterization with JWST. They span equilibrium temperatures from ˜130 K to >500 K, and radii from 0.7 to 1.43 Earth radii. Some of these planets orbit as distances potentially amenable to surface liquid water, though the actual surface temperatures will depend strongly on the albedo of the planet and the thickness and composition of its atmosphere. The stars they orbit also vary in activity levels, from the quiet LHS 1140b host star to the more active TRAPPIST-1 host star. This set of planets will form the testbed for our first chance to study the diversity of atmospheres around Earth-sized planets. Here, we will present model spectra of these 9 planets, varying the composition and the surface pressure of the atmosphere. We base our elemental compositions on three outcomes of planetary atmosphere evolution in our own solar system: Earth, Titan, and Venus. We calculate the molecular compositions in chemical equilibrium. We present both thermal emission spectra and transmission spectra for each of these objects, and make predictions for the observability of these spectra with different instrument modes with JWST.
Study in the plasma with non-equilibrium ionization state by relative intensities in K-spectra of multicharged ions

International Nuclear Information System (INIS)

Bojko, V.A.; Skobelev, I.Yu.; Faenov, A.Ya.

1984-01-01

The pressure of the K-spectra formation of multicharge h-, He-, Li-like ions in a plasma with an arbitrary ionization state are considered. It is shown that comparison of experimental and theoretical data on the intensities of f a number of spectral lines belonging to such ions allows one to determine both the plasma electron temperature and ion distribution versus the ionization degre ees. The proposed method of plasma diagnostics is used for measuring parameters of the expanding laser-produced magnesium plasme
First-Principles Fe L _2,3 -Edge and O K-Edge XANES and XMCD Spectra for Iron Oxides

Energy Technology Data Exchange (ETDEWEB)

Sassi, Michel [Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Pearce, Carolyn I. [Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Bagus, Paul S. [Department; Arenholz, Elke [Advanced; Rosso, Kevin M. [Pacific Northwest National Laboratory, Richland, Washington 99352, United States

2017-10-02

X-ray absorption near-edge structure (XANES) and X-ray magnetic circular dichroism (XMCD) spectroscopies are tools in widespread use for providing detailed local atomic structure, oxidation state, and magnetic structure information for materials and organometallic complexes. The analysis of these spectra for transition-metal L-edges is routinely performed on the basis of ligand-field multiplet theory because one- and two-particle mean-field ab initio methods typically cannot describe the multiplet structure. Here we show that multireference configuration interaction (MRCI) calculations can satisfactorily reproduce measured XANES spectra for a range of complex iron oxide materials including hematite and magnetite. MRCI Fe L2,3-edge XANES and XMCD spectra of Fe(II)O6, Fe(III)O6, and Fe(III)O4 in magnetite are found to be in very good qualitative agreement with experiment and multiplet calculations. Point-charge embedding and small distortions of the first-shell oxygen ligands have only small effects. Oxygen K-edge XANES/XMCD spectra for magnetite investigated by a real-space Green’s function approach complete the very good qualitative agreement with experiment. Material-specific differences in local coordination and site symmetry are well reproduced, making the approach useful for assigning spectral features to specific oxidation states and coordination environments.
Infrared Model Spectra for Evolving Red Supergiants

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Kyung-Won Suh

1993-06-01

Full Text Available The space and ground based infrared spectra of red supergiants are modeled and arranged in order of their evolutionary status with their theoretical model parameters. The chemical compositions of the dust shells around red supergiants are affected by the nuclear reaction and dredge-up processes of the cental stars. The processes are sensitively dependent on the initial mass, the initial chemical composition, and the evolutionary status. Miras, infrared carbon stars, and OH/IR stars have close link in their evolution in manu aspects, i,e., the chemical composition, the optical depths and the mass loss rates. The evolutionary tracks for the three classes of red supergiants on infrared two-color diagrams have been made from model calculations and IRAS observational data.
Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method.

Science.gov (United States)

Guo, Meiyuan; Sørensen, Lasse Kragh; Delcey, Mickaël G; Pinjari, Rahul V; Lundberg, Marcus

2016-01-28

The intensities and relative energies of metal K pre-edge features are sensitive to both geometric and electronic structures. With the possibility to collect high-resolution spectral data it is important to find theoretical methods that include all important spectral effects: ligand-field splitting, multiplet structures, 3d-4p orbital hybridization, and charge-transfer excitations. Here the restricted active space (RAS) method is used for the first time to calculate metal K pre-edge spectra of open-shell systems, and its performance is tested against on six iron complexes: [FeCl6](n-), [FeCl4](n-), and [Fe(CN)6](n-) in ferrous and ferric oxidation states. The method gives good descriptions of the spectral shapes for all six systems. The mean absolute deviation for the relative energies of different peaks is only 0.1 eV. For the two systems that lack centrosymmetry [FeCl4](2-/1-), the ratios between dipole and quadrupole intensity contributions are reproduced with an error of 10%, which leads to good descriptions of the integrated pre-edge intensities. To gain further chemical insight, the origins of the pre-edge features have been analyzed with a chemically intuitive molecular orbital picture that serves as a bridge between the spectra and the electronic structures. The pre-edges contain information about both ligand-field strengths and orbital covalencies, which can be understood by analyzing the RAS wavefunction. The RAS method can thus be used to predict and rationalize the effects of changes in both the oxidation state and ligand environment in a number of hard X-ray studies of small and medium-sized molecular systems.
Overview of preparedness and response for Middle East respiratory syndrome coronavirus (MERS-CoV) in Oman.

Science.gov (United States)

Al-Abaidani, I S; Al-Maani, A S; Al-Kindi, H S; Al-Jardani, A K; Abdel-Hady, D M; Zayed, B E; Al-Harthy, K S; Al-Shaqsi, K H; Al-Abri, S S

2014-12-01

Several countries in the Middle East and around 22 countries worldwide have reported cases of human infection with the Middle East respiratory syndrome coronavirus (MERS-CoV). The exceptionally high fatality rate resulting from MERS-CoV infection in conjunction with the paucity of knowledge about this emerging virus has led to major public and international concern. Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. The aim of this report is to describe the epidemiological aspects of these two cases and to highlight the importance of public health preparedness and response. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. Copyright © 2014. Published by Elsevier Ltd.
Overview of preparedness and response for Middle East respiratory syndrome coronavirus (MERS-CoV in Oman

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I.S. Al-Abaidani

2014-12-01

Full Text Available Several countries in the Middle East and around 22 countries worldwide have reported cases of human infection with the Middle East respiratory syndrome coronavirus (MERS-CoV. The exceptionally high fatality rate resulting from MERS-CoV infection in conjunction with the paucity of knowledge about this emerging virus has led to major public and international concern. Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. The aim of this report is to describe the epidemiological aspects of these two cases and to highlight the importance of public health preparedness and response. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman.
Caractéristiques biologiques de la truite de mer (Salmo trutta L. au Nord de l'Espagne, dans deux rivières des Asturies

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TOLEDO Ma Del Mar

1993-07-01

Full Text Available Une première caractérisation des truites de mer des rivières du Nord de l'Espagne (Asturies est réalisée à partir de l'analyse de la structure de taille et d'âge, ainsi que celle de l'alimentation et des paramètres reproducteurs des poissons adultes. Les truites proviennent des captures réalisées à la ligne (de juin à août sur les rivières Cares et Narcea et par pêche électrique sur les zones de frayères du Narcea durant la saison de reproduction (novembre à janvier. Les truites de mer échantillonnées durant la saison de pêche ont une structure d'âge semblable sur les deux cours d'eau. Environ 85% des individus sont restés deux ans en eau douce avant de descendre en mer, et plus de 95% d'entre eux appartiennent aux classes d'âge de mer 0 + et 1 + . L'importance relative des poissons de 0 + de mer (finnock est légèrement plus élevée dans le Cares (68% que dans le Narcea (51 %. Le rapport des sexes est en faveur des femelles, quelle que soit la classe d'âge de mer. La structure d'âge marin des truites capturées en période de reproduction ne diffère pas de celle observée durant la saison de pêche, bien que montrant une haute proportion de 0 + de mer (32% de l'ensemble des poissons matures. Le taux de maturation chez les truites de 0 + de mer est particulièrement élevé ( 81% parmi les femelles et 100% chez les mâles et tous les individus des autres classes d'âge de mer sont matures. Le nombre d'oeufs (de 571 à 2086 oeufs par femelle et l'index gonadosomatique sont positivement corrélés à la taille et à l'âge de mer des femelles. La truite de mer se nourrit activement en eau douce durant la remontée estivale, puisque 81 % des estomacs examinés étaient pleins. Elle consomme principalement des Epheméroptères, des Diptères et des Trichoptères, mais son alimentation inclut également des proies d'origine terrestre, essentiellement des Arthropodes.
A camel-derived MERS-CoV with a variant spike protein cleavage site and distinct fusion activation properties

Science.gov (United States)

Millet, Jean Kaoru; Goldstein, Monty E; Labitt, Rachael N; Hsu, Hung-Lun; Daniel, Susan; Whittaker, Gary R

2016-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) continues to circulate in both humans and camels, and the origin and evolution of the virus remain unclear. Here we characterize the spike protein of a camel-derived MERS-CoV (NRCE-HKU205) identified in 2013, early in the MERS outbreak. NRCE-HKU205 spike protein has a variant cleavage motif with regard to the S2′ fusion activation site—notably, a novel substitution of isoleucine for the otherwise invariant serine at the critical P1′ cleavage site position. The substitutions resulted in a loss of furin-mediated cleavage, as shown by fluorogenic peptide cleavage and western blot assays. Cell–cell fusion and pseudotyped virus infectivity assays demonstrated that the S2′ substitutions decreased spike-mediated fusion and viral entry. However, cathepsin and trypsin-like protease activation were retained, albeit with much reduced efficiency compared with the prototypical EMC/2012 human strain. We show that NRCE-HKU205 has more limited fusion activation properties possibly resulting in more restricted viral tropism and may represent an intermediate in the complex pattern of MERS-CoV ecology and evolution. PMID:27999426
From Prime to Extended Mission: Evolution of the MER Tactical Uplink Process

Science.gov (United States)

Mishkin, Andrew H.; Laubach, Sharon

2006-01-01

To support a 90-day surface mission for two robotic rovers, the Mars Exploration Rover mission designed and implemented an intensive tactical operations process, enabling daily commanding of each rover. Using a combination of new processes, custom software tools, a Mars-time staffing schedule, and seven-day-a-week operations, the MER team was able to compress the traditional weeks-long command-turnaround for a deep space robotic mission to about 18 hours. However, the pace of this process was never intended to be continued indefinitely. Even before the end of the three-month prime mission, MER operations began evolving towards greater sustainability. A combination of continued software tool development, increasing team experience, and availability of reusable sequences first reduced the mean process duration to approximately 11 hours. The number of workshifts required to perform the process dropped, and the team returned to a modified 'Earth-time' schedule. Additional process and tool adaptation eventually provided the option of planning multiple Martian days of activity within a single workshift, making 5-day-a-week operations possible. The vast majority of the science team returned to their home institutions, continuing to participate fully in the tactical operations process remotely. MER has continued to operate for over two Earth-years as many of its key personnel have moved on to other projects, the operations team and budget have shrunk, and the rovers have begun to exhibit symptoms of aging.
The Development of New Atmospheric Models for K and M DwarfStars with Exoplanets

Science.gov (United States)

Linsky, Jeffrey L.

2018-01-01

The ultraviolet and X-ray emissions of host stars play critical roles in the survival and chemical composition of the atmospheres of their exoplanets. The need to measure and understand this radiative output, in particular for K and M dwarfs, is the main rationale for computing a new generation of stellar models that includes magnetically heated chromospheres and coronae in addition to their photospheres. We describe our method for computing semi-empirical models that includes solutions of the statistical equilibrium equations for 52 atoms and ions and of the non-LTE radiative transfer equations for all important spectral lines. The code is an offspring of the Solar Radiation Physical Modelling system (SRPM) developed by Fontenla et al. (2007--2015) to compute one-dimensional models in hydrostatic equilibrium to fit high-resolution stellar X-ray to IR spectra. Also included are 20 diatomic molecules and their more than 2 million spectral lines. Our-proof-of-concept model is for the M1.5 V star GJ 832 (Fontenla et al. ApJ 830, 154 (2016)). We will fit the line fluxes and profiles of X-ray lines and continua observed by Chandra and XMM-Newton, UV lines observed by the COS and STIS instruments on HST (N V, C IV, Si IV, Si III, Mg II, C II, and O I), optical lines (including H$\\alpha$, Ca II, Na I), and continua. These models will allow us to compute extreme-UV spectra, which are unobservable but required to predict the hydrodynamic mass-loss rate from exoplanet atmospheres, and to predict panchromatic spectra of new exoplanet host stars discovered after the end of the HST mission.This work is supported by grant HST-GO-15038 from the Space Telescope Science Institute to the Univ. of Colorado
Towards a comprehensive X-ray approach for studying the photosynthetic manganese complex-XANES, K{alpha}/K{beta}/K{beta}-satellite emission lines, RIXS, and comparative computational approaches for selected model complexes

Energy Technology Data Exchange (ETDEWEB)

Zaharieva, I; Chernev, P; Risch, M; Gerencser, L; Haumann, M; Dau, H [Free University Berlin, FB Physik, Arnimallee 14, D-14195 Berlin (Germany); Berggren, G; Shevchenko, D; Anderlund, M [Dept. of Photochemistry and Molecular Science, Uppsala University, Box 523, S-751 20 Uppsala (Sweden); Weng, T C, E-mail: holger.dau@fu-berlin.d, E-mail: michael.haumann@fu-berlin.d [European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble Cedex (France)

2009-11-15

Advanced X-ray spectroscopy experiments can contribute to elucidation of the mechanism of water oxidation in biological (tetra-manganese complex of Photosystem II) and artificial systems. Although the electronic structure of the catalytic metal site is of high interest, it is experimentally not easily accessible. Therefore, we and other researchers are working towards a comprehensive approach involving a combination of methods, namely (1) quantitative analysis of X-ray absorption near-edge structure (XANES) spectra collected at the K-edge and, in the long run, at the L-edge of manganese; (2) high-resolution X-ray emission spectroscopy (XES) of K{alpha} and K{beta} lines, (3) two-dimensional resonant inelastic X-ray scattering (RIXS) spectra. Collection of these spectroscopic data sets requires state-of-the-art synchrotron radiation facilities as well as experimental strategies to minimize the radiation-induced modifications of the samples. Data analysis requires the use and development of appropriate theoretical tools. Here, we present exemplary data collected for three multi-nuclear synthetic Mn complexes with the Mn ions in the oxidation states II, III, and IV, and for Mn{sup VII} of the permanganate ion. Emission spectra are calculated for the Mn{sup VII} ion using both multiple-scattering (MS) approach and time-dependent density functional theory (TDDFT).
Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV: a systematic review and meta-analysis

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Alaa Badawi

2016-08-01

Full Text Available The Middle East respiratory syndrome coronavirus (MERS-CoV is associated with life-threatening severe illnesses and a mortality rate of approximately 35%, particularly in patients with underlying comorbidities. A systematic analysis of 637 MERS-CoV cases suggests that diabetes and hypertension are equally prevalent in approximately 50% of the patients. Cardiac diseases are present in 30% and obesity in 16% of the cases. These conditions down-regulate the synthesis of proinflammatory cytokines and impair the host's innate and humoral immune systems. In conclusion, protection against MERS-CoV and other respiratory infections can be improved if public health vaccination strategies are tailored to target persons with chronic disorders.
Moessbauer spectra of some complex compounds of Fe(II) with pyridine

International Nuclear Information System (INIS)

Teodorescu, M.; Filoti, G.

1975-01-01

The Moessbauer spectra of [Fe(II)py 6 ]Br 2 at 298 and 80 K and the reflectance spectra of the same compound at room temperature are presented. Isomer shift and quadrupole splitting were determined for [Fe(II)py 6 ]Br 2 at 298 and 80 K, their values being correlated with those obtained from electronic spectra measured in the solid state. (Z.S.)
Variable selection based on clustering analysis for improvement of polyphenols prediction in green tea using synchronous fluorescence spectra

Science.gov (United States)

Shan, Jiajia; Wang, Xue; Zhou, Hao; Han, Shuqing; Riza, Dimas Firmanda Al; Kondo, Naoshi

2018-04-01

Synchronous fluorescence spectra, combined with multivariate analysis were used to predict flavonoids content in green tea rapidly and nondestructively. This paper presented a new and efficient spectral intervals selection method called clustering based partial least square (CL-PLS), which selected informative wavelengths by combining clustering concept and partial least square (PLS) methods to improve models’ performance by synchronous fluorescence spectra. The fluorescence spectra of tea samples were obtained and k-means and kohonen-self organizing map clustering algorithms were carried out to cluster full spectra into several clusters, and sub-PLS regression model was developed on each cluster. Finally, CL-PLS models consisting of gradually selected clusters were built. Correlation coefficient (R) was used to evaluate the effect on prediction performance of PLS models. In addition, variable influence on projection partial least square (VIP-PLS), selectivity ratio partial least square (SR-PLS), interval partial least square (iPLS) models and full spectra PLS model were investigated and the results were compared. The results showed that CL-PLS presented the best result for flavonoids prediction using synchronous fluorescence spectra.
Estimation des caractéristiques biologiques des truites de mer adultes (Salmo trutta du Rhin supérieur

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OMBREDANE D.

1998-07-01

Full Text Available L'analyse des longueurs totales et des écailles d'un échantillon de 120 truites de mer adultes capturées essentiellement par pêche à l'électricité dans le Rhin supérieur (700 km de la mer du Nord de 1989 à 1996 a permis de caractériser la population de cette ressource piscicole en voie de restauration. L'utilisation des Captures Par Unité d'Effort (CPUE, calculées pour les pêches de 1994 à 1996, permet d'appréhender le rythme de migration et d'améliorer l'estimation des caractéristiques générales de la population. Dans cette partie du Rhin, la migration anadrome de la truite de mer se déroule en deux pics successifs de juin à décembre, les individus les plus âgés arrivant les premiers. La population est caractérisée par une très forte prédominance des groupes d'âge de mer 1 + (49,2 % et 2+ (45,8 %, soit un Age Moyen de Mer (AMM de 1,54 an. L'Age Moyen de Smoltification (AMS et de première Reproduction (AMR sont estimés respectivement à 1,30 an et 1,39 an. Par ailleurs, il est constaté que l'âge marin de première maturité des adultes du Rhin augmente quand leur âge de smoltification diminue. Les résultats sont discutés en fonction de la méthodologie employée et comparés à ceux obtenus sur d'autres populations françaises et plus nordiques. Il ressort que les caractéristiques de la population de truite de mer du Rhin traduisent bien la position latitudinale mais aussi l'importance de ce réseau hydrographique.
Duality between SU(N)k and SU(k)N WZW models

International Nuclear Information System (INIS)

Naculich, S.G.; Schnitzer, H.J.

1990-01-01

We exhibit a duality of the SU(N) k WZW model under interchange of the group parameter N and the level k. The primary fields of SU(N) k and SU(k) N are related by transposition of their associated Young tableaux. The holomorphic blocks of the four-point functions of the primary fields are in one-to-one correspondence, and satisfy orthogonality and completeness relations with respect to one another. We derive these relations through a path integral realization of the SU(N) k WZW model in terms of a theory of constrained Dirac fermions. (orig.)

High proportion of MERS-CoV shedding dromedaries at slaughterhouse with a potential epidemiological link to human cases, Qatar 2014

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Elmoubasher A. B. A. Farag

2015-07-01

Full Text Available Two of the earliest Middle East respiratory syndrome (MERS cases were men who had visited the Doha central animal market and adjoining slaughterhouse in Qatar. We show that a high proportion of camels presenting for slaughter in Qatar show evidence for nasal MERS-CoV shedding (62/105. Sequence analysis showed the circulation of at least five different virus strains at these premises, suggesting that this location is a driver of MERS-CoV circulation and a high-risk area for human exposure. No correlation between RNA loads and levels of neutralizing antibodies was observed, suggesting limited immune protection and potential for reinfection despite previous exposure.
Overexpression of a bacterial mercury transporter MerT in Arabidopsis enhances mercury tolerance.

Science.gov (United States)

Xu, Sheng; Sun, Bin; Wang, Rong; He, Jia; Xia, Bing; Xue, Yong; Wang, Ren

2017-08-19

The phytoremediation by using of green plants in the removal of environmental pollutant is an environment friendly, green technology that is cost effective and energetically inexpensive. By using Agrobacterium-mediated gene transfer, we generated transgenic Arabidopsis plants ectopically expressing mercuric transport protein gene (merT) from Pseudomonas alcaligenes. Compared with wild-type (WT) plants, overexpressing PamerT in Arabidopsis enhanced the tolerance to HgCl 2 . Further results showed that the enhanced total activities or corresponding transcripts of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT) and guaiacol peroxidase (POD) were observed in transgenic Arabidopsis under HgCl 2 stress. These results were confirmed by the alleviation of oxidative damage, as indicated by the decrease of thiobarbituric acid reactive substances (TBARS) contents and reactive oxygen species (ROS) accumulation. In addition, localization analysis of PaMerT in Arabidopsis protoplast showed that it is likely to be associated with vacuole. In all, PamerT increased mercury (Hg) tolerance in transgenic Arabidopsis, and decreased production of Hg-induced ROS, thereby protecting plants from oxidative damage. The present study has provided further evidence that bacterial MerT plays an important role in the plant tolerance to HgCl 2 and in reducing the production of ROS induced by HgCl 2 . Copyright © 2017 Elsevier Inc. All rights reserved.
Modeling degradation in SOEC impedance spectra

DEFF Research Database (Denmark)

Jensen, Søren Højgaard; Hauch, Anne; Knibbe, Ruth

2013-01-01

Solid oxide cell (SOC) performance is limited by various processes. One way to investigate these processes is by electrochemical impedance spectroscopy. In order to quantify and characterize the processes, an equivalent circuit can be used to model the SOC impedance spectra (IS). Unfortunately......, the optimal equivalent circuit is often unknown and to complicate matters further, several processes contribute to the SOC impedance - making detailed process characterization difficult. In this work we analyze and model a series of IS measured during steam electrolysis operation of an SOC. During testing......, degradation is only observed in the Ni/YSZ electrode and not in the electrolyte or the LSM/YSZ electrode. A batch fit of the differences between the IS shows that a modified Gerischer element provides a better fit to the Ni/YSZ electrode impedance than the frequently used RQ element - albeit neither...
Application of class-modelling techniques to infrared spectra for analysis of pork adulteration in beef jerkys.

Science.gov (United States)

Kuswandi, Bambang; Putri, Fitra Karima; Gani, Agus Abdul; Ahmad, Musa

2015-12-01

The use of chemometrics to analyse infrared spectra to predict pork adulteration in the beef jerky (dendeng) was explored. In the first step, the analysis of pork in the beef jerky formulation was conducted by blending the beef jerky with pork at 5-80 % levels. Then, they were powdered and classified into training set and test set. The second step, the spectra of the two sets was recorded by Fourier Transform Infrared (FTIR) spectroscopy using atenuated total reflection (ATR) cell on the basis of spectral data at frequency region 4000-700 cm(-1). The spectra was categorised into four data sets, i.e. (a) spectra in the whole region as data set 1; (b) spectra in the fingerprint region (1500-600 cm(-1)) as data set 2; (c) spectra in the whole region with treatment as data set 3; and (d) spectra in the fingerprint region with treatment as data set 4. The third step, the chemometric analysis were employed using three class-modelling techniques (i.e. LDA, SIMCA, and SVM) toward the data sets. Finally, the best result of the models towards the data sets on the adulteration analysis of the samples were selected and the best model was compared with the ELISA method. From the chemometric results, the LDA model on the data set 1 was found to be the best model, since it could classify and predict 100 % accuracy of the sample tested. The LDA model was applied toward the real samples of the beef jerky marketed in Jember, and the results showed that the LDA model developed was in good agreement with the ELISA method.
The sub-bandgap energy loss satellites in the RIXS spectra of beryllium compounds

International Nuclear Information System (INIS)

Kuusik, I.; Kaeaembre, T.; Kooser, K.; Pustovarov, V.; Ivanov, V.; Kukk, E.; Kikas, A.

2011-01-01

Research highlights: → Be 1s RIXS spectra have been measured in Be containing crystals phenakite and chrysoberyl. → A strong energy loss sideband to the elastic scattering peak similar to BeO is found in both minerals. → Additionally the Si 2p RIXS spectra of phenakite also show a strong energy loss sideband to the elastic scattering peak. → The energy loss shoulder appears to result from lattice relaxation in the absorption site. - Abstract: Resonant X-ray inelastic scattering spectra have been measured in BeO, phenakite (Be 2 SiO 4 ) and chrysoberyl (BeAl 2 O 4 ) with the excitation energy near the beryllium K edge. The RIXS spectra excited in the vicinity of the Be 1s core resonance show two principal features: the scattering on a valence excitation (which at higher excitation energies verges into the characteristic K α emission), and a remarkably strong energy loss sideband to the elastic scattering peak. The energy loss shoulder appears to result from lattice relaxation in the absorption site. The comparison of the RIXS spectra of phenakite, chrysoberyl and BeO shows that the strength of the low energy sideband differs greatly; it is strongest in BeO and weakest in phenakite. The Si 2p RIXS spectra of phenakite also display a similar strong sub-bandgap energy loss tail. To gain further insight to this process, transitions in a system with a single vibrational mode have been modelled. The phonon relaxation has been simulated empirically by 'smearing' the photoabsortion-populated vibrational levels with lower levels. This simple model is able to qualitatively explain this wide energy loss shoulder.
The sub-bandgap energy loss satellites in the RIXS spectra of beryllium compounds

Energy Technology Data Exchange (ETDEWEB)

Kuusik, I., E-mail: ivar@fi.tartu.ee [Institute of Physics, University of Tartu, Riia 142, 51014 Tartu (Estonia); Kaeaembre, T. [Institute of Physics, University of Tartu, Riia 142, 51014 Tartu (Estonia); Kooser, K. [Institute of Physics, University of Tartu, Riia 142, 51014 Tartu (Estonia); Department of Physics and Astronomy, University of Turku, Turku (Finland); Pustovarov, V.; Ivanov, V. [Ural State Technical University-UPI, Yekaterinburg (Russian Federation); Kukk, E. [Department of Physics and Astronomy, University of Turku, Turku (Finland); Kikas, A. [Institute of Physics, University of Tartu, Riia 142, 51014 Tartu (Estonia)

2011-07-15

Research highlights: {yields} Be 1s RIXS spectra have been measured in Be containing crystals phenakite and chrysoberyl. {yields} A strong energy loss sideband to the elastic scattering peak similar to BeO is found in both minerals. {yields} Additionally the Si 2p RIXS spectra of phenakite also show a strong energy loss sideband to the elastic scattering peak. {yields} The energy loss shoulder appears to result from lattice relaxation in the absorption site. - Abstract: Resonant X-ray inelastic scattering spectra have been measured in BeO, phenakite (Be{sub 2}SiO{sub 4}) and chrysoberyl (BeAl{sub 2}O{sub 4}) with the excitation energy near the beryllium K edge. The RIXS spectra excited in the vicinity of the Be 1s core resonance show two principal features: the scattering on a valence excitation (which at higher excitation energies verges into the characteristic K{sub {alpha}} emission), and a remarkably strong energy loss sideband to the elastic scattering peak. The energy loss shoulder appears to result from lattice relaxation in the absorption site. The comparison of the RIXS spectra of phenakite, chrysoberyl and BeO shows that the strength of the low energy sideband differs greatly; it is strongest in BeO and weakest in phenakite. The Si 2p RIXS spectra of phenakite also display a similar strong sub-bandgap energy loss tail. To gain further insight to this process, transitions in a system with a single vibrational mode have been modelled. The phonon relaxation has been simulated empirically by 'smearing' the photoabsortion-populated vibrational levels with lower levels. This simple model is able to qualitatively explain this wide energy loss shoulder.
Novel chimeric virus-like particles vaccine displaying MERS-CoV receptor-binding domain induce specific humoral and cellular immune response in mice.

Science.gov (United States)

Wang, Chong; Zheng, Xuexing; Gai, Weiwei; Wong, Gary; Wang, Hualei; Jin, Hongli; Feng, Na; Zhao, Yongkun; Zhang, Weijiao; Li, Nan; Zhao, Guoxing; Li, Junfu; Yan, Jinghua; Gao, Yuwei; Hu, Guixue; Yang, Songtao; Xia, Xianzhu

2017-04-01

Middle East respiratory syndrome coronavirus (MERS-CoV) has continued spreading since its emergence in 2012 with a mortality rate of 35.6%, and is a potential pandemic threat. Prophylactics and therapies are urgently needed to address this public health problem. We report here the efficacy of a vaccine consisting of chimeric virus-like particles (VLP) expressing the receptor binding domain (RBD) of MERS-CoV. In this study, a fusion of the canine parvovirus (CPV) VP2 structural protein gene with the RBD of MERS-CoV can self-assemble into chimeric, spherical VLP (sVLP). sVLP retained certain parvovirus characteristics, such as the ability to agglutinate pig erythrocytes, and structural morphology similar to CPV virions. Immunization with sVLP induced RBD-specific humoral and cellular immune responses in mice. sVLP-specific antisera from these animals were able to prevent pseudotyped MERS-CoV entry into susceptible cells, with neutralizing antibody titers reaching 1: 320. IFN-γ, IL-4 and IL-2 secreting cells induced by the RBD were detected in the splenocytes of vaccinated mice by ELISpot. Furthermore, mice inoculated with sVLP or an adjuvanted sVLP vaccine elicited T-helper 1 (Th1) and T-helper 2 (Th2) cell-mediated immunity. Our study demonstrates that sVLP displaying the RBD of MERS-CoV are promising prophylactic candidates against MERS-CoV in a potential outbreak situation. Copyright © 2017 Elsevier B.V. All rights reserved.
Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis.

Science.gov (United States)

Badawi, Alaa; Ryoo, Seung Gwan

2016-08-01

The Middle East respiratory syndrome coronavirus (MERS-CoV) is associated with life-threatening severe illnesses and a mortality rate of approximately 35%, particularly in patients with underlying comorbidities. A systematic analysis of 637 MERS-CoV cases suggests that diabetes and hypertension are equally prevalent in approximately 50% of the patients. Cardiac diseases are present in 30% and obesity in 16% of the cases. These conditions down-regulate the synthesis of proinflammatory cytokines and impair the host's innate and humoral immune systems. In conclusion, protection against MERS-CoV and other respiratory infections can be improved if public health vaccination strategies are tailored to target persons with chronic disorders. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.
Reliable typing of MERS-CoV variants with a small genome fragment

NARCIS (Netherlands)

S.L. Smits (Saskia); V.S. Raj (Stalin); S.D. Pas (Suzan); C.B.E.M. Reusken (Chantal); K.A. Mohran (Khaled A.); E. Farag (Elmoubasher); H.E. Al Romaihi (Hamad); M.M. AlHajri (Mohd); B.L. Haagmans (Bart); M.P.G. Koopmans D.V.M. (Marion)

2015-01-01

textabstractBackground: Middle East Respiratory Syndrome coronavirus (. MERS-CoV) is an emerging pathogen that causes lower respiratory tract infection in humans. Camels are the likely animal source for zoonotic infection, although exact transmission modes remain to be determined. Human-to-human
K3 projective models in scrolls

CERN Document Server

Johnsen, Trygve

2004-01-01

The exposition studies projective models of K3 surfaces whose hyperplane sections are non-Clifford general curves. These models are contained in rational normal scrolls. The exposition supplements standard descriptions of models of general K3 surfaces in projective spaces of low dimension, and leads to a classification of K3 surfaces in projective spaces of dimension at most 10. The authors bring further the ideas in Saint-Donat's classical article from 1974, lifting results from canonical curves to K3 surfaces and incorporating much of the Brill-Noether theory of curves and theory of syzygies developed in the mean time.
The geometric content of the interacting boson model for molecular spectra

International Nuclear Information System (INIS)

Levit, S.; Smilansky, U.

1981-12-01

The recently proposed algebraic model for collective spectra of diatomic molecules is analysed in terms of conventional geometrical degrees of freedom. We present a mapping of the algebraic Hamiltonian onto an exactly solvable geometrical Hamiltonian with the Morse potential. This mapping explains the success of the algebraic model in reproducing the low lying part of molecular spectra. At the same time the mapping shows that the expression for the dipole transition operator in terms of boson operators differs from the simplest IBM expression and in general must include many-body boson terms. The study also provides an insight into the problem of possible interpretations of the bosons in the nuclear IBM. (author)
Non-LTE Stellar Population Synthesis of Globular Clusters Using Synthetic Integrated Light Spectra. I. Constructing the IL Spectra

Science.gov (United States)

Young, Mitchell. E.; Short, C. Ian

2017-02-01

We present an investigation of the globular cluster population synthesis method of McWilliam & Bernstein, focusing on the impact of non-LTE (NLTE) modeling effects and color-magnitude diagram (CMD) discretization. Johnson-Cousins-Bessel U - B, B-V, V-I, and J-K colors are produced for 96 synthetic integrated light (IL) spectra with two different discretization prescriptions and three degrees of NLTE treatment. These color values are used to compare NLTE- and LTE-derived population ages. Relative contributions of different spectral types to the IL spectra for different wavebands are measured. IL NLTE spectra are shown to be more luminous in the UV and optical than LTE spectra, but show stronger absorption features in the IR. The main features showing discrepancies between NLTE and LTE IL spectra may be attributed to light metals, primarily Fe I, Ca I, and Ti I, as well as TiO molecular bands. Main-sequence stars are shown to have negligible NLTE effects at IR wavelengths compared to more evolved stars. Photometric color values are shown to vary at the millimagnitude level as a function of CMD discretization. Finer CMD sampling for the upper main sequence and turnoff, base of the red giant branch, and the horizontal branch minimizes this variation. Differences in ages derived from LTE and NLTE IL spectra are found to range from 0.55 to 2.54 Gyr, comparable to the uncertainty in GC ages derived from color indices with observational uncertainties of 0.01 mag, the limiting precision of the Harris catalog.
Slip heterogeneity, body-wave spectra, and directivity of earthquake ruptures

OpenAIRE

Bernard, P.; Herrero, A.

1994-01-01

We present a broadband kinematic model based on a self-similar k-square distribution of the coseismic slip, with an instantaneous rise-time and a constant rupture velocity. The phase of the slip spectrum at high wave number is random. This model generates an ?-squared body-wave radiation, and a particular directivity factor C2d scaling the amplitude of the body-wave spectra, where Cd is the standard directivity factor. Considering the source models with a propagating pulse and a finite rise-t...
Antibodies against MERS coronavirus in dromedaries, United Arab Emirates, 2003 and 2013

NARCIS (Netherlands)

Meyer, Benjamin; Müller, Marcel A.; Corman, Victor M.; Reusken, Chantal B E M; Ritz, Daniel; Godeke, Gert Jan; Lattwein, Erik; Kallies, Stephan; Siemens, Artem; van Beek, Janko; Drexler, Jan F.; Muth, Doreen; Bosch, Berend Jan; Wernery, Ulrich; Koopmans, Marion P G; Wernery, Renate; Drosten, Christian

2014-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) has caused an ongoing outbreak of severe acute respiratory tract infection in humans in the Arabian Peninsula since 2012. Dromedary camels have been implicated as possible viral reservoirs. We used serologic assays to analyze 651 dromedary
The clinical and virological features of the first imported case causing MERS-CoV outbreak in South Korea, 2015.

Science.gov (United States)

Lee, Ji Yeon; Kim, You-Jin; Chung, Eun Hee; Kim, Dae-Won; Jeong, Ina; Kim, Yeonjae; Yun, Mi-Ran; Kim, Sung Soon; Kim, Gayeon; Joh, Joon-Sung

2017-07-14

In 2015, the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection outside the Middle East occurred in South Korea. We summarized the epidemiological, clinical, and laboratory findings of the first Korean case of MERS-CoV and analyzed whole-genome sequences of MERS-CoV derived from the patient. A 68-year-old man developed fever and myalgia 7 days after returning to Korea, following a 10-day trip to the Middle East. Before diagnosis, he visited 4 hospitals, potentially resulting in secondary transmission to 28 patients. On admission to the National Medical Center (day 9, post-onset of clinical illness), he presented with drowsiness, hypoxia, and multiple patchy infiltrations on the chest radiograph. He was intubated (day 12) because of progressive acute respiratory distress syndrome (ARDS) and INF-α2a and ribavirin treatment was commenced. The treatment course was prolonged by superimposed ventilator associated pneumonia. MERS-CoV PCR results converted to negative from day 47 and the patient was discharged (day 137), following rehabilitation therapy. The complete genome sequence obtained from a sputum sample (taken on day 11) showed the highest sequence similarity (99.59%) with the virus from an outbreak in Riyadh, Saudi Arabia, in February 2015. The first case of MERS-CoV infection had high transmissibility and was associated with a severe clinical course. The patient made a successful recovery after early treatment with antiviral agents and adequate supportive care. This first case in South Korea became a super-spreader because of improper infection control measures, rather than variations of the virus.
Quark-antiquark annihilation and small psub(T) inclusive spectra

International Nuclear Information System (INIS)

Nandi, S.; Rittenberg, V.; Schneider, H.R.

1977-07-01

Assuming that only a part of the valence quarks contributes to the fusion process and that the amount of charmed quarks in the sea of the hadrons is one fifth, that of the strange quarks one half of the usual quarks, the fusion model provides a quantitative and consistent description of the inclusive vector meson spectra in γ, π, K and p initiated processes. For pseudoscalar meson production, the model gives only a fair approximation to the data in proton induced reactions. (orig.) [de
Sci—Thur AM: YIS - 09: Validation of a General Empirically-Based Beam Model for kV X-ray Sources

Energy Technology Data Exchange (ETDEWEB)

Poirier, Y. [CancerCare Manitoba (Canada); University of Calgary (Canada); Sommerville, M.; Johnstone, C.D. [San Diego State University (United States); Gräfe, J.; Nygren, I.; Jacso, F. [Tom Baker Cancer Centre (Canada); Khan, R.; Villareal-Barajas, J.E. [University of Calgary (Canada); Tom Baker Cancer Centre (Canada); Tambasco, M. [University of Calgary (Canada); San Diego State University (United States)

2014-08-15

Purpose: To present an empirically-based beam model for computing dose deposited by kilovoltage (kV) x-rays and validate it for radiographic, CT, CBCT, superficial, and orthovoltage kV sources. Method and Materials: We modeled a wide variety of imaging (radiographic, CT, CBCT) and therapeutic (superficial, orthovoltage) kV x-ray sources. The model characterizes spatial variations of the fluence and spectrum independently. The spectrum is derived by matching measured values of the half value layer (HVL) and nominal peak potential (kVp) to computationally-derived spectra while the fluence is derived from in-air relative dose measurements. This model relies only on empirical values and requires no knowledge of proprietary source specifications or other theoretical aspects of the kV x-ray source. To validate the model, we compared measured doses to values computed using our previously validated in-house kV dose computation software, kVDoseCalc. The dose was measured in homogeneous and anthropomorphic phantoms using ionization chambers and LiF thermoluminescent detectors (TLDs), respectively. Results: The maximum difference between measured and computed dose measurements was within 2.6%, 3.6%, 2.0%, 4.8%, and 4.0% for the modeled radiographic, CT, CBCT, superficial, and the orthovoltage sources, respectively. In the anthropomorphic phantom, the computed CBCT dose generally agreed with TLD measurements, with an average difference and standard deviation ranging from 2.4 ± 6.0% to 5.7 ± 10.3% depending on the imaging technique. Most (42/62) measured TLD doses were within 10% of computed values. Conclusions: The proposed model can be used to accurately characterize a wide variety of kV x-ray sources using only empirical values.
Spin-polarized x-ray emission of 3d transition-metal ions : A comparison via K alpha and K beta detection

NARCIS (Netherlands)

Wang, Xin; deGroot, F.M.F.; Cramer, SP

1997-01-01

This paper demonstrates that spin-polarized x-ray-excitation spectra can be obtained using K alpha emission as well as K beta lines. A spin-polarized analysis of K alpha x-ray emission and the excitation spectra by K alpha detection on a Ni compound is reported. A systematic analysis of the
Time-resolved resonance Raman spectroscopy of intermediates of bacteriorhodopsin: The bK(590) intermediate.

Science.gov (United States)

Terner, J; Hsieh, C L; Burns, A R; El-Sayed, M A

1979-07-01

We have combined microbeam and flow techniques with computer subtraction methods to obtain the resonance Raman spectrum of the short lived batho-intermediate (bK(590)) of bacteriorhodopsin. Comparison of the spectra obtained in (1)H(2)O and (2)H(2)O, as well as the fact that the bK(590) intermediate shows large optical red shifts, suggests that the Schiff base linkage of this intermediate is protonated. The fingerprint region of the spectrum of bK(590), sensitive to the isomeric configuration of the retinal chromophore, does not resemble the corresponding region of the parent bR(570) form. The resonance Raman spectrum of bK(590) as well as the spectra of all of the other main intermediates in the photoreaction cycle of bacteriorhodopsin are discussed and compared with resonance Raman spectra of published model compounds.
An Inverse Modeling Approach to Estimating Phytoplankton Pigment Concentrations from Phytoplankton Absorption Spectra

Science.gov (United States)

Moisan, John R.; Moisan, Tiffany A. H.; Linkswiler, Matthew A.

2011-01-01

Phytoplankton absorption spectra and High-Performance Liquid Chromatography (HPLC) pigment observations from the Eastern U.S. and global observations from NASA's SeaBASS archive are used in a linear inverse calculation to extract pigment-specific absorption spectra. Using these pigment-specific absorption spectra to reconstruct the phytoplankton absorption spectra results in high correlations at all visible wavelengths (r(sup 2) from 0.83 to 0.98), and linear regressions (slopes ranging from 0.8 to 1.1). Higher correlations (r(sup 2) from 0.75 to 1.00) are obtained in the visible portion of the spectra when the total phytoplankton absorption spectra are unpackaged by multiplying the entire spectra by a factor that sets the total absorption at 675 nm to that expected from absorption spectra reconstruction using measured pigment concentrations and laboratory-derived pigment-specific absorption spectra. The derived pigment-specific absorption spectra were further used with the total phytoplankton absorption spectra in a second linear inverse calculation to estimate the various phytoplankton HPLC pigments. A comparison between the estimated and measured pigment concentrations for the 18 pigment fields showed good correlations (r(sup 2) greater than 0.5) for 7 pigments and very good correlations (r(sup 2) greater than 0.7) for chlorophyll a and fucoxanthin. Higher correlations result when the analysis is carried out at more local geographic scales. The ability to estimate phytoplankton pigments using pigment-specific absorption spectra is critical for using hyperspectral inverse models to retrieve phytoplankton pigment concentrations and other Inherent Optical Properties (IOPs) from passive remote sensing observations.

Sero-prevalence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) specific antibodies in Dromedary Camels in Tabuk, Saudi Arabia.

Science.gov (United States)

Harrath, Rafik; Duhier, Faisel M Abu

2018-04-16

The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a novel Coronavirus which was responsible of the first case of human acute respiratory syndrome in the Kingdom of Saudi Arabia (KSA), 2012. Dromedary camels are considered as potential reservoirs for the virus and seem to be the only animal host which may transmit the infection to human. Further studies are required to better understand the animal sources of zoonotic transmission route and the risks of this infection. A primary sero-prevalence study of MERS-CoV preexisting neutralizing antibodies in Dromedary camel serum was conducted in Tabuk, western north region of KSA, in order to assess the seopositivity of these animals and to explain their possible role in the transmission of the infection to Human. One hundred seventy one (171) serum samples were collected from healthy dromedary camels with different ages and genders in Tabuk city and tested for specific serum IgG by ELISA using the receptor-binding S1 subunits of spike proteins of MERS-CoV. 144 (84,21%) of the total camel sera shown the presence of protein-specific antibodies against MERS-CoV. These results may provide evidence that MERS-CoV has previously infected dromedary camels in Tabuk and may support the possible role of camels in the human infection. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
The TAM-family receptor Mer mediates production of HGF through the RhoA-dependent pathway in response to apoptotic cells.

Science.gov (United States)

Park, Hyun-Jung; Baen, Ji-Yeon; Lee, Ye-Ji; Choi, Youn-Hee; Kang, Jihee Lee

2012-08-01

The TAM receptor protein tyrosine kinases Tyro3, Axl, and Mer play important roles in macrophage function. We investigated the roles of the TAM receptors in mediating the induction of hepatocyte growth factor (HGF) during the interaction of macrophages with apoptotic cells. Mer-specific neutralizing antibody, small interfering RNA (siRNA), and a recombinant Mer protein (Mer/Fc) inhibited HGF mRNA and protein expression, as well as activation of RhoA, Akt, and specific mitogen-activated protein (MAP) kinases in response to apoptotic cells. Inhibition of Axl or Tyro3 with specific antibodies, siRNA, or Fc-fusion proteins did not prevent apoptotic cell-induced HGF mRNA and protein expression and did not inhibit activation of the postreceptor signaling molecules RhoA and certain MAP kinases, including extracellular signal-regulated protein kinase and c-Jun NH(2)-terminal kinase. However, Axl- and Tyro3-specific blockers did inhibit the activation of Akt and p38 MAP kinase in response to apoptotic cells. In addition, none of the TAM receptors mediated the effects of apoptotic cells on transforming growth factor-β or epidermal growth factor mRNA expression. However, they were involved in the induction of vascular endothelial growth factor mRNA expression. Our data provide evidence that when macrophages interact with apoptotic cells, only Mer of the TAM-family receptors is responsible for mediating transcriptional HGF production through a RhoA-dependent pathway.
Retrieving CO concentrations from FT-IR spectra with nonmodeled interferences and fluctuating baselines using PCR model parameters

DEFF Research Database (Denmark)

Bak, J.

2001-01-01

It is demonstrated that good predictions of gas concentrations based on measured spectra can be made even if these spectra contain totally overlapping spectral features from nonidentified and non-modeled interfering compounds and fluctuating baselines. The prediction program (CONTOUR) is based...... solely on principal component regression (PCR) model parameters, CONTOUR consists of two smaller algorithms. The first of these is used to calculate pure component spectra based on the PCR model parameters at different concentrations. In the second algorithm, the calculated pure component spectra...... remains. The assumptions are that the background and analytical signals must be additive and that no accidental match between these signals takes place. The best results are obtained with the use of spectra with a high selectivity. The use of the program is demonstrated hg applying simple single...
Excitation spectra of an effective d-wave model for cuprate superconductivity

NARCIS (Netherlands)

Yamaguchi, M; Ohta, Y; Eder, R

An exact-diagonalization technique on finite-size clusters is used to study the ground states and some excitation spectra of the two-dimensional effective Fermi-liquid model derived from numerical studies of the t-J model. We show that there is actually a reasonable range of parameter values where
Modelling of the anti-neutrino production and spectra from a Magnox reactor

Science.gov (United States)

Mills, Robert W.; Mountford, David J.; Coleman, Jonathon P.; Metelko, Carl; Murdoch, Matthew; Schnellbach, Yan-Jie

2018-01-01

The anti-neutrino source properties of a fission reactor are governed by the production and beta decay of the radionuclides present and the summation of their individual anti-neutrino spectra. The fission product radionuclide production changes during reactor operation and different fissioning species give rise to different product distributions. It is thus possible to determine some details of reactor operation, such as power, from the anti-neutrino emission to confirm safeguards records. Also according to some published calculations, it may be feasible to observe different anti-neutrino spectra depending on the fissile contents of the reactor fuel and thus determine the reactor's fissile material inventory during operation which could considerable improve safeguards. In mid-2014 the University of Liverpool deployed a prototype anti-neutrino detector at the Wylfa R1 station in Anglesey, United Kingdom based upon plastic scintillator technology developed for the T2K project. The deployment was used to develop the detector electronics and software until the reactor was finally shutdown in December 2015. To support the development of this detector technology for reactor monitoring and to understand its capabilities, the National Nuclear Laboratory modelled this graphite moderated and natural uranium fuelled reactor with existing codes used to support Magnox reactor operations and waste management. The 3D multi-physics code PANTHER was used to determine the individual powers of each fuel element (8×6152) during the year and a half period of monitoring based upon reactor records. The WIMS/TRAIL/FISPIN code route was then used to determine the radionuclide inventory of each nuclide on a daily basis in each element. These nuclide inventories were then used with the BTSPEC code to determine the anti-neutrino spectra and source strength using JEFF-3.1.1 data. Finally the anti-neutrino source from the reactor for each day during the year and a half of monitored reactor
Modelling of the anti-neutrino production and spectra from a Magnox reactor

Directory of Open Access Journals (Sweden)

Mills Robert W

2018-01-01

Full Text Available The anti-neutrino source properties of a fission reactor are governed by the production and beta decay of the radionuclides present and the summation of their individual anti-neutrino spectra. The fission product radionuclide production changes during reactor operation and different fissioning species give rise to different product distributions. It is thus possible to determine some details of reactor operation, such as power, from the anti-neutrino emission to confirm safeguards records. Also according to some published calculations, it may be feasible to observe different anti-neutrino spectra depending on the fissile contents of the reactor fuel and thus determine the reactor's fissile material inventory during operation which could considerable improve safeguards. In mid-2014 the University of Liverpool deployed a prototype anti-neutrino detector at the Wylfa R1 station in Anglesey, United Kingdom based upon plastic scintillator technology developed for the T2K project. The deployment was used to develop the detector electronics and software until the reactor was finally shutdown in December 2015. To support the development of this detector technology for reactor monitoring and to understand its capabilities, the National Nuclear Laboratory modelled this graphite moderated and natural uranium fuelled reactor with existing codes used to support Magnox reactor operations and waste management. The 3D multi-physics code PANTHER was used to determine the individual powers of each fuel element (8×6152 during the year and a half period of monitoring based upon reactor records. The WIMS/TRAIL/FISPIN code route was then used to determine the radionuclide inventory of each nuclide on a daily basis in each element. These nuclide inventories were then used with the BTSPEC code to determine the anti-neutrino spectra and source strength using JEFF-3.1.1 data. Finally the anti-neutrino source from the reactor for each day during the year and a half of
Observations on the Morphology, Pollination and Cultivation of Coco de Mer (Lodoicea maldivica (J F Gmel. Pers., Palmae

Directory of Open Access Journals (Sweden)

Stephen Blackmore

2012-01-01

Full Text Available We present a range of observations on the reproductive morphology, pollination biology and cultivation of Lodoicea maldivica (coco de mer, an endangered species with great ecological, economic and cultural importance. We review the history of study of this charismatic species. Morphological studies of the male inflorescence indicate its importance as a year-round food source to the Seychelles fauna. In situ observations suggest a number of potential biotic and abiotic pollination mechanisms including bees, flies, slugs, and geckos; trigonid bees are identified as the most likely potential natural pollinator. We outline a successful programme for ex situ pollination, germination, and cultivation of the coco de mer, highlighting the importance of temperature, humidity and light levels as well as maintaining an undisturbed environment. In combination with continued protection and monitoring, this advice may aid the future in situ and ex situ conservation of the coco de mer.
Behavior of lambda 2800 Mg II in stellar spectra

International Nuclear Information System (INIS)

Gurzadyan, G.A.

1975-01-01

The results of measurements of the equivalent widths of the resonance doublet of ionized magnesium lambda 2800 Mg II in the spectra of 51 relatively faint stars, up to 10/sup m/, of the spectral classes B1-K5 are presented. The observed material has been obtained by means of the space observatory ''Orion-2''. Some regularities in the behavior of lambda 2800 Mg II in stellar spectra have been revealed: wide and deep depression of the continuous spectra at 2800 A in F-G type stars; the presence of the doublet lambda 2800 Mg II in the form of weak emission in the spectra of cold stars (K2-K5); the presence both of the multiplet lambda 3080 Ti II and the doublet lambda 2800 Mg II simultaneously either in emission--in the late-type stars--or in absorption in earlier types; the existence of combined profiles of lambda 2800 Mg II, i.e., a wide absorption line with a weak emission in the center, in stars of the transitional class (G5-K0), etc. A well-defined empirical relationship between the equivalent width of lambda 2800 Mg II and the spectral class of the star has been established (Fig. 8). (U.S.)
The effects of general anesthetics on ESR spectra of spin labels in phosphatidylcholine vesicles containing purified Na,K-ATPase or microsomal protein

Energy Technology Data Exchange (ETDEWEB)

Shibuya, Makiko, E-mail: shibu@den.hokudai.ac.jp [Department of Dental Anesthesiology, Graduate School of Dental Medicine, Hokkaido University (Japan); Hiraoki, Toshifumi [Division of Applied Physics, Graduate School of Engineering, Hokkaido University (Japan); Kimura, Kunie; Fukushima, Kazuaki [Department of Dental Anesthesiology, Graduate School of Dental Medicine, Hokkaido University (Japan); Suzuki, Kuniaki [Department of Molecular Cell Pharmacology, Graduate School of Dental Medicine, Hokkaido University (Japan)

2012-12-01

Highlights: Black-Right-Pointing-Pointer We studied the effects of general anesthetics on liposome using ESR spectra. Black-Right-Pointing-Pointer Two spin labels, 5-DSA and 16-DSA, were located in different position in liposome. Black-Right-Pointing-Pointer Anesthetics did not change the environment around the spin labels in the liposome. Black-Right-Pointing-Pointer Anesthetics remained on the surface of the lipid bilayer of liposome. Black-Right-Pointing-Pointer Proteins in the liposome did not change the effects of anesthetics on liposome. - Abstract: We investigated the effects of general anesthetics on liposome containing spin labels, 5-doxyl stearic acid (5-DSA) and 16-doxyl stearic acid (16-DSA), and purified Na,K-ATPase or membrane protein of microsome using an electron spin resonance (ESR) spectroscopy. The spectra of 16-DSA in liposomes with both proteins showed three sharp signals compared with 5-DSA. The difference in the order parameter S value of 5-DSA and 16-DSA suggested that the nitroxide radical location of 5-DSA and 16-DSA were different in the membrane bilayer. The results were almost the same as those obtained in liposomes without proteins. The addition of sevoflurane, isoflurane, halothane, ether, ethanol and propofol increased the intensity of the signals, but the clinical concentrations of anesthetics did not significantly alter the S and {tau} values, which are indices of the fluidity of the membrane. These results suggest that anesthetics remain on the surface of the lipid bilayer and do not act on both the inside hydrophobic area and the relatively hydrophilic area near the surface. These results and others also suggest that the existence of Na,K-ATPase and microsomal proteins did not affect the environment around the spin labels in the liposome and the effects of anesthetics on liposome as a model membrane.
Energy spectra of vibron and cluster models in molecular and nuclear systems

Science.gov (United States)

Jalili Majarshin, A.; Sabri, H.; Jafarizadeh, M. A.

2018-03-01

The relation of the algebraic cluster model, i.e., of the vibron model and its extension, to the collective structure, is discussed. In the first section of the paper, we study the energy spectra of vibron model, for diatomic molecule then we derive the rotation-vibration spectrum of 2α, 3α and 4α configuration in the low-lying spectrum of 8Be, 12C and 16O nuclei. All vibrational and rotational states with ground and excited A, E and F states appear to have been observed, moreover the transitional descriptions of the vibron model and α-cluster model were considered by using an infinite-dimensional algebraic method based on the affine \\widehat{SU(1,1)} Lie algebra. The calculated energy spectra are compared with experimental data. Applications to the rotation-vibration spectrum for the diatomic molecule and many-body nuclear clusters indicate that there are solvable models and they can be approximated very well using the transitional theory.
CHARACTERIZING THE COOL KOIs. VI. H- AND K-BAND SPECTRA OF KEPLER M DWARF PLANET-CANDIDATE HOSTS

Energy Technology Data Exchange (ETDEWEB)

Muirhead, Philip S. [Department of Astronomy, Boston University, 725 Commonwealth Avenue, Boston, MA 02215 (United States); Becker, Juliette; Price, Ellen M.; Thorp, Rachel; Riddle, Reed [California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Feiden, Gregory A. [Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala (Sweden); Rojas-Ayala, Bárbara [Centro de Astrofísica da Universidade do Porto, Rua das Estrelas, 4150-762 Oporto (Portugal); Vanderburg, Andrew; Johnson, John Asher [Harvard College Observatory, 60 Garden Street, Cambridge, MA 02138 (United States); Law, Nicholas M. [Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3255 (United States); Baranec, Christoph [Institute for Astronomy, University of Hawai' i at Mānoa, Hilo, HI 96720-2700 (United States); Hamren, Katherine [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States); Schlawin, Everett; Lloyd, James P. [Department of Astronomy, Cornell University, Ithaca, NY 14583 (United States); Covey, Kevin R., E-mail: philipm@bu.edu [Lowell Observatory, 1400 W Mars Hill Road, Flagstaff, AZ 86001 (United States)

2014-07-01

We present H- and K-band spectra for late-type Kepler Objects of Interest (the {sup C}ool KOIs{sup )}: low-mass stars with transiting-planet candidates discovered by NASA's Kepler Mission that are listed on the NASA Exoplanet Archive. We acquired spectra of 103 Cool KOIs and used the indices and calibrations of Rojas-Ayala et al. to determine their spectral types, stellar effective temperatures, and metallicities, significantly augmenting previously published values. We interpolate our measured effective temperatures and metallicities onto evolutionary isochrones to determine stellar masses, radii, luminosities, and distances, assuming the stars have settled onto the main sequence. As a choice of isochrones, we use a new suite of Dartmouth predictions that reliably include mid-to-late M dwarf stars. We identify five M4V stars: KOI-961 (confirmed as Kepler 42), KOI-2704, KOI-2842, KOI-4290, and the secondary component to visual binary KOI-1725, which we call KOI-1725 B. We also identify a peculiar star, KOI-3497, which has Na and Ca lines consistent with a dwarf star but CO lines consistent with a giant. Visible-wavelength adaptive optics imaging reveals two objects within a 1 arcsec diameter; however, the objects' colors are peculiar. The spectra and properties presented in this paper serve as a resource for prioritizing follow-up observations and planet validation efforts for the Cool KOIs and are all available for download online using the ''data behind the figure'' feature.
Cross-sectional surveillance of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels and other mammals in Egypt, August 2015 to January 2016.

Science.gov (United States)

Ali, Mohamed; El-Shesheny, Rabeh; Kandeil, Ahmed; Shehata, Mahmoud; Elsokary, Basma; Gomaa, Mokhtar; Hassan, Naglaa; El Sayed, Ahmed; El-Taweel, Ahmed; Sobhy, Heba; Fasina, Folorunso Oludayo; Dauphin, Gwenaelle; El Masry, Ihab; Wolde, Abebe Wossene; Daszak, Peter; Miller, Maureen; VonDobschuetz, Sophie; Morzaria, Subhash; Lubroth, Juan; Makonnen, Yilma Jobre

2017-03-16

A cross-sectional study was conducted in Egypt to determine the prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in imported and resident camels and bats, as well as to assess possible transmission of the virus to domestic ruminants and equines. A total of 1,031 sera, 1,078 nasal swabs, 13 rectal swabs, and 38 milk samples were collected from 1,078 camels in different types of sites. In addition, 145 domestic animals and 109 bats were sampled. Overall, of 1,031 serologically-tested camels, 871 (84.5%) had MERS-CoV neutralising antibodies. Seroprevalence was significantly higher in imported (614/692; 88.7%) than resident camels (257/339; 5.8%) (p MERS-CoV seroprevalence (p MERS-CoV antibodies except one sheep sample which showed a 1:640 titre. Of 1,078 camels, 41 (3.8%) were positive for MERS-CoV genetic material. Sequences obtained were not found to cluster with clade A or B MERS-CoV sequences and were genetically diverse. The presence of neutralising antibodies in one sheep apparently in contact with seropositive camels calls for further studies on domestic animals in contact with camels. This article is copyright of The Authors, 2017.
DPW-VI Results Using FUN3D with Focus on k-kL-MEAH2015 (k-kL) Turbulence Model

Science.gov (United States)

Abdol-Hamid, K. S.; Carlson, Jan-Renee; Rumsey, Christopher L.; Lee-Rausch, Elizabeth M.; Park, Michael A.

2017-01-01

The Common Research Model wing-body configuration is investigated with the k-kL-MEAH2015 turbulence model implemented in FUN3D. This includes results presented at the Sixth Drag Prediction Workshop and additional results generated after the workshop with a nonlinear Quadratic Constitutive Relation (QCR) variant of the same turbulence model. The workshop provided grids are used, and a uniform grid refinement study is performed at the design condition. A large variation between results with and without a reconstruction limiter is exhibited on "medium" grid sizes, indicating that the medium grid size is too coarse for drawing conclusions in comparison with experiment. This variation is reduced with grid refinement. At a fixed angle of attack near design conditions, the QCR variant yielded decreased lift and drag compared with the linear eddy-viscosity model by an amount that was approximately constant with grid refinement. The k-kL-MEAH2015 turbulence model produced wing root junction flow behavior consistent with wind tunnel observations.
Neutron and photon spectra in LINACs

International Nuclear Information System (INIS)

Vega-Carrillo, H.R.; Martínez-Ovalle, S.A.; Lallena, A.M.; Mercado, G.A.; Benites-Rengifo, J.L.

2012-01-01

A Monte Carlo calculation, using the MCNPX code, was carried out in order to estimate the photon and neutron spectra in two locations of two linacs operating at 15 and 18 MV. Detailed models of both linac heads were used in the calculations. Spectra were estimated below the flattening filter and at the isocenter. Neutron spectra show two components due to evaporation and knock-on neutrons. Lethargy spectra under the filter were compared to the spectra calculated from the function quoted by Tosi et al. that describes reasonably well neutron spectra beyond 1 MeV, though tends to underestimate the energy region between 10 –6 and 1 MeV. Neutron and the Bremsstrahlung spectra show the same features regardless of the linac voltage. - Highlights: ► With MCNPX code realistic models of two LINACs were built. ► Photon and neutron spectra below the flattening filter and at the isocenter were calculated. ► Neutron spectrum at the flattening filter was compared against the Tosi et al. source-term model. ► Tosi et al. model underestimates the neutron contribution below 1 MeV. ► Photon spectra look alike to those published in literature.
USING LANDSAT IMAGES AND GIS TO ASSESS THE CHANGES OF MER DE GLACE AND MARMOLADA GLACIERS, IN THE LAST THREE DECADES

Directory of Open Access Journals (Sweden)

M. M. NISTOR

2014-06-01

Full Text Available Using Landsat Images and GIS to Assess the Changes of Mer de Glace and Marmolada Glaciers, in the Last Three Decades. We have demonstrated that Mer de Glace Glacier (GL and Marmolada GL are in continuous retreat. The changes in size and status of terminus points were estimated in various time intervals by satellite images (SIs and Geographic Information Systems (GIS techniques, during the last three decades. The aim of the research was to found the value of the ice melting areas of Mer de Glace GL and Marmolada GL and to calculate the decline rate for both GLs. A large number of GLs have lost ice mass all over the world. Often glaciologists monitor the GLs movements under climate changes and they express their opinions about the ocean level rise, ecosystem challenges and the future implications of GLs decline. The analysed information to quantify the Mer de Glace GL and Marmolada GL areas derived from SIs. By manual vectorization we obtained the outlines of GLs in different years. For 1984, 1999, 2013 we defined the limits for Mer de Glace GL and for 1986, 1999, 2013 we defined the limits for Marmolada GL. These vector layers were compared in order to observe the melting area and to establish the withdrawal rate. The first results indicate that Mer de Glace GL area declined by 2.365 km² between 1984 and 2013 and a mean melting rate of 0.082 km²/year was obtained. Marmolada GL decreased by 1.035 km² between 1986 and 2013 and a mean melting rate of 0.038 km²/year was calculated. We believe that these results represent significant quantitative data about GLs movements regarding two different areas in the Alps Range and may provide knowledge for hydrology, geomorphology and environmental sciences.
Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography

Energy Technology Data Exchange (ETDEWEB)

Paixao, L.; Oliveira, B. B.; Nogueira, M. do S. [Centro de Desenvolvimento da Tecnologia Nuclear, Post-graduation in Science and Technology of Radiations, Minerals and Materials, Pte. Antonio Carlos 6.627, Pampulha, 31270-901 Belo Horizonte (Brazil); Viloria, C. [UFMG, Departamento de Engenharia Nuclear, Post-graduation in Nuclear Sciences and Techniques, Pte. Antonio Carlos 6.627, Pampulha, 31270-901 Belo Horizonte (Brazil); Alves de O, M. [UFMG, Department of Anatomy and Imaging, Prof. Alfredo Balena 190, 30130-100 Belo Horizonte (Brazil); Araujo T, M. H., E-mail: lpr@cdtn.br [Dr Maria Helena Araujo Teixeira Clinic, Guajajaras 40, 30180-100 Belo Horizonte (Brazil)

2014-08-15

It is widely accepted that the mean glandular dose (D{sub G}) for the glandular tissue is the more useful magnitude for characterizing the breast cancer risk. The procedure to estimate the D{sub G}, for being difficult to measure it directly in the breast, it is to make the use of conversion factors that relate incident air kerma (K{sub i}) at this dose. Generally, the conversion factors vary with the x-ray spectrum half-value layer and the breast composition and thickness. Several authors through computer simulations have calculated such factors by the Monte Carlo (Mc) method. Many spectral models for D{sub G} computer simulations purposes are available in the diagnostic range. One of the models available generates unfiltered spectra. In this work, the Monte Carlo EGSnrc code package with the C++ class library (eg spp) was employed to derive filtered tungsten x-ray spectra used in digital mammography systems. Filtered spectra for rhodium and aluminium filters were obtained for tube potentials between 26 and 32 kV. The half-value layer of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F and Mam Detector Platinum and 8201023-C Xi Base unit Platinum Plus w m As in a Hologic Selenia Dimensions system using a Direct Radiography mode. Calculated half-value layer values showed good agreement compared to those obtained experimentally. These results show that the filtered tungsten anode x-ray spectra and the EGSnrc Mc code can be used for D{sub G} determination in mammography. (Author)
Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography

International Nuclear Information System (INIS)

Paixao, L.; Oliveira, B. B.; Nogueira, M. do S.; Viloria, C.; Alves de O, M.; Araujo T, M. H.

2014-08-01

It is widely accepted that the mean glandular dose (D G ) for the glandular tissue is the more useful magnitude for characterizing the breast cancer risk. The procedure to estimate the D G , for being difficult to measure it directly in the breast, it is to make the use of conversion factors that relate incident air kerma (K i ) at this dose. Generally, the conversion factors vary with the x-ray spectrum half-value layer and the breast composition and thickness. Several authors through computer simulations have calculated such factors by the Monte Carlo (Mc) method. Many spectral models for D G computer simulations purposes are available in the diagnostic range. One of the models available generates unfiltered spectra. In this work, the Monte Carlo EGSnrc code package with the C++ class library (eg spp) was employed to derive filtered tungsten x-ray spectra used in digital mammography systems. Filtered spectra for rhodium and aluminium filters were obtained for tube potentials between 26 and 32 kV. The half-value layer of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F and Mam Detector Platinum and 8201023-C Xi Base unit Platinum Plus w m As in a Hologic Selenia Dimensions system using a Direct Radiography mode. Calculated half-value layer values showed good agreement compared to those obtained experimentally. These results show that the filtered tungsten anode x-ray spectra and the EGSnrc Mc code can be used for D G determination in mammography. (Author)
Effect of the antiestrogen ethamoxytriphetol (MER-25) on placental low density lipoprotein uptake and degradation in baboons

International Nuclear Information System (INIS)

Henson, M.C.; Babischkin, J.S.; Pepe, G.J.; Albrecht, E.D.

1988-01-01

The present study determined if the decline in placental progesterone (P4) production that results from administration of the antiestrogen ethamoxytriphetol (MER-25) to pregnant baboons results from a change in placental low density lipoprotein (LDL) uptake and/or degradation. Pregnant baboons (Papio anubis) were untreated (n = 10) or received MER-25 (25 mg/kg BW, orally; n = 10) daily on days 140-170 of gestation (term, 184 days). Placentas were removed by cesarean section on day 170 of gestation, and villous tissue was dispersed with 0.1% collagenase at 37 C for 40 min. Placental cells (10(6)) were incubated in medium 199 (pH 7.2) for 12 h at 37 C with increasing amounts (5-100 micrograms) of [125I]LDL, with or without a 100-fold excess of unlabeled baboon LDL. Mean (+/- SE) peripheral serum P4 concentrations on days 140-170 of gestation were 51% lower (P less than 0.01) in MER-25-treated (5.7 +/- 0.3 ng/ml) than in untreated (11.6 +/- 0.5 ng/ml) baboons. The uptake of LDL was 56% lower (P less than 0.01) in placental cells from antiestrogen-treated (6.3 +/- 1.6 ng/micrograms cell protein) than in those from untreated (14.4 +/- 1.9 ng/micrograms cell protein) baboons. The dissociation constants for placental LDL uptake, as assessed by Scatchard analysis, however, were similar in untreated (0.80 microgram/ml) and MER-25-treated (0.76 microgram/ml) animals. The amount of [125I]LDL concomitantly degraded by cells from baboons that received MER-25 was 54% of that degraded by cells from untreated controls. The relative decline in LDL degradation by cells of antiestrogen-treated baboons was proportionate to the decline in overall LDL uptake. The results indicate, therefore, that antiestrogen treatment decreased the amount of placental LDL uptake, but did not change the affinity for the lipoprotein
Effect of the antiestrogen ethamoxytriphetol (MER-25) on placental low density lipoprotein uptake and degradation in baboons

Energy Technology Data Exchange (ETDEWEB)

Henson, M.C.; Babischkin, J.S.; Pepe, G.J.; Albrecht, E.D.

1988-05-01

The present study determined if the decline in placental progesterone (P4) production that results from administration of the antiestrogen ethamoxytriphetol (MER-25) to pregnant baboons results from a change in placental low density lipoprotein (LDL) uptake and/or degradation. Pregnant baboons (Papio anubis) were untreated (n = 10) or received MER-25 (25 mg/kg BW, orally; n = 10) daily on days 140-170 of gestation (term, 184 days). Placentas were removed by cesarean section on day 170 of gestation, and villous tissue was dispersed with 0.1% collagenase at 37 C for 40 min. Placental cells (10(6)) were incubated in medium 199 (pH 7.2) for 12 h at 37 C with increasing amounts (5-100 micrograms) of (125I)LDL, with or without a 100-fold excess of unlabeled baboon LDL. Mean (+/- SE) peripheral serum P4 concentrations on days 140-170 of gestation were 51% lower (P less than 0.01) in MER-25-treated (5.7 +/- 0.3 ng/ml) than in untreated (11.6 +/- 0.5 ng/ml) baboons. The uptake of LDL was 56% lower (P less than 0.01) in placental cells from antiestrogen-treated (6.3 +/- 1.6 ng/micrograms cell protein) than in those from untreated (14.4 +/- 1.9 ng/micrograms cell protein) baboons. The dissociation constants for placental LDL uptake, as assessed by Scatchard analysis, however, were similar in untreated (0.80 microgram/ml) and MER-25-treated (0.76 microgram/ml) animals. The amount of (125I)LDL concomitantly degraded by cells from baboons that received MER-25 was 54% of that degraded by cells from untreated controls. The relative decline in LDL degradation by cells of antiestrogen-treated baboons was proportionate to the decline in overall LDL uptake. The results indicate, therefore, that antiestrogen treatment decreased the amount of placental LDL uptake, but did not change the affinity for the lipoprotein.
Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV.

Directory of Open Access Journals (Sweden)

Sanchita Bhadra

Full Text Available The Middle East respiratory syndrome coronavirus (MERS-CoV, an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU (5 to 50 PFU/ml of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens.

Charge exchange recombination in X-ray spectra of He-like argon measured at the tokamak TEXTOR

Energy Technology Data Exchange (ETDEWEB)

Schlummer, Tobias

2014-06-16

Charge exchange recombination between ions and atomic hydrogen is an important atomic process in magnetically confined fusion plasmas. Besides radiative cooling of the plasma edge, charge exchange causes modifications of the ionization balance and the population densities of excited ion states. The central goal of this work is to investigate the influence of charge exchange on X-ray spectra measured at the tokamak TEXTOR. A new 2D X-ray spectrometer developed for future use at the stellarator W7-X was recently installed at TEXTOR. The spectrometer is optimized for measuring the K{sub α}-spectrum of He-like argon (1s2l - 1s{sup 2}) at wavelengths close to 4 Aa. K{sub α}-spectroscopy on He-like impurity ions is an established diagnostic for electron and ion temperature measurements in fusion plasmas. Still, up to now the observed intensity ratios of the K{sub α}-lines and their associated satellites are not fully understood. They show significant deviations from the predictions made by basic corona models. In the past charge exchange with the neutral particle background and radial impurity transport have been discussed as likely explanations. Yet a detailed description of the experimental spectra still has not been achieved. To reconstruct the 2D K{sub α}-spectra measured at TEXTOR the radial argon ion distribution is modeled using an impurity transport code. The model accounts for charge exchange and transport on basis of given radial profiles of the neutral particle density n{sub 0}(r) and the diffusion coefficient D {sub perpendicular} {sub to} (r). The theoretical spectrum is then constructed based on the processes relevant for line emission. Within an iterative procedure n{sub 0}(r) and D {sub perpendicular} {sub to} (r) are varied until consistency between the theoretical and the experimental spectra is achieved. It is shown that the 2D K{sub α}-spectra allow a clear distinction of charge exchange and transport effects, ensuring unique solutions for n
MERS-CoV: Middle East respiratory syndrome corona virus: Can radiology be of help? Initial single center experience

OpenAIRE

Hamimi, Ahmed

2016-01-01

Human infection with a novel coronavirus named Middle East respiratory syndrome coronavirus (MERS-CoV) was first identified in Saudi Arabia and the Middle East in September, 2012. The aim of this study was to establish the most pathognomonic radiological sign(s) to diagnose MERS CoV. Patients and methods: This is a retrospective descriptive study. All patients were subjected to serial X-ray. High resolution non-contrast CT chest was also obtained for 10 patients. The scans were reviewed fo...
Effects of quantum chemistry models for bound electrons on positron annihilation spectra for atoms and small molecules

International Nuclear Information System (INIS)

Wang Feng; Ma Xiaoguang; Selvam, Lalitha; Gribakin, Gleb; Surko, Clifford M

2012-01-01

The Doppler-shift spectra of the γ-rays from positron annihilation in molecules were determined by using the momentum distribution of the annihilation electron–positron pair. The effect of the positron wavefunction on spectra was analysed in a recent paper (Green et al 2012 New J. Phys. 14 035021). In this companion paper, we focus on the dominant contribution to the spectra, which arises from the momenta of the bound electrons. In particular, we use computational quantum chemistry models (Hartree–Fock with two basis sets and density functional theory (DFT)) to calculate the wavefunctions of the bound electrons. Numerical results are presented for noble gases and small molecules such as H 2 , N 2 , O 2 , CH 4 and CF 4 . The calculations reveal relatively small effects on the Doppler-shift spectra from the level of inclusion of electron correlation energy in the models. For atoms, the difference in the full-width at half-maximum of the spectra obtained using the Hartree–Fock and DFT models does not exceed 2%. For molecules the difference can be much larger, reaching 8% for some molecular orbitals. These results indicate that the predicted positron annihilation spectra for molecules are generally more sensitive to inclusion of electron correlation energies in the quantum chemistry model than the spectra for atoms are. (paper)
The high energy X-ray spectra of supernova remnants

Science.gov (United States)

Pravdo, S. H.; Nugent, J. J.

The results of fitting an ionization-nonequilibrium (INE) model to the high-energy (above 5-keV) X-ray spectra of the young supernova remnants Cas A and Tycho are presented. As an additional constraint, the models must simultaneously fit lower-energy, higher-resolution data. For Cas A, a single INE component cannot adequately reproduce the features for the entire X-ray spectrum because the ionization structure of iron ions responsible for the K emission is inconsistent with that of the ions responsible for the lower-energy lines, and the flux of the highest-energy X-rays is underestimated. The iron K line and the high-energy continuum could arise from the same INE component, but the identification of this component with either the blast wave or the ejecta in the standard model is difficult. In Tycho, the high-energy data rule out a class of models for the lower-energy data which have too large a continuum contribution.
Bridging the spectral divide: a case study with PAGES2k, the CESM Last Millennium Ensemble and proxy system models

Science.gov (United States)

Zhu, F.; Emile-Geay, J.; Ault, T.; McKay, N.; Dee, S.

2017-12-01

A grand challenge for paleoclimatology is to constrain climate model behavior on timescales longer than the instrumental record. Of particular interest is the spectrum of temperature as sensed by climate proxies. The "continuum" of climate variability [Huybers & Curry, Nature 2006] is often characterized by its scaling exponent β , where the spectral density S and the frequency f satisfy the power law S ∝ f-β . Recent studies have voiced concern that climate models underestimate scaling behavior compared to proxies [Laepple & Huybers, PNAS 2014]. Part of this discrepancy is known to lie in the complex processes whereby proxies transform climate signals [Dee et al, EPSL in press], yet many questions remain open. Here we leverage a recent multiproxy compilation [PAGES 2k Consortium, Sci Data 2017] to characterize scaling behavior over the Common Era using an interpolation-free method [Kirchner & Neal, PNAS 2013]. Proxy spectra are compared to spectra derived from the CESM Last Millennium Ensemble [Otto-Bliesner et al, BAMS 2016], using: (a) a naive model where proxies are assumed linearly related to annual temperature vs (b) proxy system models [Evans et al, QSR 2013] of varying complexity. Scaling behavior varies considerably by archive: on average the strongest centennial slopes are observed for lake sediments (β =1.2), while the smallest are observed for glacier ice (β =0.24). Results confirm that the CESM Last Millennium simulation (LM) exhibits decadal-centennial scaling closer to proxy spectra than the pre-industrial control run (PI): the latter shows a "blue" spectrum (β 0), suggesting that forcings are essential to reduce the spectral divide. Yet, even with forcings, LM spectra are flatter than the proxy spectra. Subsequent work will investigate the roles of seasonal sensitivity (trees, foraminifera, alkenones), multivariate influences (corals, trees), detrending (trees) and post-depositional processes (ice cores, lake & marine sediments) on spectral
Improved spectral absorption coefficient grouping strategy of wide band k-distribution model used for calculation of infrared remote sensing signal of hot exhaust systems

Science.gov (United States)

Hu, Haiyang; Wang, Qiang

2018-07-01

A new strategy for grouping spectral absorption coefficients, considering the influences of both temperature and species mole ratio inhomogeneities on correlated-k characteristics of the spectra of gas mixtures, has been deduced to match the calculation method of spectral overlap parameter used in multiscale multigroup wide band k-distribution model. By comparison with current spectral absorption coefficient grouping strategies, for which only the influence of temperature inhomogeneity on the correlated-k characteristics of spectra of single species was considered, the improvements in calculation accuracies resulting from the new grouping strategy were evaluated using a series of 0D cases in which radiance under 3-5-μm wave band emitted by hot combustion gas of hydrocarbon fuel was attenuated by atmosphere with quite different temperature and mole ratios of water vapor and carbon monoxide to carbon dioxide. Finally, evaluations are presented on the calculation of remote sensing thermal images of transonic hot jet exhausted from a chevron ejecting nozzle with solid wall cooling system.
A theoretical study of water equilibria: the cluster distribution versus temperature and pressure for (H2O)n, n = 1-60, and ice.

Science.gov (United States)

Lenz, Annika; Ojamäe, Lars

2009-10-07

The size distribution of water clusters at equilibrium is studied using quantum-chemical calculations in combination with statistical thermodynamics. The necessary energetic data is obtained by quantum-chemical B3LYP computations and through extrapolations from the B3LYP results for the larger clusters. Clusters with up to 60 molecules are included in the equilibrium computations. Populations of different cluster sizes are calculated using both an ideal gas model with noninteracting clusters and a model where a correction for the interaction energy is included analogous to the van der Waals law. In standard vapor the majority of the water molecules are monomers. For the ideal gas model at 1 atm large clusters [56-mer (0-120 K) and 28-mer (100-260 K)] dominate at low temperatures and separate to smaller clusters [21-22-mer (170-280 K) and 4-6-mer (270-320 K) and to monomers (300-350 K)] when the temperature is increased. At lower pressure the transition from clusters to monomers lies at lower temperatures and fewer cluster sizes are formed. The computed size distribution exhibits enhanced peaks for the clusters consisting of 21 and 28 water molecules; these sizes are for protonated water clusters often referred to as magic numbers. If cluster-cluster interactions are included in the model the transition from clusters to monomers is sharper (i.e., occurs over a smaller temperature interval) than when the ideal-gas model is used. Clusters with 20-22 molecules dominate in the liquid region. When a large icelike cluster is included it will dominate for temperatures up to 325 K for the noninteracting clusters model. Thermodynamic properties (C(p), DeltaH) were calculated with in general good agreement with experimental values for the solid and gas phase. A formula for the number of H-bond topologies in a given cluster structure is derived. For the 20-mer it is shown that the number of topologies contributes to making the population of dodecahedron-shaped cluster larger
Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

Science.gov (United States)

Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G

2016-02-23

In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.
Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA

Science.gov (United States)

Tedder, Philip; Zubko, Elena; Westhead, David R.; Meyer, Peter

2009-01-01

Two pools of small RNAs were cloned from inflorescences of Petunia hybrida using a 5′-ligation dependent and a 5′-ligation independent approach. The two libraries were integrated into a public website that allows the screening of individual sequences against 359,769 unique clones. The library contains 15 clones with 100% identity and 53 clones with one mismatch to miRNAs described for other plant species. For two conserved miRNAs, miR159 and miR390, we find clear differences in tissue-specific distribution, compared with other species. This shows that evolutionary conservation of miRNA sequences does not necessarily include a conservation of the miRNA expression profile. Almost 60% of all clones in the database are 24-nucleotide clones. In accordance with the role of 24mers in marking repetitive regions, we find them distributed across retroviral and transposable element sequences but other 24mers map to promoter regions and to different transcript regions. For one target region we observe tissue-specific variation of matching 24mers, which demonstrates that, as for 21mers, 24mer concentrations are not necessarily identical in different tissues. Asymmetric distribution of a putative novel miRNA in the two libraries suggests that the cloning method can be selective for the representation of certain small RNAs in a collection. PMID:19369427
K{sup +}→μ{sup +}ν{sub μ}νν̄ and K{sup +}→e{sup +}ν{sub e}νν̄ decays within the Chiral Perturbation Theory

Energy Technology Data Exchange (ETDEWEB)

Gorbunov, D.; Mitrofanov, A. [Theoretical Physics Division, Institute for Nuclear Research of the Russian Academy of Sciences,60th October anniversary prospect, 7a, Moscow, 117312 (Russian Federation); Department of Problems of Physics and Energetics Moscow Institute of Physics and Technology,9 Institutskiy per., Dolgoprudny, Moscow Region, 141700 (Russian Federation)

2016-10-10

Decays K{sup +}→μ{sup +}ν{sub μ}νν̄ and K{sup +}→e{sup +}ν{sub e}νν̄ are examined to the leading order in momenta in the framework of Chiral Perturbation Theory. Predictions of the Standard Model for the muon and electron differential energy spectra and branching ratios of K{sub μ3ν} and K{sub e3ν} are presented.
A conservative region of the mercuric reductase gene (merA) as a molecular marker of bacterial mercury resistance Região conservada do gene da mercúrio redutase (merA) como marcador molecular da resistência bacteriana ao mercúrio

OpenAIRE

Adriana Sotero-Martins; Michele Silva de Jesus; Michele Lacerda; Josino Costa Moreira; Ana Luzia Lauria Filgueiras; Paulo Rubens Guimarães Barrocas

2008-01-01

The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg0, which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains.O mecanismo de resistência bacteriana ao mercúrio mais comum é baseada na redução do Hg(II) a Hg0, através da ativida...
Human Infection with MERS coronavirus after exposure to infected camels, Saudi Arabia, 2013

NARCIS (Netherlands)

Memish, Ziad A.; Cotten, Matthew; Meyer, Benjamin; Watson, Simon J.; Alsahafi, Abdullah J.; Al Rabeeah, Abdullah A.; Corman, Victor Max; Sieberg, Andrea; Makhdoom, Hatem Q.; Assiri, Abdullah; Al Masri, Malaki; Aldabbagh, Souhaib; Bosch, Berend Jan|info:eu-repo/dai/nl/273306049; Beer, Martin; Müller, Marcel A.; Kellam, Paul; Drosten, Christian

2014-01-01

We investigated a case of human infection with Middle East respiratory syndrome coronavirus (MERS-CoV) after exposure to infected camels. Analysis of the whole human-derived virus and 15% of the camel-derived virus sequence yielded nucleotide polymorphism signatures suggestive of cross-species
Rock properties influencing impedance spectra (IS) studied by lab measurements on porous model systems

Energy Technology Data Exchange (ETDEWEB)

Volkmann, J.; Klitzsch, N.; Mohnke, O. [RWTH Aachen Univ. (Germany). Applied Geophysics and Geothermal Energy; Schleifer, N. [Wintershall Holding GmbH, Barnstorf (Germany)

2013-08-01

The wetting condition of reservoir rocks is a crucial parameter for the estimation of reservoir characteristics like permeability and saturation with residual oil or water. Since standard methods are often costly, at least in terms of time, we aim at assessing wettability of reservoir rocks using impedance spectroscopy (IS), a frequency dependent measurement of complex electric resistivity. This approach is promising, because IS is sensitive to the electrochemical properties of the inner surface of rocks which, on the other hand, are decisively influencing wettability. Unfortunately, there is large number of rock parameters - besides wettability - influencing the impedance spectra often not exactly known for natural rock samples. Therefore, we study model systems to improve the understanding of the underlying mechanisms and to quantify the influencing parameters. The model systems consist of sintered porous silica beads of different sizes leading to samples with different pore sizes. The main advantage of these samples compared to natural rocks is their well-defined and uniform mineralogical composition and thus their uniform electrochemical surface property. In order to distinguish pore geometry and fluid electrochemistry effects on the IS properties we measured the IS response of the fully water saturated model systems in a wide frequency range - from 1 mHz to 35 MHz - to capture different often overlapping polarization processes. With these measurements we study the influence of pore or grain size, fluid conductivity, and wettability (contact angle) on the impedance spectra. The influence of wettability was studied by modifying the originally hydrophilic inner surface into a hydrophobic state. The wettability change was verified by contact angle measurements. As results, we find pore size dependent relaxation times and salinity dependent chargeabilities for the hydrophilic samples in the low frequency range (< 10 kHz), whereas for the hydrophobic samples
Ionization potential depression and optical spectra in a Debye plasma model

Science.gov (United States)

Lin, Chengliang; Röpke, Gerd; Reinholz, Heidi; Kraeft, Wolf-Dietrich

2017-11-01

We show how optical spectra in dense plasmas are determined by the shift of energy levels as well as the broadening owing to collisions with the plasma particles. In lowest approximation, the interaction with the plasma particles is described by the RPA dielectric function, leading to the Debye shift of the continuum edge. The bound states remain nearly un-shifted, their broadening is calculated in Born approximation. The role of ionization potential depression as well as the Inglis-Teller effect are shown. The model calculations have to be improved going beyond the lowest (RPA) approximation when applying to WDM spectra.
Alternative collimator for CdTe (model XR-100T), when it is used for a direct measurements of radiodiagnostic spectra

International Nuclear Information System (INIS)

Soares, C.; Guevara, M.V. Manso; Milian, F. Mas; Garcia, F.

2014-01-01

The spectrum simulation is a powerful instrument of great practical and pedagogical usefulness, because it helps to understand the technical and the instrumental limits of parameters in optimized measurements of magnitudes of interest in physics. Monte Carlo models, based on particle and radiation transport, provide easy and flexible tools for simulating complex geometries and materials. Particularly, MCNPX code is used to compare, manipulate, and quantify simulated and measured spectra. The purpose of this work is to use this tool set to estimate the characteristics of a collimation device, avoiding permanent and temporary damages into the diode-pin detector, during direct measurements of the Bremsstrahlung's spectrum, which was generated from diagnosis tubes with medical purpose. The simulations were made with a maximum voltage of 150 kVp, and typical charges used in radiological protocols in the medical area. Also, differential high pulse spectra, simulated and measured with a CdTe Detector, are reported. (author)
Raman Spectra of Methane, Ethylene, Ethane, Dimethyl ether, Formaldehyde and Propane for Combustion Applications

KAUST Repository

Magnotti, G.

2015-05-09

Spontaneous Raman scattering measurements of temperature and major species concentration in hydrocarbon-air flames require detailed knowledge of the Raman spectra of the hydrocarbons present when fuels more complex than methane are used. Although hydrocarbon spectra have been extensively studied at room temperature, there are no data available at higher temperatures. Quantum mechanical calculations, when available are not sufficiently accurate for combustion applications. This work presents experimental measurements of spontaneous Stokes-Raman scattering spectra of methane, ethylene, ethane, dimethyl ether, formaldehyde and propane in the temperature range 300-860 K. Raman spectra from heated hydrocarbons jets have been collected with a higher resolution than is generally employed for Raman measurements in combustion applications. A set of synthetic spectra have been generated for each hydrocarbon, providing the basis for extrapolation to higher temperatures. The spectra provided here will enable simultaneous measurements of multiple hydrocarbons in flames. This capability will greatly extend the range of applicability of Raman measurements in combustion applications. In addition, the experimental spectra provide a validation dataset for quantum mechanical models.
Raman Spectra of Methane, Ethylene, Ethane, Dimethyl ether, Formaldehyde and Propane for Combustion Applications

KAUST Repository

Magnotti, G.; KC, Utsav; Varghese, P.L.; Barlow, R.S.

2015-01-01

Spontaneous Raman scattering measurements of temperature and major species concentration in hydrocarbon-air flames require detailed knowledge of the Raman spectra of the hydrocarbons present when fuels more complex than methane are used. Although hydrocarbon spectra have been extensively studied at room temperature, there are no data available at higher temperatures. Quantum mechanical calculations, when available are not sufficiently accurate for combustion applications. This work presents experimental measurements of spontaneous Stokes-Raman scattering spectra of methane, ethylene, ethane, dimethyl ether, formaldehyde and propane in the temperature range 300-860 K. Raman spectra from heated hydrocarbons jets have been collected with a higher resolution than is generally employed for Raman measurements in combustion applications. A set of synthetic spectra have been generated for each hydrocarbon, providing the basis for extrapolation to higher temperatures. The spectra provided here will enable simultaneous measurements of multiple hydrocarbons in flames. This capability will greatly extend the range of applicability of Raman measurements in combustion applications. In addition, the experimental spectra provide a validation dataset for quantum mechanical models.
Measurements of π{sup ±}, K{sup ±}, p and p spectra in proton-proton interactions at 20, 31, 40, 80 and 158 GeV/c with the NA61/SHINE spectrometer at the CERN SPS

Energy Technology Data Exchange (ETDEWEB)

Aduszkiewicz, A.; Dominik, W.; Kuich, M.; Matulewicz, T.; Podlaski, P.; Posiadala, M.; Walewski, M. [University of Warsaw, Warsaw (Poland); Ali, Y.; Brzychczyk, J.; Larsen, D.; Planeta, R.; Richter-Was, E.; Staszel, P.; Wyszynski, O. [Jagiellonian University, Krakow (Poland); Andronov, E.; Feofilov, G.A.; Igolkin, S.; Kondratiev, V.P.; Kovalenko, V.; Merzlaya, A.; Seryakov, A.; Vechernin, V.V.; Vinogradov, L. [St. Petersburg State University, St. Petersburg (Russian Federation); Anticic, T.; Kadija, K.; Susa, T. [Ruder Boskovic Institute, Zagreb (Croatia); Baatar, B.; Bunyatov, S.A.; Kireyeu, V.A.; Kolesnikov, V.I.; Krasnoperov, A.; Lyubushkin, V.V.; Malakhov, A.I.; Matveev, V.; Melkumov, G.L.; Tereshchenko, V. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Baszczyk, M.; Dorosz, P.; Kucewicz, W.; Mik, L. [University of Science and Technology, Krakow (Poland); Bhosale, S.; Davis, N.; Kielbowicz, M.; Marcinek, A.; Ozvenchuk, V.; Rybicki, A. [H. Niewodniczanski Institute of Nuclear Physics of the Polish Academy of Sciences, Krakow (Poland); Blondel, A.; Bravar, A.; Damyanova, A.; Haesler, A.; Korzenev, A.; Ravonel, M. [University of Geneva, Geneva (Switzerland); Bogomilov, M.; Kolev, D.; Tsenov, R. [University of Sofia, Faculty of Physics, Sofia (Bulgaria); Brandin, A.; Selyuzhenkov, I.; Strikhanov, M.; Taranenko, A. [National Research Nuclear University (Moscow Engineering Physics Institute), Moscow (Russian Federation); Busygina, O.; Golubeva, M.; Guber, F.; Ivashkin, A.; Kurepin, A.; Sadovsky, A. [Institute for Nuclear Research, Moscow (Russian Federation); Cherif, H.; Deveaux, M.; Klochkov, V.; Koziel, M.; Renfordt, R.; Snoch, A.; Stroebele, H.; Toia, A. [University of Frankfurt, Frankfurt (Germany); Cirkovic, M.; Knezevic, N.; Manic, D.; Puzovic, J. [University of Belgrade, Belgrade (Serbia); Czopowicz, T.; Grebieszkow, K.; Mackowiak-Pawlowska, M.; Maksiak, B.; Slodkowski, M.; Tefelska, A.; Tefelski, D. [Warsaw University of Technology, Warsaw (Poland); Dembinski, H.; Engel, R.; Herve, A.E.; Mathes, H.J.; Roth, M.; Szuba, M.; Ulrich, R.; Unger, M.; Veberic, D. [Karlsruhe Institute of Technology, Karlsruhe (Germany); Dumarchez, J. [University of Paris VI and VII, LPNHE, Paris (France); Ereditato, A.; Francois, C.; Pistillo, C.; Wilkinson, C. [University of Bern, Bern (Switzerland); Fodor, Z. [Wigner Research Centre for Physics of the Hungarian Academy of Sciences, Budapest (Hungary); University of Wroclaw, Wroclaw (Poland); Garibov, A. [National Nuclear Research Center, Baku (Azerbaijan); Gazdzicki, M. [University of Frankfurt, Frankfurt (Germany); Jan Kochanowski University in Kielce, Kielce (Poland); Hylen, J.; Lundberg, B.; Marchionni, A.; Rameika, R.; Zwaska, R. [Fermilab, Batavia (United States); Johnson, S.R.; Marino, A.D.; Nagai, Y.; Rumberger, B.T.; Zimmerman, E.D. [University of Colorado, Boulder (United States); Kaptur, E.; Kowalski, S.; Lysakowski, B.; Pulawski, S.; Schmidt, K. [University of Silesia, Katowice (Poland); Kowalik, K.; Rondio, E.; Stepaniak, J. [National Centre for Nuclear Research, Warsaw (Poland); Laszlo, A.; Marton, K.; Vesztergombi, G. [Wigner Research Centre for Physics of the Hungarian Academy of Sciences, Budapest (Hungary); Lewicki, M.; Naskret, M.; Turko, L. [University of Wroclaw, Wroclaw (Poland); Messerly, B.; Paolone, V.; Wickremasinghe, A. [University of Pittsburgh, Pittsburgh (United States); Mills, G.B. [Los Alamos National Laboratory, Los Alamos (United States); Morozov, S.; Petukhov, O. [Institute for Nuclear Research, Moscow (Russian Federation); National Research Nuclear University (Moscow Engineering Physics Institute), Moscow (Russian Federation); Mrowczynski, S.; Rybczynski, M.; Seyboth, P.; Stefanek, G.; Wlodarczyk, Z.; Wojtaszek-Szwarc, A. [Jan Kochanowski University in Kielce, Kielce (Poland); Pavin, M. [Ruder Boskovic Institute, Zagreb (Croatia); University of Paris VI and VII, LPNHE, Paris (France); Popov, B.A. [University of Paris VI and VII, LPNHE, Paris (France); Joint Institute for Nuclear Research, Dubna (Russian Federation); Rauch, W. [Fachhochschule Frankfurt, Frankfurt (Germany); Roehrich, D. [University of Bergen, Bergen (Norway); Rustamov, A. [National Nuclear Research Center, Baku (Azerbaijan); University of Frankfurt, Frankfurt (Germany); Zambelli, L. [National Nuclear Research Center, Baku (Azerbaijan); University of Paris VI and VII, LPNHE, Paris (France); Collaboration: The NA61/SHINE Collaboration

2017-10-15

Measurements of inclusive spectra and mean multiplicities of π{sup ±}, K{sup ±}, p and p produced in inelastic p + p interactions at incident projectile momenta of 20, 31, 40, 80 and 158 GeV/c (√(s) = 6.3, 7.7, 8.8, 12.3 and 17.3 GeV, respectively) were performed at the CERN Super Proton Synchrotron using the large acceptance NA61/SHINE hadron spectrometer. Spectra are presented as function of rapidity and transverse momentum and are compared to predictions of current models. The measurements serve as the baseline in the NA61/SHINE study of the properties of the onset of deconfinement and search for the critical point of strongly interacting matter. (orig.)
Parametrization relating the fermionic mass spectra

International Nuclear Information System (INIS)

Kleppe, A.

1993-01-01

When parametrizing the fermionic mass spectra in terms of the unit matrix and a recursive matrix scrR 0 , which corresponds to an underlying scaling pattern in the mass spectra, each fermionic sector is characterized by three parameters: k, α, and R. Using the set of relations displayed by the parameters of the different sectors, it is possible to formulate a ''family Lagrangian'' which for each sector encompasses all the families. Relations between quark masses are furthermore deduced from these ''family Lagrangians.'' Using the relations between the parameters of the different charge sectors, it is also possible to ''derive'' the quark mass spectra from the (charged) leptonic mass spectrum
Theoretically predicted soft x-ray emission and absorption spectra of graphitic-structured BC2N

Science.gov (United States)

Muramatsu, Yasuji

Theoretical B K, C K and N K x-ray emission/absorption spectra of three possible graphitic-structured BC2N clusters are predicted based on the B2p-, C2p-, and N2p- density-of-states (DOS) calculated by discrete variational (DV)-X[alpha] molecular orbital calculations. Several prominent differences in DOS spectral features among BC2Ns, h-BN, and graphite are confirmed from comparison of calculated B2p-, C2p-, and N2p-DOS spectra. These variations in the spectra allow BC2N structures to be positively identified by high-resolution x-ray emission/absorption spectroscopy in the B K, C K, and N K regions.

Measurement of cold neutron spectra at a model of cryogenic moderator of the IBR-2M reactor

International Nuclear Information System (INIS)

Kulikov, S.A.; Chernikov, A.N.; Shabalin, E.P.; Kalinin, I.V.; Morozov, V.M.; Novikov, A.G.; Puchkov, A.V.

2010-01-01

The article is dedicated to methods and results of experimental determination of cold neutron spectra from solid mesitylene at neutron moderator temperatures 10-50 K. Experiments were fulfilled at the DIN-2PI spectrometer of the IBR-2 reactor. The main goals of this work were to examine a system of constants for Monte Carlo calculation of cryogenic moderators of the IBR-2M reactor and to determine the temperature dependence of cold neutron intensity from the moderator. A reasonable agreement of experimental and calculation results for mesitylene at 20 K has been obtained. The cold neutron intensity at temperature of moderator 10 K is about 1.8 times higher than at T=50 K
Fučík spectra for vector equations

Directory of Open Access Journals (Sweden)

Christian Fabry

2000-01-01

Full Text Available Let $L:\\hbox{dom} L\\subset L^2(\\Omega;R^N\\rightarrow L^2(\\Omega;R^N$ be a linear operator, $\\Omega$ being open and bounded in $R^M$. The aim of this paper is to study the Fu\\v c\\'\\i k spectrum for vector problems of the form $Lu=\\alpha Au^+ -\\beta Au^-$, where $A$ is an $N\\times N$ matrix, $\\alpha, \\beta$ are real numbers, $u^+$ a vector defined componentwise by $(u^+_i=\\max\\{u_i,0\\}$, $u^-$ being defined similarly. With $\\lambda^*$ an eigenvalue for the problem $Lu=\\lambda Au$, we describe (locally curves in the Fučík spectrum passing through the point $(\\lambda^*,\\lambda^*$, distinguishing different cases illustrated by examples, for which Fučík curves have been computed numerically.
Structural and Biochemical Characterization of Organotin and Organolead Compounds Binding to the Organomercurial Lyase MerB Provide New Insights into Its Mechanism of Carbon–Metal Bond Cleavage

Energy Technology Data Exchange (ETDEWEB)

Wahba, Haytham M. [Département; Faculty; Stevenson, Michael J. [Department; Mansour, Ahmed [Département; Sygusch, Jurgen [Département; Wilcox, Dean E. [Department; Omichinski, James G. [Département

2017-01-03

The organomercurial lyase MerB has the unique ability to cleave carbon–Hg bonds, and structural studies indicate that three residues in the active site (C96, D99, and C159 in E. coli MerB) play important roles in the carbon–Hg bond cleavage. However, the role of each residue in carbon–metal bond cleavage has not been well-defined. To do so, we have structurally and biophysically characterized the interaction of MerB with a series of organotin and organolead compounds. Studies with two known inhibitors of MerB, dimethyltin (DMT) and triethyltin (TET), reveal that they inhibit by different mechanisms. In both cases the initial binding is to D99, but DMT subsequently binds to C96, which induces a conformation change in the active site. In contrast, diethyltin (DET) is a substrate for MerB and the SnIV product remains bound in the active site in a coordination similar to that of HgII following cleavage of organomercurial compounds. The results with analogous organolead compounds are similar in that trimethyllead (TML) is not cleaved and binds only to D99, whereas diethyllead (DEL) is a substrate and the PbIV product remains bound in the active site. Binding and cleavage is an exothermic reaction, while binding to D99 has negligible net heat flow. These results show that initial binding of organometallic compounds to MerB occurs at D99 followed, in some cases, by cleavage and loss of the organic moieties and binding of the metal ion product to C96, D99, and C159. The N-terminus of MerA is able to extract the bound PbVI but not the bound SnIV. These results suggest that MerB could be utilized for bioremediation applications, but certain organolead and organotin compounds may present an obstacle by inhibiting the enzyme.
Satellite Atmospheric Sounder IRFS-2 1. Analysis of Outgoing Radiation Spectra Measurements

Science.gov (United States)

Polyakov, A. V.; Timofeyev, Yu. M.; Virolainen, Ya. A.; Uspensky, A. B.; Zavelevich, F. S.; Golovin, Yu. M.; Kozlov, D. A.; Rublev, A. N.; Kukharsky, A. V.

2017-12-01

The outgoing radiation spectra measured by the IRFS-2 spectrometer onboard Meteor-M no. 2 satellite have been analyzed. Some statistical parameters of more than 106 spectra measured in spring in 2015 have been calculated. The radiation brightness temperature varied from ˜300 K (surface temperature) up to ˜210 K (tropopause temperature). The quite high variability of the longwave measured radiation has been demonstrated. The signal-to-noise ratio distinctively decreases in the shortwave region (higher than 1300 cm-1). Intercomparisons of IR sounders IRFS-2 with IASI and CrIS spectra showed that the discrepancies in the average spectra and their variability do not exceed measurement errors in the spectral region 660-1300 cm-1. A comparison of specially chosen pairs of the simultaneously measured spectra showed that the differences between IRFS-2 and European instruments in the region of the 15-μm CO2 band and the transparency windows 8-12 μm are less than 1 mW/(m2 sr cm-1) and no more than the differences between the two IASI instruments (-A and -B). The differences between measured and simulated spectra are less than 1 mW/(m2 sr cm-1) in the mean part of CO2 band. However, starting from 720 cm-1, values appear that reach 2-4 mW/(m2 sr cm-1). This is caused by the absence of precise information about the surface temperature. Further investigations into the possible reasons for the observed disagreements are required in order to improve both the method of initial processing and the radiative model of the atmosphere.
Middle East respiratory syndrome coronavirus (MERS Cov outbreak so far exempted Sub Saharan Africa; is it good news or call for action?

Directory of Open Access Journals (Sweden)

Ballah Akawu Denue

2015-01-01

Full Text Available The reported cases of MERS Cov in Arabian Peninsula and sporadic cases elsewhere except in sub Saharan Africa at present is disquieting considering its initial clinical feature that mimic flu like symptoms caused by other viruses. However MERS Cov is associated with organ dysfunction and high mortality. Although the mode of transmission is still unclear, it is postulated that it spreads through close contact, possibly via respiratory route. High similarities of MERS CoV carried by humans and camels may suggest that the diseases are zoonotic. Furthermore, airborne nosocomial transmission can occur in the room shared by the patients in the hospitals. There is still the confusion of transmission through body fluids or clinical samples, including stools and a cross transmission with medical devices or hands. Currently, all known cases can be directly or indirectly linked to Middle East from where it derives its name. Cases reported outside the Middle East first developed infection in the Middle East and then were exported outside the region. Several hospital-acquired outbreaks that resulted in upsurge of MERS Cov cases in Jeddah revealed lack of systematic implementation of infection prevention and control measures to effectively control emerging infectious diseases. The causative agent is detected and identified using Enzyme Linked Immuunosorbent Assay (ELISA and real-time polymerase chain reaction (RT-PCR that is expensive and not readily available in hospitals located in resource poor settings such as sub Saharan Africa. Although, so far no case of MERS Cov has been reported from sub Saharan Africa, the devastating consequences of MERS epidemic will be more catastrophic if it emerges in developing nations especially in sub Saharan Africa where there are no up to date facilities for investigations and management of such cases. Against this backdrop, we review this hazardous and incurable disease believing that it would create the necessary
The effects of general anesthetics on ESR spectra of spin labels in phosphatidylcholine vesicles containing purified Na,K-ATPase or microsomal protein

Science.gov (United States)

Shibuya, Makiko; Hiraoki, Toshifumi; Kimura, Kunie; Fukushima, Kazuaki; Suzuki, Kuniaki

2012-12-01

We investigated the effects of general anesthetics on liposome containing spin labels, 5-doxyl stearic acid (5-DSA) and 16-doxyl stearic acid (16-DSA), and purified Na,K-ATPase or membrane protein of microsome using an electron spin resonance (ESR) spectroscopy. The spectra of 16-DSA in liposomes with both proteins showed three sharp signals compared with 5-DSA. The difference in the order parameter S value of 5-DSA and 16-DSA suggested that the nitroxide radical location of 5-DSA and 16-DSA were different in the membrane bilayer. The results were almost the same as those obtained in liposomes without proteins. The addition of sevoflurane, isoflurane, halothane, ether, ethanol and propofol increased the intensity of the signals, but the clinical concentrations of anesthetics did not significantly alter the S and τ values, which are indices of the fluidity of the membrane. These results suggest that anesthetics remain on the surface of the lipid bilayer and do not act on both the inside hydrophobic area and the relatively hydrophilic area near the surface. These results and others also suggest that the existence of Na,K-ATPase and microsomal proteins did not affect the environment around the spin labels in the liposome and the effects of anesthetics on liposome as a model membrane.
Measurement of spectra for intra-oral X-ray beams using biological materials as attenuator

International Nuclear Information System (INIS)

Zenóbio, Madelon A.F.; Nogueira-Tavares, Maria S.; Zenóbio, Elton G.; Squair, Peterson Lima; Santos, Marcus A.P.; Silva, Teógenes A. da

2011-01-01

In diagnostic radiology, the radiation interaction probability in matter is a strong function of the X-ray energy. The knowledge of the X-ray energy spectral distribution allows optimizing the radiographic imaging system in order to obtain high quality images with as low as reasonably achievable patient doses. In this study, transmitted X-ray spectra through dentin and enamel that are existing materials in intra-oral radiology were experimentally determined in an X-ray equipment with 40–70 kV variable range. Dentin and enamel samples with 0.4–3.8 and 0.6–2.6 mm thick were used as attenuators. X-ray transmitted spectra were measured with XR-100T model CdTe detector and half-value layers (HVL) were determined. Characteristics of both dentin and enamel transmitted spectra showed that they have differences in the penetration power in matter and in the spectrum distribution. The results will be useful for phantom developments based on dentin and enamel for image quality control in dental radiology. - Highlights: ► The X-ray energy spectral distribution, optimize the radiographic imaging system. Transmitted X-ray spectra through dentin and enamel were experimentally determined. X-ray transmitted spectra were measured (XR-100T model CdTe detector). The transmitted spectra showed differences in the penetration power and spectrum distribution. Dentin and enamel transmitted spectra will be useful for phantom developments.
Water on Mars: Evidence from MER Mission Results

Science.gov (United States)

Landis, Geoffrey A.

2004-01-01

The Viking and the Mars Exploration Rover missions observed that the surface of Mars is encrusted by a thinly cemented layer, or "duricrust". Elemental analyzes at five sites on Mars show that these soils have sulfur content and chlorine content consistent with the presence of sulfates and halides as mineral cements. The soil is highly enriched in the salt-forming elements compared with rock. Analysis of the soil cementation indicates some features which may be evidence of liquid water. At both MER sites, duricrust textures revealed by the Microscopic Imager show features including the presence of fine sand-sized grains, some of which may be aggregates of fine silt and clay, surrounded by a pervasive light colored material that is associated with microtubular structures and networks of microfractures. Stereo views of undisturbed duricrust surfaces reveal rugged microrelief between 2-3 mm and minimal loose material. Comparisons of microscopic images of duricrust soils obtain before and after placement of the Mossbauer spectrometer indicate differing degrees of compaction and cementation. Two models of a transient water hypothesis are offered, a "top down" hypothesis that emphasizes the surface deposition of frost, melting and downward migration of liquid water and a "bottom up" alternative that proposes the presence of interstitial ice/brine, with the upward capillary migration of liquid water. The viability of both of these models ultimately hinges on the availability of seasonally transient liquid water for brief periods.
The atmospheric parameters of FGK stars using wavelet analysis of CORALIE spectra

Science.gov (United States)

Gill, S.; Maxted, P. F. L.; Smalley, B.

2018-05-01

Context. Atmospheric properties of F-, G- and K-type stars can be measured by spectral model fitting or with the analysis of equivalent width (EW) measurements. These methods require data with good signal-to-noise ratios (S/Ns) and reliable continuum normalisation. This is particularly challenging for the spectra we have obtained with the CORALIE échelle spectrograph for FGK stars with transiting M-dwarf companions. The spectra tend to have low S/Ns, which makes it difficult to analyse them using existing methods. Aims: Our aim is to create a reliable automated spectral analysis routine to determine Teff, [Fe/H], V sini from the CORALIE spectra of FGK stars. Methods: We use wavelet decomposition to distinguish between noise, continuum trends, and stellar spectral features in the CORALIE spectra. A subset of wavelet coefficients from the target spectrum are compared to those from a grid of models in a Bayesian framework to determine the posterior probability distributions of the atmospheric parameters. Results: By testing our method using synthetic spectra we found that our method converges on the best fitting atmospheric parameters. We test the wavelet method on 20 FGK exoplanet host stars for which higher-quality data have been independently analysed using EW measurements. We find that we can determine Teff to a precision of 85 K, [Fe/H] to a precision of 0.06 dex and V sini to a precision of 1.35 km s-1 for stars with V sini ≥ 5 km s-1. We find an offset in metallicity ≈- 0.18 dex relative to the EW fitting method. We can determine log g to a precision of 0.13 dex but find systematic trends with Teff. Measurements of log g are only reliable enough to confirm dwarf-like surface gravity (log g ≈ 4.5). Conclusions: The wavelet method can be used to determine Teff, [Fe/H], and V sini for FGK stars from CORALIE échelle spectra. Measurements of log g are unreliable but can confirm dwarf-like surface gravity. We find that our method is self consistent, and
Treatment outcomes for patients with Middle Eastern Respiratory Syndrome Coronavirus (MERS CoV) infection at a coronavirus referral center in the Kingdom of Saudi Arabia.

Science.gov (United States)

Al Ghamdi, Mohammed; Alghamdi, Khalid M; Ghandoora, Yasmeen; Alzahrani, Ameera; Salah, Fatmah; Alsulami, Abdulmoatani; Bawayan, Mayada F; Vaidya, Dhananjay; Perl, Trish M; Sood, Geeta

2016-04-21

Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV) is a poorly understood disease with no known treatments. We describe the clinical features and treatment outcomes of patients with laboratory confirmed MERS-CoV at a regional referral center in the Kingdom of Saudi Arabia. In 2014, a retrospective chart review was performed on patients with a laboratory confirmed diagnosis of MERS-CoV to determine clinical and treatment characteristics associated with death. Confounding was evaluated and a multivariate logistic regression was performed to assess the independent effect of treatments administered. Fifty-one patients had an overall mortality of 37 %. Most patients were male (78 %) with a mean age of 54 years. Almost a quarter of the patients were healthcare workers (23.5 %) and 41 % had a known exposure to another person with MERS-CoV. Survival was associated with male gender, working as a healthcare worker, history of hypertension, vomiting on admission, elevated respiratory rate, abnormal lung exam, elevated alanine transaminase (ALT), clearance of MERS-CoV on repeat PCR polymerase chain reaction (PCR) testing, and mycophenolate mofetil treatment. Survival was reduced in the presence of coronary artery disease, hypotension, hypoxemia, CXR (chest X-ray) abnormalities, leukocytosis, creatinine >1 · 5 mg/dL, thrombocytopenia, anemia, and renal failure. In a multivariate analysis of treatments administered, severity of illness was the greatest predictor of reduced survival. Care for patients with MERS-CoV remains a challenge. In this retrospective cohort, interferon beta and mycophenolate mofetil treatment were predictors of increased survival in the univariate analysis. Severity of illness was the greatest predictor of reduced survival in the multivariate analysis. Larger randomized trials are needed to better evaluate the efficacy of these treatment regimens for MERS-CoV.
Applications of the k – ω Model in Stellar Evolutionary Models

Energy Technology Data Exchange (ETDEWEB)

Li, Yan, E-mail: ly@ynao.ac.cn [Yunnan Observatories, Chinese Academy of Sciences, Kunming 650216 (China)

2017-05-20

The k – ω model for turbulence was first proposed by Kolmogorov. A new k – ω model for stellar convection was developed by Li, which could reasonably describe turbulent convection not only in the convectively unstable zone, but also in the overshooting regions. We revised the k – ω model by improving several model assumptions (including the macro-length of turbulence, convective heat flux, and turbulent mixing diffusivity, etc.), making it applicable not only for convective envelopes, but also for convective cores. Eight parameters are introduced in the revised k – ω model. It should be noted that the Reynolds stress (turbulent pressure) is neglected in the equation of hydrostatic support. We applied it into solar models and 5 M {sub ⊙} stellar models to calibrate the eight model parameters, as well as to investigate the effects of the convective overshooting on the Sun and intermediate mass stellar models.
FTIR spectra of the solid solutions (Na0.88K0.12)VO3, (Na0.5K0.5)VO3, and Na(V0.66P0.34)O3

Science.gov (United States)

de Waal, D.; Heyns, A. M.

1992-03-01

It is known that three different solid solutions, (Na0.88K0.12)VO3, (Na0.5K0.5)VO3 and Na(V0.66P0.34)O3, form in the (Na,K)(V,P)O3 system. These compounds all have monoclinic crystal structures similar to the pure alkali metal metavanadates containing small cations, e.g. Li+ and Na+ (Space group C2/c). Metavanadates with large cations like K+, Rb+, C+s and NH+4 form orthorhombic crystals, space group Pbcm. All those are structurally related to the silicate pyroxenes. Na(V0.66P0.34)O3 and (Na0.88K0.12)VO3 have the same modified diopside structure as (alpha) - NaVO3 while (Na0.5K0.5)VO3 adopts the true diopside structure. The infrared spectra of the three solid solutions are reported here in comparison with those of (alpha) -NaVO3 and KVO3. The results are also correlated with those obtained in two independent high pressure Raman studies of NH4VO3 and RbVO3 as the introduction of a larger cation like K+ should increase the pressure in the structure.
Calculations of the energy spectra of Zn, Ga and Ge isotopes by the shell model

International Nuclear Information System (INIS)

Sakakura, M.; Shikata, Y.; Arima, A.; Sebe, T.

1979-01-01

The effective Hamiltonian which was determined empirically by Koops and Glaudemans is tested in shell model calculations for the 65-68 Zn, 67-69 Ga, and 68-70 Ge nuclei in the full (1p 3 / 2 , 0f 5 / 2 , 1p 1 / 2 )n space. The resulting energy spectra are compared with the experimental spectra and results of previous calculations. The overall agreement with experiment is as satisfactory for these nuclei as for the Ni and Cu isotopes, by which the Hamiltonian was determined. It is noticed that the spectra of 67 Zn and 67 , 69 Ga calculated in this work are similar to those provided by the Alaga model. (orig.) [de
A model study of tunneling conductance spectra of ferromagnetically ordered manganites

Science.gov (United States)

Panda, Saswati; Kar, J. K.; Rout, G. C.

2018-02-01

We report here the interplay of ferromagnetism (FM) and charge density wave (CDW) in manganese oxide systems through the study of tunneling conductance spectra. The model Hamiltonian consists of strong Heisenberg coupling in core t2g band electrons within mean-field approximation giving rise to ferromagnetism. Ferromagnetism is induced in the itinerant eg electrons due to Kubo-Ohata type double exchange (DE) interaction among the t2g and eg electrons. The charge ordering (CO) present in the eg band giving rise to CDW interaction is considered as the extra-mechanism to explain the colossal magnetoresistance (CMR) property of manganites. The magnetic and CDW order parameters are calculated using Zubarev's Green's function technique and solved self-consistently and numerically. The eg electron density of states (DOS) calculated from the imaginary part of the Green's function explains the experimentally observed tunneling conductance spectra. The DOS graph exhibits a parabolic gap near the Fermi energy as observed in tunneling conductance spectra experiments.
A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray

Directory of Open Access Journals (Sweden)

Fairbanks Benjamin D

2006-04-01

Full Text Available Abstract Background DNA microarrays have proven powerful for functional genomics studies. Several technologies exist for the generation of whole-genome arrays. It is well documented that 25mer probes directed against different regions of the same gene produce variable signal intensity values. However, the extent to which this is true for probes of greater length (60mers is not well characterized. Moreover, this information has not previously been reported for whole-genome arrays designed against bacteria, whose genomes may differ substantially in characteristics directly affecting microarray performance. Results We report here an analysis of alternative 60mer probe designs for an in-situ synthesized oligonucleotide array for the GC rich, β-proteobacterium Burkholderia cenocepacia. Probes were designed using the ArrayOligoSel3.5 software package and whole-genome microarrays synthesized by Agilent, Inc. using their in-situ, ink-jet technology platform. We first validated the quality of the microarrays as demonstrated by an average signal to noise ratio of >1000. Next, we determined that the variance of replicate probes (1178 total probes examined of identical sequence was 3.8% whereas the variance of alternative probes (558 total alternative probes examined designs was 9.5%. We determined that depending upon the definition, about 2.4% of replicate and 7.8% of alternative probes produced outlier conclusions. Finally, we determined none of the probe design subscores (GC content, internal repeat, binding energy and self annealment produced by ArrayOligoSel3.5 were predictive or probes that produced outlier signals. Conclusion Our analysis demonstrated that the use of multiple probes per target sequence is not essential for in-situ synthesized 60mer oligonucleotide arrays designed against bacteria. Although probes producing outlier signals were identified, the use of ratios results in less than 10% of such outlier conclusions. We also determined that
Deconvolution of Complex 1D NMR Spectra Using Objective Model Selection.

Directory of Open Access Journals (Sweden)

Travis S Hughes

Full Text Available Fluorine (19F NMR has emerged as a useful tool for characterization of slow dynamics in 19F-labeled proteins. One-dimensional (1D 19F NMR spectra of proteins can be broad, irregular and complex, due to exchange of probe nuclei between distinct electrostatic environments; and therefore cannot be deconvoluted and analyzed in an objective way using currently available software. We have developed a Python-based deconvolution program, decon1d, which uses Bayesian information criteria (BIC to objectively determine which model (number of peaks would most likely produce the experimentally obtained data. The method also allows for fitting of intermediate exchange spectra, which is not supported by current software in the absence of a specific kinetic model. In current methods, determination of the deconvolution model best supported by the data is done manually through comparison of residual error values, which can be time consuming and requires model selection by the user. In contrast, the BIC method used by decond1d provides a quantitative method for model comparison that penalizes for model complexity helping to prevent over-fitting of the data and allows identification of the most parsimonious model. The decon1d program is freely available as a downloadable Python script at the project website (https://github.com/hughests/decon1d/.
Studying the highly bent spectra of FR II-type radio galaxies with the KDA EXT model

Science.gov (United States)

Kuligowska, Elżbieta

2018-04-01

Context. The Kaiser, Dennett-Thorpe & Alexander (KDA, 1997, MNRAS, 292, 723) EXT model, that is, the extension of the KDA model of Fanaroff & Riley (FR) II-type source evolution, is applied and confronted with the observational data for selected FR II-type radio sources with significantly aged radio spectra. Aim. A sample of FR II-type radio galaxies with radio spectra strongly bent at their highest frequencies is used for testing the usefulness of the KDA EXT model. Methods: The dynamical evolution of FR II-type sources predicted with the KDA EXT model is briefly presented and discussed. The results are then compared to the ones obtained with the classical KDA approach, assuming the source's continuous injection and self-similarity. Results: The results and corresponding diagrams obtained for the eight sample sources indicate that the KDA EXT model predicts the observed radio spectra significantly better than the best spectral fit provided by the original KDA model.
Nonclassical dynamics of the methyl group in 1,1,1-triphenylethane. Evidence from powder 1H NMR spectra

KAUST Repository

Osior, Agnieszka

2017-03-14

According to the damped quantum rotation (DQR) theory, hindered rotation of methyl groups, evidenced in nuclear magnetic resonance (NMR) line shapes, is a nonclassical process. It comprises a number of quantum-rate processes measured by two different quantum-rate constants. The classical jump model employing only one rate constant is reproduced if these quantum constants happen to be equal. The values of their ratio, or the nonclassicallity coefficient, determined hitherto from NMR spectra of single crystals and solutions range from about 1.20 to 1.30 in the latter case to above 5.0 in the former, with the value of 1 corresponding to the jump model. Presently, first systematic investigations of the DQR effects in wide-line NMR spectra of a powder sample are reported. For 1,1,1-triphenylethane deuterated in the aromatic positions, the relevant line-shape effects were monitored in the range 99–121 K. The values of the nonclassicality coefficient dropping from 2.7 to 1.7 were evaluated in line shape fits to the experimental powder spectra from the range 99–108 K. At these temperatures, the fits with the conventional line-shape model are visibly inferior to the DQR fits. Using a theoretical model reported earlier, a semiquantitative interpretation of the DQR parameters evaluated from the spectra is given. It is shown that the DQR effects as such can be detected in wide-line NMR spectra of powdered samples, which are relatively facile to measure. However, a fully quantitative picture of these effects can only be obtained from the much more demanding experiments on single crystals.
General document environmental impact report (m.e.r.) oil and gas exploitation industry. Update and supplement of the general document; Generiek document m.e.r. offshore olie- en gaswinningsindustrie. Update en aanvulling van het generiek document environmental impact report (m.e.r.) offshore, 1999

Energy Technology Data Exchange (ETDEWEB)

NONE

2008-04-15

The generic environmental impact assessment (EIA or MER in Dutch) in 1999 is intended to serve as a template for specific environmental impact assessments for oil and gas exploitation projects at sea. Since 1999, a number of innovations and changes were implemented. Particularly in offshore technologies and regulations new insights and ideas came up in recent years. Therefore the existing generic document has to be updated with new information, relevant in the preparation of specific environmental impact assessments in the offshore oil and gas exploitation industry in the Dutch part of the Continental Shelf [Dutch] De generieke milieu effect rapportage (MER) uit 1999 is bedoeld om te dienen als een sjabloon voor specifieke Milieueffectrapportages bij olie- en gaswinningprojecten op zee. Sinds 1999 is een aantal vernieuwingen en veranderingen doorgevoerd. Met name in offshore technologieen en wet- en regelgeving zijn de afgelopen jaren nieuwe inzichten en ideeen ontstaan. Hierdoor is de wens ontstaan om het bestaande generieke document aan te vullen met nieuwe informatie die relevant is voor het opstellen van specifieke Milieueffectrapportages in de offshore olie- en gaswinningsindustrie op het Nederlands deel van het Continentaal Plat.
Correction of diagnostic x-ray spectra measured with CdTe and CdZnTe detectors

Energy Technology Data Exchange (ETDEWEB)

Matsumoto, M [Osaka Univ., Suita (Japan). Medical School; Kanamori, H; Toragaito, T; Taniguchi, A

1996-07-01

We modified the formula of stripping procedure presented by E. Di. Castor et al. We added the Compton scattering and separated K{sub {alpha}} radiation of Cd and Te (23 and 27keV, respectively). Using the new stripping procedure diagnostic x-ray spectra (object 4mm-Al) of tube voltage 50kV to 100kV for CdTe and CdZnTe detectors are corrected with comparison of those spectra for the Ge detector. The corrected spectra for CdTe and CdZnTe detectors coincide with those for Ge detector at lower tube voltage than 70kV. But the corrected spectra at higher tube voltage than 70kV do not coincide with those for Ge detector. The reason is incomplete correction for full energy peak efficiencies of real CdTe and CdZnTe detectors. (J.P.N.)

MAGNETIC ENERGY SPECTRA IN SOLAR ACTIVE REGIONS

International Nuclear Information System (INIS)

Abramenko, Valentyna; Yurchyshyn, Vasyl

2010-01-01

Line-of-sight magnetograms for 217 active regions (ARs) with different flare rates observed at the solar disk center from 1997 January until 2006 December are utilized to study the turbulence regime and its relationship to flare productivity. Data from the SOHO/MDI instrument recorded in the high-resolution mode and data from the BBSO magnetograph were used. The turbulence regime was probed via magnetic energy spectra and magnetic dissipation spectra. We found steeper energy spectra for ARs with higher flare productivity. We also report that both the power index, α, of the energy spectrum, E(k) ∼ k -α , and the total spectral energy, W = ∫E(k)dk, are comparably correlated with the flare index, A, of an AR. The correlations are found to be stronger than those found between the flare index and the total unsigned flux. The flare index for an AR can be estimated based on measurements of α and W as A = 10 b (αW) c , with b = -7.92 ± 0.58 and c = 1.85 ± 0.13. We found that the regime of the fully developed turbulence occurs in decaying ARs and in emerging ARs (at the very early stage of emergence). Well-developed ARs display underdeveloped turbulence with strong magnetic dissipation at all scales.
A Tn5051-like mer-containing transposon identified in a heavy metal tolerant strain Achromobacter sp. AO22

Directory of Open Access Journals (Sweden)

Bhave Mrinal

2009-03-01

Full Text Available Abstract Background Achromobacter sp. AO22 (formerly Alcaligenes sp. AO22, a bacterial strain isolated from a lead-contaminated industrial site in Australia, was previously found to be resistant to moderate to high levels of mercury, copper and other heavy metals. However, the nature and location of the genetic basis for mercuric ion resistance in this strain, had not been previously identified. Findings Achromobacter sp. AO22 contains a functional mer operon with all four essential genes (merRTPA and shows >99% DNA sequence identity to that of Tn501. The mer operon was present on a transposon, designated TnAO22, captured by introducing a broad-host-range IncP plasmid into Achromobacter sp. AO22 and subsequently transferring it to E. coli recipients. The transposition frequency of TnAO22 was 10-2 to 10-3 per target plasmid transferred. Analysis of TnAO22 sequence revealed it belonged to the Tn21 subgroup of the Tn3 superfamily of transposons, with the transposition module having >99% identity with Tn5051 of a Pseudomonas putida strain isolated from a water sample in New York. Conclusion TnAO22 is thus a new variant of Tn5051 of the Tn3 superfamily and the transposon and its associated mercury resistance system are among the few such systems reported in a soil bacterium. Achromobacter sp. AO22 can thus be exploited for applications such as in situ mercury bioremediation of contaminated sites, or the mobile unit and mer operon could be mobilized to other bacteria for similar purposes.
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach

Directory of Open Access Journals (Sweden)

Shoyaib Mohammad

2008-10-01

Full Text Available Abstract Background Eukaryotic promoter prediction using computational analysis techniques is one of the most difficult jobs in computational genomics that is essential for constructing and understanding genetic regulatory networks. The increased availability of sequence data for various eukaryotic organisms in recent years has necessitated for better tools and techniques for the prediction and analysis of promoters in eukaryotic sequences. Many promoter prediction methods and tools have been developed to date but they have yet to provide acceptable predictive performance. One obvious criteria to improve on current methods is to devise a better system for selecting appropriate features of promoters that distinguish them from non-promoters. Secondly improved performance can be achieved by enhancing the predictive ability of the machine learning algorithms used. Results In this paper, a novel approach is presented in which 128 4-mer motifs in conjunction with a non-linear machine-learning algorithm utilising a Support Vector Machine (SVM are used to distinguish between promoter and non-promoter DNA sequences. By applying this approach to plant, Drosophila, human, mouse and rat sequences, the classification model has showed 7-fold cross-validation percentage accuracies of 83.81%, 94.82%, 91.25%, 90.77% and 82.35% respectively. The high sensitivity and specificity value of 0.86 and 0.90 for plant; 0.96 and 0.92 for Drosophila; 0.88 and 0.92 for human; 0.78 and 0.84 for mouse and 0.82 and 0.80 for rat demonstrate that this technique is less prone to false positive results and exhibits better performance than many other tools. Moreover, this model successfully identifies location of promoter using TATA weight matrix. Conclusion The high sensitivity and specificity indicate that 4-mer frequencies in conjunction with supervised machine-learning methods can be beneficial in the identification of RNA pol II promoters comparative to other methods. This
DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.

Science.gov (United States)

Ma, Wenxiu; Yang, Lin; Rohs, Remo; Noble, William Stafford

2017-10-01

Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, a limitation of these methods is that they typically require a training set of aligned TF binding sites. We describe a sequence + shape kernel that leverages DNA sequence and shape information to better understand protein-DNA binding preference and affinity. This kernel extends an existing class of k-mer based sequence kernels, based on the recently described di-mismatch kernel. Using three in vitro benchmark datasets, derived from universal protein binding microarrays (uPBMs), genomic context PBMs (gcPBMs) and SELEX-seq data, we demonstrate that incorporating DNA shape information improves our ability to predict protein-DNA binding affinity. In particular, we observe that (i) the k-spectrum + shape model performs better than the classical k-spectrum kernel, particularly for small k values; (ii) the di-mismatch kernel performs better than the k-mer kernel, for larger k; and (iii) the di-mismatch + shape kernel performs better than the di-mismatch kernel for intermediate k values. The software is available at https://bitbucket.org/wenxiu/sequence-shape.git. rohs@usc.edu or william-noble@uw.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.
K-distribution models for gas mixtures in hypersonic nonequilibrium flows

Science.gov (United States)

Bansal, Ankit

Calculation of nonequilibrium radiation field in plasmas around a spacecraft entering into an atmosphere at hypersonic velocities is a very complicated and computationally expensive task. The objective of this Dissertation is to collect state-of-the art spectroscopic data for the evaluation of spectral absorption and emission coefficients of atomic and molecular gases, develop efficient and accurate spectral models and databases, and study the effect of radiation on wall heat loads and flowfield around the spacecraft. The most accurate simulation of radiative transport in the shock layer requires calculating the gas properties at a large number of wavelengths and solving the Radiative Transfer Equation (RTE) in a line-by-line (LBL) fashion, which is prohibitively expensive for coupled simulations. A number of k-distribution based spectral models are developed for atomic lines, continuum and molecular bands that allow efficient evaluation of radiative properties and heat loads in hypersonic shock layer plasma. Molecular radiation poses very different challenges than atomic radiation. A molecular spectrum is governed by simultaneous electronic, vibrational and rotational transitions, making the spectrum very strongly dependent on wavelength. In contrast to an atomic spectrum, where line wings play a major role in heat transfer, most of the heat transfer in molecular spectra occurs near line centers. As the first step, k-distribution models are developed separately for atomic and molecular species, taking advantage of the fact that in the Earth's atmosphere the radiative field is dominated by atomic species (N and O) and in Titan's and Mars' atmospheres molecular bands of CN and CO are dominant. There are a number of practical applications where both atomic and molecular species are present, for example, the vacuum-ultra-violet spectrum during Earth's reentry conditions is marked by emission from atomic bound-bound lines and continuum and simultaneous absorption by
Tuning in and catching on? Examining the relationship between pandemic communication and awareness and knowledge of MERS in the USA.

Science.gov (United States)

Lin, Leesa; McCloud, Rachel F; Bigman, Cabral A; Viswanath, Kasisomayajula

2017-06-01

Large-scale influenza outbreaks over the last decade, such as SARS and H1N1, have brought to global attention the importance of emergency risk communication and prompted the international community to develop communication responses. Since pandemic outbreaks are relatively infrequent, there is a dearth of evidence addressing the following questions: (i) Have the resources invested in strategic and routine communication for past pandemic outbreaks yielded public health preparedness benefits? (ii) Have past efforts sensitized people to pay attention to new pandemic threats? The Middle East Respiratory Syndrome (MERS) that was followed closely by major media outlets in the USA provides an opportunity to examine the relationship between exposure to public communication about epidemics and public awareness and knowledge about new risks. In December, 2013, we surveyed a nationally representative sample of 627 American adults and examined the associations between people's awareness to prior pandemics and their awareness of and knowledge about MERS. Awareness of prior pandemics was significantly associated with awareness and knowledge of MERS. The most common sources from which people first heard about MERS were also identified. Communication inequalities were observed between racial/ethnic and socioeconomic positions, suggesting a need for more effective pandemic communication. © The Author 2016. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Modelling impacts of offshore wind farms on trophic web: the Courseulles-sur-Mer case study

Science.gov (United States)

Raoux, Aurore; Pezy, Jean-Philippe; Dauvin, Jean-Claude; Tecchio, samuele; Degraer, Steven; Wilhelmsson, Dan; Niquil, Nathalie

2016-04-01

The French government is planning the construction of three offshore wind farms in Normandy. These offshore wind farms will integrate into an ecosystem already subject to a growing number of anthropogenic disturbances such as transportation, fishing, sediment deposit, and sediment extraction. The possible effects of this cumulative stressors on ecosystem functioning are still unknown, but they could impact their resilience, making them susceptible to changes from one stable state to another. Understanding the behaviour of these marine coastal complex systems is essential in order to anticipate potential state changes, and to implement conservation actions in a sustainable manner. Currently, there are no global and integrated studies on the effects of construction and exploitation of offshore wind farms. Moreover, approaches are generally focused on the conservation of some species or groups of species. Here, we develop a holistic and integrated view of ecosystem impacts through the use of trophic webs modelling tools. Trophic models describe the interaction between biological compartments at different trophic levels and are based on the quantification of flow of energy and matter in ecosystems. They allow the application of numerical methods for the characterization of emergent properties of the ecosystem, also called Ecological Network Analysis (ENA). These indices have been proposed as ecosystem health indicators as they have been demonstrated to be sensitive to different impacts on marine ecosystems. We present here in detail the strategy for analysing the potential environmental impacts of the construction of the Courseulles-sur-Mer offshore wind farm (Bay of Seine) such as the reef effect through the use of the Ecopath with Ecosim software. Similar Ecopath simulations will be made in the future on the Le Tréport offshore wind farm site. Results will contribute to a better knowledge of the impacts of the offshore wind farms on ecosystems. They also allow to
Temperature dependence of Q-band electron paramagnetic resonance spectra of nitrosyl heme proteins

Energy Technology Data Exchange (ETDEWEB)

Flores, Marco; Wajnberg, Eliane; Bemski, George

1997-11-01

The Q-band (35 GHz) electron paramagnetic resonance (EPR) spectra of nitrosyl hemoglobin (Hb N O) and nitrosyl myoglobin (Mb NO) were studied as a function of temperature between 19 K and 200 K. The spectra of both heme proteins show classes of variations as a function of temperature. The first one has previously been associated with the existence of two paramagnetic species, one with rhombic and the other with axial symmetry. The second one manifests itself in changes in the g-factors and linewidths of each species. These changes are correlated with the conformational substates model and associate the variations of g-values with changes in the angle of the N(his)-Fe-N (NO) bond in the rhombic species and with changes in the distance between Fe and N of the proximal (F8) histidine in the axial species. (author) 24 refs., 6 figs.
Modeling Blazar Spectra by Solving an Electron Transport Equation

Science.gov (United States)

Lewis, Tiffany; Finke, Justin; Becker, Peter A.

2018-01-01

Blazars are luminous active galaxies across the entire electromagnetic spectrum, but the spectral formation mechanisms, especially the particle acceleration, in these sources are not well understood. We develop a new theoretical model for simulating blazar spectra using a self-consistent electron number distribution. Specifically, we solve the particle transport equation considering shock acceleration, adiabatic expansion, stochastic acceleration due to MHD waves, Bohm diffusive particle escape, synchrotron radiation, and Compton radiation, where we implement the full Compton cross-section for seed photons from the accretion disk, the dust torus, and 26 individual broad lines. We used a modified Runge-Kutta method to solve the 2nd order equation, including development of a new mathematical method for normalizing stiff steady-state ordinary differential equations. We show that our self-consistent, transport-based blazar model can qualitatively fit the IR through Fermi g-ray data for 3C 279, with a single-zone, leptonic configuration. We use the solution for the electron distribution to calculate multi-wavelength SED spectra for 3C 279. We calculate the particle and magnetic field energy densities, which suggest that the emitting region is not always in equipartition (a common assumption), but sometimes matter dominated. The stratified broad line region (based on ratios in quasar reverberation mapping, and thus adding no free parameters) improves our estimate of the location of the emitting region, increasing it by ~5x. Our model provides a novel view into the physics at play in blazar jets, especially the relative strength of the shock and stochastic acceleration, where our model is well suited to distinguish between these processes, and we find that the latter tends to dominate.
Time resolved EUV spectra from Zpinching capillary discharge plasma

Science.gov (United States)

Jancarek, Alexandr; Nevrkla, Michal; Nawaz, Fahad

2015-09-01

We developed symmetrically charged driver to obtain high voltage, high current Z-pinching capillary discharge. Plasma is created by up to 70 kA, 29 ns risetime current pulse passing through a 5 mm inner diameter, 224 mm long capillary filled with gas to initial pressure in the range of 1 kPa. Due to the low inductance design of the driver, the pinch is observable directly from the measured current curve. Time-integrated and time-resolved spectra of discharge plasma radiation are recorded together with the capillary current and analyzed. The most encouraging spectra were captured in the wavelength range 8.3 ÷ 14 nm. This spectral region contains nitrogen Balmer series lines including potentially lasing NVII 2 - 3 transition. Spectral lines are identified in the NIST database using the FLY kinetic code. The line of 13.38 nm wavelength, transition NVII 2 - 3, was observed in gated, and also in time-integrated spectra for currents >60 kA. This work has been supported by the Ministry of Education, Youth and Sports of the Czech Republic grants LG13029.
Generation of floor response spectra for a model structure of nuclear power plant

International Nuclear Information System (INIS)

Vaidyanathan, C.V.; Kamatchi, P.; Ravichandran, R.; Lakshmanan, N.

2003-01-01

The importance of Nuclear power plants and the consequences of a nuclear accident require that the nuclear structures be designed for the most severe environmental conditions. Earthquakes constitutes major design consideration for the system, structures and equipment of a nuclear power plant. The design of structures on ground is based on the ground response spectra. Many important parts of a nuclear power plant facility are attached to the principal parts of the structure and respond in a manner determined by the structural response rather than by the general ground motion to which the structure is supported. Hence the seismic response of equipment is generally based on the response spectrum of the floor on which it is mounted. In this paper such floor response spectra have been generated at different nodes of a chosen model structure of a nuclear power plant. In the present study a detailed nonlinear time history analysis has been carried out on the mathematical model of the chosen Nuclear Power Plant model structure with the spectrum compatible time history. The acceleration response results of the time history analysis has been used in the spectral analysis and the response spectra are generated. Further peak broadening has been done to account for uncertainties in the material properties and soil characteristics. (author)
Nitrosyl hemoglobins: EPR above 80 K

Energy Technology Data Exchange (ETDEWEB)

Wajnberg, E.; Bemski, G.; El-Jaick, L.J.; Alves, O.C.

1995-03-01

The EPR spectra of nitrosyl hemoglobin and myoglobin in different conditions (native, denatured and lyophilized), as well as of hematin-NO were obtained in the temperature range of 80 K-280 K. There is a substantial and reversible.decrease of the areas of the EPR spectra of all the hemoglobin samples above 150 K. The interpretation of the results implies the existence of two conformational states in thermal equilibrium only one of which is EPR detectable. Thermodynamical parameters are determined for the hexa and penta-coordinated cases. (author). 25 refs, 3 figs.
Nitrosyl hemoglobins: EPR above 80 K

International Nuclear Information System (INIS)

Wajnberg, E.; Bemski, G.; El-Jaick, L.J.; Alves, O.C.

1995-03-01

The EPR spectra of nitrosyl hemoglobin and myoglobin in different conditions (native, denatured and lyophilized), as well as of hematin-NO were obtained in the temperature range of 80 K-280 K. There is a substantial and reversible.decrease of the areas of the EPR spectra of all the hemoglobin samples above 150 K. The interpretation of the results implies the existence of two conformational states in thermal equilibrium only one of which is EPR detectable. Thermodynamical parameters are determined for the hexa and penta-coordinated cases. (author). 25 refs, 3 figs
Photoionization Modeling and the K Lines of Iron

Science.gov (United States)

Kallman, T. R.; Palmeri, P.; Bautista, M. A.; Mendoza, C.; Krolik, J. H.

2004-01-01

We calculate the efficiency of iron K line emission and iron K absorption in photoionized models using a new set of atomic data. These data are more comprehensive than those previously applied to the modeling of iron K lines from photoionized gases, and allow us to systematically examine the behavior of the properties of line emission and absorption as a function of the ionization parameter, density and column density of model constant density clouds. We show that, for example, the net fluorescence yield for the highly charged ions is sensitive to the level population distribution produced by photoionization, and these yields are generally smaller than those predicted assuming the population is according to statistical weight. We demonstrate that the effects of the many strongly damped resonances below the K ionization thresholds conspire to smear the edge, thereby potentially affecting the astrophysical interpretation of absorption features in the 7-9 keV energy band. We show that the centroid of the ensemble of K(alpha) lines, the K(beta) energy, and the ratio of the K(alpha(sub 1)) to K(alpha(sub 2)) components are all diagnostics of the ionization parameter of our model slabs.
Nutrient availability at Mer Bleue bog measured by PRSTM probes

Science.gov (United States)

Wang, M.; Moore, T. R.; Talbot, J.

2015-12-01

Bogs, covering ~0.7 million km2 in Canada, store a large amount of C and N. As nutrient deficient ecosystems, it's critical to examine the nutrient availabilities and seasonal dynamics. We used Plant Root Simulators (PRSTM) at Mer Bleue bog to provide some baseline data on nutrient availability and its variability. In particular, we focused on ammonium, nitrate, phosphate, calcium, magnesium and potassium, iron, sulphate and aluminum. We placed PRS probes at a depth of 5 - 15 cm in pristine plots and plots with long term N, P and K fertilization for 4 weeks and determined the availability of these nutrients, from spring through to fall. Probes were also placed beneath the water table in hummock and hollow microtopography and along a transect including part of the bog which had been drained through the creation of a ditch 80 years ago. The result showed that there was limited available ammonium, nitrate and phosphate in the bog, the seasonal variation of nutrient availabilities probably due to mineralization, an increase in the availability of some nutrients between different water table depths or as a result of drainage, and the relative availability of nutrients compared to the input from fertilization. We suggest that PRS probes could be a useful tool to examine nutrient availability and dynamics in wetlands, with careful consideration of installing condition, for example, proper exposure period, depth relative to water table etc.
Investigation of the pp→K+nΣ+ reaction at the magnetic spectrometer ANKE-COSY

International Nuclear Information System (INIS)

Valdau, Yury

2009-01-01

This thesis describes measurements of the pp→K + nΣ + reaction near threshold. The work was largely motivated by the lack of data for Σ + hyperon production in pp collisions and, in particular, by recent measurements of pp→K + nΣ + by the COSY11 collaboration. The experiment performed by this group using a neutron detector reported surprisingly high Σ + cross sections that are hard to reconcile with isospin considerations. The experiment discussed in the thesis has been performed at the ANKE-COSY facility at four close-to-threshold energies. It relies on the almost background-free K + identification using the delayed-veto technique and the fact that below the threshold for pp→K + nΛπ + there is no source of the K + π + correlations other than the Σ + →nπ + decay. Thus, the detection of K + π + pairs allows one to identify the pp→K + nΣ + reaction without the need for a neutron detector. The analysis of three simultaneously measured spectra has been carried out, searching for any signal from a possible high Σ + cross section. All the K + production channels allowed at the energy of the experiment contribute to the K + inclusive and K + p correlation spectra. In the K + inclusive distributions, signals from the different production channels are summed and can only be isolated using theoretical models. In the K + p correlation spectra, there are not only signals from the direct reaction protons but also protons from hyperon decays can be observed. Thus, the signal from Σ + →pπ 0 decay contributes to the K + p missing mass. The study of the K + π + correlations allows one to identify the Σ + reaction channels and to estimate the total production cross section. This method has been successfully applied to existing ANKE data collected in August 2003 and resulted in a publication a refereed journal. Analysis of experimental data collected in September 2007 yielded following results: -The pp→K + nΣ + total cross sections measured at four
Atomic physics modeling of transmission spectra of Sc-doped aerogel foams to support OMEGA experiments

Energy Technology Data Exchange (ETDEWEB)

Johns, H. M., E-mail: hjohns@lanl.gov; Lanier, N. E.; Kline, J. L.; Fontes, C. J.; Perry, T. S.; Fryer, C. L.; Sherrill, M. E. [Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87544 (United States); Brown, C. R. D.; Morton, J. W. [AWE Aldermaston, Berkshire, Reading RG7 4PR (United Kingdom); Hager, J. D. [Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87544 (United States); Lockheed-Martin, 497 Electronics Parkway, Syracuse, New York 13221 (United States)

2016-11-15

We present synthetic transmission spectra generated with PrismSPECT utilizing both the ATBASE model and the Los Alamos opacity library (OPLIB) to evaluate whether an alternative choice in atomic data will impact modeling of experimental data from radiation transport experiments using Sc-doped aerogel foams (ScSi{sub 6}O{sub 12} at 75 mg/cm{sup 3} density). We have determined that in the 50-200 eV T{sub e} range there is a significant difference in the 1s-3p spectra, especially below 100 eV, and for T{sub e} = 200 eV above 5000 eV in photon energy. Examining synthetic spectra generated using OPLIB with 300 resolving power reveals spectral sensitivity to T{sub e} changes of ∼3 eV.
Analytical Model of Doppler Spectra of Light Backscattered from Rotating Convex Bodies of Revolution in the Global Cartesian Coordinate System

International Nuclear Information System (INIS)

Yan-Jun, Gong; Zhen-Sen, Wu; Jia-Ji, Wu

2009-01-01

We present an analytical model of Doppler spectra in backscattering from arbitrary rough convex bodies of revolution rotating around their axes in the global Cartesian coordinate system. This analytical model is applied to analyse Doppler spectra in backscatter from two cones and two cylinders, as well as two ellipsoids of revolution. We numerically analyse the influences of attitude and geometry size of objects on Doppler spectra. The analytical model can give contribution of the surface roughness, attitude and geometry size of convex bodies of revolution to Doppler spectra and may contribute to laser Doppler velocimetry as well as ladar applications
Strength and Deformability of Light-toned Layered Deposits Observed by MER Opportunity: Eagle to Erebus Craters

Science.gov (United States)

Okubo, C. H.; Schultz, R. A.; Nahm, A. L.

2007-07-01

The strength and deformability of light-toned layered deposits are estimated based on measurements of porosity from Microscopic Imager data acquired by MER Opportunity during its traverse from Eagle Crater to Erebus Crater.
Using Molecular Modeling in Teaching Group Theory Analysis of the Infrared Spectra of Organometallic Compounds

Science.gov (United States)

Wang, Lihua

2012-01-01

A new method is introduced for teaching group theory analysis of the infrared spectra of organometallic compounds using molecular modeling. The main focus of this method is to enhance student understanding of the symmetry properties of vibrational modes and of the group theory analysis of infrared (IR) spectra by using visual aids provided by…

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers

DEFF Research Database (Denmark)

Lundegaard, Claus; Lund, Ole; Nielsen, Morten

2008-01-01

Several accurate prediction systems have been developed for prediction of class I major histocompatibility complex (MHC):peptide binding. Most of these are trained on binding affinity data of primarily 9mer peptides. Here, we show how prediction methods trained on 9mer data can be used for accurate...
A self-consistent model for the Galactic cosmic ray, antiproton and positron spectra

CERN Multimedia

CERN. Geneva

2015-01-01

In this talk I will present the escape model of Galactic cosmic rays. This model explains the measured cosmic ray spectra of individual groups of nuclei from TeV to EeV energies. It predicts an early transition to extragalactic cosmic rays, in agreement with recent Auger data. The escape model also explains the soft neutrino spectrum 1/E^2.5 found by IceCube in concordance with Fermi gamma-ray data. I will show that within the same model one can explain the excess of positrons and antiprotons above 20 GeV found by PAMELA and AMS-02, the discrepancy in the slopes of the spectra of cosmic ray protons and heavier nuclei in the TeV-PeV energy range and the plateau in cosmic ray dipole anisotropy in the 2-50 TeV energy range by adding the effects of a 2 million year old nearby supernova.
Feasibility of N-Gram Data-Structures for Next-Generation Pathogen Signature Design

Energy Technology Data Exchange (ETDEWEB)

Gardner, S N

2009-01-26

We determined the most appropriate data structure for handling n-gram (also known as k-mer) string comparisons and storage for genomic sequence data that will scale in terms of memory and speed. This is critical to maintain LLNL as the leader in pathogen detection, as it will guide the design of the 'Next Generation' system for computational signature prediction. There are two parts to k-mer analysis for signature prediction that we investigated. First is the enumeration and frequency counting of all observed k-mers in a sequence database (k-mer is a biological term equivalent to the CS term n-gram). Second is the down-selection and pairing of k-mers to generate a signature. We determined that for the first part, suffix arrays are the preferred method to enumerate k-mers, being memory efficient and relatively easy and fast to compute. For the second part, a subset of the k-mers can be stored and manipulated in a hash, that subset determination based on desired frequency characteristics such as most/least frequent from a set, shared among sequence sets, or discriminating across sequence sets.
OPTICAL CONSTANTS AND LAB SPECTRA OF WATER ICE V1.0

Data.gov (United States)

National Aeronautics and Space Administration — Transmission spectra of amorphous and crystalline H2O-ice at temperatures from 20-150 K for a wavelength range from 1.11 to 2.63 microns. These spectra have not been...
OPTICAL CONSTANTS AND LAB SPECTRA OF WATER ICE V1.1

Data.gov (United States)

National Aeronautics and Space Administration — Transmission spectra of amorphous and crystalline H2O-ice at temperatures from 20-150 K for a wavelength range from 1.11 to 2.63 microns. These spectra have not been...
Measurement of the infrared optical constants for spectral modeling: n and k values for (NH4)2SO4 via single-angle reflectance and ellipsometric methods

Energy Technology Data Exchange (ETDEWEB)

Blake, Thomas A.; Brauer, Carolyn S.; Kelly-Gorham, Molly Rose K.; Burton, Sarah D.; Bliss, Mary; Myers, Tanya L.; Johnson, Timothy J.; Tiwald, Thomas E.

2017-05-05

The optical constants n and k can be used to model infrared spectra, including refraction, absorption, reflectance, and emissivity, but obtaining reliable values for solid materials (pure or otherwise) presents a challenge: In the past, the best results for n and k have been obtained from bulk, homogeneous materials, free of defects. That is, materials where the Fresnel equations are operant since there is no light scattering. Since it is often not possible to obtain a pure macroscopic (crystalline) material, it may be possible to press the material into a (uniform, void-free) disk. We have recently been able to do this with ammonium sulfate powder and then measured the n & k values via two independent methods: 1) Ellipsometry - which measures the changes in amplitude and phase of light reflected from the material of interest as a function of wavelength and angle of incidence, and 2) Single angle specular reflectance with an FT spectrometer using a specular reflectance device within an FT instrument which measures the change in amplitude of light reflected from the material of interest as a function of wavelength and angle of incidence over a wide wavelength range. The quality of the derived n & k values was tested by generating the reflectance spectra of the pellet and comparing to the calculated to measured reflectance spectra of the pure material which has been previously published. The comparison to literature values showed good accuracy and good agreement, indicating promise to measure other materials by such methods.
Characterization of K-complexes and slow wave activity in a neural mass model.

Directory of Open Access Journals (Sweden)

Arne Weigenand

2014-11-01

Full Text Available NREM sleep is characterized by two hallmarks, namely K-complexes (KCs during sleep stage N2 and cortical slow oscillations (SOs during sleep stage N3. While the underlying dynamics on the neuronal level is well known and can be easily measured, the resulting behavior on the macroscopic population level remains unclear. On the basis of an extended neural mass model of the cortex, we suggest a new interpretation of the mechanisms responsible for the generation of KCs and SOs. As the cortex transitions from wake to deep sleep, in our model it approaches an oscillatory regime via a Hopf bifurcation. Importantly, there is a canard phenomenon arising from a homoclinic bifurcation, whose orbit determines the shape of large amplitude SOs. A KC corresponds to a single excursion along the homoclinic orbit, while SOs are noise-driven oscillations around a stable focus. The model generates both time series and spectra that strikingly resemble real electroencephalogram data and points out possible differences between the different stages of natural sleep.
Cl K-edge XANES spectra of atmospheric rust on Fe, Fe-Cr and Fe-Ni alloys exposed to saline environment

International Nuclear Information System (INIS)

Konishi, Hiroyuki; Mizuki, Jun'ichiro; Yamashita, Masato; Uchida, Hitoshi

2004-01-01

Cl K-edge XANES measurements of atmospheric corrosion products (rust) formed on Fe, Fe-Ni and Fe-Cr alloys in chloride pollution have been performed using synchrotron radiation in order to clarify roles of anticorrosive alloying elements and of Cl in the corrosion resistance of weathering steel. The spectra of binary alloys show a shoulder structure near the absorption edge. The intensity of the shoulder peak depends on the kind and amount of the alloying element, whereas the energy position is invariant. This indicates that Cl is not combined directly with alloying elements in the rust. (author)
The Role of Social Work for Foreign Residents in an Epidemic: The MERS Crisis in the Republic of Korea.

Science.gov (United States)

Park, Hong-Jae; Lee, Bong Joo

2016-01-01

This article explores the experiences of foreign residents during the period of the Middle East Respiratory Syndrome (MERS) outbreak in (South) Korea and discusses from a social work perspective the implications of their experiences and their needs. Data were obtained from interviews with 22 foreigners who either live and work or study in Korea. The data were then interpreted using a thematic analysis approach in a multilingual research context. The findings from the study show that foreign residents experienced a wide range of social and psychoemotional difficulties during the MERS health threat. Implications for social work practice in an epidemic emergency are presented.
The ultrasonic relaxation spectra for furfural molecules undergoing conformational changes

International Nuclear Information System (INIS)

Mirzaev, S. Z.; Telyaev, S. Q.; Egamberdiev, K.

2011-01-01

The acoustic spectra of liquid furfural have been investigated in the frequency range from 0.1MHz to 150 MHz and at the temperatures from 303.15 K to 333.15 K. The ultrasonic spectra of pure furfural show two relaxation processes. One relaxation process is located in the frequency range ∼0.2 MHz, and the second in the frequency range ∼2 MHz. The process with the lower relaxation frequency has been assigned to the 'X0-cis and X0-trans' internal rotation of furfural molecules. (authors)
Rezension: Ada Lovelace. Die Pionierin der Computertechnik und ihre Nachfolgerinnen von Sybille Krämer (Hg.)

OpenAIRE

Bettina Schabschneider

2015-01-01

Ein aktueller von Sybille Krämer herausgegebener Sammelband beleuchtet die Bedeutung der Computertechnik-Pionierin Ada Lovelace. Bettina Schabschneider hat den Band einer detaillierten Lektüre unterzogen und für die MEDIENIMPULSE rezensiert …
Modelling of oscillations in two-dimensional echo-spectra of the Fenna-Matthews-Olson complex

International Nuclear Information System (INIS)

Hein, Birgit; Kreisbeck, Christoph; Kramer, Tobias; Rodríguez, Mirta

2012-01-01

Recent experimental observations of time-dependent beatings in the two-dimensional echo-spectra of light-harvesting complexes at ambient temperatures have opened up the question of whether coherence and wave-like behaviour play a significant role in photosynthesis. We carry out a numerical study of the absorption and echo-spectra of the Fenna-Matthews-Olson (FMO) complex in Chlorobium tepidum and analyse the requirements in the theoretical model needed to reproduce beatings in the calculated spectra. The energy transfer in the FMO pigment-protein complex is theoretically described by an exciton Hamiltonian coupled to a phonon bath which accounts for the pigments' electronic and vibrational excitations, respectively. We use the hierarchical equations of motions method to treat the strong couplings in a non-perturbative way. We show that the oscillations in the two-dimensional echo-spectra persist in the presence of thermal noise and static disorder. (paper)
Evolution of complex organic molecules in hot molecular cores. Synthetic spectra at (sub-)mm wavebands

Science.gov (United States)

Choudhury, R.; Schilke, P.; Stéphan, G.; Bergin, E.; Möller, T.; Schmiedeke, A.; Zernickel, A.

2015-03-01

Context. Hot molecular cores (HMCs) are intermediate stages of high-mass star formation and are also known for their rich chemical reservoirs and emission line spectra at (sub-)mm wavebands. Complex organic molecules (COMs) such as methanol (CH3OH), ethanol (C2H5OH), dimethyl ether (CH3OCH3), and methyl formate (HCOOCH3) produce most of these observed lines. The observed spectral feature of HMCs such as total number of emission lines and associated line intensities are also found to vary with evolutionary stages. Aims: We aim to investigate the spectral evolution of these COMs to explore the initial evolutionary stages of high-mass star formation including HMCs. Methods: We developed various 3D models for HMCs guided by the evolutionary scenarios proposed by recent empirical and modeling studies. We then investigated the spatio-temporal variation of temperature and molecular abundances in HMCs by consistently coupling gas-grain chemical evolution with radiative transfer calculations. We explored the effects of varying physical conditions on molecular abundances including density distribution and luminosity evolution of the central protostar(s) among other parameters. Finally, we simulated the synthetic spectra for these models at different evolutionary timescales to compare with observations. Results: Temperature has a profound effect on the formation of COMs through the depletion and diffusion on grain surface to desorption and further gas-phase processing. The time-dependent temperature structure of the hot core models provides a realistic framework for investigating the spatial variation of ice mantle evaporation as a function of evolutionary timescales. We find that a slightly higher value (15 K) than the canonical dark cloud temperature (10 K) provides a more productive environment for COM formation on grain surface. With increasing protostellar luminosity, the water ice evaporation font (~100 K) expands and the spatial distribution of gas phase abundances of
Predictive modelling of the dielectric response of plasmonic substrates: application to the interpretation of ellipsometric spectra

Science.gov (United States)

Pugliara, A.; Bayle, M.; Bonafos, C.; Carles, R.; Respaud, M.; Makasheva, K.

2018-03-01

A predictive modelling of plasmonic substrates appropriate to read ellipsometric spectra is presented in this work. We focus on plasmonic substrates containing a single layer of silver nanoparticles (AgNPs) embedded in silica matrices. The model uses the Abeles matrix formalism and is based on the quasistatic approximation of the classical Maxwell-Garnett mixing rule, however accounting for the electronic confinement effect through the damping parameter. It is applied on samples elaborated by: (i) RF-diode sputtering followed by Plasma Enhanced Chemical Vapor Deposition (PECVD) and (ii) Low Energy Ion Beam Synthesis (LE-IBS), and represents situations with increasing degree of complexity that can be accounted for by the model. It allows extraction of the main characteristics of the AgNPs population: average size, volume fraction and distance of the AgNPs layer from the matrix free surface. Model validation is achieved through comparison with results obtained from transmission electron microscopy approving for its applicability. The advantages and limitations of the proposed model are discussed after eccentricity-based statistical analysis along with further developments related to the quality of comparison between the model-generated spectra and the experimentally-recorded ellipsometric spectra.
Extracting Optical Fiber Background from Surface-Enhanced Raman Spectroscopy Spectra Based on Bi-Objective Optimization Modeling.

Science.gov (United States)

Huang, Jie; Shi, Tielin; Tang, Zirong; Zhu, Wei; Liao, Guanglan; Li, Xiaoping; Gong, Bo; Zhou, Tengyuan

2017-08-01

We propose a bi-objective optimization model for extracting optical fiber background from the measured surface-enhanced Raman spectroscopy (SERS) spectrum of the target sample in the application of fiber optic SERS. The model is built using curve fitting to resolve the SERS spectrum into several individual bands, and simultaneously matching some resolved bands with the measured background spectrum. The Pearson correlation coefficient is selected as the similarity index and its maximum value is pursued during the spectral matching process. An algorithm is proposed, programmed, and demonstrated successfully in extracting optical fiber background or fluorescence background from the measured SERS spectra of rhodamine 6G (R6G) and crystal violet (CV). The proposed model not only can be applied to remove optical fiber background or fluorescence background for SERS spectra, but also can be transferred to conventional Raman spectra recorded using fiber optic instrumentation.
Reflectance Spectra Diversity of Silica-Rich Materials: Sensitivity to Environment and Implications for Detections on Mars

Science.gov (United States)

Rice, M. S.; Cloutis, E. A.; Bell, J. F., III; Bish, D. L.; Horgan, B. H.; Mertzman, S. A.; Craig, M. A.; Renault, R. W.; Gautason, B.; Mountain, B.

2013-01-01

Hydrated silica-rich materials have recently been discovered on the surface of Mars by the Mars Exploration Rover (MER) Spirit, the Mars Reconnaissance Orbiter (MRO) Compact Reconnaissance Imaging Spectrometer for Mars (CRISM), and the Mars Express Observatoire pour la Mineralogie, l'Eau, les Glaces, et l'Activite'(OMEGA) in several locations. Having been interpreted as hydrothermal deposits and aqueous alteration products, these materials have important implications for the history of water on the martian surface. Spectral detections of these materials in visible to near infrared (Vis NIR) wavelengths have been based on a H2O absorption feature in the 934-1009 nm region seen with Spirit s Pancam instrument, and on SiOH absorption features in the 2.21-2.26 micron range seen with CRISM. Our work aims to determine how the spectral reflectance properties of silica-rich materials in Vis NIR wavelengths vary as a function of environmental conditions and formation. Here we present laboratory reflectance spectra of a diverse suite of silica-rich materials (chert, opal, quartz, natural sinters and synthetic silica) under a range of grain sizes and temperature, pressure, and humidity conditions. We find that the H2O content and form of H2O/OH present in silica-rich materials can have significant effects on their Vis NIR spectra. Our main findings are that the position of the approx.1.4 microns OH feature and the symmetry of the approx.1.9 microns feature can be used to discern between various forms of silica-rich materials, and that the ratio of the approx.2.2 microns (SiOH) and approx.1.9 microns (H2O) band depths can aid in distinguishing between silica phases (opal-A vs. opal-CT) and formation conditions (low vs. high temperature). In a case study of hydrated silica outcrops in Valles Marineris, we show that careful application of a modified version of these spectral parameters to orbital near-infrared spectra (e.g., from CRISM and OMEGA) can aid in characterizing the
Discriminating model for diagnosis of basal cell carcinoma and melanoma in vitro based on the Raman spectra of selected biochemicals

Science.gov (United States)

Silveira, Landulfo; Silveira, Fabrício Luiz; Bodanese, Benito; Zângaro, Renato Amaro; Pacheco, Marcos Tadeu T.

2012-07-01

Raman spectroscopy has been employed to identify differences in the biochemical constitution of malignant [basal cell carcinoma (BCC) and melanoma (MEL)] cells compared to normal skin tissues, with the goal of skin cancer diagnosis. We collected Raman spectra from compounds such as proteins, lipids, and nucleic acids, which are expected to be represented in human skin spectra, and developed a linear least-squares fitting model to estimate the contributions of these compounds to the tissue spectra. We used a set of 145 spectra from biopsy fragments of normal (30 spectra), BCC (96 spectra), and MEL (19 spectra) skin tissues, collected using a near-infrared Raman spectrometer (830 nm, 50 to 200 mW, and 20 s exposure time) coupled to a Raman probe. We applied the best-fitting model to the spectra of biochemicals and tissues, hypothesizing that the relative spectral contribution of each compound to the tissue Raman spectrum changes according to the disease. We verified that actin, collagen, elastin, and triolein were the most important biochemicals representing the spectral features of skin tissues. A classification model applied to the relative contribution of collagen III, elastin, and melanin using Euclidean distance as a discriminator could differentiate normal from BCC and MEL.
XUV spectra of laser-produced zirconium plasmas

Czech Academy of Sciences Publication Activity Database

Li, B.; Higashiguchi, T.; Otsuka, T.; Jiang, W.; Endo, Akira; Dunne, P.; O'Sullivan, G.

2012-01-01

Roč. 45, č. 24 (2012), "245004-1"-"245004-6" ISSN 0953-4075 R&D Projects: GA MŠk ED2.1.00/01.0027; GA MŠk EE2.3.20.0143 Grant - others:HILASE(XE) CZ.1.05/2.1.00/01.0027; OP VK 6 k HILASE(XE) CZ.1.07/2.3.00/20.0143 Program:EE Institutional support: RVO:68378271 Keywords : x-ray-spectra * dielectronic recombination * transitions * spectroscopy * microscopy * ions Subject RIV: BH - Optics, Masers, Lasers Impact factor: 2.031, year: 2012
A passive physical model for DnaK chaperoning

Science.gov (United States)

Uhl, Lionel; Dumont, Audrey; Dukan, Sam

2018-03-01

Almost all living organisms use protein chaperones with a view to preventing proteins from misfolding or aggregation either spontaneously or during cellular stress. This work uses a reaction-diffusion stochastic model to describe the dynamic localization of the Hsp70 chaperone DnaK in Escherichia coli cells during transient proteotoxic collapse characterized by the accumulation of insoluble proteins. In the model, misfolded (‘abnormal’) proteins are produced during alcoholic stress and have the propensity to aggregate with a polymerization-like kinetics. When aggregates diffuse more slowly they grow larger. According to Michaelis-Menten-type kinetics, DnaK has the propensity to bind with misfolded proteins or aggregates in order to catalyse refolding. To match experimental fluorescence microscopy data showing clusters of DnaK-GFP localized in multiple foci, the model includes spatial zones with local reduced diffusion rates to generate spontaneous assemblies of DnaK called ‘foci’. Numerical simulations of our model succeed in reproducing the kinetics of DnaK localization experimentally observed. DnaK starts from foci, moves to large aggregates during acute stress, resolves those aggregates during recovery and finally returns to its initial punctate localization pattern. Finally, we compare real biological events with hypothetical repartitions of the protein aggregates or DnaK. We then notice that DnaK action is more efficient on protein aggregates than on protein homogeneously distributed.
Maintenance energy requirements in miniature colony dogs.

Science.gov (United States)

Serisier, S; Weber, M; Feugier, A; Fardet, M-O; Garnier, F; Biourge, V; German, A J

2013-05-01

There are numerous reports of maintenance energy requirements (MER) in dogs, but little information is available about energy requirements of miniature dog breeds. In this prospective, observational, cohort study, we aimed to determine MER in dogs from a number of miniature breeds and to determine which factors were associated with it. Forty-two dogs participated in the study. MER was calculated by determining daily energy intake (EI) during a period of 196 days (28-359 days) when body weight did not change significantly (e.g. ±2% in 12 weeks). Estimated median MER was 473 kJ/kg(0.75) /day (285-766 kJ/kg(0.75) /day), that is, median 113 kcal/kg(0.75) /day (68-183 kcal/kg(0.75) /day). In the obese dogs that lost weight, median MER after weight loss was completed was 360 kJ/kg(0.75) /day (285-515 kJ/kg(0.75) /day), that is, 86 kcal/kg(0.75) /day, (68-123 kcal/kg(0.75) /day). Simple linear regression analysis suggested that three breeds (e.g. Chihuahua, p = 0.002; Yorkshire terrier, p = 0.039; dachshund, p = 0.035) had an effect on MER. In addition to breed, simple linear regression revealed that neuter status (p = 0.079) and having previously been overweight (p = 0.002) were also of significance. However, with multiple linear regression analysis, only previous overweight status (MER less in dogs previously overweight p = 0.008) and breed (MER greater in Yorkshire terriers [p = 0.029] and less in Chihuahuas [p = 0.089]) remained in the final model. This study is the first to estimate MER in dogs of miniature breeds. Although further information from pet dogs is now needed, the current work will be useful for setting energy and nutrient requirement in such dogs for the future. Journal of Animal Physiology and Animal Nutrition © 2013 Blackwell Verlag GmbH.

Avoiding student infection during a Middle East respiratory syndrome (MERS) outbreak: a single medical school experience.

Science.gov (United States)

Park, Seung Won; Jang, Hye Won; Choe, Yon Ho; Lee, Kyung Soo; Ahn, Yong Chan; Chung, Myung Jin; Lee, Kyu-Sung; Lee, Kyunghoon; Han, Taehee

2016-06-01

In outbreaks of infectious disease, medical students are easily overlooked in the management of healthcare personnel protection although they serve in clinical clerkships in hospitals. In the early summer of 2015, Middle East respiratory syndrome (MERS) struck South Korea, and students of Sungkyunkwan University School of Medicine (SKKUSOM) were at risk of contracting the disease. The purpose of this report is to share SKKUSOM's experience against the MERS outbreak and provide suggestions for medical schools to consider in the face of similar challenges. Through a process of reflection-on-action, we examined SKKUSOM's efforts to avoid student infection during the MERS outbreak and derived a few practical guidelines that medical schools can adopt to ensure student safety in outbreaks of infectious disease. The school leadership conducted ongoing risk assessment and developed contingency plans to balance student safety and continuity in medical education. They rearranged the clerkships to another hospital and offered distant lectures and tutorials. Five suggestions are extracted for medical schools to consider in infection outbreaks: instant cessation of clinical clerkships; rational decision making on a school closure; use of information technology; constant communication with hospitals; and open communication with faculty, staff, and students. Medical schools need to take the initiative and actively seek countermeasures against student infection. It is essential that medical schools keep constant communication with their index hospitals and the involved personnel. In order to assure student learning, medical schools may consider offering distant education with online technology.
On Developments of k-τ and k-ω Models for Near-Wall Turbulence of Engineering Duct Flows

DEFF Research Database (Denmark)

Rokni, Masoud; Sundén, Bengt

2009-01-01

-epsilon model namely, the lack of natural boundary conditions. Based on idea of Kolmogorov time-scale a boundary condition at the wall is also proposed. A bounded k-omega model for near wall turbulence is also presented and comparison with other well established two-equation models (k-epsilon model and Wilcox k...
Low-frequency vibrational spectra of crystals of tutton salts

Science.gov (United States)

Barashkov, M. V.; Zazhogin, A. A.; Komyak, A. I.; Shashkov, S. N.

2000-07-01

IR absorption spectra and polarized Raman spectra of crystals of Tutton salts K2M(SO4)26H2O and (NH4)2M(SO4)2·6H2O, where M=Co, Ni, Zn, have been obtained by experiment at 93 K and at room temperature. The frequencies and forms of normal modes of the [Zn(H2O)6]2+ octahedral complex have been calculated. The observed lines are assigned to the internal modes of the [M(H2O)6]2+ complex and external modes of the crystal lattice in accordance with the results of the calculations and factor-group analysis.
An IR investigation of solid amorphous ethanol - Spectra, properties, and phase changes

Science.gov (United States)

Hudson, Reggie L.

2017-12-01

Mid- and far-infrared spectra of condensed ethanol (CH3CH2OH) at 10-160 K are presented, with a special focus on amorphous ethanol, the form of greatest astrochemical interest, and with special attention given to changes at 155-160 K. Infrared spectra of amorphous and crystalline forms are shown. The refractive index at 670 nm of amorphous ethanol at 16 K is reported, along with three IR band strengths and a density. A comparison is made to recent work on the isoelectronic compound ethanethiol (CH3CH2SH), and several astrochemical applications are suggested for future study.
Spectroscopic properties of K5Li2UF10

International Nuclear Information System (INIS)

Karbowiak, M.; Gajek, Z.; Drozdzynski, J.

2005-01-01

A new uranium (III) fluoro-complex of the formula K 5 Li 2 UF 10 has been synthesised and characterised by X-ray powder diffraction and electronic absorption spectra measurements. The compound crystallises in the orthorhombic system, space group Pnma, with a = 20.723, b = 7.809, c = 6.932 A, V = 1121.89 A 3 , Z = 4 and is isostructural with its K 5 Li 2 NdF 10 and K 5 Li 2 LaF 10 analogous. The absorption spectrum of a polycrystalline sample of K 5 Li 2 UF 10 was recorded at 4.2 K in the 3500-45,000 cm -1 range and is discussed. The observed crystal-field levels were assigned and fitted to parameters of the simplified angular overlap model (AOM) and next to those of a semi-empirical Hamiltonian, which was representing the combined atomic and one-electron crystal-field interactions. The starting values of the AOM parameters were obtained from ab initio calculations. The analysis of the spectra enabled the assignment of 71 crystal-field levels of U 3+ with a relatively small r.m.s. deviation of 37 cm -1 . The total splitting of 714 cm -1 was calculated for the 4 I 9/2 ground multiplet
Spectroscopic properties of K 5Li 2UF 10

Science.gov (United States)

Karbowiak, M.; Gajek, Z.; Drożdżyński, J.

2005-04-01

A new uranium (III) fluoro-complex of the formula K 5Li 2UF 10 has been synthesised and characterised by X-ray powder diffraction and electronic absorption spectra measurements. The compound crystallises in the orthorhombic system, space group Pnma, with a = 20.723, b = 7.809, c = 6.932 Å, V = 1121.89 Å 3, Z = 4 and is isostructural with its K 5Li 2NdF 10 and K 5Li 2LaF 10 analogous. The absorption spectrum of a polycrystalline sample of K 5Li 2UF 10 was recorded at 4.2 K in the 3500-45,000 cm -1 range and is discussed. The observed crystal-field levels were assigned and fitted to parameters of the simplified angular overlap model (AOM) and next to those of a semi-empirical Hamiltonian, which was representing the combined atomic and one-electron crystal-field interactions. The starting values of the AOM parameters were obtained from ab initio calculations. The analysis of the spectra enabled the assignment of 71 crystal-field levels of U 3+ with a relatively small r.m.s. deviation of 37 cm -1. The total splitting of 714 cm -1 was calculated for the 4I 9/2 ground multiplet.
Rezension: Ada Lovelace. Die Pionierin der Computertechnik und ihre Nachfolgerinnen von Sybille Krämer (Hg.

Directory of Open Access Journals (Sweden)

Bettina Schabschneider

2015-12-01

Full Text Available Ein aktueller von Sybille Krämer herausgegebener Sammelband beleuchtet die Bedeutung der Computertechnik-Pionierin Ada Lovelace. Bettina Schabschneider hat den Band einer detaillierten Lektüre unterzogen und für die MEDIENIMPULSE rezensiert …
Prevalence of MERS-CoV nasal carriage and compliance with the Saudi health recommendations among pilgrims attending the 2013 Hajj.

Science.gov (United States)

Memish, Ziad A; Assiri, Abdullah; Almasri, Malak; Alhakeem, Rafat F; Turkestani, Abdulhafeez; Al Rabeeah, Abdullah A; Al-Tawfiq, Jaffar A; Alzahrani, Abdullah; Azhar, Essam; Makhdoom, Hatem Q; Hajomar, Waleed H; Al-Shangiti, Ali M; Yezli, Saber

2014-10-01

Annually, Saudi Arabia is the host of the Hajj mass gathering. We aimed to determine the Middle East respiratory syndrome coronavirus (MERS-CoV) nasal carriage rate among pilgrims performing the 2013 Hajj and to describe the compliance with the Saudi Ministry of Health vaccine recommendations. Nasopharyngeal samples were collected from 5235 adult pilgrims from 22 countries and screened for MERS-CoV using reverse transcriptase-polymerase chain reaction. Information regarding the participants' age, gender, country of origin, medical conditions, and vaccination history were obtained. The mean age of the screened population was 51.8 years (range, 18-93 years) with a male/female ratio of 1.17:1. MERS-CoV was not detected in any of the samples tested (3210 pre-Hajj and 2025 post-Hajj screening). According to the vaccination documents, all participants had received meningococcal vaccination and the majority of those from at-risk countries were vaccinated against yellow fever and polio. Only 22% of the pilgrims (17.5% of those ≥65 years and 36.3% of diabetics) had flu vaccination, and 4.4% had pneumococcal vaccination. There was no evidence of MERS-CoV nasal carriage among Hajj pilgrims. While rates of compulsory vaccinations uptake were high, uptake of pneumococcal and flu seasonal vaccinations were low, including among the high-risk population. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
On the dynamics of k-essence models

International Nuclear Information System (INIS)

Jorge, Pedro; Mimoso, Jose P; Wands, David

2007-01-01

We investigate cosmological dynamics of models with higher-order corrections to the canonical (second-order) kinetic lagrangian for a scalar field, which have been termed k -essence . We study the qualitative dynamics of simple purely kinetic k-essence models and find that the simplest attempts to construct non-singular cosmological models by including higher-order terms in the kinetic lagrangian fail because of a different type of singularity where the scalar field theory becomes ill-defined
Multivariate analysis of electrical impedance spectra for relaxed and contracted skeletal muscle

International Nuclear Information System (INIS)

Zagar, T; Krizaj, D

2008-01-01

Four-electrode impedance spectra of relaxed and contracted muscle biceps brachii were analyzed in an adult human subject over the frequency range from 300 Hz to 75 kHz. A feasibility of the principal component analysis of bioimpedance measurement for the evaluation of skeletal muscle contractile state was examined. The principal components score plots show a data grouping of the impedance spectra from the two muscle groups. The classification was performed using a soft independent modeling of class analogy (SIMCA) method. The data set comprised 32 samples (16 samples of contracted muscle and 16 samples of relaxed muscle). The leave-one-out test of the classification yields about 80% of correctly classified samples (11 samples for contracted and 15 samples for relaxed muscle)
Can a one-layer optical skin model including melanin and inhomogeneously distributed blood explain spatially resolved diffuse reflectance spectra?

Science.gov (United States)

Karlsson, Hanna; Pettersson, Anders; Larsson, Marcus; Strömberg, Tomas

2011-02-01

Model based analysis of calibrated diffuse reflectance spectroscopy can be used for determining oxygenation and concentration of skin chromophores. This study aimed at assessing the effect of including melanin in addition to hemoglobin (Hb) as chromophores and compensating for inhomogeneously distributed blood (vessel packaging), in a single-layer skin model. Spectra from four humans were collected during different provocations using a twochannel fiber optic probe with source-detector separations 0.4 and 1.2 mm. Absolute calibrated spectra using data from either a single distance or both distances were analyzed using inverse Monte Carlo for light transport and Levenberg-Marquardt for non-linear fitting. The model fitting was excellent using a single distance. However, the estimated model failed to explain spectra from the other distance. The two-distance model did not fit the data well at either distance. Model fitting was significantly improved including melanin and vessel packaging. The most prominent effect when fitting data from the larger separation compared to the smaller separation was a different light scattering decay with wavelength, while the tissue fraction of Hb and saturation were similar. For modeling spectra at both distances, we propose using either a multi-layer skin model or a more advanced model for the scattering phase function.
A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.

Science.gov (United States)

Smith, Robin P; Riesenfeld, Samantha J; Holloway, Alisha K; Li, Qiang; Murphy, Karl K; Feliciano, Natalie M; Orecchia, Lorenzo; Oksenberg, Nir; Pollard, Katherine S; Ahituv, Nadav

2013-07-18

Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from the activity of short, transcription factor binding sequences. We describe a comprehensive promoter extension assay in which the regulatory potential of all 6 base-pair (bp) sequences was tested in the context of a minimal promoter. To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence exactly once. Our library multiplexes all 4,096 unique 6-mers into 184 double-stranded 15-bp oligomers, which is sufficiently compact for in vivo testing. We injected each multiplexed construct into zebrafish embryos and scored GFP expression in 15 tissues at two developmental time points. Twenty-seven constructs produced consistent expression patterns, with the majority doing so in only one tissue. Functional sequences are enriched near biologically relevant genes, match motifs for developmental transcription factors, and are required for enhancer activity. By concatenating tissue-specific functional sequences, we generated completely synthetic enhancers for the notochord, epidermis, spinal cord, forebrain and otic lateral line, and show that short regulatory sequences do not always function modularly. This work introduces a unique in vivo catalog of short, functional regulatory sequences and demonstrates several important principles of regulatory element organization. Furthermore, we provide resources for designing compact, reverse-complement aware k-mer libraries.
Modeling X-ray Spectra of Astrophysical Plasmas: Current Status and Future Needs

Science.gov (United States)

Smith, Randall

Existing high-resolution astrophysical X-ray spectra has exposed the need for high-quality atomic data of all stripes: wavelengths, collisional and absorption cross sections, and radiative rates. The Astro-H soft X-ray spectrometer (2015 launch) will vastly increase the number and type of high-resolution X-ray spectra available and likely expose a number of shortcomings in our models. I will describe recent advances in theoretical calculations and laboratory measurements, as well as a number of existing needs in the field. These include accurate soft X-ray wavelengths for L-shell ions, diagnostic emission line ratios with estimated error bars, and high-resolution absorption cross sections for abundant ions and molecules. Finally, new models of emission from non-equilibrium ionization plasmas and astrophysical charge exchange will be discussed. This latter emission arises due to the interaction of highly charged ions with neutral atoms, forming a diffuse background in the case of solar wind ions and possibly also arising in more distant environments.
Nonscaling parametrization of hadronic spectra and dual parton model

International Nuclear Information System (INIS)

Gaponenko, O.N.

2001-01-01

Using the popular Wdowczyk-Wolfendale parametrization (WW-parametrization) as an example one studies restrictions imposed by a dual parton model for different nonscaling parametrizations of the pulsed hadron spectra in soft hadron-hadron and hadron-nuclear interactions. One derived a new parametrization free from basic drawback of the WW-formulae. In the central range the determined parametrization show agreement with the Wdowczyk-Wolfendale formula, but in contrast to the last-named one it does not result in contradiction with the experiment due to fast reduction of inelastic factor reduction with energy increase [ru
Search for the Theta+ pentaquark in the reactions gammap-->[overline K]0K+n and gammap-->[overline K]0K0p

Energy Technology Data Exchange (ETDEWEB)

Raffaella De Vita; Marco Battaglieri; V. Kubarovsky; Nathan Baltzell; Matthew Bellis; John Goett; Lei Guo; Gordon Mutchler; Paul Stoler; Maurizio Ungaro; Dennis Weygand; Moscov Amaryan; Pawel Ambrozewicz; Marco Anghinolfi; Gegham Asryan; Harutyun AVAKIAN; Harutyun Avakian; Hovhannes Baghdasaryan; Nathan Baillie; Jacques Ball; Vitaly Baturin; Ivan Bedlinski; Ivan Bedlinskiy; Nawal Benmouna; Barry Berman; Angela Biselli; Sergey Boyarinov; Sylvain Bouchigny; Robert Bradford; Derek Branford; William Briscoe; William Brooks; Stephen Bueltmann; Volker Burkert; Cornel Butuceanu; John Calarco; Sharon Careccia; Daniel Carman; Shifeng Chen; Eric Clinton; Philip Cole; Patrick Collins; Philip Coltharp; Donald Crabb; Hall Crannell; Volker Crede; John Cummings; D. Dale; Raffaella De Vita; Enzo De Sanctis; Pavel Degtiarenko; Alexandre Deur; Kahanawita Dharmawardane; Chaden Djalali; Gail Dodge; Joseph Donnelly; David Doughty; Michael Dugger; Oleksandr Dzyubak; Hovanes Egiyan; Kim Egiyan; Lamiaa Elfassi; Latifa Elouadrhiri; Paul Eugenio; Gleb Fedotov; Herbert Funsten; Marianna Gabrielyan; Liping Gan; Michel Garcon; Ashot Gasparian; Gagik Gavalian; Gerard Gilfoyle; Kevin Giovanetti; Francois-Xavier Girod; Oleksandr Glamazdin; John Goetz; Evgueni Golovatch; Atilla Gonenc; Christopher Gordon; Ralf Gothe; Keith Griffioen; Michel Guidal; Nevzat Guler; Harutyun Gyurjyan; Cynthia Hadjidakis; Kawtar Hafidi; Hayk Hakobyan; Rafael Hakobyan; John Hardie; F. Hersman; Kenneth Hicks; Ishaq Hleiqawi; Maurik Holtrop; Charles Hyde-Wright; Yordanka Ilieva; David Ireland; Boris Ishkhanov; Eugeny Isupov; Mark Ito; D. Jenkins; Hyon-Suk Jo; Kyungseon Joo; Henry Juengst; James Kellie; Mahbubul Khandaker; Wooyoung Kim; Andreas Klein; Franz Klein; Alexei Klimenko; Mikhail Kossov; Laird Kramer; Joachim Kuhn; Sebastian Kuhn; Sergey Kuleshov; Jeff Lachniet; Jean Laget; Jorn Langheinrich; Dave Lawrence; Tsung-shung Lee; Ji Li; K. Livingston; Haiyun Lu; Marion MacCormick; Nikolai Markov; Bryan McKinnon; Bernhard Mecking; Joseph Melone; Mac Mestayer; Curtis Meyer; Tsutomu Mibe; Konstantin Mikhaylov; Ralph Minehart; Marco Mirazita; R. Miskimen; Vasiliy Mochalov; Viktor Mokeev; Ludyvine Morand; Steven Morrow; Maryam Moteabbed; Pawel Nadel-Turonski; Itaru Nakagawa; Rakhsha Nasseripour; Silvia Niccolai; Gabriel Niculescu; Maria-Ioana Niculescu; Bogdan Niczyporuk; Megh Niroula; Rustam Niyazov; Mina Nozar; Mikhail Osipenko; Alexander Ostrovidov; Kijun Park; Evgueni Pasyuk; Craig Paterson; Joshua Pierce; Nikolay Pivnyuk; Dinko Pocanic; Oleg Pogorelko; Sergey Pozdnyakov; John Price; Yelena Prok; Dan Protopopescu; Brian Raue; Gregory Riccardi; Giovanni Ricco; Marco Ripani; Barry Ritchie; Federico Ronchetti; Guenther Rosner; Patrizia Rossi; Franck Sabatie; Carlos Salgado; Joseph Santoro; Vladimir Sapunenko; Reinhard Schumacher; Vladimir Serov; Youri Sharabian; Nikolay Shvedunov; Elton Smith; Lee Smith; Daniel Sober; Aleksey Stavinskiy; Samuel Stepanyan; Stepan Stepanyan; Burnham Stokes; Igor Strakovski; Steffen Strauch; Mauro Taiuti; David Tedeschi; Aram Teymurazyan; Ulrike Thoma; Avtandil Tkabladze; Svyatoslav Tkachenko; Luminita Todor; Clarisse Tur; Michael Vineyard; Alexander Vlassov; Daniel Watts; Lawrence Weinstein; M. Williams; Elliott Wolin; Michael Wood; Amrit Yegneswaran; Lorenzo Zana; Jixie Zhang; Bo Zhao; Zhiwen Zhao

2006-11-16

The exclusive reactions {gamma}p {yields} {bar K}{sup 0} K{sup +} n and {gamma}p {yields} {bar K}{sup 0} K{sup 0} p have been studied in the photon energy range 1.6--3.8 GeV, searching for evidence of the exotic baryon {Theta}{sup +}(1540) in the decays {Theta}{sup +} {yields} nK{sup +} and {Theta}{sup +} {yields} pK{sup 0}. Data were collected with the CLAS detector at the Thomas Jefferson National Accelerator Facility. The integrated luminosity was about 70 pb{sup -1}. The reactions have been isolated by detecting the K{sup +} and proton directly, the neutral kaon via its decay to K{sub S} {yields} {pi}{sup +}{pi}{sup -} and the neutron or neutral kaon via the missing mass technique. The mass and width of known hyperons such as {Sigma}{sup +}, {Sigma}{sup -} and {Lambda}(1116) were used as a check of the mass determination accuracy and experimental resolution. Approximately 100,000 {Lambda}*(1520)'s and 150,000 {phi}'s were observed in the {bar K}{sup 0} K{sup +} n and {bar K}{sup 0} K{sup 0} p final state respectively. No evidence for the {Theta}{sup +} pentaquark was found in the nK{sup +} or pK{sub S} invariant mass spectra. Upper limits were set on the production cross section of the reaction {gamma}p {yields} {Theta}{sup +} {bar K}{sup 0} as functions of center-of-mass angle, nK{sup +} and pK{sub S} masses. Combining the results of the two reactions, the 95% C.L. upper limit on the total cross section for a resonance peaked at 1540 MeV was found to be 0.7 nb. Within most of the available theoretical models, this corresponds to an upper limit on the {Theta}{sup +} width, {Gamma}{sub {Theta}{sup +}}, ranging between 0.01 and 7 MeV.
Nonlinear optical and electroabsorption spectra of polydiacetylene crystals and films

Science.gov (United States)

Mukhopadhyay, D.; Soos, Z. G.

1996-01-01

Vibronic structure of nonlinear optical (NLO) coefficients is developed within the Condon approximation, displaced harmonic oscillators, and crude adiabatic states. The displacements of backbone modes of conjugated polymers are taken from vibrational data on the ground and 1B excited state. NLO resonances are modeled by three excitations and transition moments taken from Pariser-Parr-Pople (PPP) theory and optimized to polydiacetylene (PDA) spectra in crystals and films, with blue-shifted 1B exciton. The joint analysis of third-harmonic-generation, two-photon absorption, and nondegenerate four-wave-mixing spectra of PDA crystals and films shows weak two-photon absorption to 2A below 1B, leading to overlapping resonances in the THG spectrum, strong two-photon absorption to an nA state some 35% above 1B, and weak Raman resonances in nondegenerate FWM spectra. The full π-π* spectrum contributes to Stark shifts and field-induced transitions, as shown by PPP results for PDA oligomers. The Stark shift dominates high-resolution electroabsorption (EA) spectra of PDA crystals below 10 K. The close correspondence between EA and the first-derivative I'(ω) of the linear absorption above the 1B exciton in PDA crystals provides an experimental separation of vibrational and electronic contributions that limits any even-parity state in this 0.5 eV interval. An oscillator-strength sum rule is applied to the convergence of PDA oligomers with increasing length, N, and the crystal oscillator strengths are obtained without adjustable parameters. The sum rule for the 1B exciton implies large transition moments to higher-energy Ag states, whose locations in recent models are contrasted to PPP results. Joint analysis of NLO and EA spectra clarifies when a few electronic excitations are sufficient, distinguishes between vibrational and electronic contributions, and supports similar π-electron interactions in conjugated molecules and polymers.
INFRARED SPECTRA AND OPTICAL CONSTANTS OF NITRILE ICES RELEVANT TO TITAN's ATMOSPHERE

International Nuclear Information System (INIS)

Moore, Marla H.; Hudson, Reggie; Ferrante, Robert F.; James Moore, W.

2010-01-01

Spectra and optical constants of nitrile ices known or suspected to be in Titan's atmosphere are presented from 2.0 to 333.3 μm (∼5000-30 cm -1 ). These results are relevant to the ongoing modeling of Cassini CIRS observations of Titan's winter pole. Ices studied are: HCN, hydrogen cyanide; C 2 N 2 , cyanogen; CH 3 CN, acetonitrile; C 2 H 5 CN, propionitrile; and HC 3 N, cyanoacetylene. For each of these molecules, we also report new cryogenic measurements of the real refractive index, n, determined in both the amorphous and crystalline phases at 670 nm. These new values have been incorporated into our optical constant calculations. Spectra were measured and optical constants were calculated for each nitrile at a variety of temperatures, including, but not limited to, 20, 35, 50, 75, 95, and 110 K, in both the amorphous phase and the crystalline phase. This laboratory effort used a dedicated FTIR spectrometer to record transmission spectra of thin-film ice samples. Laser interference was used to measure film thickness during condensation onto a transparent cold window attached to the tail section of a closed-cycle helium cryostat. Optical constants, real (n) and imaginary (k) refractive indices, were determined using Kramers-Kronig analysis. Our calculation reproduces the complete spectrum, including all interference effects.
Quantifying the effect of anode surface roughness on diagnostic x-ray spectra using Monte Carlo simulation

Energy Technology Data Exchange (ETDEWEB)

Mehranian, A.; Ay, M. R.; Alam, N. Riyahi; Zaidi, H. [Department of Medical Physics and Biomedical Engineering, Tehran University of Medical Sciences, P.O. Box 14155-6447, Tehran (Iran, Islamic Republic of) and Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, P.O. Box 14185-615, Tehran (Iran, Islamic Republic of); Department of Medical Physics and Biomedical Engineering, Tehran University of Medical Sciences, P.O. Box 14155-6447, Tehran (Iran, Islamic Republic of); Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, P.O. Box 14185-615, Tehran (Iran, Islamic Republic of) and Research Institute for Nuclear Medicine, Tehran University of Medical Sciences, P.O. Box 14155-6447, Tehran (Iran, Islamic Republic of); Department of Medical Physics and Biomedical Engineering, Tehran University of Medical Sciences, P.O. Box 14155-6447, Tehran (Iran, Islamic Republic of); Division of Nuclear Medicine, Geneva University Hospital, CH-1211 Geneva (Switzerland) and Geneva Neuroscience Center, Geneva University, CH-1205 Geneva (Switzerland)

2010-02-15

Purpose: The accurate prediction of x-ray spectra under typical conditions encountered in clinical x-ray examination procedures and the assessment of factors influencing them has been a long-standing goal of the diagnostic radiology and medical physics communities. In this work, the influence of anode surface roughness on diagnostic x-ray spectra is evaluated using MCNP4C-based Monte Carlo simulations. Methods: An image-based modeling method was used to create realistic models from surface-cracked anodes. An in-house computer program was written to model the geometric pattern of cracks and irregularities from digital images of focal track surface in order to define the modeled anodes into MCNP input file. To consider average roughness and mean crack depth into the models, the surface of anodes was characterized by scanning electron microscopy and surface profilometry. It was found that the average roughness (R{sub a}) in the most aged tube studied is about 50 {mu}m. The correctness of MCNP4C in simulating diagnostic x-ray spectra was thoroughly verified by calling its Gaussian energy broadening card and comparing the simulated spectra with experimentally measured ones. The assessment of anode roughness involved the comparison of simulated spectra in deteriorated anodes with those simulated in perfectly plain anodes considered as reference. From these comparisons, the variations in output intensity, half value layer (HVL), heel effect, and patient dose were studied. Results: An intensity loss of 4.5% and 16.8% was predicted for anodes aged by 5 and 50 {mu}m deep cracks (50 kVp, 6 deg. target angle, and 2.5 mm Al total filtration). The variations in HVL were not significant as the spectra were not hardened by more than 2.5%; however, the trend for this variation was to increase with roughness. By deploying several point detector tallies along the anode-cathode direction and averaging exposure over them, it was found that for a 6 deg. anode, roughened by 50 {mu}m deep
Statistical thermodynamics of aligned rigid rods with attractive lateral interactions: Theory and Monte Carlo simulations

Science.gov (United States)

dos Santos, G. J.; Linares, D. H.; Ramirez-Pastor, A. J.

2018-04-01

The phase behaviour of aligned rigid rods of length k (k-mers) adsorbed on two-dimensional square lattices has been studied by Monte Carlo (MC) simulations and histogram reweighting technique. The k-mers, containing k identical units (each one occupying a lattice site) were deposited along one of the directions of the lattice. In addition, attractive lateral interactions were considered. The methodology was applied, particularly, to the study of the critical point of the condensation transition occurring in the system. The process was monitored by following the fourth order Binder cumulant as a function of temperature for different lattice sizes. The results, obtained for k ranging from 2 to 7, show that: (i) the transition coverage exhibits a decreasing behaviour when it is plotted as a function of the k-mer size and (ii) the transition temperature, Tc, exhibits a power law dependence on k, Tc ∼k 0 , 4, shifting to higher values as k increases. Comparisons with an analytical model based on a generalization of the Bragg-Williams approximation (BWA) were performed in order to support the simulation technique. A significant qualitative agreement was obtained between BWA and MC results.
Infrared Spectra, Index of Refraction, and Optical Constants of Nitrile Ices Relevant to Titan's Atmosphere

Science.gov (United States)

Moore, Marla; Ferrante, Robert; Moore, William; Hudson, Reggie

2010-01-01

Spectra and optical constants of nitrite ices known or suspected to be in Titan's atmosphere are presented from 2.5 to 200 microns (4000 to 50 per cm ). These results are relevant to the ongoing modeling of Cassini CIRS observations of Titan's winter pole. Ices studied include: HCN, hydrogen cyanide; C2N2, cyanogen; CH3CN, acetonitrile; C 2H5CN, propionitrile; and HC3N, cyanoacetylene. For each of these molecules we report new measurements of the index of refraction, n, determined in both the amorphous- and crystallinephase at 670 nm. Spectra were measured and optical constants were calculated for each nitrite at a variety of temperatures including 20, 35, 50, 75, 95, and 110 K, in the amorphous- and crystalline-phase. This laboratory effort uses a dedicated FTIR spectrometer to record transmission spectra of thin-film ice samples. Laser interference is used to measure film thickness during condensation onto a transparent cold window attached to the tail section of a closed-cycle helium cryostat. Optical constants, real (n) and imaginary (k) refractive indices, are determined using Kramers-Kronig (K-K) analysis. Our calculation reproduces the complete spectrum, including all interference effects. Index of refraction measurements are made in a separate dedicated FTIR spectrometer where interference deposit fringes are measured using two 670 nm lasers at different angles to the ice substrate. A survey of these new measurements will be presented along with a discussion of their validation, errors, and application to Titan data.

Late time optical spectra from the 56Ni model for Type I supernovae

International Nuclear Information System (INIS)

Axelrod, T.S.

1980-07-01

The hypothesis that the optical luminosity of Type I supernovae results from the radioactive decay of 56 Ni synthesized and ejected by the explosion has been investigated by numerical simulation of the optical spectrum resulting from a homologously expanding shell composed initially of pure 56 Ni core. This model, which neglects the effects of material external to the 56 Ni core, is expected to provide a reasonable representation of the supernova at late times when the star is nearly transparent to optical photons. The numerical simulation determines the temperature, ionization state, and non-LTE level populations which result from energy deposition by the radioactive decay products of 56 Ni and 56 Co. The optical spectrum includes the effects of both allowed and forbidden lines. The optical spectra resulting from the simulation are found to be sensitive to the mass and ejection velocity of the 56 Ni shell. A range of these parameters has been found which results in good agreement with the observed spectra of SN1972e over a considerable range of time. In particular, evidence for the expected decaying abundance of 56 Co has been found in the spectra of SN1972e. These results are used to assess the validity of the 56 Ni model and set limits on the mass and explosion mechanism of the Type I progenitor. The possibilities for improvement of the numerical model are discussed and future atomic data requirements defined
Assessment by regional modelling of the impact of monopile foundations on the hydrodynamics and sediment transport: case of Courseulles-sur-Mer (France) wind farm

Science.gov (United States)

Rivier, Aurélie; Bennis, Anne-Claire; Pinon, Grégory; Magar, Vanesa; Gross, Markus

2015-04-01

Offshore monopile foundations of wind turbines modify hydrodynamics and sediment transport at local scale and also at regional scale. The aim of this work is to assess these changes and to parametrize them in a regional model. These modifications were previously evaluated using the regional circulation model MARS3D (Lazure and Dumas, 2008) in tests-cases (Rivier et al., 2014) using two approaches: in the first approach, monopiles are explicitly modelled in the mesh as dry cells and in the second approach a sub-grid parametrization which considers the drag force exerted by a monopile on the flow is used. The sub-grid parametrization is improved close to the bed in this paper by adding a drag force term in the momentum equations, source terms in the turbulence model and by increasing the bed shear stress at monopile location. Changes in hydrodynamics regime, especially near-bed, affect sediment transport regime and modifications due to monopiles on sediment dynamics is also investigated using the MARS3D sediment transport module (Le Hir et al., 2011) which solves the advection-diffusion equations. Test-cases are run using hydrodynamical conditions and sediment grain sizes typical from the area located off Courseulles-sur-Mer (Normandy, France) where an offshore wind farm is planned to be built. Velocity, turbulent kinetic energy and bed thickness changes due to the monopile simulated by both approaches are compared to each other and to experimental measurements made in a flume at the University of Caen or to published data (e.g. Roulund et al., 2005; Dargahi,1989). Then the model is applied in a real configuration on an area including the future offshore wind farm of Courseulles-sur-Mer. Four monopiles are represented in the model using both approaches and modifications of the hydrodynamics and sediment transport are assessed along a tidal cycle. Currents increase at the side edge of the monopile and decrease in front of and downstream the monopile. Turbulent kinetic
A model of tungsten anode x-ray spectra

Energy Technology Data Exchange (ETDEWEB)

Hernández, G.; Fernández, F., E-mail: fdz@usal.es [Física Fundamental, Universidad de Salamanca, Salamanca 37008 (Spain)

2016-08-15

Purpose: A semiempirical model for x-ray production in tungsten thick-targets was evaluated using a new characterization of electron fluence. Methods: Electron fluence is modeled taking into account both the energy and angular distributions, each of them adjusted to Monte Carlo simulated data. Distances were scaled by the CSDA range to reduce the energy dependence. Bremsstrahlung production was found by integrating the cross section with the fluence in a 1D penetration model. Characteristic radiation was added using a semiempirical law whose validity was checked. The results were compared the experimental results of Bhat et al., with the SpekCalc numerical tool, and with MCNPX simulation results from the work of Hernandez and Boone. Results: The model described shows better agreement with the experimental results than the SpekCalc predictions in the sense of area between the spectra. A general improvement of the predictions of half-value layers is also found. The results are also in good agreement with the simulation results in the 50–640 keV energy range. Conclusions: A complete model for x-ray production in thick bremsstrahlung targets has been developed, improving the results of previous works and extending the energy range covered to the 50–640 keV interval.
Determination of half value layer and applied voltage from emitted spectra by an X-ray tube

International Nuclear Information System (INIS)

Santos, Josilene C.; Gonzales, Alejandro H.L.; Terini, Ricardo A.; Costa, Paulo R.

2016-01-01

This work describes a method for assessment of half value layer (HVL) and peak tube voltage (kVp) applied in an X-ray tube by means of experimental X-ray spectra measured using a CdTe detector. It was assessed some parameters that can affect the evaluation of these quantities such as dead time, count rate and tube current (mA). For this study, two sets of X-ray spectra were measured: Set A), spectra measurements using Cu filters with different thicknesses (1.8 - 5.4 mm) and fixed tube current; Set B), spectra measurements keeping a fixed Cu filtration and varying tube current (0.5 - 3.0 mA). The experimental setup for the Set A spectra measurements allowed the assessment of the HVL and kVp for different count rates and dead time in the detection system, while the Set B setup allowed to assess the dependence of these quantities with the tube current. The spectrometer was energy calibrated using standard X/γ rays radioactive sources. The tube voltage values were estimated by means of experimental measured X-ray spectra, using linear regression in order to search the end point of each spectrum. The spectra correction was performed using the stripping procedure developed for the Matlab® software and the HVL values were derived from these corrected spectra. For comparison, HVL was also determined using a 30 cm"3 ion chamber and high purity Al filters. The results show that it is possible to determine the kVp with accuracy and reproducibility using spectra with dead time of up to 10%. In spite of this, the values obtained showed a deviation of up to 7 kV, for spectra measured using the same nominal tube voltage different tube current values, indicating dependence between these two parameters. (author)
Long-term MST radar observations of vertical wave number spectra of gravity waves in the tropical troposphere over Gadanki (13.5° N, 79.2° E: comparison with model spectra

Directory of Open Access Journals (Sweden)

S. Vijaya Bhaskara Rao

2008-06-01

Full Text Available The potential utility of Mesosphere-Stratosphere-Troposphere (MST radar measurements of zonal, meridional and vertical winds for divulging the gravity wave vertical wave number spectra is discussed. The data collected during the years 1995–2004 are used to obtain the mean vertical wave number spectra of gravity wave kinetic energy in the tropical troposphere over Gadanki (13.5° N, 79.2° E. First, the climatology of 3-dimensional wind components is developed using ten years of radar observations, for the first time, over this latitude. This climatology brought out the salient features of background tropospheric winds over Gadanki. Further, using the second order polynomial fit as background, the day-to-day wind anomalies are estimated. These wind anomalies in the 4–14 km height regions are used to estimate the profiles of zonal, meridional and vertical kinetic energy per unit mass, which are then used to estimate the height profile of total kinetic energy. Finally, the height profiles of total kinetic energy are subjected to Fourier analysis to obtain the monthly mean vertical wave number spectra of gravity wave kinetic energy. The monthly mean vertical wave number spectra are then compared with a saturation spectrum predicted by gravity wave saturation theory. A slope of 5/3 is used for the model gravity wave spectrum estimation. In general, the agreement is good during all the months. However, it is noticed that the model spectrum overestimates the PSD at lower vertical wave numbers and underestimates it at higher vertical wave numbers, which is consistently observed during all the months. The observed discrepancies are attributed to the differences in the slopes of theoretical and observed gravity wave spectra. The slopes of the observed vertical wave number spectra are estimated and compared with the model spectrum slope, which are in good agreement. The estimated slopes of the observed monthly vertical wave number spectra are in the
Cross-spectra over the sea from observations and mesoscale modelling

DEFF Research Database (Denmark)

Vincent, Claire Louise; Larsén, Xiaoli Guo; Larsen, Søren Ejling

2013-01-01

of the cross-correlation function and an exponentially decaying coherence function are fitted to the normalized cospectra and quadrature spectra. The expressions are shown to be a good fit to the spectra calculated from the WRF simulations and to the observed spectra for directions with a long sea-fetch, which...
Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography*

Science.gov (United States)

Paixão, Lucas; Oliveira, Bruno Beraldo; Viloria, Carolina; de Oliveira, Marcio Alves; Teixeira, Maria Helena Araújo; Nogueira, Maria do Socorro

2015-01-01

Objective Derive filtered tungsten X-ray spectra used in digital mammography systems by means of Monte Carlo simulations. Materials and Methods Filtered spectra for rhodium filter were obtained for tube potentials between 26 and 32 kV. The half-value layer (HVL) of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F & MAM Detector Platinum and 8201023-C Xi Base unit Platinum Plus w mAs in a Hologic Selenia Dimensions system using a direct radiography mode. Results Calculated HVL values showed good agreement as compared with those obtained experimentally. The greatest relative difference between the Monte Carlo calculated HVL values and experimental HVL values was 4%. Conclusion The results show that the filtered tungsten anode X-ray spectra and the EGSnrc Monte Carlo code can be used for mean glandular dose determination in mammography. PMID:26811553
Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography

Directory of Open Access Journals (Sweden)

Lucas Paixão

2015-12-01

Full Text Available Abstract Objective: Derive filtered tungsten X-ray spectra used in digital mammography systems by means of Monte Carlo simulations. Materials and Methods: Filtered spectra for rhodium filter were obtained for tube potentials between 26 and 32 kV. The half-value layer (HVL of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F & MAM Detector Platinum and 8201023-C Xi Base unit Platinum Plus w mAs in a Hologic Selenia Dimensions system using a direct radiography mode. Results: Calculated HVL values showed good agreement as compared with those obtained experimentally. The greatest relative difference between the Monte Carlo calculated HVL values and experimental HVL values was 4%. Conclusion: The results show that the filtered tungsten anode X-ray spectra and the EGSnrc Monte Carlo code can be used for mean glandular dose determination in mammography.
Development of a risk-prediction model for Middle East respiratory syndrome coronavirus infection in dialysis patients.

Science.gov (United States)

Ahmed, Anwar E; Alshukairi, Abeer N; Al-Jahdali, Hamdan; Alaqeel, Mody; Siddiq, Salma S; Alsaab, Hanan A; Sakr, Ezzeldin A; Alyahya, Hamed A; Alandonisi, Munzir M; Subedar, Alaa T; Aloudah, Nouf M; Baharoon, Salim; Alsalamah, Majid A; Al Johani, Sameera; Alghamdi, Mohammed G

2018-04-14

Introduction The Middle East respiratory syndrome coronavirus (MERS-CoV) infection can cause transmission clusters and high mortality in hemodialysis facilities. We attempted to develop a risk-prediction model to assess the early risk of MERS-CoV infection in dialysis patients. Methods This two-center retrospective cohort study included 104 dialysis patients who were suspected of MERS-CoV infection and diagnosed with rRT-PCR between September 2012 and June 2016 at King Fahd General Hospital in Jeddah and King Abdulaziz Medical City in Riyadh. We retrieved data on demographic, clinical, and radiological findings, and laboratory indices of each patient. Findings A risk-prediction model to assess early risk for MERS-CoV in dialysis patients has been developed. Independent predictors of MERS-CoV infection were identified, including chest pain (OR = 24.194; P = 0.011), leukopenia (OR = 6.080; P = 0.049), and elevated aspartate aminotransferase (AST) (OR = 11.179; P = 0.013). The adequacy of this prediction model was good (P = 0.728), with a high predictive utility (area under curve [AUC] = 76.99%; 95% CI: 67.05% to 86.38%). The prediction of the model had optimism-corrected bootstrap resampling AUC of 71.79%. The Youden index yielded a value of 0.439 or greater as the best cut-off for high risk of MERS infection. Discussion This risk-prediction model in dialysis patients appears to depend markedly on chest pain, leukopenia, and elevated AST. The model accurately predicts the high risk of MERS-CoV infection in dialysis patients. This could be clinically useful in applying timely intervention and control measures to prevent clusters of infections in dialysis facilities or other health care settings. The predictive utility of the model warrants further validation in external samples and prospective studies. © 2018 International Society for Hemodialysis.
CASTHY, Statistical Model for Neutron Cross-Sections and Gamma-Ray Spectra

International Nuclear Information System (INIS)

Igarasi, Sin-iti; Fukahori, Tokio

1998-01-01

Description of program or function: CASTHY calculates neutron cross sections of total, shape elastic scattering and compound nucleus formation with the optical model, and compound elastic, inelastic and capture cross sections by the statistical model. The other cross sections, such as (n,2n), (n,p), (n,f) reactions are treated as cross sections of competing processes, and their sum is given through input data. Capture gamma-ray spectra can also be calculated. The branching ratio for primary transition can be treated in a particular way, if required
VNIR Reflectance and MIR Emissivity Spectra of Ordinary Chondrite Meteorites Under Simulated Asteroid Surface Conditions

Science.gov (United States)

Gemma, M.; Shirley, K.; Glotch, T. D.; Ebel, D. S. S.

2017-12-01

Recent missions have revealed much about the nature of many Near-Earth asteroids, including the NEAR-Shoemaker target 433 Eros and Hayabusa target 25142 Itokawa. Both asteroids appear to have mineralogy consistent with ordinary chondrite meteorites. Laboratory spectral analysis of well-constrained meteorite samples can be employed as a reference tool to characterize and constrain data from current and future asteroid studies. A sample set of ordinary chondrite meteorites was chosen from the collection at the American Museum of Natural History. Six meteorites, spanning groups H, L, and LL, were prepared at four different size fractions (25-63 μm, 63-90 μm, 90-125 μm, 125-250 μm) in an attempt to mimic regolith known to exist on asteroids such as 433 Eros and 25142 Itokawa. At the Center for Planetary Exploration at Stony Brook University, spectra of the ordinary chondrite material were measured under simulated asteroid surface conditions ( 10-6 mbar, 150 K chamber temperature, low intensity illumination). The samples were used in two experiments: one measuring visible and near-infrared (VNIR) reflectance spectra at a series of temperatures, and the other measuring mid-infrared (MIR) emissivity spectra. The emissivity measurements require accurate simulation of the thermal environment within asteroid regolith, achieved by inducing a thermal gradient within the sample that results in a surface brightness temperature around 323 K (similar to the surface of 25142 Itokawa). Mid-IR emissivity spectra were collected for each sample at a surface temperature of 323 K, and reflectance spectra were collected in increments of 10 K, over the range 283 K to 373 K. Preliminary VNIR spectra show spreads similar to those seen in Hinrichs and Lucey (2002). Preliminary MIR emissivity spectra suggest that under asteroid surface conditions, the position of the Christiansen feature shifts to shorter wavelengths and emissivity is lower in the Reststrahlen bands when compared to
Avoiding student infection during a Middle East respiratory syndrome (MERS outbreak: a single medical school experience

Directory of Open Access Journals (Sweden)

Seung Won Park

2016-06-01

Full Text Available Purpose: In outbreaks of infectious disease, medical students are easily overlooked in the management of healthcare personnel protection although they serve in clinical clerkships in hospitals. In the early summer of 2015, Middle East respiratory syndrome (MERS struck South Korea, and students of Sungkyunkwan University School of Medicine (SKKUSOM were at risk of contracting the disease. The purpose of this report is to share SKKUSOM’s experience against the MERS outbreak and provide suggestions for medical schools to consider in the face of similar challenges. Methods: Through a process of reflection-on-action, we examined SKKUSOM’s efforts to avoid student infection during the MERS outbreak and derived a few practical guidelines that medical schools can adopt to ensure student safety in outbreaks of infectious disease. Results: The school leadership conducted ongoing risk assessment and developed contingency plans to balance student safety and continuity in medical education. They rearranged the clerkships to another hospital and offered distant lectures and tutorials. Five suggestions are extracted for medical schools to consider in infection outbreaks: instant cessation of clinical clerkships; rational decision making on a school closure; use of information technology; constant communication with hospitals; and open communication with faculty, staff, and students. Conclusion: Medical schools need to take the initiative and actively seek countermeasures against student infection. It is essential that medical schools keep constant communication with their index hospitals and the involved personnel. In order to assure student learning, medical schools may consider offering distant education with online technology.
Advanced k-epsilon modeling of heat transfer

Science.gov (United States)

Kwon, Okey; Ames, Forrest E.

1995-01-01

This report describes two approaches to low Reynolds-number k-epsilon turbulence modeling which formulate the eddy viscosity on the wall-normal component of turbulence and a length scale. The wall-normal component of turbulence is computed via integration of the energy spectrum based on the local dissipation rate and is bounded by the isotropic condition. The models account for the anisotropy of the dissipation and the reduced mixing length due to the high strain rates present in the near-wall region. The turbulent kinetic energy and its dissipation rate were computed from the k and epsilon transport equations of Durbin. The models were tested for a wide range of turbulent flows and proved to be superior to other k-epsilon models, especially for nonequilibrium anisotropic flows. For the prediction of airfoil heat transfer, the models included a set of empirical correlations for predicting laminar-turbulent transition and laminar heat transfer augmentation due to the presence of freestream turbulence. The predictions of surface heat transfer were generally satisfactory.
Tailoring subunit vaccine immunity with adjuvant combinations and delivery routes using the Middle East respiratory coronavirus (MERS-CoV receptor-binding domain as an antigen.

Directory of Open Access Journals (Sweden)

Jiaming Lan

Full Text Available The development of an effective vaccine is critical for prevention of a Middle East respiratory syndrome coronavirus (MERS-CoV pandemic. Some studies have indicated the receptor-binding domain (RBD protein of MERS-CoV spike (S is a good candidate antigen for a MERS-CoV subunit vaccine. However, highly purified proteins are typically not inherently immunogenic. We hypothesised that humoral and cell-mediated immunity would be improved with a modification of the vaccination regimen. Therefore, the immunogenicity of a novel MERS-CoV RBD-based subunit vaccine was tested in mice using different adjuvant formulations and delivery routes. Different vaccination regimens were compared in BALB/c mice immunized 3 times intramuscularly (i.m. with a vaccine containing 10 µg of recombinant MERS-CoV RBD in combination with either aluminium hydroxide (alum alone, alum and polyriboinosinic acid (poly I:C or alum and cysteine-phosphate-guanine (CpG oligodeoxynucleotides (ODN. The immune responses of mice vaccinated with RBD, incomplete Freund's adjuvant (IFA and CpG ODN by a subcutaneous (s.c. route were also investigated. We evaluated the induction of RBD-specific humoral immunity (total IgG and neutralizing antibodies and cellular immunity (ELISpot assay for IFN-γ spot-forming cells and splenocyte cytokine production. Our findings indicated that the combination of alum and CpG ODN optimized the development of RBD-specific humoral and cellular immunity following subunit vaccination. Interestingly, robust RBD-specific antibody and T-cell responses were induced in mice immunized with the rRBD protein in combination with IFA and CpG ODN, but low level of neutralizing antibodies were elicited. Our data suggest that murine immunity following subunit vaccination can be tailored using adjuvant combinations and delivery routes. The vaccination regimen used in this study is promising and could improve the protection offered by the MERS-CoV subunit vaccine by eliciting
Reactivity feedback models for SSC-K

Energy Technology Data Exchange (ETDEWEB)

Han, Do Hee; Kwon, Young Min; Kim, Kyung Du; Chang, Won Pyo [Korea Atomic Energy Research Institute, Taejon (Korea)

1998-06-01

Safety of KALIMER is assured by the inherent safety of the core and passive safety of the safety-related systems. For the safety analysis of a new reactor design such as KALIMER, analysis models, which are consistent with the design, have to be developed for a plant-wide transient and safety analysis code. Efforts for the development of reactivity feedback models for SSC-K, which is now being developed for the safety analysis of KALIMER, is described in this report. Models for Doppler, sodium density/void, fuel axial expansion, core radial expansion, and CRDL expansion have been developed. Test runs have been performed for the unprotected accident for the verification of the models. Use of KALIMER reactivity coefficients and future development of models for GEM and PSDRS would make it possible to analyze the response of KALIMER under TOP as well as LOF and LOHS accident conditions using SSC-K. (author). 5 refs., 64 figs., 2 tabs.
Redefining Tactical Operations for MER Using Cloud Computing

Science.gov (United States)

Joswig, Joseph C.; Shams, Khawaja S.

2011-01-01

The Mars Exploration Rover Mission (MER) includes the twin rovers, Spirit and Opportunity, which have been performing geological research and surface exploration since early 2004. The rovers' durability well beyond their original prime mission (90 sols or Martian days) has allowed them to be a valuable platform for scientific research for well over 2000 sols, but as a by-product it has produced new challenges in providing efficient and cost-effective tactical operational planning. An early stage process adaptation was the move to distributed operations as mission scientists returned to their places of work in the summer of 2004, but they would still came together via teleconference and connected software to plan rover activities a few times a week. This distributed model has worked well since, but it requires the purchase, operation, and maintenance of a dedicated infrastructure at the Jet Propulsion Laboratory. This server infrastructure is costly to operate and the periodic nature of its usage (typically heavy usage for 8 hours every 2 days) has made moving to a cloud based tactical infrastructure an extremely tempting proposition. In this paper we will review both past and current implementations of the tactical planning application focusing on remote plan saving and discuss the unique challenges present with long-latency, distributed operations. We then detail the motivations behind our move to cloud based computing services and as well as our system design and implementation. We will discuss security and reliability concerns and how they were addressed
Automated generation and ensemble-learned matching of X-ray absorption spectra

Science.gov (United States)

Zheng, Chen; Mathew, Kiran; Chen, Chi; Chen, Yiming; Tang, Hanmei; Dozier, Alan; Kas, Joshua J.; Vila, Fernando D.; Rehr, John J.; Piper, Louis F. J.; Persson, Kristin A.; Ong, Shyue Ping

2018-03-01

X-ray absorption spectroscopy (XAS) is a widely used materials characterization technique to determine oxidation states, coordination environment, and other local atomic structure information. Analysis of XAS relies on comparison of measured spectra to reliable reference spectra. However, existing databases of XAS spectra are highly limited both in terms of the number of reference spectra available as well as the breadth of chemistry coverage. In this work, we report the development of XASdb, a large database of computed reference XAS, and an Ensemble-Learned Spectra IdEntification (ELSIE) algorithm for the matching of spectra. XASdb currently hosts more than 800,000 K-edge X-ray absorption near-edge spectra (XANES) for over 40,000 materials from the open-science Materials Project database. We discuss a high-throughput automation framework for FEFF calculations, built on robust, rigorously benchmarked parameters. FEFF is a computer program uses a real-space Green's function approach to calculate X-ray absorption spectra. We will demonstrate that the ELSIE algorithm, which combines 33 weak "learners" comprising a set of preprocessing steps and a similarity metric, can achieve up to 84.2% accuracy in identifying the correct oxidation state and coordination environment of a test set of 19 K-edge XANES spectra encompassing a diverse range of chemistries and crystal structures. The XASdb with the ELSIE algorithm has been integrated into a web application in the Materials Project, providing an important new public resource for the analysis of XAS to all materials researchers. Finally, the ELSIE algorithm itself has been made available as part of veidt, an open source machine-learning library for materials science.
Model-independent separation of poorly resolved hypperfine split spectra by a linear combination method

International Nuclear Information System (INIS)

Nagy, D.L.; Dengler, J.; Ritter, G.

1988-01-01

A model-independent evaluation of the components of poorly resolved Moessbauer spectra based on a linear combination method is possible if there is a parameter as a function of which the shape of the individual components do not but their intensities do change and the dependence of the intensities on this parameter is known. The efficiency of the method is demonstrated on the example of low temperature magnetically split spectra of the high-T c superconductor YBa 2 (Cu 0.9 Fe 0 .1 ) 3 O 7-y . (author)
A new k-epsilon model consistent with Monin-Obukhov similarity theory

DEFF Research Database (Denmark)

van der Laan, Paul; Kelly, Mark C.; Sørensen, Niels N.

2017-01-01

A new k-" model is introduced that is consistent with Monin–Obukhov similarity theory (MOST). The proposed k-" model is compared with another k-" model that was developed in an attempt to maintain inlet profiles compatible with MOST. It is shown that the previous k-" model is not consistent with ...
K0 → π0γγ decays in chiral perturbation theory

International Nuclear Information System (INIS)

Ecker, G.; Pich, A.; Rafael, E. de

1987-01-01

The decays K L,S → π 0 γγ are calculated within the framework of chiral perturbation theory. The amplitude for K L → π 0 γγ is found to be finite at the one-loop level yielding a branching ratio of 6.8 · 10 -7 . The decay spectra of both decays are very characteristic and provide good tests of the effective chiral symmetry realization of the Standard Model. (Author)

Measurement of the MACS of {sup 181}Ta(n,γ) at kT=30 keV as a test of a method for Maxwellian neutron spectra generation

Energy Technology Data Exchange (ETDEWEB)

Praena, J., E-mail: jpraena@us.es [Universidad de Sevilla (Spain); Centro Nacional de Aceleradores, Sevilla (Spain); Mastinu, P.F. [Laboratori Nazionali di Legnaro, INFN, Padova (Italy); Pignatari, M. [Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel (Switzerland); Quesada, J.M. [Universidad de Sevilla (Spain); García-López, J. [Universidad de Sevilla (Spain); Centro Nacional de Aceleradores, Sevilla (Spain); Lozano, M. [Universidad de Sevilla (Spain); Dzysiuk, N. [International Nuclear Safety Center of Ukraine, Kyiv (Ukraine); Capote, R. [NAPC–Nuclear Data Section, International Atomic Energy Agency, Vienna (Austria); Martín-Hernández, G. [Centro de Aplicaciones Tecnólogicas y Desarrollo Nuclear, 5ta y 30, Playa, La Habana (Cuba)

2013-11-01

Measurement of the Maxwellian-Averaged Cross-Section (MACS) of the {sup 181}Ta(n,γ) reaction at kT=30 keV by the activation technique using an innovative method for the generation of Maxwellian neutron spectra is presented. The method is based on the shaping of the proton beam to produce a desired neutron spectrum using the {sup 7}Li(p,n) reaction as a neutron source. The characterization of neutron spectra has been performed by combining measured proton distributions, an analytical description of the differential neutron yield in angle and energy of the {sup 7}Li(p,n) reaction, and with Monte Carlo simulations of the neutron transport. A measured value equal to 815±73 mbarn is reported for the MACS of the reaction {sup 181}Ta(n,γ) at kT=30 keV. The MACS of the reaction {sup 197}Au(n,γ) provided by KADoNiS has been used as a reference. -- Author-Highlights: • Generation of Maxwellian neutron spectrum for astrophysics and nuclear data validation. • {sup 7}Li(p,n) reaction and proton distributions conformed by aluminum as a shaper foil. • Measurement of the proton distributions and simulation of the neutron transport. • MACS of {sup 181}Ta(n,γ) at kT=30 keV measured by the activation technique. • First accelerator-based neutron source in Spain.
ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

Science.gov (United States)

Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

2015-01-01

Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.
Oxygen K-edge absorption spectra of small molecules in the gas phase

International Nuclear Information System (INIS)

Yang, B.X.; Kirz, J.; Sham, T.K.

1986-01-01

The absorption spectra of O 2 , CO, CO 2 and OCS have been recorded in a transmission mode in the energy region from 500 to 950 eV. Recent observation of EXAFS in these molecules is confirmed in this study. 7 refs., 3 figs
A digital processing method for the analysis of complex nuclear spectra

International Nuclear Information System (INIS)

Madan, V.K.; Abani, M.C.; Bairi, B.R.

1994-01-01

This paper describes a digital processing method using frequency power spectra for the analysis of complex nuclear spectra. The power spectra were estimated by employing modified discrete Fourier transform. The method was applied to observed spectral envelopes. The results for separating closely-spaced doublets in nuclear spectra of low statistical precision compared favorably with those obtained by using a popular peak fitting program SAMPO. The paper also describes limitations of the peak fitting methods. It describes the advantages of digital processing techniques for type II digital signals including nuclear spectra. A compact computer program occupying less than 2.5 kByte of memory space was written in BASIC for the processing of observed spectral envelopes. (orig.)
Monte Carlo simulation of x-ray spectra in diagnostic radiology and mammography using MCNP4C

Energy Technology Data Exchange (ETDEWEB)

Ay, M R [Department of Physics and Nuclear Sciences, AmirKabir University of Technology, Tehran (Iran, Islamic Republic of); Shahriari, M [Department of Nuclear Engineering, Shahid Beheshti University, Tehran (Iran, Islamic Republic of); Sarkar, S [Department of Medical Physics, Tehran University of Medical Science, Tehran (Iran, Islamic Republic of); Adib, M [TPP Co., GE Medical Systems, Iran Authorized Distributor, Tehran (Iran, Islamic Republic of); Zaidi, H [Division of Nuclear Medicine, Geneva University Hospital, 1211 Geneva (Switzerland)

2004-11-07

The general purpose Monte Carlo N-particle radiation transport computer code (MCNP4C) was used for the simulation of x-ray spectra in diagnostic radiology and mammography. The electrons were transported until they slow down and stop in the target. Both bremsstrahlung and characteristic x-ray production were considered in this work. We focus on the simulation of various target/filter combinations to investigate the effect of tube voltage, target material and filter thickness on x-ray spectra in the diagnostic radiology and mammography energy ranges. The simulated x-ray spectra were compared with experimental measurements and spectra calculated by IPEM report number 78. In addition, the anode heel effect and off-axis x-ray spectra were assessed for different anode angles and target materials and the results were compared with EGS4-based Monte Carlo simulations and measured data. Quantitative evaluation of the differences between our Monte Carlo simulated and comparison spectra was performed using student's t-test statistical analysis. Generally, there is a good agreement between the simulated x-ray and comparison spectra, although there are systematic differences between the simulated and reference spectra especially in the K-characteristic x-rays intensity. Nevertheless, no statistically significant differences have been observed between IPEM spectra and the simulated spectra. It has been shown that the difference between MCNP simulated spectra and IPEM spectra in the low energy range is the result of the overestimation of characteristic photons following the normalization procedure. The transmission curves produced by MCNP4C have good agreement with the IPEM report especially for tube voltages of 50 kV and 80 kV. The systematic discrepancy for higher tube voltages is the result of systematic differences between the corresponding spectra.
Monte Carlo simulation of x-ray spectra in diagnostic radiology and mammography using MCNP4C

Science.gov (United States)

Ay, M. R.; Shahriari, M.; Sarkar, S.; Adib, M.; Zaidi, H.

2004-11-01

The general purpose Monte Carlo N-particle radiation transport computer code (MCNP4C) was used for the simulation of x-ray spectra in diagnostic radiology and mammography. The electrons were transported until they slow down and stop in the target. Both bremsstrahlung and characteristic x-ray production were considered in this work. We focus on the simulation of various target/filter combinations to investigate the effect of tube voltage, target material and filter thickness on x-ray spectra in the diagnostic radiology and mammography energy ranges. The simulated x-ray spectra were compared with experimental measurements and spectra calculated by IPEM report number 78. In addition, the anode heel effect and off-axis x-ray spectra were assessed for different anode angles and target materials and the results were compared with EGS4-based Monte Carlo simulations and measured data. Quantitative evaluation of the differences between our Monte Carlo simulated and comparison spectra was performed using student's t-test statistical analysis. Generally, there is a good agreement between the simulated x-ray and comparison spectra, although there are systematic differences between the simulated and reference spectra especially in the K-characteristic x-rays intensity. Nevertheless, no statistically significant differences have been observed between IPEM spectra and the simulated spectra. It has been shown that the difference between MCNP simulated spectra and IPEM spectra in the low energy range is the result of the overestimation of characteristic photons following the normalization procedure. The transmission curves produced by MCNP4C have good agreement with the IPEM report especially for tube voltages of 50 kV and 80 kV. The systematic discrepancy for higher tube voltages is the result of systematic differences between the corresponding spectra.
Image simulation and a model of noise power spectra across a range of mammographic beam qualities

Energy Technology Data Exchange (ETDEWEB)

Mackenzie, Alistair, E-mail: alistairmackenzie@nhs.net; Dance, David R.; Young, Kenneth C. [National Coordinating Centre for the Physics of Mammography, Royal Surrey County Hospital, Guildford GU2 7XX, United Kingdom and Department of Physics, University of Surrey, Guildford GU2 7XH (United Kingdom); Diaz, Oliver [Centre for Vision, Speech and Signal Processing, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom and Computer Vision and Robotics Research Institute, University of Girona, Girona 17071 (Spain)

2014-12-15

Purpose: The aim of this work is to create a model to predict the noise power spectra (NPS) for a range of mammographic radiographic factors. The noise model was necessary to degrade images acquired on one system to match the image quality of different systems for a range of beam qualities. Methods: Five detectors and x-ray systems [Hologic Selenia (ASEh), Carestream computed radiography CR900 (CRc), GE Essential (CSI), Carestream NIP (NIPc), and Siemens Inspiration (ASEs)] were characterized for this study. The signal transfer property was measured as the pixel value against absorbed energy per unit area (E) at a reference beam quality of 28 kV, Mo/Mo or 29 kV, W/Rh with 45 mm polymethyl methacrylate (PMMA) at the tube head. The contributions of the three noise sources (electronic, quantum, and structure) to the NPS were calculated by fitting a quadratic at each spatial frequency of the NPS against E. A quantum noise correction factor which was dependent on beam quality was quantified using a set of images acquired over a range of radiographic factors with different thicknesses of PMMA. The noise model was tested for images acquired at 26 kV, Mo/Mo with 20 mm PMMA and 34 kV, Mo/Rh with 70 mm PMMA for three detectors (ASEh, CRc, and CSI) over a range of exposures. The NPS were modeled with and without the noise correction factor and compared with the measured NPS. A previous method for adapting an image to appear as if acquired on a different system was modified to allow the reference beam quality to be different from the beam quality of the image. The method was validated by adapting the ASEh flat field images with two thicknesses of PMMA (20 and 70 mm) to appear with the imaging characteristics of the CSI and CRc systems. Results: The quantum noise correction factor rises with higher beam qualities, except for CR systems at high spatial frequencies, where a flat response was found against mean photon energy. This is due to the dominance of secondary quantum noise
A protein-targeting strategy used to develop a selective inhibitor of the E17K point mutation in the PH domain of Akt1

Science.gov (United States)

Deyle, Kaycie M.; Farrow, Blake; Qiao Hee, Ying; Work, Jeremy; Wong, Michelle; Lai, Bert; Umeda, Aiko; Millward, Steven W.; Nag, Arundhati; Das, Samir; Heath, James R.

2015-05-01

Ligands that can bind selectively to proteins with single amino-acid point mutations offer the potential to detect or treat an abnormal protein in the presence of the wild type (WT). However, it is difficult to develop a selective ligand if the point mutation is not associated with an addressable location, such as a binding pocket. Here we report an all-chemical synthetic epitope-targeting strategy that we used to discover a 5-mer peptide with selectivity for the E17K-transforming point mutation in the pleckstrin homology domain of the Akt1 oncoprotein. A fragment of Akt1 that contained the E17K mutation and an I19[propargylglycine] substitution was synthesized to form an addressable synthetic epitope. Azide-presenting peptides that clicked covalently onto this alkyne-presenting epitope were selected from a library using in situ screening. One peptide exhibits a 10:1 in vitro selectivity for the oncoprotein relative to the WT, with a similar selectivity in cells. This 5-mer peptide was expanded into a larger ligand that selectively blocks the E17K Akt1 interaction with its PIP3 (phosphatidylinositol (3,4,5)-trisphosphate) substrate.
Drag Coefficient Comparisons Between Observed and Model Simulated Directional Wave Spectra Under Hurricane Conditions

Science.gov (United States)

2016-04-19

the Wave Model (WAM; Hasselmann t al., 1988 ), and Simulating Waves Nearshore ( SWAN ; Booij et al., 999...of the circle represents the maximum wind speed of the hurricane. The black lines in the vicinity of the hurricane track represent the aircraft...contour maps and black contour lines for the model spec- ra at the same location. Then, the model spectra energy exceeds RA pk are plotted as
Systematic evaluation of prompt neutron spectra in fission

International Nuclear Information System (INIS)

Osawa, Takaaki

1995-01-01

To create the nuclear data fail JEND-32, the prompt fission neutron spectra X(E) of 233 U, 235 U, 238 U and 239 Pu were reevaluated and some improvement were added to the calculation models. We tried to extend the calculation method of fission spectra of nuclides with poor measurement data in consideration of increasing the importance of nuclear data of minor actinoids. We improved and extended the following five points. (1) On JENDL-3.1, the fission spectra of principal fissible materials had been calculated by the Modland-Nix model which the neutron emissions of fragments were calculated under the approximation of the constant inverse process cross section. In the paper, the spectra were calculated by the use of the inverse process cross section depend on the energy obtained by the calculation of the optical model. The result showed the increase of low energy components and the softening effect of spectra (2) On JENDL-3.1, the all fission processes were assumed to undergo (n,f) reaction. In the paper, they were calculated by the multi-chance fission such as (n, n'f), (n, 2nf) and (n, 3nf) etc. Softening of the spectra (En > 6 MeV) was obtained by this method. (3) The level density parameter (LDP) has been assumed as a = A/C in either case of light fragment (LF) and heavy fragment (HF) in the original Madland-Nix model. But we used LDP based on the Ignatyuk model under consideration of the shell effects of nuclear fragments, hence the neutron spectra of heavy fragments were hardening. (4) Nuclear temperature of both fragments had been assumed to be the same at original model, but now R T = Tm/TmH was derived to calculate them. The ratio of middle/both side components of spectra was changed. (5) Unknown neutron fission spectra of minor actinide were able to the assumed on the basis of Moriyama-Ohnishi model. (S.Y.)
K → πι+ι- decays in the effective chiral lagrangian of the standard model

International Nuclear Information System (INIS)

Pich, A.; Rafael, E. de; Ecker, G.

1986-01-01

The decay amplitudes of K → πι + ι - transitions (ι = e or μ) are calculated in chiral perturbation theory to lowest non-trivial order. This includes one-loop contributions as well as contributions from all possible tree level counterterms to the corresponding order in momenta and meson masses. Only one combination of counterterm coupling constants appearing in the decay amplitudes remains unknown. Two possible solutions for this constant are found from a comparison with the experimentally known K + → π + e + e - decay rate. Predictions are then obtained for the rates of K + → π + μ + μ - , K S o → π o e + e - and K S o → π o μ + μ - decays as well as for the corresponding spectra in the invariant mass of the lepton pair. The CP-violating transition K L o → π o 'γ' → π o ι + ι - is also discussed. (Author)
Application of some Hartree-Fock model calculations to the analysis of atomic and free-ion optical spectra

International Nuclear Information System (INIS)

Hayhurst, T.L.

1980-05-01

Techniques for applying ab-initio calculations to the analysis of atomic spectra are investigated, along with the relationship between the semi-empirical and ab-initio forms of Slater-Condon theory. Slater-Condon theory is reviewed with a focus on the essential features that lead to the effective Hamiltonians associated with the semi-empirical form of the theory. Ab-initio spectroscopic parameters are calculated from wavefunctions obtained via self-consistent field methods, while multi-configuration Hamiltonian matrices are constructed and diagonalized with computer codes written by Robert Cowan of Los Alamos Scientific Laboratory. Group theoretical analysis demonstrates that wavefunctions more general than Slater determinants (i.e., wavefunctions with radial correlations between electrons) lead to essentially the same parameterization of effective Hamiltonians. In the spirit of this analysis, a strategy is developed for adjusting ab-initio values of the spectroscopic parameters, reproducing parameters obtained by fitting the corresponding effective Hamiltonian. Secondary parameters are used to screen the calculated (primary) spectroscopic parameters, their values determined by least squares. Extrapolations of the secondary parameters determined from analyzed spectra are attempted to correct calculations of atoms and ions without experimental levels. The adjustment strategy and extrapolations are tested on the K I sequence from K 0+ through Fe 7+ , fitting to experimental levels for V 4+ , and Cr 5+ ; unobserved levels and spectra are predicted for several members of the sequence. A related problem is also discussed: energy levels of the uranium hexahalide complexes, (UX 6 ) 2- for X = F, Cl, Br, and I, are fit to an effective Hamiltonian (the f 2 configuration in O/sub h/ symmetry) with corrections proposed by Brian Judd
Ömer Seyfeddin'in Değiş(tirilen Andı The Manipulated And Of Ömer Seyfeddin

Directory of Open Access Journals (Sweden)

Fundagül APAK

2013-07-01

adaptation, word/meaning oriented translation… in the target culture as a result of the act of translation. Therefore this research intends to examine what kind of changes in terms of structure and meaning And has undergone and/or been exposed to, in its editions published after the passing away of its author and in which part of the map developed by Holmes these changes have originated from. According to the theory suggested by Vermeer and Reiss, decision making bodies effective in reshaping the source text during the process of translation, will be tried to be described. Thus covering the period from the establishment of the Republic until today, a pilot study, in terms of the functions of patronage and ideologies in Turkish literature influencing the reshaping of a literary product will be presented. And; Türk edebiyatında “modern öykücülüğün babası” kabul edilen Ömer Seyfeddin’in (1884-1920 yazdığı öykülerden birinin adıdır. Bu öykünün, yazarın ölümünden sonraki baskıları incelendiğinde, kurgunun, yapı ve anlam açısından bozulduğu ve birbirinden oldukça farklı metinlere dönüştüğü görülür. Kaynak metin; yabancı bir kültürün diline çevrilmişçesine, biçim ve içerik açısından pek çok darbe almıştır. 20. yüz yılda, James Holmes (1924-1986 tarafından salt ve uygulamalı olmak üzere ikiye ayrılıp kendi içinde dallanıp budaklanan çeviribilimde, salt alandaki ürün-süreç-işlev odaklı betimleyici çalışmaların yanı sıra, içinde hem genel hem de araç-alan-düzey-metin türü-zaman-sorun ile sınırlandırılmış bölütlü çalışmaların bulunduğu kuramsal aşamalar yer alır. Çevirmen eğitimi, çeviri destekleri ve çeviri eleştirisi ise çeviribilimin uygulamalı kolunu oluşturur. Hans Vermeer ve Katharina Reiss’in geliştirdiği Skopos (amaç kuramındaysa bir kaynak metni erek kültürde yeniden biçimlendirirken belirlenen amacın çevrilen kültüre ya da çevirmenin (ki
Resonant Ni and Fe KLL Auger spectra photoexcited from NiFe alloys

International Nuclear Information System (INIS)

Koever, L.; Cserny, I.; Berenyi, Z.; Egri, S.; Novak, M.

2005-01-01

Complete text of publication follows. KLL Auger spectra of 3d transition metal atoms in solid environment, measured using high energy resolution, give an insight into the details of the local electronic structure surrounding the particular atoms emitting the signal Auger electrons. Fine tuning the energy of the exciting monochromatic photons across the K-absorption edge, features characteristic to resonant phenomena can be identified in the spectra. The shapes of the resonantly photoexcited KLL Auger spectra induced from 3d transition metals and alloys are well interpreted by the single step model of the Auger process, based on the resonant scattering theory. The peak shapes are strongly influenced by the 4p partial density of unoccupied electronic states around the excited atom. High energy resolution studies of KLL Auger spectra of 3d transition metals using laboratory X-ray sources, however, request very demanding experiments and yield spectra of limited statistical quality making the evaluation of the fine details in the spectra difficult. The Tunable High Energy XPS (THE- XPS) instrument at BW2 offers optimum photon x and energy resolution for spectroscopy of deep core Auger transitions. For the present measurements high purity polycrystalline Ni and Fe sheets as well as NiFe alloy samples of different compositions (Ni 80 Fe 20 , Ni 50 Fe 50 , Ni 20 Fe 80 ) were used. The surfaces of the samples were cleaned by in-situ argon ion sputtering. The measurements of the Ni and Fe KL 23 L 23 Auger spectra of the metal and alloy samples were performed with the THE-XPS instrument using high electron energy resolution (0.2 eV). In Fig.1, the measured Fe KL 23 L 23 spectrum, photoexcited at the Fe K absorption edge from Fe metal, is compared with the respective spectrum excited from a Ni 50 Fe 50 alloy. A significant broadening of the 1 D 2 peak and an enhancement of the spectral intensity at the low energy loss part of this peak observed in the alloy sample, while the
Oxygen K-edge absorption spectra of small molecules in the gas phase

Energy Technology Data Exchange (ETDEWEB)

Yang, B.X.; Kirz, J.; Sham, T.K.

1986-01-01

The absorption spectra of O/sub 2/, CO, CO/sub 2/ and OCS have been recorded in a transmission mode in the energy region from 500 to 950 eV. Recent observation of EXAFS in these molecules is confirmed in this study. 7 refs., 3 figs.
AN EMPIRICAL METHOD FOR IMPROVING THE QUALITY OF RXTE HEXTE SPECTRA

Energy Technology Data Exchange (ETDEWEB)

Garcia, Javier A.; Steiner, James F.; McClintock, Jeffrey E. [Harvard-Smithsonian Center for Astrophysics, 60 Garden St., Cambridge, MA 02138 (United States); Grinberg, Victoria [MIT Kavli Institute for Astrophysics and Space Research, MIT, 70 Vassar Street, Cambridge, MA 02139 (United States); Pottschmidt, Katja [Department of Physics and Center for Space Science and Technology, UMBC, Baltimore, MD 21250 (United States); Rothschild, Richard E., E-mail: javier@head.cfa.harvard.edu, E-mail: jem@cfa.harvard.edu, E-mail: jsteiner@mit.edu, E-mail: grinberg@space.mit.edu, E-mail: katja@milkyway.gsfc.nasa.gov, E-mail: rrothschild@ucsd.edu [Center for Astrophysics and Space Sciences, University of California at San Diego, La Jolla, CA (United States)

2016-03-01

We have developed a correction tool to improve the quality of Rossi X-ray Timing Explorer (RXTE) High Energy X-ray Timing Experiment (HEXTE) spectra by employing the same method we used earlier to improve the quality of RXTE Proportional Counter Array (PCA) spectra. We fit all of the hundreds of HEXTE spectra of the Crab individually to a simple power-law model, some 37 million counts in total for Cluster A and 39 million counts for Cluster B, and we create for each cluster a combined spectrum of residuals. We find that the residual spectrum of Cluster A is free of instrumental artifacts while that of Cluster B contains significant features with amplitudes ∼1%; the most prominent is in the energy range 30–50 keV, which coincides with the iodine K edge. Starting with the residual spectrum for Cluster B, via an iterative procedure we created the calibration tool hexBcorr for correcting any Cluster B spectrum of interest. We demonstrate the efficacy of the tool by applying it to Cluster B spectra of two bright black holes, which contain several million counts apiece. For these spectra, application of the tool significantly improves the goodness of fit, while affecting only slightly the broadband fit parameters. The tool may be important for the study of spectral features, such as cyclotron lines, a topic that is beyond the scope of this paper.
Application of simulated standard spectra in natural radioactivity measurements using gamma spectrometry

International Nuclear Information System (INIS)

Narayani, K.; Pant, A.D.; Bhosle, Nitin; Anilkumar, S.; Singh, Rajvir; Pradeepkumar, K.S.

2014-01-01

Gamma ray spectrometry is one of the well known analytical techniques for environmental radioactivity measurements. Gamma spectrometer based on NaI(Tl) scintillation detectors is very popular since it offers high efficiency, low cost and case in handling. The poor energy resolution of the NaI(TI) detector is the major disadvantage making tile analysis of complex gamma ray spectra difficult. Least square method or the full spectrum analysis method is widely used for the analysis of complex spectra from scintillation detectors. The main requirement of this method is that the individual standard spectra of all nuclides expected in the complex spectrum in the same measurement geometry must be available. It is not always possible and feasible to have all the standards of nuclides in the desired geometry. A methodology based on the use of simulated standard spectra generated by Monte Carlo technique was proposed for analysis of complex spectra of nuclides. In the present work, for the analysis of 238 U, 233 Th and 40 K in soil samples, the same methodology was applied by using the simulated standard spectra in soil matrix. The details of the simulation method and results analysis of 238 U, 232 Th and 40 K in environmental samples are discussed in this paper
Adaptation aux répercussions de l'élévation du niveau de la mer ...

International Development Research Centre (IDRC) Digital Library (Canada)

, la pollution, l'utilisation intensive des terres, la croissance démographique et la dégradation des écosystèmes. Elles sont par ailleurs exposées aux répercussions de la hausse du niveau de la mer et notamment aux inondations. Réduire la ...
Lattice vibration spectra. 16

International Nuclear Information System (INIS)

Lutz, H.D.; Willich, P.

1977-01-01

The FIR absorption spectra of pyrite type compounds RuS 2 , RuSsub(2-x)Sesub(x), RuSe 2 , RuTe 2 , OsS 2 , OsSe 2 , and PtP 2 as well as loellingite type phosphides FeP 2 , RuP 2 , and OsP 2 are reported. For RuS 2 , RuSe 2 , RuTe 2 , OsS 2 , and PtP 2 all of the five infrared allowed modes (k = 0) are observed. As a first result of a numerical normal coordinate treatment vibration forms of pyrite structure are communicated. The spectra show that lattice forces of corresponding sulfides, tellurides, and phosphides are about the same strength, but increase strongly by substitution of iron by ruthenium and especially of ruthenium by osmium. The lattice constants of the RuSsub(2-x)Sesub(x) solid solution obey Vegard's rule. (author)
Heavy components coupling effect on building response spectra generation

International Nuclear Information System (INIS)

Liu, T.H.; Johnson, E.R.

1985-01-01

This study investigates the dynamic coupling effect on the floor response spectra between the heavy components and the Reactor Interior (R/I) building in a PWR. The following cases were studied: (I) simplified models of one and two lump mass models representing building and heavy components, and (II) actual plant building and heavy component models. Response spectra are developed at building nodes for all models, using time-history analysis methods. Comparisons of response spectra from various models are made to observe the coupling effects. In some cases, this study found that the coupling would reduce the response spectra values in certain frequency regions even if the coupling is not required according to the above criteria. (orig./HP)

Computer model for calculating gamma-ray pulse-height spectra for logging applications

International Nuclear Information System (INIS)

Evans, M.L.

1981-01-01

A generalized computer model has been devised to simulate the emission, transport, and detection of natural gamma radiation from various logging environments. The model yields high-resolution gamma-ray pulse-height spectra that can be used to correct both gross gamma and spectral gamma-ray logs. The technique can help provide corrections to airborne and surface radiometric survey logs for the effects of varying altitude, formation composition, and overburden. Applied to borehole logging, the model can yield estimates of the effects of varying borehole fluid and casing attenuations, as well as varying formation porosity and saturation
Duality relations between SU(N)k and SU(k)NWZW models and their braid matrices

International Nuclear Information System (INIS)

Naculich, S.G.; Schnitzer, H.J.

1990-01-01

Dual relations are found between the primary fields, correlators, and conformal blocks of SU(N) k and SU(k) N WZW models, which in turn imply dual relations between the braid matrices of the two theories. These results are a consequence of the fact that the spaces of conformal blocks of SU(N) k and SU(k) N correlation functions are dual. (orig.)
Radiative-Transfer Modeling of Spectra of Densely Packed Particulate Media

Science.gov (United States)

Ito, G.; Mishchenko, M. I.; Glotch, T. D.

2017-12-01

Remote sensing measurements over a wide range of wavelengths from both ground- and space-based platforms have provided a wealth of data regarding the surfaces and atmospheres of various solar system bodies. With proper interpretations, important properties, such as composition and particle size, can be inferred. However, proper interpretation of such datasets can often be difficult, especially for densely packed particulate media with particle sizes on the order of wavelength of light being used for remote sensing. Radiative transfer theory has often been applied to the study of densely packed particulate media like planetary regoliths and snow, but with difficulty, and here we continue to investigate radiative transfer modeling of spectra of densely packed media. We use the superposition T-matrix method to compute scattering properties of clusters of particles and capture the near-field effects important for dense packing. Then, the scattering parameters from the T-matrix computations are modified with the static structure factor correction, accounting for the dense packing of the clusters themselves. Using these corrected scattering parameters, reflectance (or emissivity via Kirchhoff's Law) is computed with the method of invariance imbedding solution to the radiative transfer equation. For this work we modeled the emissivity spectrum of the 3.3 µm particle size fraction of enstatite, representing some common mineralogical and particle size components of regoliths, in the mid-infrared wavelengths (5 - 50 µm). The modeled spectrum from the T-matrix method with static structure factor correction using moderate packing densities (filling factors of 0.1 - 0.2) produced better fits to the laboratory measurement of corresponding spectrum than the spectrum modeled by the equivalent method without static structure factor correction. Future work will test the method of the superposition T-matrix and static structure factor correction combination for larger particles
Modification of K{sup 0}{sub s} and Λ(anti Λ) transverse momentum spectra in Pb-Pb collisions at √(s{sub NN})=2.76 TeV with ALICE

Energy Technology Data Exchange (ETDEWEB)

Schuchmann, Simone

2015-07-22

of R{sub AA}, where a mass hierarchy is discovered among the baryons and mesons, respectively, with the heaviest particle being least suppressed. When comparing the results from RHIC and LHC, the R{sub CP} is found to be similar at low-to-intermediate p{sub T}, while a significantly smaller R{sub AA} of K{sup 0}{sub s} and Λ in central and peripheral events at the LHC is observed in this p{sub T} region as compared to the RHIC results. This can be attributed to the larger radial flow in AA collisions and to the harder spectra at the LHC. At high p{sub T}(p{sub T}>8 GeV/c), a strong suppression in central Pb-Pb collisions with respect to pp collisions is found for K{sup 0}{sub s} and Λ(anti Λ). A significant high-p{sub T} suppression of these hadrons is also observed in the ratio of central-to-peripheral collisions. The nuclear modification of K{sup 0}{sub s} and Λ(anti Λ) is compatible with the modification of charged hadrons at high p{sub T}. The calculations with the transport model BAMPS agree with these results suggesting a similar energy loss for all light quarks, i.e. u, d and s. Moreover, a compatible suppression for c-quarks appears in the ALICE measurements via the D meson R{sub AA} as well as in the BAMPS calculations, which hints to a flavour-independent suppression if light- and c-quarks are regarded. Within this consideration, no indication for a medium-modified fragmentation is found yet. To summarize, for the particle production in Pb-Pb collisions at the LHC relative to pp neither at lower p{sub T} (rapidity density) nor at higher p{sub T} (nuclear modification factor) a significant difference of K{sup 0}{sub s} and Λ(anti Λ) carrying strangeness to hadrons made of u- and d-quarks was found.
Superposition of the luminescence spectra of free and bound excitons in ZnP2-D48

International Nuclear Information System (INIS)

Stamov, Ion; Nemerenco, Lucretia; Ivanenco, Iurii; Syrbu, Nicolae

2011-01-01

The luminescence spectra of ZnP 2 tetragonal crystals doped Mn, Sn, Cd, Sb at 10 K emission lines of bound excitons is detected. In the spectra non-phonon emission lines of bound and free excitons and their phonon replicas is isolated. The emission lines by the levels of the axial center are described. The composition of the luminescence of free and bound excitons at the axial center is investigated. In the region of phonon replicas of free excitons observed enhancement of lines due to forbidden transitions involving the recombination of excitons. A model of optic recombination transitions of the axial centre is proposed
Scaling of turbulence spectra measured in strong shear flow near the Earth’s surface

Science.gov (United States)

Mikkelsen, T.; Larsen, S. E.; Jørgensen, H. E.; Astrup, P.; Larsén, X. G.

2017-12-01

in the lowest part of the atmospheric surface layer with the form ˜ {u}* 2{k}-1, where {u}* is the surface friction velocity and k is the wavenumber. Tchen’s turbulence theory is shown to be able to predict the measured spectra of the wind velocity component parallel to the mean wind direction for eddy sizes larger than the measurement height above the ground. An amended analytical model for the near-neutral surface layer spectrum is then proposed. This model, which is applicable to the scaling of the u spectrum at all heights in the surface layer, is obtained by a combination of Kaimal’s classical spectral model for scaling the inertial subrange with Tchen’s 1953 and 1954 proposed shear production subrange theory. The shear production-amended spectral model is compared with observations of ensemble-averaged near-neutral spectra selected during a nine-month measurement period from recordings from six sonic anemometers at heights of 10, 20, 40, 60, 80, and 100 m in the meteorological tower at the test site for large wind turbines in Høvsøre, Denmark. Finally, potential applications of the new spectral model are discussed, in particular for use within the lowest one-third of the surface layer in which the production subrange component of the spectrum is most prominent. The new spectral model can supply wavenumber-resolved turbulent kinetic energies for the prediction of wind loads on buildings, bridges, and wind turbines, and its spectral parameterization can also be used for scale-dependent parameterization of, e.g., surface-released atmospheric dispersion calculations for regions close to the ground.
Laser-induced fluorescence spectra of Ba+*-He exciplexes produced in cold He gas

International Nuclear Information System (INIS)

Fukuyama, Yoshimitsu; Matsuo, Yukari; Moriwaki, Yoshiki

2004-01-01

We report the observation of laser-induced fluorescence spectra of Ba +* -He exciplexes. The experiment is carried out in an environment of cold gaseous helium at a temperature range of 3-30 K. We have observed the emission spectra of exciplexes by means of excitation of the 6p 2 P 32 2 S 12 transition of Ba + ions. It is found that these spectra are redshifted from the D2 emission line in the free space and are composed of several peaks. The experimental results are reproduced well by theoretical calculation of the emission spectra for vibrational levels of Ba +* -He. We also investigate the vibrational dynamics of the 6p 2 Π 32 state of Ba + *-He, and we have determined the collision-induced vibrational relaxation cross sections of the 6p 2 Π 32 state to be 9.7±1.1 A 2 at 15 K
Late time optical spectra from the /sup 56/Ni model for Type I supernovae

Energy Technology Data Exchange (ETDEWEB)

Axelrod, T.S.

1980-07-01

The hypothesis that the optical luminosity of Type I supernovae results from the radioactive decay of /sup 56/Ni synthesized and ejected by the explosion has been investigated by numerical simulation of the optical spectrum resulting from a homologously expanding shell composed initially of pure /sup 56/Ni core. This model, which neglects the effects of material external to the /sup 56/Ni core, is expected to provide a reasonable representation of the supernova at late times when the star is nearly transparent to optical photons. The numerical simulation determines the temperature, ionization state, and non-LTE level populations which result from energy deposition by the radioactive decay products of /sup 56/Ni and /sup 56/Co. The optical spectrum includes the effects of both allowed and forbidden lines. The optical spectra resulting from the simulation are found to be sensitive to the mass and ejection velocity of the /sup 56/Ni shell. A range of these parameters has been found which results in good agreement with the observed spectra of SN1972e over a considerable range of time. In particular, evidence for the expected decaying abundance of /sup 56/Co has been found in the spectra of SN1972e. These results are used to assess the validity of the /sup 56/Ni model and set limits on the mass and explosion mechanism of the Type I progenitor. The possibilities for improvement of the numerical model are discussed and future atomic data requirements defined.
Photoinduced Effects in the ZnO Luminescence Spectra

Science.gov (United States)

Akopyan, I. Kh.; Labzovskaya, M. E.; Novikov, B. V.; Lisachenko, A. A.; Serov, A. Yu.; Filosofov, N. G.

2018-02-01

The effect of intense UV irradiation on the photoluminescence (PL) spectra of ZnO powders and nanocrystalline films obtained by atomic layer deposition (ALD) was investigated. At room temperature, the behavior of the spectra under continuous UV irradiation in multiple vacuum-atmosphere cycles was studied. The changes in the intensities of exciton radiation and radiation in the "green" band region, associated with the phenomena of oxygen photodesorption and photoadsorption, are discussed. In the temperature range of 5-300 K, the effect of strong UV irradiation on the near-edge luminescence spectrum of ZnO films was studied. The nature of a new line arising in the photoluminescence spectra of an irradiated film in the region of emission of bound excitons is discussed.
Influence of smoothing of X-ray spectra on parameters of calibration model

International Nuclear Information System (INIS)

Antoniak, W.; Urbanski, P.; Kowalska, E.

1998-01-01

Parameters of the calibration model before and after smoothing of X-ray spectra have been investigated. The calibration model was calculated using multivariate procedure - namely the partial least square regression (PLS). Investigations have been performed on an example of six sets of various standards used for calibration of some instruments based on X-ray fluorescence principle. The smoothing methods were compared: regression splines, Savitzky-Golay and Discrete Fourier Transform. The calculations were performed using a software package MATLAB and some home-made programs. (author)
Prediction of in vivo background in phoswich lung count spectra

International Nuclear Information System (INIS)

Richards, N.W.

1999-01-01

Phoswich scintillation counters are used to detect actinides deposited in the lungs. The resulting spectra, however, contain Compton background from the decay of 40 K, which occurs naturally in the striated muscle tissue of the body. To determine the counts due to actinides in a lung count spectrum, the counts due to 40 K scatter must first be subtracted out. The 40 K background in the phoswich NaI(Tl) spectrum was predicted from an energy region of interest called the monitor region, which is above the 238 Pu region and the 241 Am region, where photopeaks from 238 Pu and 241 Am region, where photopeaks from 238 Pu and 241 Am occur. Empirical models were developed to predict the backgrounds in the 238 Pu and 241 Am regions by testing multiple linear and nonlinear regression models. The initial multiple regression models contain a monitor region variable as well as the variables gender, (weight/height) α , and interaction terms. Data were collected from 64 male and 63 female subjects with no internal exposure. For the 238 Pu region, the only significant predictor was found to be the monitor region. For the 241 Am region, the monitor region was found to have the greatest effect on prediction, while gender was significantly only when weight/height was included in a model. Gender-specific models were thus developed. The empirical models for the 241 Am region that contain weight/height were shown to have the best coefficients of determination (R 2 ) and the lowest mean squares for error (MSE)
Optical conductivity calculation of a k.p model semiconductor GaAs incorporating first-order electron-hole vertex correction

Science.gov (United States)

Nurhuda, Maryam; Aziz Majidi, Muhammad

2018-04-01

The role of excitons in semiconducting materials carries potential applications. Experimental results show that excitonic signals also appear in optical absorption spectra of semiconductor system with narrow gap, such as Gallium Arsenide (GaAs). While on the theoretical side, calculation of optical spectra based purely on Density Functional Theory (DFT) without taking electron-hole (e-h) interactions into account does not lead to the appearance of any excitonic signal. Meanwhile, existing DFT-based algorithms that include a full vertex correction through Bethe-Salpeter equation may reveal an excitonic signal, but the algorithm has not provided a way to analyze the excitonic signal further. Motivated to provide a way to isolate the excitonic effect in the optical response theoretically, we develop a method of calculation for the optical conductivity of a narrow band-gap semiconductor GaAs within the 8-band k.p model that includes electron-hole interactions through first-order electron-hole vertex correction. Our calculation confirms that the first-order e-h vertex correction reveals excitonic signal around 1.5 eV (the band gap edge), consistent with the experimental data.
'Mathematical model of K Capture and its implications'

International Nuclear Information System (INIS)

Angus, Andrew C.

2000-01-01

The mechanism of K Capture, the nuclear absorption of electron in the K shell, as induced by electricity, is explained in this article. Furthermore, a mathematical model of K Capture is formulated. Then, K Capture is applied to explain the negative results obtained by Steven Jones and the positive results obtained by Pons-Fleischmann in Deuterium Oxide Electrolysis Experiments. The most important implication of K Capture is the possibility of obtaining nuclear energy by fusion at low temperature from heavy water
Modeling of aircraft exhaust emissions and infrared spectra for remote measurement of nitrogen oxides

Directory of Open Access Journals (Sweden)

K. Beier

1994-08-01

Full Text Available Infrared (IR molecular spectroscopy is proposed to perform remote measurements of NOx concentrations in the exhaust plume and wake of aircraft. The computer model NIRATAM is applied to simulate the physical and chemical properties of the exhaust plume and to generate low resolution IR spectra and synthetical thermal images of the aircraft in its natural surroundings. High-resolution IR spectra of the plume, including atmospheric absorption and emission, are simulated using the molecular line-by-line radiation model FASCODE2. Simulated IR spectra of a Boeing 747-400 at cruising altitude for different axial and radial positions in the jet region of the exhaust plume are presented. A number of spectral lines of NO can be identified that can be discriminated from lines of other exhaust gases and the natural atmospheric background in the region around 5.2 µm. These lines can be used to determine NO concentration profiles in the plume. The possibility of measuring nitrogen dioxide NO2 is also discussed briefly, although measurements turn out to be substantially less likely than those of NO. This feasibility study compiles fundamental data for the optical and radiometric design of an airborne Fourier transform spectrometer and the preparation of in-flight measurements for monitoring of aircraft pollutants.
Modeling of aircraft exhaust emissions and infrared spectra for remote measurement of nitrogen oxides

Directory of Open Access Journals (Sweden)

K. Beier

Full Text Available Infrared (IR molecular spectroscopy is proposed to perform remote measurements of NO_x concentrations in the exhaust plume and wake of aircraft. The computer model NIRATAM is applied to simulate the physical and chemical properties of the exhaust plume and to generate low resolution IR spectra and synthetical thermal images of the aircraft in its natural surroundings. High-resolution IR spectra of the plume, including atmospheric absorption and emission, are simulated using the molecular line-by-line radiation model FASCODE2. Simulated IR spectra of a Boeing 747-400 at cruising altitude for different axial and radial positions in the jet region of the exhaust plume are presented. A number of spectral lines of NO can be identified that can be discriminated from lines of other exhaust gases and the natural atmospheric background in the region around 5.2 µm. These lines can be used to determine NO concentration profiles in the plume. The possibility of measuring nitrogen dioxide NO₂ is also discussed briefly, although measurements turn out to be substantially less likely than those of NO. This feasibility study compiles fundamental data for the optical and radiometric design of an airborne Fourier transform spectrometer and the preparation of in-flight measurements for monitoring of aircraft pollutants.
Identify High-Quality Protein Structural Models by Enhanced K-Means.

Science.gov (United States)

Wu, Hongjie; Li, Haiou; Jiang, Min; Chen, Cheng; Lv, Qiang; Wu, Chuang

2017-01-01

Background. One critical issue in protein three-dimensional structure prediction using either ab initio or comparative modeling involves identification of high-quality protein structural models from generated decoys. Currently, clustering algorithms are widely used to identify near-native models; however, their performance is dependent upon different conformational decoys, and, for some algorithms, the accuracy declines when the decoy population increases. Results. Here, we proposed two enhanced K -means clustering algorithms capable of robustly identifying high-quality protein structural models. The first one employs the clustering algorithm SPICKER to determine the initial centroids for basic K -means clustering ( SK -means), whereas the other employs squared distance to optimize the initial centroids ( K -means++). Our results showed that SK -means and K -means++ were more robust as compared with SPICKER alone, detecting 33 (59%) and 42 (75%) of 56 targets, respectively, with template modeling scores better than or equal to those of SPICKER. Conclusions. We observed that the classic K -means algorithm showed a similar performance to that of SPICKER, which is a widely used algorithm for protein-structure identification. Both SK -means and K -means++ demonstrated substantial improvements relative to results from SPICKER and classical K -means.
Phylogenetic Distribution of Leaf Spectra and Optically Derived Functional Traits in the American Oaks

Science.gov (United States)

Cavender-Bares, J.; Meireles, J. E.; Couture, J. J.; Kaproth, M.; Townsend, P. A.

2015-12-01

Detecting functional traits of species, genotypes and phylogenetic lineages is critical in monitoring functional biodiversity remotely. We examined the phylogenetic distribution of leaf spectra across the American Oaks for 35 species under greenhouse conditions as well as genetic variation in leaf spectra across Central American populations of a single species grown in common gardens in Honduras. We found significant phylogenetic signal in the leaf spectra (Blomberg's K > 1.0), indicating similarity in spectra among close relatives. Across species, full range leaf spectra were used in a Partial Least Squares Discriminant Analysis (PLS-DA) that allowed species calibration (kappa statistic = 0.55). Validation of the model used to detect species (kappa statistic = 0.4) indicated reasonably good detection of individual species within the same the genus. Among four populations from Belize, Costa Rica, Honduras, and Mexico within a single species (Quercus oleoides), leaf spectra were also able to differentiate populations. Ordination of population-level data using dissimilarities of predicted foliar traits, including leaf mass per area (LMA), lignin content, fiber content, chlorophyll a+b, and C:N ratio in genotypes in either watered or unwatered conditions showed significant differentiation among populations and treatments. These results provide promise for remote detection and differentiation of plant functional traits among plant phylogenetic lineages and genotypes, even among closely related populations and species.
Thermal Infrared Spectra of a Suite of Forsterite Samples and Ab-initio Modelling of theirs Spectra

Science.gov (United States)

Maturilli, A.; Stangarone, C.; Helbert, J.; Tribaudino, M.; Prencipe, M.

2017-12-01

Forsterite is the dominating component in olivine, a major constituent in ultrafemic rocks, as well as planetary bodies. Messenger X-ray spectrometer has shown that Mg-rich silicate minerals, such as enstatite and forsterite, dominate Mercury's surface (Weider et al 2012). A careful and detailed acquaintance with the forsterite spectral features and their dependence wrt environmental conditions on Mercury is needed to interpret the remote sensing data from previous and forthcoming missions. We propose an experimental vs calculation approach to reproduce and describe the spectral features of forsterite. TIR emissivity measurements are performed by the Planetary Spectroscopy Laboratory (PSL) of DLR. PSL offers the unique capability to measure the emissivity of samples at temperature up to 1000K under vacuum conditions. TIR emissivity and reflectance measurements are performed on 11 olivine samples having a different composition within the forsterite-fayalite series. When available, the sample has been measured in 2 different grain sizes (chameleon-like effects of Mercury surface already observed (Helbert et al. 2013), this study wants to point out the main spectral features due to the composition and temperature. Our results are used to create a theoretical background to interpret the high temperature infrared emissivity spectra from MERTIS onboard the ESA BepiColombo mission to Mercury (Helbert et al. 2010).
Loop quantum cosmology of k=1 FRW models

International Nuclear Information System (INIS)

Ashtekar, Abhay; Pawlowski, Tomasz; Singh, Parampreet; Vandersloot, Kevin

2007-01-01

The closed, k=1, FRW model coupled to a massless scalar field is investigated in the framework of loop quantum cosmology using analytical and numerical methods. As in the k=0 case, the scalar field can be again used as emergent time to construct the physical Hilbert space and introduce Dirac observables. The resulting framework is then used to address a major challenge of quantum cosmology: resolving the big-bang singularity while retaining agreement with general relativity at large scales. It is shown that the framework fulfills this task. In particular, for states which are semiclassical at some late time, the big bang is replaced by a quantum bounce and a recollapse occurs at the value of the scale factor predicted by classical general relativity. Thus, the ''difficulties'' pointed out by Green and Unruh in the k=1 case do not arise in a more systematic treatment. As in k=0 models, quantum dynamics is deterministic across the deep Planck regime. However, because it also retains the classical recollapse, in contrast to the k=0 case one is now led to a cyclic model. Finally, we clarify some issues raised by Laguna's recent work addressed to computational physicists
Measurements of production properties of $K^{0}_{S}$ mesons and $\\Lambda$ hyperons in proton-carbon interactions at 31 GeV/c

CERN Document Server

Abgrall, N.; Ali, Y.; Anticic, T.; Antoniou, N.; Argyriades, J.; Baatar, B.; Blondel, A.; Blumer, J.; Bogomilov, M.; Bravar, A.; Brooks, W.; Brzychczyk, J.; Bunyatov, S.A.; Busygina, O.; Christakoglou, P.; Czopowicz, T.; Davis, N.; Debieux, S.; Dembinski, H.; Diakonos, F.; Di Luise, S.; Dominik, W.; Drozhzhova, T.; Dumarchez, J.; Dynowski, K.; Engel, R.; Ereditato, A.; Esposito, L.; Feofilov, G.A.; Fodor, Z.; Fulop, A.; Gazdzicki, M.; Golubeva, M.; Grebieszkow, K.; Grzeszczuk, A.; Guber, F.; Hakobyan, H.; Haesler, A.; Hasegawa, T.; Hierholzer, M.; Idczak, R.; Igolkin, S.; Ivanov, Y.; Ivashkin, A.; Jokovic, D.; Kadija, K.; Kapoyannis, A.; Katrynska, N.; Kaptur, E.; Kielczewska, D.; Kikola, D.; Kirejczyk, M.; Kisiel, J.; Kiss, T.; Kleinfelder, S.; Kobayashi, T.; Kolesnikov, V.I.; Kolev, D.; Kondratiev, V.P.; Korzenev, A.; Kowalski, S.; Krasnoperov, A.; Kuleshov, S.; Kurepin, A.; Larsen, D.; Laszlo, A.; Lyubushkin, V.V.; Mackowiak-Pawlowska, M.; Majka, Z.; Maksiak, B.; Malakhov, A.I.; Maletic, D.; Manic, D.; Marchionni, A.; Marcinek, A.; Marin, V.; Marton, K.; Mathes, H-J.; Matulewicz, T.; Matveev, V.; Melkumov, G.L.; Mrowczynski, St.; Murphy, S.; Nakadaira, T.; Nirkko, M.; Nishikawa, K.; Palczewski, T.; Palla, G.; Panagiotou, A.D.; Paul, T.; Peryt, W.; Pistillo, C.; Redij, A.; Petukhov, O.; Planeta, R.; Pluta, J.; Popov, B.A.; Posiada la, M.; Pulawski, S.; Puzovic, J.; Rauch, W.; Ravonel, M.; Renfordt, R.; Robert, A.; Rohrich, D.; Rondio, E.; Roth, M.; Rubbia, A.; Rustamov, A.; Rybczynski, M.; Sadovsky, A.; Sakashita, K.; Savic, M.; Schmidt, K.; Sekiguchi, T.; Seyboth, P.; Shibata, M.; Sipos, R.; Skrzypczak, E.; Slodkowski, M.; Staszel, P.; Stefanek, G.; Stepaniak, J.; Susa, T.; Szuba, M.; Tada, M.; Tereshchenko, V.; Tolyhi, T.; Tsenov, R.; Turko, L.; Ulrich, R.; Unger, M.; Vassiliou, M.; Veberic, D.; Vechernin, V.V.; Vesztergombi, G.; Vinogradov, L.; Wilczek, A.; Wlodarczyk, Z.; Wojtaszek, A.; Wyszynski, O.; Zambelli, L.; Zipper, W.

2014-02-28

Spectra of $K^0_S$ mesons and $\\Lambda$ hyperons were measured in p+C interactions at 31 GeV/c with the large acceptance NA61/SHINE spectrometer at the CERN SPS. The data were collected with an isotropic graphite target with a thickness of 4% of a nuclear interaction length. Interaction cross sections, charged pion spectra, and charged kaon spectra were previously measured using the same data set. Results on $K^0_S$ and $\\Lambda$ production in p+C interactions serve as reference for the understanding of the enhancement of strangeness production in nucleus-nucleus collisions. Moreover, they provide important input for the improvement of neutrino flux predictions for the T2K long baseline neutrino oscillation experiment in Japan. Inclusive production cross sections for $K^0_S$ and $\\Lambda$ are presented as a function of laboratory momentum in intervals of the laboratory polar angle covering the range from 0 up to 240 mrad. The results are compared with predictions of several hadron production models. The $K^0_...

Insularité et démographie dans la mer Intérieure japonaise

Directory of Open Access Journals (Sweden)

Philippe PELLETIER

1992-12-01

Full Text Available Les îles éloignées (ritô tiennent une place importante dans l’espace japonais. Les îles de la mer Intérieure se dépeuplèrent fortement pendant la Haute Croissance. Un graphique corrélant leur évolution démographique et leur distance par rapport à Honshû et Shikoku nous aide à comprendre que l’éloignement insulaire joua un rôle relatif.
QUALITATIVE INTERPRETATION OF GALAXY SPECTRA

Energy Technology Data Exchange (ETDEWEB)

Sanchez Almeida, J.; Morales-Luis, A. B. [Instituto de Astrofisica de Canarias, E-38205 La Laguna, Tenerife (Spain); Terlevich, R.; Terlevich, E. [Instituto Nacional de Astrofisica, Optica y Electronica, Tonantzintla, Puebla (Mexico); Cid Fernandes, R., E-mail: jos@iac.es, E-mail: abml@iac.es, E-mail: rjt@ast.cam.ac.uk, E-mail: eterlevi@inaoep.mx, E-mail: cid@astro.ufsc.br [Departamento de Fisica-CFM, Universidade Federal de Santa Catarina, P.O. Box 476, 88040-900 Florianopolis, SC (Brazil)

2012-09-10

We describe a simple step-by-step guide to qualitative interpretation of galaxy spectra. Rather than an alternative to existing automated tools, it is put forward as an instrument for quick-look analysis and for gaining physical insight when interpreting the outputs provided by automated tools. Though the recipe is for general application, it was developed for understanding the nature of the Automatic Spectroscopic K-means-based (ASK) template spectra. They resulted from the classification of all the galaxy spectra in the Sloan Digital Sky Survey data release 7, thus being a comprehensive representation of the galaxy spectra in the local universe. Using the recipe, we give a description of the properties of the gas and the stars that characterize the ASK classes, from those corresponding to passively evolving galaxies, to H II galaxies undergoing a galaxy-wide starburst. The qualitative analysis is found to be in excellent agreement with quantitative analyses of the same spectra. We compare the mean ages of the stellar populations with those inferred using the code STARLIGHT. We also examine the estimated gas-phase metallicity with the metallicities obtained using electron-temperature-based methods. A number of byproducts follow from the analysis. There is a tight correlation between the age of the stellar population and the metallicity of the gas, which is stronger than the correlations between galaxy mass and stellar age, and galaxy mass and gas metallicity. The galaxy spectra are known to follow a one-dimensional sequence, and we identify the luminosity-weighted mean stellar age as the affine parameter that describes the sequence. All ASK classes happen to have a significant fraction of old stars, although spectrum-wise they are outshined by the youngest populations. Old stars are metal-rich or metal-poor depending on whether they reside in passive galaxies or in star-forming galaxies.
Evidence of mercury trapping in biofilm-EPS and mer operon-based volatilization of inorganic mercury in a marine bacterium Bacillus cereus BW-201B.

Science.gov (United States)

Dash, Hirak R; Basu, Subham; Das, Surajit

2017-04-01

Biofilm-forming mercury-resistant marine bacterium Bacillus cereus BW-201B has been explored to evident that the bacterial biofilm-EPS (exopolymers) trap inorganic mercury but subsequently release EPS-bound mercury for induction of mer operon-mediated volatilization of inorganic mercury. The isolate was able to tolerate 50 ppm of mercury and forms biofilm in presence of mercury. mer operon-mediated volatilization was confirmed, and -SH was found to be the key functional group of bacterial EPS responsible for mercury binding. Biofilm-EPS-bound mercury was found to be internalized to the bacterial system as confirmed by reversible conformational change of -SH group and increased expression level of merA gene in a timescale experiment. Biofilm-EPS trapped Hg after 24 h of incubation, and by 96 h, the volatilization process reaches to its optimum confirming the internalization of EPS-bound mercury to the bacterial cells. Biofilm disintegration at the same time corroborates the results.
Second-order Raman spectra of LiHxD1-x crystals

International Nuclear Information System (INIS)

Plekhanov, V.G.

1994-01-01

High-resolution Raman spectra of LiH x D 1-x cubic crystals were measured for the first time in a wide concentration range (0≤x≤1) at room temperature. The results agree well with data on inelastic neutron scattering and direct calculations of the lattice dynamics for LiH and LiD crystals. This allows one to assign the observed spectral features to the phonon excitations in X-, W-, L-, and K-points of the Brillouin zone. Spectra of LiD exhibit the high-frequency maximum with a pronounced doubled structure. This fact and the dependence of the maximum intensity on the excitation laser frequency provide clear evidence that the maximum is due to excitation of LO(Γ)-phonons in pure or mixed crystals. In the x approx-lt 0.4 range, the LO-phonons manifest themselves in the spectra of both pure LiD and mixed LiH x D 1-x crystals, which demonstrates for the first time their two-mode character in this concentration range. This conclusion is in contradiction with predictions of the coherent potential model. In this paper, causes of this conflict are briefly discussed. 36 refs., 5 figs., 2 tabs
Synthesis of audio spectra using a diffraction model.

Science.gov (United States)

Vijayakumar, V; Eswaran, C

2006-12-01

It is shown that the intensity variations of an audio signal in the frequency domain can be obtained by using a mathematical function containing a series of weighted complex Bessel functions. With proper choice of values for two parameters, this function can transform an input spectrum of discrete frequencies of unit intensity into the known spectra of different musical instruments. Specific examples of musical instruments are considered for evaluating the performance of this method. It is found that this function yields musical spectra with a good degree of accuracy.
Probabilistic topic modeling for the analysis and classification of genomic sequences

Science.gov (United States)

2015-01-01

Background Studies on genomic sequences for classification and taxonomic identification have a leading role in the biomedical field and in the analysis of biodiversity. These studies are focusing on the so-called barcode genes, representing a well defined region of the whole genome. Recently, alignment-free techniques are gaining more importance because they are able to overcome the drawbacks of sequence alignment techniques. In this paper a new alignment-free method for DNA sequences clustering and classification is proposed. The method is based on k-mers representation and text mining techniques. Methods The presented method is based on Probabilistic Topic Modeling, a statistical technique originally proposed for text documents. Probabilistic topic models are able to find in a document corpus the topics (recurrent themes) characterizing classes of documents. This technique, applied on DNA sequences representing the documents, exploits the frequency of fixed-length k-mers and builds a generative model for a training group of sequences. This generative model, obtained through the Latent Dirichlet Allocation (LDA) algorithm, is then used to classify a large set of genomic sequences. Results and conclusions We performed classification of over 7000 16S DNA barcode sequences taken from Ribosomal Database Project (RDP) repository, training probabilistic topic models. The proposed method is compared to the RDP tool and Support Vector Machine (SVM) classification algorithm in a extensive set of trials using both complete sequences and short sequence snippets (from 400 bp to 25 bp). Our method reaches very similar results to RDP classifier and SVM for complete sequences. The most interesting results are obtained when short sequence snippets are considered. In these conditions the proposed method outperforms RDP and SVM with ultra short sequences and it exhibits a smooth decrease of performance, at every taxonomic level, when the sequence length is decreased. PMID:25916734
Analysis of the K-epsilon turbulence model

International Nuclear Information System (INIS)

Mohammadi, B.; Pironneau, O.

1993-12-01

This book is aimed at applied mathematicians interested in numerical simulation of turbulent flows. The book is centered around the k - ε model but it also deals with other models such as subgrid scale models, one equation models and Reynolds Stress models. The reader is expected to have some knowledge of numerical methods for fluids and, if possible, some understanding of fluid mechanics, the partial differential equations used and their variational formulations. This book presents the k - ε method for turbulence in a language familiar to applied mathematicians, stripped bare of all the technicalities of turbulence theory. The model is justified from a mathematical standpoint rather than from a physical one. The numerical algorithms are investigated and some theoretical and numerical results presented. This book should prove an invaluable tool for those studying a subject that is still controversial but very useful for industrial applications. (authors). 71 figs., 200 refs
MERS-CoV: Middle East respiratory syndrome corona virus: Can radiology be of help? Initial single center experience

Directory of Open Access Journals (Sweden)

Ahmed Hamimi

2016-03-01

Conclusions: MERS CoV virus may have a specific pattern in chest X-ray and CT developing a single or multiple opacities progressing into a widespread multifocal bilateral patches of ground glass opacities or confluent consolidation resembling organizing pneumonia.
Investigation of the pp{yields}K{sup +}n{sigma}{sup +} reaction at the magnetic spectrometer ANKE-COSY

Energy Technology Data Exchange (ETDEWEB)

Valdau, Yury

2009-10-20

This thesis describes measurements of the pp{yields}K{sup +}n{sigma}{sup +} reaction near threshold. The work was largely motivated by the lack of data for {sigma}{sup +} hyperon production in pp collisions and, in particular, by recent measurements of pp{yields}K{sup +}n{sigma}{sup +} by the COSY11 collaboration. The experiment performed by this group using a neutron detector reported surprisingly high {sigma}{sup +} cross sections that are hard to reconcile with isospin considerations. The experiment discussed in the thesis has been performed at the ANKE-COSY facility at four close-to-threshold energies. It relies on the almost background-free K{sup +} identification using the delayed-veto technique and the fact that below the threshold for pp{yields}K{sup +}n{lambda}{pi}{sup +} there is no source of the K{sup +}{pi}{sup +} correlations other than the {sigma}{sup +}{yields}n{pi}{sup +} decay. Thus, the detection of K{sup +}{pi}{sup +} pairs allows one to identify the pp{yields}K{sup +}n{sigma}{sup +} reaction without the need for a neutron detector. The analysis of three simultaneously measured spectra has been carried out, searching for any signal from a possible high {sigma}{sup +} cross section. All the K{sup +} production channels allowed at the energy of the experiment contribute to the K{sup +} inclusive and K{sup +}p correlation spectra. In the K{sup +} inclusive distributions, signals from the different production channels are summed and can only be isolated using theoretical models. In the K{sup +}p correlation spectra, there are not only signals from the direct reaction protons but also protons from hyperon decays can be observed. Thus, the signal from {sigma}{sup +}{yields}p{pi}{sup 0} decay contributes to the K{sup +}p missing mass. The study of the K{sup +}{pi}{sup +} correlations allows one to identify the {sigma}{sup +} reaction channels and to estimate the total production cross section. This method has been successfully applied to existing ANKE
Raman spectra of lignin model compounds

Science.gov (United States)

Umesh P. Agarwal; Richard S. Reiner; Ashok K. Pandey; Sally A. Ralph; Kolby C. Hirth; Rajai H. Atalla

2005-01-01

To fully exploit the value of Raman spectroscopy for analyzing lignins and lignin containing materials, a detailed understanding of ligninsâ Raman spectra needs to be achieved. Although advances made thus far have led to significant growth in application of Raman techniques, further developments are needed to improve upon the existing knowledge. Considering that lignin...
Stellar model chromospheres. VIII - 70 Ophiuchi A /K0 V/ and Epsilon Eridani /K2 V/

Science.gov (United States)

Kelch, W. L.

1978-01-01

Model atmospheres for the late-type active-chromosphere dwarf stars 70 Oph A and Epsilon Eri are computed from high-resolution Ca II K line profiles as well as Mg II h and k line fluxes. A method is used which determines a plane-parallel homogeneous hydrostatic-equilibrium model of the upper photosphere and chromosphere which differs from theoretical models by lacking the constraint of radiative equilibrium (RE). The determinations of surface gravities, metallicities, and effective temperatures are discussed, and the computational methods, model atoms, atomic data, and observations are described. Temperature distributions for the two stars are plotted and compared with RE models for the adopted effective temperatures and gravities. The previously investigated T min/T eff vs. T eff relation is extended to Epsilon Eri and 70 Oph A, observed and computed Ca II K and Mg II h and k integrated emission fluxes are compared, and full tabulations are given for the proposed models. It is suggested that if less than half the observed Mg II flux for the two stars is lost in noise, the difference between an active-chromosphere star and a quiet-chromosphere star lies in the lower-chromospheric temperature gradient.
When Information from Public Health Officials is Untrustworthy: The Use of Online News, Interpersonal Networks, and Social Media during the MERS Outbreak in South Korea.

Science.gov (United States)

Jang, Kyungeun; Baek, Young Min

2018-03-20

Public health officials (PHOs) are responsible for providing trustworthy information during a public health crisis; however, there is little research on how the public behaves when their expectations for such information are violated. Drawing on media dependency theory and source credibility research as our primary theoretical framework, we tested how credibility of information from PHOs is associated with people's reliance on a particular communication channel in the context of the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea. Using nationally representative data (N = 1036) collected during the MERS outbreak, we found that less credible information from PHOs led to more frequent use of online news, interpersonal networks, and social media for acquiring MERS-related information. However, credibility of information from PHOs was not associated with the use of television news or print newspapers. The theoretical and practical implications of our results on communication channels usage are discussed.
Absorption spectra analysis of hydrated uranium(III) complex chlorides

Science.gov (United States)

Karbowiak, M.; Gajek, Z.; Drożdżyński, J.

2000-11-01

Absorption spectra of powdered samples of hydrated uranium(III) complex chlorides of the formulas NH 4UCl 4 · 4H 2O and CsUCl 4 · 3H 2O have been recorded at 4.2 K in the 4000-26 000 cm -1 range. The analysis of the spectra enabled the determination of crystal-field parameters and assignment of 83 and 77 crystal-field levels for the tetrahydrate and trihydrate, respectively. The energies of the levels were computed by applying a simplified angular overlap model as well as a semiempirical Hamiltonian representing the combined atomic and crystal-field interactions. Ab initio calculations have enabled the application of a simplified parameterization and the determination of the starting values of the AOM parameters. The received results have proved that the AOM approach can quite well predict both the structure of the ground multiplet and the positions of the crystal-field levels in the 17 000-25 000 cm -1 range, usually obscured by strong f-d bands.
RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data.

Directory of Open Access Journals (Sweden)

Simon H Tausch

Full Text Available The assembly of viral or endosymbiont genomes from Next Generation Sequencing (NGS data is often hampered by the predominant abundance of reads originating from the host organism. These reads increase the memory and CPU time usage of the assembler and can lead to misassemblies.We developed RAMBO-K (Read Assignment Method Based On K-mers, a tool which allows rapid and sensitive removal of unwanted host sequences from NGS datasets. Reaching a speed of 10 Megabases/s on 4 CPU cores and a standard hard drive, RAMBO-K is faster than any tool we tested, while showing a consistently high sensitivity and specificity across different datasets.RAMBO-K rapidly and reliably separates reads from different species without data preprocessing. It is suitable as a straightforward standard solution for workflows dealing with mixed datasets. Binaries and source code (java and python are available from http://sourceforge.net/projects/rambok/.
77 FR 49059 - Requested Administrative Waiver of the Coastwise Trade Laws: Vessel CHAT DE MER; Invitation for...

Science.gov (United States)

2012-08-15

... Administrative Waiver of the Coastwise Trade Laws: Vessel CHAT DE MER; Invitation for Public Comments AGENCY....gov . SUPPLEMENTARY INFORMATION: As described by the applicant the intended service of the vessel CHAT... Francisco Bay. Geographic Region: ``California.'' The complete application is given in DOT docket MARAD-2012...
Monte Carlo simulation of x-ray spectra in mammography

Energy Technology Data Exchange (ETDEWEB)

Ng, K.P. [Department of Optometry and Radiography, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong (China). E-mail: benngkp at netvigator.com; Kwok, C.S.; Ng, K.P.; Tang, F.H. [Department of Optometry and Radiography, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong (China)

2000-05-01

A model for generating x-ray spectra in mammography is presented. This model used the ITS version 3 Monte Carlo code for simulating the radiation transport. Various target/filter combinations such as tungsten/aluminium, molybdenum/molybdenum, molybdenum/rhodium and rhodium/rhodium were used in the simulation. Both bremsstrahlung and characteristic x-ray production were included in the model. The simulated x-ray emission spectra were compared with two sets of spectra, those of Boone et al (1997 Med. Phys. 24 1863-74) and IPEM report 78. The {chi}{sup 2} test was used for the overall goodness of fit of the spectral data. There is good agreement between the simulated x-ray spectra and the comparison spectra as the test yielded a probability value of nearly 1. When the transmitted x-ray spectra for specific target/filter combinations were generated and compared with a measured molybdenum/rhodium spectrum and spectra generated in IPEM report 78, close agreement is also observed. This was demonstrated by the probability value for the {chi}{sup 2} test being almost 1 for all the cases. However, minor differences between the simulated spectra and the 'standard' ones are observed. (author)
Monte Carlo simulation of x-ray spectra in mammography

International Nuclear Information System (INIS)

Ng, K.P.

2000-01-01

A model for generating x-ray spectra in mammography is presented. This model used the ITS version 3 Monte Carlo code for simulating the radiation transport. Various target/filter combinations such as tungsten/aluminium, molybdenum/molybdenum, molybdenum/rhodium and rhodium/rhodium were used in the simulation. Both bremsstrahlung and characteristic x-ray production were included in the model. The simulated x-ray emission spectra were compared with two sets of spectra, those of Boone et al (1997 Med. Phys. 24 1863-74) and IPEM report 78. The χ 2 test was used for the overall goodness of fit of the spectral data. There is good agreement between the simulated x-ray spectra and the comparison spectra as the test yielded a probability value of nearly 1. When the transmitted x-ray spectra for specific target/filter combinations were generated and compared with a measured molybdenum/rhodium spectrum and spectra generated in IPEM report 78, close agreement is also observed. This was demonstrated by the probability value for the χ 2 test being almost 1 for all the cases. However, minor differences between the simulated spectra and the 'standard' ones are observed. (author)
Portable microcomputer unit for the analysis of plutonium gamma-ray spectra

International Nuclear Information System (INIS)

Ruhter, W.D.; Camp, D.C.

1981-10-01

A portable microcomputer has been developed for the IAEA to perform in-field analysis of plutonium gamma-ray spectra. The unit includes a 16-bit LSI-11/2 microprocessor, 32K words of memory, a 20-character display for user prompting, and a 20-character thermal printer for hardcopy output. Only the positions of the 148-keV Pu-241 and 208-keV U-237 peaks are required for spectral analysis. The unit was tested against gamma-ray spectra taken of NBS plutonium standards and IAEA spectra. Results obtained are presented
Numerical simulation of stratified flows with different k-ε turbulence models

International Nuclear Information System (INIS)

Dagestad, S.

1991-01-01

The thesis comprises the numerical simulation of stratified flows with different k-ε models. When using the k-ε model, two equations are solved to describe the turbulence. The k-equation represents the turbulent kinetic energy of the turbulence and the ε-equation is the turbulent dissipation. Different k-ε models predict stratified flows differently. The standard k-ε model leads to higher turbulent mixing than the low-Reynolds model does. For lower Froude numbers, F 0 , this effect becomes enhanced. Buoyancy extension of the k-ε model also leads to less vertical mixing in cases with strong stratification. When the stratification increases, buoyancy-extension becomes larger influence. The turbulent Prandtl number effects have large impact on the transport of heat and the development of the flow. Two different formulae which express the turbulent Prandtl effects have been tested. For unstably stratified flows, the rapid mixing and three-dimensionality of the flow can in fact be computed using a k-ε model when buoyancy-extended is employed. The turbulent heat transfer and thus turbulent production in unstable stratified flows depends strongly upon the turbulent Prandtl number effect. The main conclusions are: Stable stratified flows should be computed with a buoyancy-extended low-Reynolds k-ε model; Unstable stratified flows should be computed with a buoyancy-extended standard k-ε model; The turbulent Prandtl number effects should be included in the computations; Buoyancy-extension has lead to more correct description of the physics for all of the investigated flows. 78 refs., 128 figs., 17 tabs
Non-equilibrium ionization by a periodic electron beam. II. Synthetic Si IV and O IV transition region spectra

Science.gov (United States)

Dzifčáková, Elena; Dudík, Jaroslav

2018-03-01

Context. Transition region (TR) spectra typically show the Si IV 1402.8 Å line to be enhanced by a factor of 5 or more compared to the neighboring O IV 1401.2 Å, contrary to predictions of ionization equilibrium models and the Maxwellian distribution of particle energies. Non-equilibrium effects in TR spectra are therefore expected. Aims: To investigate the combination of non-equilibrium ionization and high-energy particles, we apply the model of the periodic electron beam, represented by a κ-distribution that recurs at periods of several seconds, to plasma at chromospheric temperatures of 104 K. This simple model can approximate a burst of energy release involving accelerated particles. Methods: Instantaneous time-dependent charge states of silicon and oxygen were calculated and used to synthesize the instantaneous and period-averaged spectra of Si IV and O IV. Results: The electron beam drives the plasma out of equilibrium. At electron densities of Ne = 1010 cm-3, the plasma is out of ionization equilibrium at all times in all cases we considered, while for a higher density of Ne = 1011 cm-3, ionization equilibrium can be reached toward the end of each period, depending on the conditions. In turn, the character of the period-averaged synthetic spectra also depends on the properties of the beam. While the case of κ = 2 results in spectra with strong or even dominant O IV, higher values of κ can approximate a range of observed TR spectra. Spectra similar to typically observed spectra, with the Si IV 1402.8 Å line about a factor 5 higher than O IV 1401.2 Å, are obtained for κ = 3. An even higher value of κ = 5 results in spectra that are exclusively dominated by Si IV, with negligible O IV emission. This is a possible interpretation of the TR spectra of UV (Ellerman) bursts, although an interpretation that requires a density that is 1-3 orders of magnitude lower than for equilibrium estimates. Movies associated to Fig. A.1 are available at http://https://www.aanda.org

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