Log-Log Convexity of Type-Token Growth in Zipf's Systems

NASA Astrophysics Data System (ADS)

Font-Clos, Francesc; Corral, Álvaro

2015-06-01

It is traditionally assumed that Zipf's law implies the power-law growth of the number of different elements with the total number of elements in a system—the so-called Heaps' law. We show that a careful definition of Zipf's law leads to the violation of Heaps' law in random systems, with growth curves that have a convex shape in log-log scale. These curves fulfill universal data collapse that only depends on the value of Zipf's exponent. We observe that real books behave very much in the same way as random systems, despite the presence of burstiness in word occurrence. We advance an explanation for this unexpected correspondence.

Using Zipf-Mandelbrot law and graph theory to evaluate animal welfare

NASA Astrophysics Data System (ADS)

de Oliveira, Caprice G. L.; Miranda, José G. V.; Japyassú, Hilton F.; El-Hani, Charbel N.

2018-02-01

This work deals with the construction and testing of metrics of welfare based on behavioral complexity, using assumptions derived from Zipf-Mandelbrot law and graph theory. To test these metrics we compared yellow-breasted capuchins (Sapajus xanthosternos) (Wied-Neuwied, 1826) (PRIMATES CEBIDAE) found in two institutions, subjected to different captive conditions: a Zoobotanical Garden (hereafter, ZOO; n = 14), in good welfare condition, and a Wildlife Rescue Center (hereafter, WRC; n = 8), in poor welfare condition. In the Zipf-Mandelbrot-based analysis, the power law exponent was calculated using behavior frequency values versus behavior rank value. These values allow us to evaluate variations in individual behavioral complexity. For each individual we also constructed a graph using the sequence of behavioral units displayed in each recording (average recording time per individual: 4 h 26 min in the ZOO, 4 h 30 min in the WRC). Then, we calculated the values of the main graph attributes, which allowed us to analyze the complexity of the connectivity of the behaviors displayed in the individuals' behavioral sequences. We found significant differences between the two groups for the slope values in the Zipf-Mandelbrot analysis. The slope values for the ZOO individuals approached -1, with graphs representing a power law, while the values for the WRC individuals diverged from -1, differing from a power law pattern. Likewise, we found significant differences for the graph attributes average degree, weighted average degree, and clustering coefficient when comparing the ZOO and WRC individual graphs. However, no significant difference was found for the attributes modularity and average path length. Both analyses were effective in detecting differences between the patterns of behavioral complexity in the two groups. The slope values for the ZOO individuals indicated a higher behavioral complexity when compared to the WRC individuals. Similarly, graph construction and the

Towards a seascape typology. I. Zipf versus Pareto laws

NASA Astrophysics Data System (ADS)

Seuront, Laurent; Mitchell, James G.

Two data analysis methods, referred to as the Zipf and Pareto methods, initially introduced in economics and linguistics two centuries ago and subsequently used in a wide range of fields (word frequency in languages and literature, human demographics, finance, city formation, genomics and physics), are described and proposed here as a potential tool to classify space-time patterns in marine ecology. The aim of this paper is, first, to present the theoretical bases of Zipf and Pareto laws, and to demonstrate that they are strictly equivalent. In that way, we provide a one-to-one correspondence between their characteristic exponents and argue that the choice of technique is a matter of convenience. Second, we argue that the appeal of this technique is that it is assumption-free for the distribution of the data and regularity of sampling interval, as well as being extremely easy to implement. Finally, in order to allow marine ecologists to identify and classify any structure in their data sets, we provide a step by step overview of the characteristic shapes expected for Zipf's law for the cases of randomness, power law behavior, power law behavior contaminated by internal and external noise, and competing power laws illustrated on the basis of typical ecological situations such as mixing processes involving non-interacting and interacting species, phytoplankton growth processes and differential grazing by zooplankton.

Greedy algorithms and Zipf laws

NASA Astrophysics Data System (ADS)

Moran, José; Bouchaud, Jean-Philippe

2018-04-01

We consider a simple model of firm/city/etc growth based on a multi-item criterion: whenever entity B fares better than entity A on a subset of M items out of K, the agent originally in A moves to B. We solve the model analytically in the cases K  =  1 and . The resulting stationary distribution of sizes is generically a Zipf-law provided M  >  K/2. When , no selection occurs and the size distribution remains thin-tailed. In the special case M  =  K, one needs to regularize the problem by introducing a small ‘default’ probability ϕ. We find that the stationary distribution has a power-law tail that becomes a Zipf-law when . The approach to the stationary state can also be characterized, with strong similarities with a simple ‘aging’ model considered by Barrat and Mézard.

Mapping of the Tuple1 gene to mouse chromosome 16A-B1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mattei, M.G.; Halford, S.; Scambler, P.J.

The human TUPLE1 gene encodes a putative transcriptional regulator and maps to chromosome 22, and therefore may play a role in Di-George syndrome (DGS), relo-cardio-facial syndrome (VCFS), or a related pathology. The murine TUPLE1 gene has also been cloned and shows strong sequence similarity to TUPLE1. Comparative mapping is useful in the study of chromosome evolution and is sometimes able to indicate possible mouse mutations that are potential models of human genetic disorders. As TIPLE1 is a candidate gene for the haploinsufficient phenotype in DGS, we mapped TUPLE1 to mouse chromosome 16A-B1. 6 refs., 1 fig.

Zipf rank approach and cross-country convergence of incomes

NASA Astrophysics Data System (ADS)

Shao, Jia; Ivanov, Plamen Ch.; Urošević, Branko; Stanley, H. Eugene; Podobnik, Boris

2011-05-01

We employ a concept popular in physics —the Zipf rank approach— in order to estimate the number of years that EU members would need in order to achieve "convergence" of their per capita incomes. Assuming that trends in the past twenty years continue to hold in the future, we find that after t≈30 years both developing and developed EU countries indexed by i will have comparable values of their per capita gross domestic product {\\cal G}_{i,t} . Besides the traditional Zipf rank approach we also propose a weighted Zipf rank method. In contrast to the EU block, on the world level the Zipf rank approach shows that, between 1960 and 2009, cross-country income differences increased over time. For a brief period during the 2007-2008 global economic crisis, at world level the {\\cal G}_{i,t} of richer countries declined more rapidly than the {\\cal G}_{i,t} of poorer countries, in contrast to EU where the {\\cal G}_{i,t} of developing EU countries declined faster than the {\\cal G}_{i,t} of developed EU countries, indicating that the recession interrupted the convergence between EU members. We propose a simple model of GDP evolution that accounts for the scaling we observe in the data.

Zipf's law and city size distribution: A survey of the literature and future research agenda

NASA Astrophysics Data System (ADS)

Arshad, Sidra; Hu, Shougeng; Ashraf, Badar Nadeem

2018-02-01

This study provides a systematic review of the existing literature on Zipf's law for city size distribution. Existing empirical evidence suggests that Zipf's law is not always observable even for the upper-tail cities of a territory. However, the controversy with empirical findings arises due to sample selection biases, methodological weaknesses and data limitations. The hypothesis of Zipf's law is more likely to be rejected for the entire city size distribution and, in such case, alternative distributions have been suggested. On the contrary, the hypothesis is more likely to be accepted if better empirical methods are employed and cities are properly defined. The debate is still far from to be conclusive. In addition, we identify four emerging areas in Zipf's law and city size distribution research including the size distribution of lower-tail cities, the size distribution of cities in sub-national regions, the alternative forms of Zipf's law, and the relationship between Zipf's law and the coherence property of the urban system.

Variation of Zipf's exponent in one hundred live languages: A study of the Holy Bible translations

NASA Astrophysics Data System (ADS)

Mehri, Ali; Jamaati, Maryam

2017-08-01

Zipf's law, as a power-law regularity, confirms long-range correlations between the elements in natural and artificial systems. In this article, this law is evaluated for one hundred live languages. We calculate Zipf's exponent for translations of the holy Bible to several languages, for this purpose. The results show that, the average of Zipf's exponent in studied texts is slightly above unity. All studied languages in some families have Zipf's exponent lower/higher than unity. It seems that geographical distribution impresses the communication between speakers of different languages in a language family, and affect similarity between their Zipf's exponent. The Bible has unique concept regardless of its language, but the discrepancy in grammatical rules and syntactic regularities in applying stop words to make sentences and imply a certain concept, lead to difference in Zipf's exponent for various languages.

Pareto-Zipf law in growing systems with multiplicative interactions

NASA Astrophysics Data System (ADS)

Ohtsuki, Toshiya; Tanimoto, Satoshi; Sekiyama, Makoto; Fujihara, Akihiro; Yamamoto, Hiroshi

2018-06-01

Numerical simulations of multiplicatively interacting stochastic processes with weighted selections were conducted. A feedback mechanism to control the weight w of selections was proposed. It becomes evident that when w is moderately controlled around 0, such systems spontaneously exhibit the Pareto-Zipf distribution. The simulation results are universal in the sense that microscopic details, such as parameter values and the type of control and weight, are irrelevant. The central ingredient of the Pareto-Zipf law is argued to be the mild control of interactions.

Zipf's word frequency law in natural language: a critical review and future directions.

PubMed

Piantadosi, Steven T

2014-10-01

The frequency distribution of words has been a key object of study in statistical linguistics for the past 70 years. This distribution approximately follows a simple mathematical form known as Zipf's law. This article first shows that human language has a highly complex, reliable structure in the frequency distribution over and above this classic law, although prior data visualization methods have obscured this fact. A number of empirical phenomena related to word frequencies are then reviewed. These facts are chosen to be informative about the mechanisms giving rise to Zipf's law and are then used to evaluate many of the theoretical explanations of Zipf's law in language. No prior account straightforwardly explains all the basic facts or is supported with independent evaluation of its underlying assumptions. To make progress at understanding why language obeys Zipf's law, studies must seek evidence beyond the law itself, testing assumptions and evaluating novel predictions with new, independent data.

Deviation of Zipf's and Heaps' Laws in Human Languages with Limited Dictionary Sizes

PubMed Central

Lü, Linyuan; Zhang, Zi-Ke; Zhou, Tao

2013-01-01

Zipf's law on word frequency and Heaps' law on the growth of distinct words are observed in Indo-European language family, but it does not hold for languages like Chinese, Japanese and Korean. These languages consist of characters, and are of very limited dictionary sizes. Extensive experiments show that: (i) The character frequency distribution follows a power law with exponent close to one, at which the corresponding Zipf's exponent diverges. Indeed, the character frequency decays exponentially in the Zipf's plot. (ii) The number of distinct characters grows with the text length in three stages: It grows linearly in the beginning, then turns to a logarithmical form, and eventually saturates. A theoretical model for writing process is proposed, which embodies the rich-get-richer mechanism and the effects of limited dictionary size. Experiments, simulations and analytical solutions agree well with each other. This work refines the understanding about Zipf's and Heaps' laws in human language systems. PMID:23378896

Zipf's Law for Word Frequencies: Word Forms versus Lemmas in Long Texts.

PubMed

Corral, Álvaro; Boleda, Gemma; Ferrer-i-Cancho, Ramon

2015-01-01

Zipf's law is a fundamental paradigm in the statistics of written and spoken natural language as well as in other communication systems. We raise the question of the elementary units for which Zipf's law should hold in the most natural way, studying its validity for plain word forms and for the corresponding lemma forms. We analyze several long literary texts comprising four languages, with different levels of morphological complexity. In all cases Zipf's law is fulfilled, in the sense that a power-law distribution of word or lemma frequencies is valid for several orders of magnitude. We investigate the extent to which the word-lemma transformation preserves two parameters of Zipf's law: the exponent and the low-frequency cut-off. We are not able to demonstrate a strict invariance of the tail, as for a few texts both exponents deviate significantly, but we conclude that the exponents are very similar, despite the remarkable transformation that going from words to lemmas represents, considerably affecting all ranges of frequencies. In contrast, the low-frequency cut-offs are less stable, tending to increase substantially after the transformation.

Deviations in the Zipf and Heaps laws in natural languages

NASA Astrophysics Data System (ADS)

Bochkarev, Vladimir V.; Lerner, Eduard Yu; Shevlyakova, Anna V.

2014-03-01

This paper is devoted to verifying of the empirical Zipf and Hips laws in natural languages using Google Books Ngram corpus data. The connection between the Zipf and Heaps law which predicts the power dependence of the vocabulary size on the text size is discussed. In fact, the Heaps exponent in this dependence varies with the increasing of the text corpus. To explain it, the obtained results are compared with the probability model of text generation. Quasi-periodic variations with characteristic time periods of 60-100 years were also found.

Understanding Zipf's law of word frequencies through sample-space collapse in sentence formation

PubMed Central

Thurner, Stefan; Hanel, Rudolf; Liu, Bo; Corominas-Murtra, Bernat

2015-01-01

The formation of sentences is a highly structured and history-dependent process. The probability of using a specific word in a sentence strongly depends on the ‘history’ of word usage earlier in that sentence. We study a simple history-dependent model of text generation assuming that the sample-space of word usage reduces along sentence formation, on average. We first show that the model explains the approximate Zipf law found in word frequencies as a direct consequence of sample-space reduction. We then empirically quantify the amount of sample-space reduction in the sentences of 10 famous English books, by analysis of corresponding word-transition tables that capture which words can follow any given word in a text. We find a highly nested structure in these transition tables and show that this ‘nestedness’ is tightly related to the power law exponents of the observed word frequency distributions. With the proposed model, it is possible to understand that the nestedness of a text can be the origin of the actual scaling exponent and that deviations from the exact Zipf law can be understood by variations of the degree of nestedness on a book-by-book basis. On a theoretical level, we are able to show that in the case of weak nesting, Zipf's law breaks down in a fast transition. Unlike previous attempts to understand Zipf's law in language the sample-space reducing model is not based on assumptions of multiplicative, preferential or self-organized critical mechanisms behind language formation, but simply uses the empirically quantifiable parameter ‘nestedness’ to understand the statistics of word frequencies. PMID:26063827

Understanding Zipf's law of word frequencies through sample-space collapse in sentence formation.

PubMed

Thurner, Stefan; Hanel, Rudolf; Liu, Bo; Corominas-Murtra, Bernat

2015-07-06

The formation of sentences is a highly structured and history-dependent process. The probability of using a specific word in a sentence strongly depends on the 'history' of word usage earlier in that sentence. We study a simple history-dependent model of text generation assuming that the sample-space of word usage reduces along sentence formation, on average. We first show that the model explains the approximate Zipf law found in word frequencies as a direct consequence of sample-space reduction. We then empirically quantify the amount of sample-space reduction in the sentences of 10 famous English books, by analysis of corresponding word-transition tables that capture which words can follow any given word in a text. We find a highly nested structure in these transition tables and show that this 'nestedness' is tightly related to the power law exponents of the observed word frequency distributions. With the proposed model, it is possible to understand that the nestedness of a text can be the origin of the actual scaling exponent and that deviations from the exact Zipf law can be understood by variations of the degree of nestedness on a book-by-book basis. On a theoretical level, we are able to show that in the case of weak nesting, Zipf's law breaks down in a fast transition. Unlike previous attempts to understand Zipf's law in language the sample-space reducing model is not based on assumptions of multiplicative, preferential or self-organized critical mechanisms behind language formation, but simply uses the empirically quantifiable parameter 'nestedness' to understand the statistics of word frequencies. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Zipf's law in city size from a resource utilization model.

PubMed

Ghosh, Asim; Chatterjee, Arnab; Chakrabarti, Anindya S; Chakrabarti, Bikas K

2014-10-01

We study a resource utilization scenario characterized by intrinsic fitness. To describe the growth and organization of different cities, we consider a model for resource utilization where many restaurants compete, as in a game, to attract customers using an iterative learning process. Results for the case of restaurants with uniform fitness are reported. When fitness is uniformly distributed, it gives rise to a Zipf law for the number of customers. We perform an exact calculation for the utilization fraction for the case when choices are made independent of fitness. A variant of the model is also introduced where the fitness can be treated as an ability to stay in the business. When a restaurant loses customers, its fitness is replaced by a random fitness. The steady state fitness distribution is characterized by a power law, while the distribution of the number of customers still follows the Zipf law, implying the robustness of the model. Our model serves as a paradigm for the emergence of Zipf law in city size distribution.

Zipf's law in city size from a resource utilization model

NASA Astrophysics Data System (ADS)

Ghosh, Asim; Chatterjee, Arnab; Chakrabarti, Anindya S.; Chakrabarti, Bikas K.

2014-10-01

We study a resource utilization scenario characterized by intrinsic fitness. To describe the growth and organization of different cities, we consider a model for resource utilization where many restaurants compete, as in a game, to attract customers using an iterative learning process. Results for the case of restaurants with uniform fitness are reported. When fitness is uniformly distributed, it gives rise to a Zipf law for the number of customers. We perform an exact calculation for the utilization fraction for the case when choices are made independent of fitness. A variant of the model is also introduced where the fitness can be treated as an ability to stay in the business. When a restaurant loses customers, its fitness is replaced by a random fitness. The steady state fitness distribution is characterized by a power law, while the distribution of the number of customers still follows the Zipf law, implying the robustness of the model. Our model serves as a paradigm for the emergence of Zipf law in city size distribution.

Detection of core-periphery structure in networks based on 3-tuple motifs

NASA Astrophysics Data System (ADS)

Ma, Chuang; Xiang, Bing-Bing; Chen, Han-Shuang; Small, Michael; Zhang, Hai-Feng

2018-05-01

Detecting mesoscale structure, such as community structure, is of vital importance for analyzing complex networks. Recently, a new mesoscale structure, core-periphery (CP) structure, has been identified in many real-world systems. In this paper, we propose an effective algorithm for detecting CP structure based on a 3-tuple motif. In this algorithm, we first define a 3-tuple motif in terms of the patterns of edges as well as the property of nodes, and then a motif adjacency matrix is constructed based on the 3-tuple motif. Finally, the problem is converted to find a cluster that minimizes the smallest motif conductance. Our algorithm works well in different CP structures: including single or multiple CP structure, and local or global CP structures. Results on the synthetic and the empirical networks validate the high performance of our method.

Term Dependence: A Basis for Luhn and Zipf Models.

ERIC Educational Resources Information Center

Losee, Robert M.

2001-01-01

Discusses relationships between the frequency-based characteristics of neighboring terms in natural language and the rank or frequency of the terms. Topics include information theory measures, including expected mutual information measure (EMIM); entropy and rank; Luhn's model of term aboutness; Zipf's law; and implications for indexing and…

Zipf 's law and the effect of ranking on probability distributions

NASA Astrophysics Data System (ADS)

Günther, R.; Levitin, L.; Schapiro, B.; Wagner, P.

1996-02-01

Ranking procedures are widely used in the description of many different types of complex systems. Zipf's law is one of the most remarkable frequency-rank relationships and has been observed independently in physics, linguistics, biology, demography, etc. We show that ranking plays a crucial role in making it possible to detect empirical relationships in systems that exist in one realization only, even when the statistical ensemble to which the systems belong has a very broad probability distribution. Analytical results and numerical simulations are presented which clarify the relations between the probability distributions and the behavior of expected values for unranked and ranked random variables. This analysis is performed, in particular, for the evolutionary model presented in our previous papers which leads to Zipf's law and reveals the underlying mechanism of this phenomenon in terms of a system with interdependent and interacting components as opposed to the “ideal gas” models suggested by previous researchers. The ranking procedure applied to this model leads to a new, unexpected phenomenon: a characteristic “staircase” behavior of the mean values of the ranked variables (ranked occupation numbers). This result is due to the broadness of the probability distributions for the occupation numbers and does not follow from the “ideal gas” model. Thus, it provides an opportunity, by comparison with empirical data, to obtain evidence as to which model relates to reality.

Two Universality Properties Associated with the Monkey Model of Zipf's Law

NASA Astrophysics Data System (ADS)

Perline, Richard; Perline, Ron

2016-03-01

The distribution of word probabilities in the monkey model of Zipf's law is associated with two universality properties: (1) the power law exponent converges strongly to $-1$ as the alphabet size increases and the letter probabilities are specified as the spacings from a random division of the unit interval for any distribution with a bounded density function on $[0,1]$; and (2), on a logarithmic scale the version of the model with a finite word length cutoff and unequal letter probabilities is approximately normally distributed in the part of the distribution away from the tails. The first property is proved using a remarkably general limit theorem for the logarithm of sample spacings from Shao and Hahn, and the second property follows from Anscombe's central limit theorem for a random number of i.i.d. random variables. The finite word length model leads to a hybrid Zipf-lognormal mixture distribution closely related to work in other areas.

Zipf's Law and the Visible Stars

NASA Astrophysics Data System (ADS)

Upgren, A. R.

2003-12-01

Zipf's law is a power law that describes the frequency of occurrence of many events in nature and in human affairs. It has recently found a resonance among some of the natural phenomena in the Earth sciences. Here we extend its applicability to astronomy. The essence of this law is that the sizes of objects or the frequencies of events adhere closely to a linear power law in which P, their frequency or size is a function of its rank; that is, P(i) ˜ 1/ia with the exponent, a, lying close to unity for many widely differing phenomena. Thus, i = 1, 2, 3, 4, . . . and P(i) ˜ 1, \\onehalf, . . . We examine the brightnesses of the naked-eye stars and compare their distribution to city populations and other examples of Zipf's law in other disciplines. At first glance it would seem that everything about these stars has long been known, but this is far from the case. In their classic 1953 text, Statistical Astronomy, Robert Trumpler and Harold Weaver (along with other authors since) list eight parameters that can define a star rather uniquely, to which we add a ninth. At that time, the only reliably known data for all or almost all of the 9110 BSC stars were their apparent magnitudes and proper motions. Reliable distances and parallaxes were known for few, and accurate radial velocities for almost none. But today photoelectric photometry and radial velocities are known for most, and parallaxes from the recent Hipparcos Catalogue for all. Only the age, through [Fe/H] or other, is not known for many of the stars; we can hope that this will be corrected in years to come.

Weiqi games as a tree: Zipf's law of openings and beyond

NASA Astrophysics Data System (ADS)

Xu, Li-Gong; Li, Ming-Xia; Zhou, Wei-Xing

2015-06-01

Weiqi is one of the most complex board games played by two persons. The placement strategies adopted by Weiqi players are often used to analog the philosophy of human wars. Contrary to the western chess, Weiqi games are less studied by academics partially because Weiqi is popular only in East Asia, especially in China, Japan and Korea. Here, we propose to construct a directed tree using a database of extensive Weiqi games and perform a quantitative analysis of the Weiqi tree. We find that the popularity distribution of Weiqi openings with the same number of moves is distributed according to a power law and the tail exponent increases with the number of moves. Intriguingly, the superposition of the popularity distributions of Weiqi openings with a number of moves not higher than a given number also has a power-law tail in which the tail exponent increases with the number of moves, and the superposed distribution approaches the Zipf law. These findings are the same as for chess and support the conjecture that the popularity distribution of board game openings follows the Zipf law with a universal exponent. We also find that the distribution of out-degrees has a power-law form, the distribution of branching ratios has a very complicated pattern, and the distribution of uniqueness scores defined by the path lengths from the root vertex to the leaf vertices exhibits a unimodal shape. Our work provides a promising direction for the study of the decision-making process of Weiqi playing from the perspective of directed branching tree.

Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

NASA Technical Reports Server (NTRS)

Mantegna, R. N.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

Zipf's Law of Abbreviation and the Principle of Least Effort: Language users optimise a miniature lexicon for efficient communication.

PubMed

Kanwal, Jasmeen; Smith, Kenny; Culbertson, Jennifer; Kirby, Simon

2017-08-01

The linguist George Kingsley Zipf made a now classic observation about the relationship between a word's length and its frequency; the more frequent a word is, the shorter it tends to be. He claimed that this "Law of Abbreviation" is a universal structural property of language. The Law of Abbreviation has since been documented in a wide range of human languages, and extended to animal communication systems and even computer programming languages. Zipf hypothesised that this universal design feature arises as a result of individuals optimising form-meaning mappings under competing pressures to communicate accurately but also efficiently-his famous Principle of Least Effort. In this study, we use a miniature artificial language learning paradigm to provide direct experimental evidence for this explanatory hypothesis. We show that language users optimise form-meaning mappings only when pressures for accuracy and efficiency both operate during a communicative task, supporting Zipf's conjecture that the Principle of Least Effort can explain this universal feature of word length distributions. Copyright © 2017 Elsevier B.V. All rights reserved.

Dual-function photonic integrated circuit for frequency octo-tupling or single-side-band modulation.

PubMed

Hasan, Mehedi; Maldonado-Basilio, Ramón; Hall, Trevor J

2015-06-01

A dual-function photonic integrated circuit for microwave photonic applications is proposed. The circuit consists of four linear electro-optic phase modulators connected optically in parallel within a generalized Mach-Zehnder interferometer architecture. The photonic circuit is arranged to have two separate output ports. A first port provides frequency up-conversion of a microwave signal from the electrical to the optical domain; equivalently single-side-band modulation. A second port provides tunable millimeter wave carriers by frequency octo-tupling of an appropriate amplitude RF carrier. The circuit exploits the intrinsic relative phases between the ports of multi-mode interference couplers to provide substantially all the static optical phases needed. The operation of the proposed dual-function photonic integrated circuit is verified by computer simulations. The performance of the frequency octo-tupling and up-conversion functions is analyzed in terms of the electrical signal to harmonic distortion ratio and the optical single side band to unwanted harmonics ratio, respectively.

An interval-valued 2-tuple linguistic group decision-making model based on the Choquet integral operator

NASA Astrophysics Data System (ADS)

Liu, Bingsheng; Fu, Meiqing; Zhang, Shuibo; Xue, Bin; Zhou, Qi; Zhang, Shiruo

2018-01-01

The Choquet integral (IL) operator is an effective approach for handling interdependence among decision attributes in complex decision-making problems. However, the fuzzy measures of attributes and attribute sets required by IL are difficult to achieve directly, which limits the application of IL. This paper proposes a new method for determining fuzzy measures of attributes by extending Marichal's concept of entropy for fuzzy measure. To well represent the assessment information, interval-valued 2-tuple linguistic context is utilised to represent information. Then, we propose a Choquet integral operator in an interval-valued 2-tuple linguistic environment, which can effectively handle the correlation between attributes. In addition, we apply these methods to solve multi-attribute group decision-making problems. The feasibility and validity of the proposed operator is demonstrated by comparisons with other models in illustrative example part.

Applying the Tuple Space-Based Approach to the Simulation of the Caspases, an Essential Signalling Pathway.

PubMed

Cárdenas-García, Maura; González-Pérez, Pedro Pablo

2013-03-01

Apoptotic cell death plays a crucial role in development and homeostasis. This process is driven by mitochondrial permeabilization and activation of caspases. In this paper we adopt a tuple spaces-based modelling and simulation approach, and show how it can be applied to the simulation of this intracellular signalling pathway. Specifically, we are working to explore and to understand the complex interaction patterns of the caspases apoptotic and the mitochondrial role. As a first approximation, using the tuple spacesbased in silico approach, we model and simulate both the extrinsic and intrinsic apoptotic signalling pathways and the interactions between them. During apoptosis, mitochondrial proteins, released from mitochondria to cytosol are decisively involved in the process. If the decision is to die, from this point there is normally no return, cancer cells offer resistance to the mitochondrial induction.

Applying the tuple space-based approach to the simulation of the caspases, an essential signalling pathway.

PubMed

Cárdenas-García, Maura; González-Pérez, Pedro Pablo

2013-04-11

Apoptotic cell death plays a crucial role in development and homeostasis. This process is driven by mitochondrial permeabilization and activation of caspases. In this paper we adopt a tuple spaces-based modelling and simulation approach, and show how it can be applied to the simulation of this intracellular signalling pathway. Specifically, we are working to explore and to understand the complex interaction patterns of the caspases apoptotic and the mitochondrial role. As a first approximation, using the tuple spaces-based in silico approach, we model and simulate both the extrinsic and intrinsic apoptotic signalling pathways and the interactions between them. During apoptosis, mitochondrial proteins, released from mitochondria to cytosol are decisively involved in the process. If the decision is to die, from this point there is normally no return, cancer cells offer resistance to the mitochondrial induction.

Zipf exponent of trajectory distribution in the hidden Markov model

NASA Astrophysics Data System (ADS)

Bochkarev, V. V.; Lerner, E. Yu

2014-03-01

This paper is the first step of generalization of the previously obtained full classification of the asymptotic behavior of the probability for Markov chain trajectories for the case of hidden Markov models. The main goal is to study the power (Zipf) and nonpower asymptotics of the frequency list of trajectories of hidden Markov frequencys and to obtain explicit formulae for the exponent of the power asymptotics. We consider several simple classes of hidden Markov models. We prove that the asymptotics for a hidden Markov model and for the corresponding Markov chain can be essentially different.

Zipf's law from scale-free geometry.

PubMed

Lin, Henry W; Loeb, Abraham

2016-03-01

The spatial distribution of people exhibits clustering across a wide range of scales, from household (∼10(-2) km) to continental (∼10(4) km) scales. Empirical data indicate simple power-law scalings for the size distribution of cities (known as Zipf's law) and the population density fluctuations as a function of scale. Using techniques from random field theory and statistical physics, we show that these power laws are fundamentally a consequence of the scale-free spatial clustering of human populations and the fact that humans inhabit a two-dimensional surface. In this sense, the symmetries of scale invariance in two spatial dimensions are intimately connected to urban sociology. We test our theory by empirically measuring the power spectrum of population density fluctuations and show that the logarithmic slope α=2.04 ± 0.09, in excellent agreement with our theoretical prediction α=2. The model enables the analytic computation of many new predictions by importing the mathematical formalism of random fields.

A DAG Scheduling Scheme on Heterogeneous Computing Systems Using Tuple-Based Chemical Reaction Optimization

PubMed Central

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems. PMID:25143977

A DAG scheduling scheme on heterogeneous computing systems using tuple-based chemical reaction optimization.

PubMed

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems.

Stable power laws in variable economies; Lotka-Volterra implies Pareto-Zipf

NASA Astrophysics Data System (ADS)

Solomon, S.; Richmond, P.

2002-05-01

In recent years we have found that logistic systems of the Generalized Lotka-Volterra type (GLV) describing statistical systems of auto-catalytic elements posses power law distributions of the Pareto-Zipf type. In particular, when applied to economic systems, GLV leads to power laws in the relative individual wealth distribution and in market returns. These power laws and their exponent α are invariant to arbitrary variations in the total wealth of the system and to other endogenously and exogenously induced variations.

Co-ordination of Mobile Information Agents in TuCSoN.

ERIC Educational Resources Information Center

Omicini, Andrea; Zambonelli, Franco

1998-01-01

Examines mobile agent coordination and presents TuCSoN, a coordination model for Internet applications based on mobile information agents that uses a tuple centre, a tuple space enhanced with the capability of programming its behavior in response to communication events. Discusses the effectiveness of the TuCSoN model in the contexts of Internet…

Where Gibrat meets Zipf: Scale and scope of French firms

NASA Astrophysics Data System (ADS)

Bee, Marco; Riccaboni, Massimo; Schiavo, Stefano

2017-09-01

The proper characterization of the size distribution and growth of firms represents an important issue in economics and business. We use the Maximum Entropy approach to assess the plausibility of the assumption that firm size follows Lognormal or Pareto distributions, which underlies most recent works on the subject. A comprehensive dataset covering the universe of French firms allows us to draw two major conclusions. First, the Pareto hypothesis for the whole distribution should be rejected. Second, by discriminating across firms based on the number of products sold and markets served, we find that, within the class of multi-product companies active in multiple markets, the distribution converges to a Zipf's law. Conversely, Lognormal distribution is a good benchmark for small single-product firms. The size distribution of firms largely depends on firms' diversification patterns.

A consensus reaching model for 2-tuple linguistic multiple attribute group decision making with incomplete weight information

NASA Astrophysics Data System (ADS)

Zhang, Wancheng; Xu, Yejun; Wang, Huimin

2016-01-01

The aim of this paper is to put forward a consensus reaching method for multi-attribute group decision-making (MAGDM) problems with linguistic information, in which the weight information of experts and attributes is unknown. First, some basic concepts and operational laws of 2-tuple linguistic label are introduced. Then, a grey relational analysis method and a maximising deviation method are proposed to calculate the incomplete weight information of experts and attributes respectively. To eliminate the conflict in the group, a weight-updating model is employed to derive the weights of experts based on their contribution to the consensus reaching process. After conflict elimination, the final group preference can be obtained which will give the ranking of the alternatives. The model can effectively avoid information distortion which is occurred regularly in the linguistic information processing. Finally, an illustrative example is given to illustrate the application of the proposed method and comparative analysis with the existing methods are offered to show the advantages of the proposed method.

Spectral and textural processing of ERTS imagery. [Kansas

NASA Technical Reports Server (NTRS)

Haralick, R. M.; Bosley, R. J.

1974-01-01

A procedure is developed to simultaneously extract textural features from all bands of ERTS multispectral scanner imagery for automatic analysis. Multi-images lead to excessively large grey tone N-tuple co-occurrence matrices; therefore, neighboring grey N-tuple differences are measured and an ellipsoidally symmetric functional form is assumed for the co-occurrence distribution of multiimage greytone N-tuple differences. On the basis of past data the ellipsoidally symmetric approximation is shown to be reasonable. Initial evaluation of the procedure is encouraging.

PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition.

PubMed

Chen, Wei; Lei, Tian-Yu; Jin, Dian-Chuan; Lin, Hao; Chou, Kuo-Chen

2014-07-01

The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

Explaining the uneven distribution of numbers in nature: the laws of Benford and Zipf

NASA Astrophysics Data System (ADS)

Pietronero, L.; Tosatti, E.; Tosatti, V.; Vespignani, A.

2001-04-01

The distribution of first digits in numbers series obtained from very different origins shows a marked asymmetry in favor of small digits that goes under the name of Benford's law. We analyze in detail this property for different data sets and give a general explanation for the origin of the Benford's law in terms of multiplicative processes. We show that this law can be also generalized to series of numbers generated from more complex systems like the catalogs of seismic activity. Finally, we derive a relation between the generalized Benford's law and the popular Zipf's law which characterize the rank order statistics and has been extensively applied to many problems ranging from city population to linguistics.

Finding exact constants in a Markov model of Zipfs law generation

NASA Astrophysics Data System (ADS)

Bochkarev, V. V.; Lerner, E. Yu.; Nikiforov, A. A.; Pismenskiy, A. A.

2017-12-01

According to the classical Zipfs law, the word frequency is a power function of the word rank with an exponent -1. The objective of this work is to find multiplicative constant in a Markov model of word generation. Previously, the case of independent letters was mathematically strictly investigated in [Bochkarev V V and Lerner E Yu 2017 International Journal of Mathematics and Mathematical Sciences Article ID 914374]. Unfortunately, the methods used in this paper cannot be generalized in case of Markov chains. The search of the correct formulation of the Markov generalization of this results was performed using experiments with different ergodic matrices of transition probability P. Combinatory technique allowed taking into account all the words with probability of more than e -300 in case of 2 by 2 matrices. It was experimentally proved that the required constant in the limit is equal to the value reciprocal to conditional entropy of matrix row P with weights presenting the elements of the vector π of the stationary distribution of the Markov chain.

PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition.

PubMed

Zuo, Yongchun; Li, Yuan; Chen, Yingli; Li, Guangpeng; Yan, Zhenhe; Yang, Lei

2017-01-01

The reduced amino acids perform powerful ability for both simplifying protein complexity and identifying functional conserved regions. However, dealing with different protein problems may need different kinds of cluster methods. Encouraged by the success of pseudo-amino acid composition algorithm, we developed a freely available web server, called PseKRAAC (the pseudo K-tuple reduced amino acids composition). By implementing reduced amino acid alphabets, the protein complexity can be significantly simplified, which leads to decrease chance of overfitting, lower computational handicap and reduce information redundancy. PseKRAAC delivers more capability for protein research by incorporating three crucial parameters that describes protein composition. Users can easily generate many different modes of PseKRAAC tailored to their needs by selecting various reduced amino acids alphabets and other characteristic parameters. It is anticipated that the PseKRAAC web server will become a very useful tool in computational proteomics and protein sequence analysis. Freely available on the web at http://bigdata.imu.edu.cn/psekraac CONTACTS: yczuo@imu.edu.cn or imu.hema@foxmail.com or yanglei_hmu@163.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Emergence of good conduct, scaling and zipf laws in human behavioral sequences in an online world.

PubMed

Thurner, Stefan; Szell, Michael; Sinatra, Roberta

2012-01-01

We study behavioral action sequences of players in a massive multiplayer online game. In their virtual life players use eight basic actions which allow them to interact with each other. These actions are communication, trade, establishing or breaking friendships and enmities, attack, and punishment. We measure the probabilities for these actions conditional on previous taken and received actions and find a dramatic increase of negative behavior immediately after receiving negative actions. Similarly, positive behavior is intensified by receiving positive actions. We observe a tendency towards antipersistence in communication sequences. Classifying actions as positive (good) and negative (bad) allows us to define binary 'world lines' of lives of individuals. Positive and negative actions are persistent and occur in clusters, indicated by large scaling exponents α ~ 0.87 of the mean square displacement of the world lines. For all eight action types we find strong signs for high levels of repetitiveness, especially for negative actions. We partition behavioral sequences into segments of length n (behavioral 'words' and 'motifs') and study their statistical properties. We find two approximate power laws in the word ranking distribution, one with an exponent of κ ~ -1 for the ranks up to 100, and another with a lower exponent for higher ranks. The Shannon n-tuple redundancy yields large values and increases in terms of word length, further underscoring the non-trivial statistical properties of behavioral sequences. On the collective, societal level the timeseries of particular actions per day can be understood by a simple mean-reverting log-normal model.

Information Theory Applied to Animal Communication Systems and Its Possible Application to SETI

NASA Astrophysics Data System (ADS)

Hanser, Sean F.; Doyle, Laurance R.; McCowan, Brenda; Jenkins, Jon M.

2004-06-01

Information theory, as first introduced by Claude Shannon (Shannon &Weaver 1949) quantitatively evaluates the organizational complexity of communication systems. At the same time George Zipf was examining linguistic structure in a way that was mathematically similar to the components of the Shannon first-order entropy (Zipf 1949). Both Shannon's and Zipf's mathematical procedures have been applied to animal communication and recently have been providing insightful results. The Zipf plot is a useful tool for a first estimate of the characterization of a communication system's complexity (which can later be examined for complex structure at deeper levels using Shannon entropic analysis). In this paper we shall discuss some of the applications and pitfalls of using the Zipf distribution as a preliminary evaluator of the communication complexity of a signaling system.

Statistical Analysis of the Indus Script Using n-Grams

PubMed Central

Yadav, Nisha; Joglekar, Hrishikesh; Rao, Rajesh P. N.; Vahia, Mayank N.; Adhikari, Ronojoy; Mahadevan, Iravatham

2010-01-01

The Indus script is one of the major undeciphered scripts of the ancient world. The small size of the corpus, the absence of bilingual texts, and the lack of definite knowledge of the underlying language has frustrated efforts at decipherment since the discovery of the remains of the Indus civilization. Building on previous statistical approaches, we apply the tools of statistical language processing, specifically n-gram Markov chains, to analyze the syntax of the Indus script. We find that unigrams follow a Zipf-Mandelbrot distribution. Text beginner and ender distributions are unequal, providing internal evidence for syntax. We see clear evidence of strong bigram correlations and extract significant pairs and triplets using a log-likelihood measure of association. Highly frequent pairs and triplets are not always highly significant. The model performance is evaluated using information-theoretic measures and cross-validation. The model can restore doubtfully read texts with an accuracy of about 75%. We find that a quadrigram Markov chain saturates information theoretic measures against a held-out corpus. Our work forms the basis for the development of a stochastic grammar which may be used to explore the syntax of the Indus script in greater detail. PMID:20333254

Filterless frequency 12-tupling optical millimeter-wave generation using two cascaded dual-parallel Mach-Zehnder modulators.

PubMed

Zhu, Zihang; Zhao, Shanghong; Zheng, Wanze; Wang, Wei; Lin, Baoqin

2015-11-10

A novel frequency 12-tupling optical millimeter-wave (mm-wave) generation using two cascaded dual-parallel Mach-Zehnder modulators (DP-MZMs) without an optical filter is proposed and demonstrated by computer simulation. By properly adjusting the amplitude and phase of radio frequency (RF) driving signal and the direct current (DC) bias points of two DP-MZMs, a 120 GHz mm-wave with an optical sideband suppression ratio (OSSR) of 25.1 dB and a radio frequency spurious suppression ratio (RFSSR) of 19.1 dB is shown to be generated from a 10 GHz RF driving signal, which largely reduces the response frequency of electronic devices. Furthermore, it is also proved to be valid that even if the phase difference of RF driving signals, the RF driving voltage, and the DC bias voltage deviate from the ideal values to a certain degree, the performance is still acceptable. Since no optical filter is employed to suppress the undesired optical sidebands, a high-spectral-purity mm-wave signal tunable from 48 to 216 GHz can be obtained theoretically when a RF driving signal from 4 to 18 GHz is applied to the DP-MZMs, and the system can be readily implemented in wavelength-division-multiplexing upconversion systems to provide high-quality optical local oscillator signal.

Scaling Property of Period-n-Tupling Sequences in One-Dimensional Mappings

NASA Astrophysics Data System (ADS)

Zeng, Wan-Zhen; Hao, Bai-Lin; Wang, Guang-Rui; Chen, Shi-Gang

1984-05-01

We calculated the universal scaling function g(x) and the scaling factor α as well as the convergence rate δ for periodtripling, -quadrapling and-quintupling sequences of RL, RL^2, RLR^2, RL2 R and RL^3 types. The superstable periods are closely connected to a set of polynomial P_n defined recursively by the original mapping. Some notable properties of these polynomials are studied. Several approaches to solving the renormalization group equation and estimating the scaling factors are suggested.

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

PubMed Central

Lin, Hao; Deng, En-Ze; Ding, Hui; Chen, Wei; Chou, Kuo-Chen

2014-01-01

The σ54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the σ54 promoters. Here, a predictor called ‘iPro54-PseKNC’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k-tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the σ54 promoters. PMID:25361964

Exploring the QSAR's predictive truthfulness of the novel N-tuple discrete derivative indices on benchmark datasets.

PubMed

Martínez-Santiago, O; Marrero-Ponce, Y; Vivas-Reyes, R; Rivera-Borroto, O M; Hurtado, E; Treto-Suarez, M A; Ramos, Y; Vergara-Murillo, F; Orozco-Ugarriza, M E; Martínez-López, Y

2017-05-01

Graph derivative indices (GDIs) have recently been defined over N-atoms (N = 2, 3 and 4) simultaneously, which are based on the concept of derivatives in discrete mathematics (finite difference), metaphorical to the derivative concept in classical mathematical analysis. These molecular descriptors (MDs) codify topo-chemical and topo-structural information based on the concept of the derivative of a molecular graph with respect to a given event (S) over duplex, triplex and quadruplex relations of atoms (vertices). These GDIs have been successfully applied in the description of physicochemical properties like reactivity, solubility and chemical shift, among others, and in several comparative quantitative structure activity/property relationship (QSAR/QSPR) studies. Although satisfactory results have been obtained in previous modelling studies with the aforementioned indices, it is necessary to develop new, more rigorous analysis to assess the true predictive performance of the novel structure codification. So, in the present paper, an assessment and statistical validation of the performance of these novel approaches in QSAR studies are executed, as well as a comparison with those of other QSAR procedures reported in the literature. To achieve the main aim of this research, QSARs were developed on eight chemical datasets widely used as benchmarks in the evaluation/validation of several QSAR methods and/or many different MDs (fundamentally 3D MDs). Three to seven variable QSAR models were built for each chemical dataset, according to the original dissection into training/test sets. The models were developed by using multiple linear regression (MLR) coupled with a genetic algorithm as the feature wrapper selection technique in the MobyDigs software. Each family of GDIs (for duplex, triplex and quadruplex) behaves similarly in all modelling, although there were some exceptions. However, when all families were used in combination, the results achieved were quantitatively

Bankruptcy risk model and empirical tests

PubMed Central

Podobnik, Boris; Horvatic, Davor; Petersen, Alexander M.; Urošević, Branko; Stanley, H. Eugene

2010-01-01

We analyze the size dependence and temporal stability of firm bankruptcy risk in the US economy by applying Zipf scaling techniques. We focus on a single risk factor—the debt-to-asset ratio R—in order to study the stability of the Zipf distribution of R over time. We find that the Zipf exponent increases during market crashes, implying that firms go bankrupt with larger values of R. Based on the Zipf analysis, we employ Bayes’s theorem and relate the conditional probability that a bankrupt firm has a ratio R with the conditional probability of bankruptcy for a firm with a given R value. For 2,737 bankrupt firms, we demonstrate size dependence in assets change during the bankruptcy proceedings. Prepetition firm assets and petition firm assets follow Zipf distributions but with different exponents, meaning that firms with smaller assets adjust their assets more than firms with larger assets during the bankruptcy process. We compare bankrupt firms with nonbankrupt firms by analyzing the assets and liabilities of two large subsets of the US economy: 2,545 Nasdaq members and 1,680 New York Stock Exchange (NYSE) members. We find that both assets and liabilities follow a Pareto distribution. The finding is not a trivial consequence of the Zipf scaling relationship of firm size quantified by employees—although the market capitalization of Nasdaq stocks follows a Pareto distribution, the same distribution does not describe NYSE stocks. We propose a coupled Simon model that simultaneously evolves both assets and debt with the possibility of bankruptcy, and we also consider the possibility of firm mergers. PMID:20937903

Design and Implementation of A Backend Multiple-Processor Relational Data Base Computer System.

DTIC Science & Technology

1981-12-01

propogated to other parts of the data base. 18 Cost. As mentioned earlier, a primary motivation for the backend DBMS work is the development of an...uniquely identify the n- tuples of the relation is called the primary key. For example, in Figure 3, the primary key is NUMBER. A primary key is said to...identifying the tuple. For example, in Figure 3, (NUMBER,TITLE) would not be a nonredundant primary key for COURSE. A relation can contain more than one

Evolution of scaling emergence in large-scale spatial epidemic spreading.

PubMed

Wang, Lin; Li, Xiang; Zhang, Yi-Qing; Zhang, Yan; Zhang, Kan

2011-01-01

Zipf's law and Heaps' law are two representatives of the scaling concepts, which play a significant role in the study of complexity science. The coexistence of the Zipf's law and the Heaps' law motivates different understandings on the dependence between these two scalings, which has still hardly been clarified. In this article, we observe an evolution process of the scalings: the Zipf's law and the Heaps' law are naturally shaped to coexist at the initial time, while the crossover comes with the emergence of their inconsistency at the larger time before reaching a stable state, where the Heaps' law still exists with the disappearance of strict Zipf's law. Such findings are illustrated with a scenario of large-scale spatial epidemic spreading, and the empirical results of pandemic disease support a universal analysis of the relation between the two laws regardless of the biological details of disease. Employing the United States domestic air transportation and demographic data to construct a metapopulation model for simulating the pandemic spread at the U.S. country level, we uncover that the broad heterogeneity of the infrastructure plays a key role in the evolution of scaling emergence. The analyses of large-scale spatial epidemic spreading help understand the temporal evolution of scalings, indicating the coexistence of the Zipf's law and the Heaps' law depends on the collective dynamics of epidemic processes, and the heterogeneity of epidemic spread indicates the significance of performing targeted containment strategies at the early time of a pandemic disease.

Evolution of Scaling Emergence in Large-Scale Spatial Epidemic Spreading

PubMed Central

Wang, Lin; Li, Xiang; Zhang, Yi-Qing; Zhang, Yan; Zhang, Kan

2011-01-01

Background Zipf's law and Heaps' law are two representatives of the scaling concepts, which play a significant role in the study of complexity science. The coexistence of the Zipf's law and the Heaps' law motivates different understandings on the dependence between these two scalings, which has still hardly been clarified. Methodology/Principal Findings In this article, we observe an evolution process of the scalings: the Zipf's law and the Heaps' law are naturally shaped to coexist at the initial time, while the crossover comes with the emergence of their inconsistency at the larger time before reaching a stable state, where the Heaps' law still exists with the disappearance of strict Zipf's law. Such findings are illustrated with a scenario of large-scale spatial epidemic spreading, and the empirical results of pandemic disease support a universal analysis of the relation between the two laws regardless of the biological details of disease. Employing the United States domestic air transportation and demographic data to construct a metapopulation model for simulating the pandemic spread at the U.S. country level, we uncover that the broad heterogeneity of the infrastructure plays a key role in the evolution of scaling emergence. Conclusions/Significance The analyses of large-scale spatial epidemic spreading help understand the temporal evolution of scalings, indicating the coexistence of the Zipf's law and the Heaps' law depends on the collective dynamics of epidemic processes, and the heterogeneity of epidemic spread indicates the significance of performing targeted containment strategies at the early time of a pandemic disease. PMID:21747932

Isolation of a transcription factor expressed in neural crest from the region of 22q11 deleted in DiGeorge syndrome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wadey, R.; Roberts, C.; Daw, S.

1994-09-01

Deletions within chromosome 22q11 cause a wide variety of birth defects including DiGeorge syndrome and Shprintzen syndrome. We have defined a commonly deleted region of over 2 Mb, and a critical region of 300 kb. A gene, TUPLE1, has been isolated from this critical region encoding a transcriptional regulator similar to the yeast HIR1 histone regulator gene. Since it has been suggested that DGS results from a defective neural crest, the expression of Tuple1 was examined in whole mouse and chick embryos, tissue sections and neural tube explants: Tuple1 is expressed in a dynamic pattern with high levels in regionsmore » containing migrating crest. Prior to crest migration Tuple1 is expressed in a rhombomere-specific expression pattern. Later Tuple1 is expressed in discrete domains within the developing neural tube. A remarkable feature of the experiments was the detection of a similar dynamic pattern with sense probe; i.e., there is an antisense Tuple1 transcript. This was confirmed using RPA. Tuple1 is being screened for mutations in non-deletion patients and constructs assembled for homologous recombination in ES cells. Tuple1 maps to MMU16 extending the homology of linkage with human chromosome 22. From these data we predict that the human homologue of the murine scid mutation maps to 22q11.« less

Word frequencies: A comparison of Pareto type distributions

NASA Astrophysics Data System (ADS)

Wiegand, Martin; Nadarajah, Saralees; Si, Yuancheng

2018-03-01

Mehri and Jamaati (2017) [18] used Zipf's law to model word frequencies in Holy Bible translations for one hundred live languages. We compare the fit of Zipf's law to a number of Pareto type distributions. The latter distributions are shown to provide the best fit, as judged by a number of comparative plots and error measures. The fit of Zipf's law appears generally poor.

Modeling Fractal Structure of City-Size Distributions Using Correlation Functions

PubMed Central

Chen, Yanguang

2011-01-01

Zipf's law is one the most conspicuous empirical facts for cities, however, there is no convincing explanation for the scaling relation between rank and size and its scaling exponent. Using the idea from general fractals and scaling, I propose a dual competition hypothesis of city development to explain the value intervals and the special value, 1, of the power exponent. Zipf's law and Pareto's law can be mathematically transformed into one another, but represent different processes of urban evolution, respectively. Based on the Pareto distribution, a frequency correlation function can be constructed. By scaling analysis and multifractals spectrum, the parameter interval of Pareto exponent is derived as (0.5, 1]; Based on the Zipf distribution, a size correlation function can be built, and it is opposite to the first one. By the second correlation function and multifractals notion, the Pareto exponent interval is derived as [1, 2). Thus the process of urban evolution falls into two effects: one is the Pareto effect indicating city number increase (external complexity), and the other the Zipf effect indicating city size growth (internal complexity). Because of struggle of the two effects, the scaling exponent varies from 0.5 to 2; but if the two effects reach equilibrium with each other, the scaling exponent approaches 1. A series of mathematical experiments on hierarchical correlation are employed to verify the models and a conclusion can be drawn that if cities in a given region follow Zipf's law, the frequency and size correlations will follow the scaling law. This theory can be generalized to interpret the inverse power-law distributions in various fields of physical and social sciences. PMID:21949753

Uniqueness of the joint measurement and the structure of the set of compatible quantum measurements

NASA Astrophysics Data System (ADS)

Guerini, Leonardo; Terra Cunha, Marcelo

2018-04-01

We address the problem of characterising the compatible tuples of measurements that admit a unique joint measurement. We derive a uniqueness criterion based on the method of perturbations and apply it to show that extremal points of the set of compatible tuples admit a unique joint measurement, while all tuples that admit a unique joint measurement lie in the boundary of such a set. We also provide counter-examples showing that none of these properties are both necessary and sufficient, thus completely describing the relation between the joint measurement uniqueness and the structure of the compatible set. As a by-product of our investigations, we completely characterise the extremal and boundary points of the set of general tuples of measurements and of the subset of compatible tuples.

Design of a lattice-based faceted classification system

NASA Technical Reports Server (NTRS)

Eichmann, David A.; Atkins, John

1992-01-01

We describe a software reuse architecture supporting component retrieval by facet classes. The facets are organized into a lattice of facet sets and facet n-tuples. The query mechanism supports precise retrieval and flexible browsing.

Quantiprot - a Python package for quantitative analysis of protein sequences.

PubMed

Konopka, Bogumił M; Marciniak, Marta; Dyrka, Witold

2017-07-17

The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids. Besides basic measures, Quantiprot performs quantitative analysis of recurrence and determinism in the sequence, calculates distribution of n-grams and computes the Zipf's law coefficient. We propose three main fields of application of the Quantiprot package. First, quantitative characteristics can be used in alignment-free similarity searches, and in clustering of large and/or divergent sequence sets. Second, a feature space defined by quantitative properties can be used in comparative studies of protein families and organisms. Third, the feature space can be used for evaluating generative models, where large number of sequences generated by the model can be compared to actually observed sequences.

Use of feature extraction techniques for the texture and context information in ERTS imagery: Spectral and textural processing of ERTS imagery. [classification of Kansas land use

NASA Technical Reports Server (NTRS)

Haralick, R. H. (Principal Investigator); Bosley, R. J.

1974-01-01

The author has identified the following significant results. A procedure was developed to extract cross-band textural features from ERTS MSS imagery. Evolving from a single image texture extraction procedure which uses spatial dependence matrices to measure relative co-occurrence of nearest neighbor grey tones, the cross-band texture procedure uses the distribution of neighboring grey tone N-tuple differences to measure the spatial interrelationships, or co-occurrences, of the grey tone N-tuples present in a texture pattern. In both procedures, texture is characterized in such a way as to be invariant under linear grey tone transformations. However, the cross-band procedure complements the single image procedure by extracting texture information and spectral information contained in ERTS multi-images. Classification experiments show that when used alone, without spectral processing, the cross-band texture procedure extracts more information than the single image texture analysis. Results show an improvement in average correct classification from 86.2% to 88.8% for ERTS image no. 1021-16333 with the cross-band texture procedure. However, when used together with spectral features, the single image texture plus spectral features perform better than the cross-band texture plus spectral features, with an average correct classification of 93.8% and 91.6%, respectively.

On power series expansions of the S-resolvent operator and the Taylor formula

NASA Astrophysics Data System (ADS)

Colombo, Fabrizio; Gantner, Jonathan

2016-12-01

The S-functional calculus is based on the theory of slice hyperholomorphic functions and it defines functions of n-tuples of not necessarily commuting operators or of quaternionic operators. This calculus relays on the notion of S-spectrum and of S-resolvent operator. Since most of the properties that hold for the Riesz-Dunford functional calculus extend to the S-functional calculus, it can be considered its non commutative version. In this paper we show that the Taylor formula of the Riesz-Dunford functional calculus can be generalized to the S-functional calculus. The proof is not a trivial extension of the classical case because there are several obstructions due to the non commutativity of the setting in which we work that have to be overcome. To prove the Taylor formula we need to introduce a new series expansion of the S-resolvent operators associated to the sum of two n-tuples of operators. This result is a crucial step in the proof of our main results, but it is also of independent interest because it gives a new series expansion for the S-resolvent operators. This paper is addressed to researchers working in operator theory and in hypercomplex analysis.

A knowledge base architecture for distributed knowledge agents

NASA Technical Reports Server (NTRS)

Riedesel, Joel; Walls, Bryan

1990-01-01

A tuple space based object oriented model for knowledge base representation and interpretation is presented. An architecture for managing distributed knowledge agents is then implemented within the model. The general model is based upon a database implementation of a tuple space. Objects are then defined as an additional layer upon the database. The tuple space may or may not be distributed depending upon the database implementation. A language for representing knowledge and inference strategy is defined whose implementation takes advantage of the tuple space. The general model may then be instantiated in many different forms, each of which may be a distinct knowledge agent. Knowledge agents may communicate using tuple space mechanisms as in the LINDA model as well as using more well known message passing mechanisms. An implementation of the model is presented describing strategies used to keep inference tractable without giving up expressivity. An example applied to a power management and distribution network for Space Station Freedom is given.

Delay correlation analysis and representation for vital complaint VHDL models

DOEpatents

Rich, Marvin J.; Misra, Ashutosh

2004-11-09

A method and system unbind a rise/fall tuple of a VHDL generic variable and create rise time and fall time generics of each generic variable that are independent of each other. Then, according to a predetermined correlation policy, the method and system collect delay values in a VHDL standard delay file, sort the delay values, remove duplicate delay values, group the delay values into correlation sets, and output an analysis file. The correlation policy may include collecting all generic variables in a VHDL standard delay file, selecting each generic variable, and performing reductions on the set of delay values associated with each selected generic variable.

The mathematical relationship between Zipf’s law and the hierarchical scaling law

NASA Astrophysics Data System (ADS)

Chen, Yanguang

2012-06-01

The empirical studies of city-size distribution show that Zipf's law and the hierarchical scaling law are linked in many ways. The rank-size scaling and hierarchical scaling seem to be two different sides of the same coin, but their relationship has never been revealed by strict mathematical proof. In this paper, the Zipf's distribution of cities is abstracted as a q-sequence. Based on this sequence, a self-similar hierarchy consisting of many levels is defined and the numbers of cities in different levels form a geometric sequence. An exponential distribution of the average size of cities is derived from the hierarchy. Thus we have two exponential functions, from which follows a hierarchical scaling equation. The results can be statistically verified by simple mathematical experiments and observational data of cities. A theoretical foundation is then laid for the conversion from Zipf's law to the hierarchical scaling law, and the latter can show more information about city development than the former. Moreover, the self-similar hierarchy provides a new perspective for studying networks of cities as complex systems. A series of mathematical rules applied to cities such as the allometric growth law, the 2n principle and Pareto's law can be associated with one another by the hierarchical organization.

Optimal shortening of uniform covering arrays

PubMed Central

Rangel-Valdez, Nelson; Avila-George, Himer; Carrizalez-Turrubiates, Oscar

2017-01-01

Software test suites based on the concept of interaction testing are very useful for testing software components in an economical way. Test suites of this kind may be created using mathematical objects called covering arrays. A covering array, denoted by CA(N; t, k, v), is an N × k array over Zv={0,…,v-1} with the property that every N × t sub-array covers all t-tuples of Zvt at least once. Covering arrays can be used to test systems in which failures occur as a result of interactions among components or subsystems. They are often used in areas such as hardware Trojan detection, software testing, and network design. Because system testing is expensive, it is critical to reduce the amount of testing required. This paper addresses the Optimal Shortening of Covering ARrays (OSCAR) problem, an optimization problem whose objective is to construct, from an existing covering array matrix of uniform level, an array with dimensions of (N − δ) × (k − Δ) such that the number of missing t-tuples is minimized. Two applications of the OSCAR problem are (a) to produce smaller covering arrays from larger ones and (b) to obtain quasi-covering arrays (covering arrays in which the number of missing t-tuples is small) to be used as input to a meta-heuristic algorithm that produces covering arrays. In addition, it is proven that the OSCAR problem is NP-complete, and twelve different algorithms are proposed to solve it. An experiment was performed on 62 problem instances, and the results demonstrate the effectiveness of solving the OSCAR problem to facilitate the construction of new covering arrays. PMID:29267343

The span of correlations in dolphin whistle sequences

NASA Astrophysics Data System (ADS)

Ferrer-i-Cancho, Ramon; McCowan, Brenda

2012-06-01

Long-range correlations are found in symbolic sequences from human language, music and DNA. Determining the span of correlations in dolphin whistle sequences is crucial for shedding light on their communicative complexity. Dolphin whistles share various statistical properties with human words, i.e. Zipf's law for word frequencies (namely that the probability of the ith most frequent word of a text is about i-α) and a parallel of the tendency of more frequent words to have more meanings. The finding of Zipf's law for word frequencies in dolphin whistles has been the topic of an intense debate on its implications. One of the major arguments against the relevance of Zipf's law in dolphin whistles is that it is not possible to distinguish the outcome of a die-rolling experiment from that of a linguistic or communicative source producing Zipf's law for word frequencies. Here we show that statistically significant whistle-whistle correlations extend back to the second previous whistle in the sequence, using a global randomization test, and to the fourth previous whistle, using a local randomization test. None of these correlations are expected by a die-rolling experiment and other simple explanations of Zipf's law for word frequencies, such as Simon's model, that produce sequences of unpredictable elements.

A probabilistic NF2 relational algebra for integrated information retrieval and database systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fuhr, N.; Roelleke, T.

The integration of information retrieval (IR) and database systems requires a data model which allows for modelling documents as entities, representing uncertainty and vagueness and performing uncertain inference. For this purpose, we present a probabilistic data model based on relations in non-first-normal-form (NF2). Here, tuples are assigned probabilistic weights giving the probability that a tuple belongs to a relation. Thus, the set of weighted index terms of a document are represented as a probabilistic subrelation. In a similar way, imprecise attribute values are modelled as a set-valued attribute. We redefine the relational operators for this type of relations such thatmore » the result of each operator is again a probabilistic NF2 relation, where the weight of a tuple gives the probability that this tuple belongs to the result. By ordering the tuples according to decreasing probabilities, the model yields a ranking of answers like in most IR models. This effect also can be used for typical database queries involving imprecise attribute values as well as for combinations of database and IR queries.« less

Estimates of Storage Capacity of Multilayer Perceptron with Threshold Logic Hidden Units.

PubMed

Kowalczyk, Adam

1997-11-01

We estimate the storage capacity of multilayer perceptron with n inputs, h(1) threshold logic units in the first hidden layer and 1 output. We show that if the network can memorize 50% of all dichotomies of a randomly selected N-tuple of points of R(n) with probability 1, then NNn and h(1). The results are based on the derivation of an explicit expression for the number of dichotomies which can be implemented by such a network for a special class of N-tuples of input patterns which has a positive probability of being randomly chosen.

Typed Multiset Rewriting Specifications of Security Protocols

DTIC Science & Technology

2011-10-01

to define the type of a tuple as the sequence of the types of its components. Therefore, if A is a principal name and kA is a public key for A, the...tuple (A, kA ) would have type “principal × pubK A” (the Cartesian product symbol “×” is the standard constructor for tuple types). This construction...allows us to associate a generic principal with A’s public key: if B is another principal, then (B, kA ) will have this type as well. We will often need

Phylogenetic Invariants for Metazoan Mitochondrial Genome Evolution.

PubMed

Sankoff; Blanchette

1998-01-01

The method of phylogenetic invariants was developed to apply to aligned sequence data generated, according to a stochastic substitution model, for N species related through an unknown phylogenetic tree. The invariants are functions of the probabilities of the observable N-tuples, which are identically zero, over all choices of branch length, for some trees. Evaluating the invariants associated with all possible trees, using observed N-tuple frequencies over all sequence positions, enables us to rapidly infer the generating tree. An aspect of evolution at the genomic level much studied recently is the rearrangements of gene order along the chromosome from one species to another. Instead of the substitutions responsible for sequence evolution, we examine the non-local processes responsible for genome rearrangements such as inversion of arbitrarily long segments of chromosomes. By treating the potential adjacency of each possible pair of genes as a position", an appropriate substitution" model can be recognized as governing the rearrangement process, and a probabilistically principled phylogenetic inference can be set up. We calculate the invariants for this process for N=5, and apply them to mitochondrial genome data from coelomate metazoans, showing how they resolve key aspects of branching order.

A self-similar hierarchy of the Korean stock market

NASA Astrophysics Data System (ADS)

Lim, Gyuchang; Min, Seungsik; Yoo, Kun-Woo

2013-01-01

A scaling analysis is performed on market values of stocks listed on Korean stock exchanges such as the KOSPI and the KOSDAQ. Different from previous studies on price fluctuations, market capitalizations are dealt with in this work. First, we show that the sum of the two stock exchanges shows a clear rank-size distribution, i.e., the Zipf's law, just as each separate one does. Second, by abstracting Zipf's law as a γ-sequence, we define a self-similar hierarchy consisting of many levels, with the numbers of firms at each level forming a geometric sequence. We also use two exponential functions to describe the hierarchy and derive a scaling law from them. Lastly, we propose a self-similar hierarchical process and perform an empirical analysis on our data set. Based on our findings, we argue that all money invested in the stock market is distributed in a hierarchical way and that a slight difference exists between the two exchanges.

Forensic Memory Analysis for Apple OS X

DTIC Science & Technology

2012-06-14

x86. Table 5. Template interface fields. Variable Python Type Description template dict template implementing the C stuct interface MBR_NAME str ...dictionary key, variable name for a struct member template[MBR_NAME] tuple dictionary value, a struct member description MBR_TYPE str C type of the...named member OFFSET int offset in bytes for the member SIZE int size in bytes for the member type FIELD str lsof field represented by member

Modeling stock price dynamics by continuum percolation system and relevant complex systems analysis

NASA Astrophysics Data System (ADS)

Xiao, Di; Wang, Jun

2012-10-01

The continuum percolation system is developed to model a random stock price process in this work. Recent empirical research has demonstrated various statistical features of stock price changes, the financial model aiming at understanding price fluctuations needs to define a mechanism for the formation of the price, in an attempt to reproduce and explain this set of empirical facts. The continuum percolation model is usually referred to as a random coverage process or a Boolean model, the local interaction or influence among traders is constructed by the continuum percolation, and a cluster of continuum percolation is applied to define the cluster of traders sharing the same opinion about the market. We investigate and analyze the statistical behaviors of normalized returns of the price model by some analysis methods, including power-law tail distribution analysis, chaotic behavior analysis and Zipf analysis. Moreover, we consider the daily returns of Shanghai Stock Exchange Composite Index from January 1997 to July 2011, and the comparisons of return behaviors between the actual data and the simulation data are exhibited.

Coding Instead of Splitting - Algebraic Combinations in Time and Space

DTIC Science & Technology

2016-06-09

sources message. For certain classes of two-unicast-Z networks, we show that the rate-tuple ( N ,1) is achievable as long as the individual source...destination cuts for the two source-destination pairs are respectively at least as large as N and 1, and the generalized network sharing cut - a bound...previously defined by Kamath et. al. - is at least as large as N + 1. We show this through a novel achievable scheme which is based on random linear coding at

A Trust-Based Adaptive Probability Marking and Storage Traceback Scheme for WSNs

PubMed Central

Liu, Anfeng; Liu, Xiao; Long, Jun

2016-01-01

Security is a pivotal issue for wireless sensor networks (WSNs), which are emerging as a promising platform that enables a wide range of military, scientific, industrial and commercial applications. Traceback, a key cyber-forensics technology, can play an important role in tracing and locating a malicious source to guarantee cybersecurity. In this work a trust-based adaptive probability marking and storage (TAPMS) traceback scheme is proposed to enhance security for WSNs. In a TAPMS scheme, the marking probability is adaptively adjusted according to the security requirements of the network and can substantially reduce the number of marking tuples and improve network lifetime. More importantly, a high trust node is selected to store marking tuples, which can avoid the problem of marking information being lost. Experimental results show that the total number of marking tuples can be reduced in a TAPMS scheme, thus improving network lifetime. At the same time, since the marking tuples are stored in high trust nodes, storage reliability can be guaranteed, and the traceback time can be reduced by more than 80%. PMID:27043566

Systems of conservation laws with third-order Hamiltonian structures

NASA Astrophysics Data System (ADS)

Ferapontov, Evgeny V.; Pavlov, Maxim V.; Vitolo, Raffaele F.

2018-06-01

We investigate n-component systems of conservation laws that possess third-order Hamiltonian structures of differential-geometric type. The classification of such systems is reduced to the projective classification of linear congruences of lines in P^{n+2} satisfying additional geometric constraints. Algebraically, the problem can be reformulated as follows: for a vector space W of dimension n+2, classify n-tuples of skew-symmetric 2-forms A^{α } \\in Λ^2(W) such that φ _{β γ }A^{β }\\wedge A^{γ }=0, for some non-degenerate symmetric φ.

Amoeba-inspired Tug-of-War algorithms for exploration-exploitation dilemma in extended Bandit Problem.

PubMed

Aono, Masashi; Kim, Song-Ju; Hara, Masahiko; Munakata, Toshinori

2014-03-01

The true slime mold Physarum polycephalum, a single-celled amoeboid organism, is capable of efficiently allocating a constant amount of intracellular resource to its pseudopod-like branches that best fit the environment where dynamic light stimuli are applied. Inspired by the resource allocation process, the authors formulated a concurrent search algorithm, called the Tug-of-War (TOW) model, for maximizing the profit in the multi-armed Bandit Problem (BP). A player (gambler) of the BP should decide as quickly and accurately as possible which slot machine to invest in out of the N machines and faces an "exploration-exploitation dilemma." The dilemma is a trade-off between the speed and accuracy of the decision making that are conflicted objectives. The TOW model maintains a constant intracellular resource volume while collecting environmental information by concurrently expanding and shrinking its branches. The conservation law entails a nonlocal correlation among the branches, i.e., volume increment in one branch is immediately compensated by volume decrement(s) in the other branch(es). Owing to this nonlocal correlation, the TOW model can efficiently manage the dilemma. In this study, we extend the TOW model to apply it to a stretched variant of BP, the Extended Bandit Problem (EBP), which is a problem of selecting the best M-tuple of the N machines. We demonstrate that the extended TOW model exhibits better performances for 2-tuple-3-machine and 2-tuple-4-machine instances of EBP compared with the extended versions of well-known algorithms for BP, the ϵ-Greedy and SoftMax algorithms, particularly in terms of its short-term decision-making capability that is essential for the survival of the amoeba in a hostile environment. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Learning to Understand Natural Language with Less Human Effort

DTIC Science & Technology

2015-05-01

j ); if one of these has the correct logical form, ` j = `i, then tj is taken as the approximate maximizer. 29 2.3 Discussion This chapter...where j indexes entity tuples (e1, e2). Training optimizes the semantic parser parameters θ to predict Y = yj,Z = zj given S = sj . The parameters θ...be au tif ul / J J N 1 /N 1 λ f .f L on do n /N N P N λ x .M (x ,“ lo nd on ”, C IT Y ) N : λ x .M (x ,“ lo nd on ”, C IT Y ) (S [d cl ]\\N

Rank-frequency relation for Chinese characters

NASA Astrophysics Data System (ADS)

Deng, Weibing; Allahverdyan, Armen E.; Li, Bo; Wang, Qiuping A.

2014-02-01

We show that the Zipf's law for Chinese characters perfectly holds for sufficiently short texts (few thousand different characters). The scenario of its validity is similar to the Zipf's law for words in short English texts. For long Chinese texts (or for mixtures of short Chinese texts), rank-frequency relations for Chinese characters display a two-layer, hierarchic structure that combines a Zipfian power-law regime for frequent characters (first layer) with an exponential-like regime for less frequent characters (second layer). For these two layers we provide different (though related) theoretical descriptions that include the range of low-frequency characters (hapax legomena). We suggest that this hierarchic structure of the rank-frequency relation connects to semantic features of Chinese characters (number of different meanings and homographies). The comparative analysis of rank-frequency relations for Chinese characters versus English words illustrates the extent to which the characters play for Chinese writers the same role as the words for those writing within alphabetical systems.

Nonlinear, nonbinary cyclic group codes

NASA Technical Reports Server (NTRS)

Solomon, G.

1992-01-01

New cyclic group codes of length 2(exp m) - 1 over (m - j)-bit symbols are introduced. These codes can be systematically encoded and decoded algebraically. The code rates are very close to Reed-Solomon (RS) codes and are much better than Bose-Chaudhuri-Hocquenghem (BCH) codes (a former alternative). The binary (m - j)-tuples are identified with a subgroup of the binary m-tuples which represents the field GF(2 exp m). Encoding is systematic and involves a two-stage procedure consisting of the usual linear feedback register (using the division or check polynomial) and a small table lookup. For low rates, a second shift-register encoding operation may be invoked. Decoding uses the RS error-correcting procedures for the m-tuple codes for m = 4, 5, and 6.

Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

PubMed Central

Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

2016-01-01

This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

Beyond description. Comment on "Approaching human language with complex networks" by Cong and Liu

NASA Astrophysics Data System (ADS)

Ferrer-i-Cancho, R.

2014-12-01

In their historical overview, Cong & Liu highlight Sausurre as the father of modern linguistics [1]. They apparently miss G.K. Zipf as a pioneer of the view of language as a complex system. His idea of a balance between unification and diversification forces in the organization of natural systems, e.g., vocabularies [2], can be seen as a precursor of the view of complexity as a balance between order (unification) and disorder (diversification) near the edge of chaos [3]. Although not mentioned by Cong & Liu somewhere else, trade-offs between hearer and speaker needs are very important in Zipf's view, which has inspired research on the optimal networks mapping words into meanings [4-6]. Quantitative linguists regard G.K. Zipf as the funder of modern quantitative linguistics [7], a discipline where statistics plays a central role as in network science. Interestingly, that centrality of statistics is missing Saussure's work and that of many of his successors.

Analysis of mass incident diffusion in Weibo based on self-organization theory

NASA Astrophysics Data System (ADS)

Pan, Jun; Shen, Huizhang

2018-02-01

This study introduces some theories and methods of self-organization system to the research of the diffusion mechanism of mass incidents in Weibo (Chinese Twitter). Based on the analysis on massive Weibo data from Songjiang battery factory incident happened in 2013 and Jiiangsu Qidong OJI PAPER incident happened in 2012, we find out that diffusion system of mass incident in Weibo satisfies Power Law, Zipf's Law, 1/f noise and Self-similarity. It means this system is the self-organization criticality system and dissemination bursts can be understood as one kind of Self-organization behavior. As the consequence, self-organized criticality (SOC) theory can be used to explain the evolution of mass incident diffusion and people may come up with the right strategy to control such kind of diffusion if they can handle the key ingredients of Self-organization well. Such a study is of practical importance which can offer opportunities for policy makers to have good management on these events.

Efficient Synthesis of Network Updates

DTIC Science & Technology

2015-06-17

model include switches S i , links L j , and a single controller element C, and a network N is a tuple containing these. Each switch S i is encoded as a...and the ports they should be forwarded to respec- tively. Each link L j is represented by a record consisting of two locations loc and loc0 and a list...the union of multisets m1 and m2. We write [x] for a singleton list, and l1@l2 for concatenation of l1 and l2. Each transition N o ! N 0 is anno - tated

A Study of Memory Effects in a Chess Database.

PubMed

Schaigorodsky, Ana L; Perotti, Juan I; Billoni, Orlando V

2016-01-01

A series of recent works studying a database of chronologically sorted chess games-containing 1.4 million games played by humans between 1998 and 2007- have shown that the popularity distribution of chess game-lines follows a Zipf's law, and that time series inferred from the sequences of those game-lines exhibit long-range memory effects. The presence of Zipf's law together with long-range memory effects was observed in several systems, however, the simultaneous emergence of these two phenomena were always studied separately up to now. In this work, by making use of a variant of the Yule-Simon preferential growth model, introduced by Cattuto et al., we provide an explanation for the simultaneous emergence of Zipf's law and long-range correlations memory effects in a chess database. We find that Cattuto's Model (CM) is able to reproduce both, Zipf's law and the long-range correlations, including size-dependent scaling of the Hurst exponent for the corresponding time series. CM allows an explanation for the simultaneous emergence of these two phenomena via a preferential growth dynamics, including a memory kernel, in the popularity distribution of chess game-lines. This mechanism results in an aging process in the chess game-line choice as the database grows. Moreover, we find burstiness in the activity of subsets of the most active players, although the aggregated activity of the pool of players displays inter-event times without burstiness. We show that CM is not able to produce time series with bursty behavior providing evidence that burstiness is not required for the explanation of the long-range correlation effects in the chess database. Our results provide further evidence favoring the hypothesis that long-range correlations effects are a consequence of the aging of game-lines and not burstiness, and shed light on the mechanism that operates in the simultaneous emergence of Zipf's law and long-range correlations in a community of chess players.

SH c realization of minimal model CFT: triality, poset and Burge condition

NASA Astrophysics Data System (ADS)

Fukuda, M.; Nakamura, S.; Matsuo, Y.; Zhu, R.-D.

2015-11-01

Recently an orthogonal basis of {{W}}_N -algebra (AFLT basis) labeled by N-tuple Young diagrams was found in the context of 4D/2D duality. Recursion relations among the basis are summarized in the form of an algebra SH c which is universal for any N. We show that it has an {{S}}_3 automorphism which is referred to as triality. We study the level-rank duality between minimal models, which is a special example of the automorphism. It is shown that the nonvanishing states in both systems are described by N or M Young diagrams with the rows of boxes appropriately shuffled. The reshuffling of rows implies there exists partial ordering of the set which labels them. For the simplest example, one can compute the partition functions for the partially ordered set (poset) explicitly, which reproduces the Rogers-Ramanujan identities. We also study the description of minimal models by SH c . Simple analysis reproduces some known properties of minimal models, the structure of singular vectors and the N-Burge condition in the Hilbert space.

A novel approach to photonic generate microwave signals based on optical injection locking and four-wave mixing

NASA Astrophysics Data System (ADS)

Zhu, Huatao; Wang, Rong; Xiang, Peng; Pu, Tao; Fang, Tao; Zheng, Jilin; Li, Yuandong

2017-10-01

In this paper, a novel approach for photonic generation of microwave signals based on frequency multiplication using an injected distributed-feedback (DFB) semiconductor laser is proposed and demonstrated by a proof-of-concept experiment. The proposed system is mainly made up of a dual-parallel Mach-Zehnder modulator (DPMZM) and an injected DFB laser. By properly setting the bias voltage of the DPMZM, ±2-order sidebands with carrier suppression are generated, which are then injected into the slave laser. Due to the optical sideband locking and four-wave mixing (FWM) nonlinearity in the slave laser, new sidebands are generated. Then these sidebands are sent to an optical notch filter where all the undesired sidebands are removed. Finally, after photodetector detection, frequency multiplied microwave signals can be generated. Thanks to the flexibility of the optical sideband locking and FWM, frequency octupling, 12-tupling, 14-tupling and 16-tupling can be obtained.

Comments on, Xuan Li, Shanghong Zhao, Zihang Zhu, Bing Gong, Xingchun Chu, Yongjun Li, Jing Zhao and Yun Liu `an optical millimeter-wave generation scheme based on two parallel dual-parallel Mach-Zehnder modulators and polarization multiplexing', Journal of Modern Optics, 2015

NASA Astrophysics Data System (ADS)

Hasan, Mehedi; Hall, Trevor

2016-11-01

In the title paper, Li et al. have presented a scheme for filter-less photonic millimetre-wave (mm-wave) generation based on two polarization multiplexed parallel dual-parallel Mach-Zehnder modulators (DP-MZMs). For frequency octo-tupling, all the harmonics are suppressed except those of order 4l, where l is the integer. The carrier is then suppressed by the polarization multiplexing technique, which is the principal innovative step in their design. Frequency 12-tupling and 16-tupling is also described following a similar method. The two DP-MZM are similarly driven and provide identical outputs for the same RF modulation indices. Consequently, a demerit of their design is the requirement to apply two different RF signal modulation indexes in a particular range and set the polarizer to a precise angle which depends on the pair of modulation indices used in order to suppress the unwanted harmonics (e.g. the carrier) without simultaneously suppressing the wanted harmonics. The aim of this comment is to show that, an adjustment of the RF drive phases with a fixed polarizer angle with the design presented by Li, all harmonics can be suppressed except those of order4l, where l is an odd integer. Hence, a filter-less frequency octo-tupling can be generated whose performance is not limited by the careful adjustment of the RF drive signal, rather it can be operated for a wide range of modulation indexes (m 2.5 → 7.5). If the modulation index is adjusted to suppress 4th harmonics, then the design can be used to perform frequency 24-tupling. Since, the carrier is suppressed by design in the modified architecture, the strict requirement to adjust the RF drive (and polarizer angle) can be avoided without any significant change to the circuit complexity.

A Logical Basis In The Layered Computer Vision Systems Model

NASA Astrophysics Data System (ADS)

Tejwani, Y. J.

1986-03-01

In this paper a four layer computer vision system model is described. The model uses a finite memory scratch pad. In this model planar objects are defined as predicates. Predicates are relations on a k-tuple. The k-tuple consists of primitive points and relationship between primitive points. The relationship between points can be of the direct type or the indirect type. Entities are goals which are satisfied by a set of clauses. The grammar used to construct these clauses is examined.

WWWinda Orchestrator: a mechanism for coordinating distributed flocks of Java Applets

NASA Astrophysics Data System (ADS)

Gutfreund, Yechezkal-Shimon; Nicol, John R.

1997-01-01

The WWWinda Orchestrator is a simple but powerful tool for coordinating distributed Java applets. Loosely derived from the Linda programming language developed by David Gelernter and Nicholas Carriero of Yale, WWWinda implements a distributed shared object space called TupleSpace where applets can post, read, or permanently store arbitrary Java objects. In this manner, applets can easily share information without being aware of the underlying communication mechanisms. WWWinda is a very useful for orchestrating flocks of distributed Java applets. Coordination event scan be posted to WWWinda TupleSpace and used to orchestrate the actions of remote applets. Applets can easily share information via the TupleSpace. The technology combines several functions in one simple metaphor: distributed web objects, remote messaging between applets, distributed synchronization mechanisms, object- oriented database, and a distributed event signaling mechanisms. WWWinda can be used a s platform for implementing shared VRML environments, shared groupware environments, controlling remote devices such as cameras, distributed Karaoke, distributed gaming, and shared audio and video experiences.

Smart Drill-Down: A New Data Exploration Operator

PubMed Central

Joglekar, Manas; Garcia-Molina, Hector; Parameswaran, Aditya

2015-01-01

We present a data exploration system equipped with smart drill-down, a novel operator for interactively exploring a relational table to discover and summarize “interesting” groups of tuples. Each such group of tuples is represented by a rule. For instance, the rule (a, b, ★, 1000) tells us that there are a thousand tuples with value a in the first column and b in the second column (and any value in the third column). Smart drill-down presents an analyst with a list of rules that together describe interesting aspects of the table. The analyst can tailor the definition of interesting, and can interactively apply smart drill-down on an existing rule to explore that part of the table. In the demonstration, conference attendees will be able to use the data exploration system equipped with smart drill-down, and will be able to contrast smart drill-down to traditional drill-down, for various interestingness measures, and resource constraints. PMID:26844008

Multiplexing N-glycan analysis by DNA analyzer.

PubMed

Feng, Hua-Tao; Li, Pingjing; Rui, Guo; Stray, James; Khan, Shaheer; Chen, Shiaw-Min; Li, Sam F Y

2017-07-01

Analysis of N-glycan structures has been gaining attentions over the years due to their critical importance to biopharma-based applications and growing roles in biological research. Glycan profiling is also critical to the development of biosimilar drugs. The detailed characterization of N-glycosylation is mandatory because it is a nontemplate driven process and that significantly influences critical properties such as bio-safety and bio-activity. The ability to comprehensively characterize highly complex mixtures of N-glycans has been analytically challenging and stimulating because of the difficulties in both the structure complexity and time-consuming sample pretreatment procedures. CE-LIF is one of the typical techniques for N-glycan analysis due to its high separation efficiency. In this paper, a 16-capillary DNA analyzer was coupled with a magnetic bead glycan purification method to accelerate the sample preparation procedure and therefore increase N-glycan assay throughput. Routinely, the labeling dye used for CE-LIF is 8-aminopyrene-1,3,6-trisulfonic acid, while the typical identification method involves matching migration times with database entries. Two new fluorescent dyes were used to either cross-validate and increase the glycan identification precision or simplify sample preparation steps. Exoglycosidase studies were carried out using neuramididase, galactosidase, and fucosidase to confirm the results of three dye cross-validation. The optimized method combines the parallel separation capacity of multiple-capillary separation with three labeling dyes, magnetic bead assisted preparation, and exoglycosidase treatment to allow rapid and accurate analysis of N-glycans. These new methods provided enough useful structural information to permit N-glycan structure elucidation with only one sample injection. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Infrared Reflectance Analysis of Epitaxial n-Type Doped GaN Layers Grown on Sapphire.

PubMed

Tsykaniuk, Bogdan I; Nikolenko, Andrii S; Strelchuk, Viktor V; Naseka, Viktor M; Mazur, Yuriy I; Ware, Morgan E; DeCuir, Eric A; Sadovyi, Bogdan; Weyher, Jan L; Jakiela, Rafal; Salamo, Gregory J; Belyaev, Alexander E

2017-12-01

Infrared (IR) reflectance spectroscopy is applied to study Si-doped multilayer n + /n 0 /n + -GaN structure grown on GaN buffer with GaN-template/sapphire substrate. Analysis of the investigated structure by photo-etching, SEM, and SIMS methods showed the existence of the additional layer with the drastic difference in Si and O doping levels and located between the epitaxial GaN buffer and template. Simulation of the experimental reflectivity spectra was performed in a wide frequency range. It is shown that the modeling of IR reflectance spectrum using 2 × 2 transfer matrix method and including into analysis the additional layer make it possible to obtain the best fitting of the experimental spectrum, which follows in the evaluation of GaN layer thicknesses which are in good agreement with the SEM and SIMS data. Spectral dependence of plasmon-LO-phonon coupled modes for each GaN layer is obtained from the spectral dependence of dielectric of Si doping impurity, which is attributed to compensation effects by the acceptor states.

There is More than a Power Law in Zipf

PubMed Central

Cristelli, Matthieu; Batty, Michael; Pietronero, Luciano

2012-01-01

The largest cities, the most frequently used words, the income of the richest countries, and the most wealthy billionaires, can be all described in terms of Zipf’s Law, a rank-size rule capturing the relation between the frequency of a set of objects or events and their size. It is assumed to be one of many manifestations of an underlying power law like Pareto’s or Benford’s, but contrary to popular belief, from a distribution of, say, city sizes and a simple random sampling, one does not obtain Zipf’s law for the largest cities. This pathology is reflected in the fact that Zipf’s Law has a functional form depending on the number of events N. This requires a fundamental property of the sample distribution which we call ‘coherence’ and it corresponds to a ‘screening’ between various elements of the set. We show how it should be accounted for when fitting Zipf’s Law. PMID:23139862

Analysis of waveguide architectures of InGaN/GaN diode lasers by nearfield optical microscopy

NASA Astrophysics Data System (ADS)

Friede, Sebastian; Tomm, Jens W.; Kühn, Sergei; Hoffmann, Veit; Wenzel, Hans

2017-02-01

Waveguide (WG) architectures of 420-nm emitting InAlGaN/GaN diode lasers are analyzed by photoluminescence (PL) and photocurrent (PC) spectroscopy using a nearfield scanning optical microscope (NSOM) for excitation and detection. The measurements with a spatial resolution of 100 nm are implemented by scanning the fiber tip along the unprepared front facets of standard devices. PL is collected by the fiber tip, whereas PCs are extracted from the contacts that are anyway present for power supply. The mechanisms of signal generation are addressed in detail. The components of the `optical active region', multiple quantum wells (MQW), WGs, and cladding layers are separately inspected. Even separate analysis of p- and n-sections of the WG become possible. Defect levels are detected in the p-part of the WG. Their presence is consistent with the doping by Mg. An increased efficiency of carrier capture into InGaN/GaN WGs compared to GaN WGs is observed. Thus, beyond the improved optical confinement, the electrical confinement is improved, as well. NSOM PL and PC at GaN based devices do not reach the clarity and spatial resolution for WG mode analysis as seen before for GaAs based devices. This is due to higher modal absorption and higher WG losses. NSOM based optical analysis turns out to be an efficient tool for analysis of single layers grown into InAlGaN/GaN diode laser structures, even if this analysis is done at a packaged ready-to-work device.

Design and Implementation of a Pretty Printer for the Functional Specification Language SPEC

DTIC Science & Technology

1988-06-01

language independent pretty printer using Kodiyak and attribute grammars. These general guidelines are a direct result of the insight gained from the...outlined. The final subject in this chapter is the general and specific rules for the pretty printer. A user of the pretty printer code needs only a working...an extension of a context-free grammar whose generated language includes syntax and semantics. A context-free grammar (CFG) is a four tuple G (N,T, P ,S

On spectra of Lüders operations

NASA Astrophysics Data System (ADS)

Nagy, Gabriel

2008-02-01

We show that all the eigenvalues of certain generalized Lüders operations are non-negative real numbers in two cases of interest. In particular, given a commuting n-tuple A =(A1,…,An) consisting of positive operators on a Hilbert space H, satisfying ∑j =1nAj=I, we show that the spectrum of the Lüders operation: ΛA:B(H)∋X↦∑j =1nAj1/2XAj1/2∈B(H) is contained in [0,∞), so the only solution of the equation ΛA(X)=I-X is the "expected" one: X =1/2I.

Computer systems and methods for the query and visualization of multidimensional databases

DOEpatents

Stolte, Chris; Tang, Diane L.; Hanrahan, Patrick

2006-08-08

A method and system for producing graphics. A hierarchical structure of a database is determined. A visual table, comprising a plurality of panes, is constructed by providing a specification that is in a language based on the hierarchical structure of the database. In some cases, this language can include fields that are in the database schema. The database is queried to retrieve a set of tuples in accordance with the specification. A subset of the set of tuples is associated with a pane in the plurality of panes.

Computer systems and methods for the query and visualization of multidimensional database

DOEpatents

Stolte, Chris; Tang, Diane L.; Hanrahan, Patrick

2010-05-11

A method and system for producing graphics. A hierarchical structure of a database is determined. A visual table, comprising a plurality of panes, is constructed by providing a specification that is in a language based on the hierarchical structure of the database. In some cases, this language can include fields that are in the database schema. The database is queried to retrieve a set of tuples in accordance with the specification. A subset of the set of tuples is associated with a pane in the plurality of panes.

Interactive Data Exploration with Smart Drill-Down

PubMed Central

Joglekar, Manas; Garcia-Molina, Hector; Parameswaran, Aditya

2017-01-01

We present smart drill-down, an operator for interactively exploring a relational table to discover and summarize “interesting” groups of tuples. Each group of tuples is described by a rule. For instance, the rule (a, b, ⋆, 1000) tells us that there are a thousand tuples with value a in the first column and b in the second column (and any value in the third column). Smart drill-down presents an analyst with a list of rules that together describe interesting aspects of the table. The analyst can tailor the definition of interesting, and can interactively apply smart drill-down on an existing rule to explore that part of the table. We demonstrate that the underlying optimization problems are NP-Hard, and describe an algorithm for finding the approximately optimal list of rules to display when the user uses a smart drill-down, and a dynamic sampling scheme for efficiently interacting with large tables. Finally, we perform experiments on real datasets on our experimental prototype to demonstrate the usefulness of smart drill-down and study the performance of our algorithms. PMID:28210096

Does mean mean MEAN!? Digits For A Very Long Time Giving Us The Finger!: 1881 Statistics Log-Law was: Quanta=Digits!: BEC; Zipf 1/f-Law; Information-Thy; Random-#s = Euler V Bernoulli; Q-Computing = Arithmetic; P=/=NP SANS Complexity: Euclid 3-Mille

NASA Astrophysics Data System (ADS)

Siegel, Edward

2008-03-01

Classic statistics digits Newcomb[Am.J.Math.4,39,1881]-Weyl[Goett.Nachr.1912]-Benford[Proc.Am.Phil.Soc.78,4,51,1938]("NeWBe")probability ON-AVERAGE/MEAN log-law: =log[1+1/d]=log[(d+1)/d][google:``Benford's-Law'';"FUZZYICS": Siegel[AMS Nat.-Mtg.:2002&2008)]; Raimi[Sci.Am.221,109,1969]; Hill[Proc.AMS,123,3,887,1996]=log-base=units=SCALE-INVARIANCE!. Algebraic-inverse d=1/[ê(w)-1]: BOSONS(1924)=DIGITS(<1881): Energy-levels:ground=(d=0),first-(d=1)-excited ,... No fractions; only digit-integer-differences=quanta! Quo vadis digit =oo vs. <<Zipf-law Pareto power-law decay algebraicity, Siegel[Symp.Fractals,MRS Fall-Mtg.,1989-5!] ``FUZZYICS'' explains INEVITABILITY via Lawvere-Goguen-Siegel-Baez ``CATEGORICAL-SEMANTICS'' HYBRID:CATEGORY-THEORY+COGNITIVE-SEMANTICS! Averages dominate physics: expectations,ensemble, time,ANY/ALL experiments!: What if any don't follow digits log-law? Must they always?; Do YOURS?; ALWAYS?; No fluctuations from it allowed?; Never?; Ever?; Never Ever? Ponder long/hard digits' log-law's MEANING for physics/ sciences! Could statistics' ``mean'' REALLY MEANS ``MEAN!''? "Does `mean' mean ``MEAN''!?": ``quantum-computing'' is/was always alive/well in/since 1881: in <1 + 1 = 2>,... simple-arithmetic!

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes.

PubMed

León-Palmero, Elizabeth; Joglar, Vanessa; Álvarez, Pedro A; Martín-Platero, Antonio; Llamas, Inmaculada; Reche, Isabel

2018-01-01

Marine invertebrates, as holobionts, contain symbiotic bacteria that coevolve and develop antimicrobial substances. These symbiotic bacteria are an underexplored source of new bioactive molecules to face the emerging antibiotic resistance in pathogens. Here, we explored the antimicrobial activity of bacteria retrieved from the microbiota of two sea anemones (Anemonia sulcata, Actinia equina) and two holothurians (Holothuria tubulosa, Holothuria forskali). We tested the antimicrobial activity of the isolated bacteria against pathogens with interest for human health, agriculture and aquaculture. We isolated 27 strains with antibacterial activity and 12 of these isolates also showed antifungal activity. We taxonomically identified these strains being Bacillus and Vibrio species the most representative producers of antimicrobial substances. Microbiome species composition of the two sea anemones was similar between them but differed substantially of seawater bacteria. In contrast, microbiome species composition of the two holothurian species was different between them and in comparison with the bacteria in holothurian feces and seawater. In all the holobiont microbiomes Bacteroidetes was the predominant phylum. For each microbiome, we determined diversity and the rank-abundance dominance using five fitted models (null, pre-emption, log-Normal, Zipf and Zipf-Mandelbrot). The models with less evenness (i.e. Zipf and Zipf-Mandelblot) showed the best fits in all the microbiomes. Finally, we tracked (using the V4 hypervariable region of 16S rRNA gene) the relative abundance of these 27 isolates with antibacterial activity in the total pool of sequences obtained for the microbiome of each holobiont. Coincidences, although with extremely low frequencies, were detected only in the microbiome of H. forskali. This fact suggests that these isolated bacteria belong to the long tail of rare symbiotic bacteria. Therefore, more and more sophisticated culture techniques are necessary

Analysis of (n,2n) cross-section measurements for nuclei up to mass 238

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davey, W.G.; Goin, R.W.; Ross, J.R.

All suitable measurements of the energy dependence of (n,2n) cross sections of all isotopes up to mass 238 have been analyzed. The objectives were to display the quality of the measured data for each isotope and to examine the systematic dependence of the (n,2n) cross section upon N, Z, and A. Graphs and tables are presented of the ratio of the asymptotic (n,2n) and nonelastic cross section to the neutron-asymmetry parameter (N--Z)/A. Similar data are presented for the derived nuclear temperature, T, and level-density parameter, $alpha$, as a function of N, Z, and A. This analysis of the results ofmore » over 145 experiments on 61 isotopes is essentially a complete review of the current status of (n,2n) cross-section measurements. (auth)« less

Zipf's Law in Gene Expression

NASA Astrophysics Data System (ADS)

Furusawa, Chikara; Kaneko, Kunihiko

2003-02-01

Using data from gene expression databases on various organisms and tissues, including yeast, nematodes, human normal and cancer tissues, and embryonic stem cells, we found that the abundances of expressed genes exhibit a power-law distribution with an exponent close to -1; i.e., they obey Zipf’s law. Furthermore, by simulations of a simple model with an intracellular reaction network, we found that Zipf’s law of chemical abundance is a universal feature of cells where such a network optimizes the efficiency and faithfulness of self-reproduction. These findings provide novel insights into the nature of the organization of reaction dynamics in living cells.

Cross sections for n+{sup 14}N from an R-matrix analysis of the {sup 15}N system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hale, G.M.; Young, P.G.; Chadwick, M.B.

1994-06-01

As part of the Hiroshima-Nagasaki Dose Reevaluation Program, a new evaluation of the neutron cross sections for {sup 14}N was made for ENDF/B-VI, based at energies below 2.5 MeV on a multichannel R-matrix analysis of reactions in the {sup 15}N system. The types of data used in the analysis, and the resulting cross sections and resonance structure for {sup 15}N are briefly described. The resonant features of the neutron cross sections were especially well determined by including precise, high-resolution neutron total cross section measurements from ORNL. While the new evaluated cross section appear to be significant improvements over the earliermore » ones, they still need to be tested more extensively against recent measurements of the differential elastic cross section from Oak Ridge.« less

Coupled-cluster based basis sets for valence correlation calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Claudino, Daniel; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu; Gargano, Ricardo

Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These newmore » sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via 〈r{sup n}〉 (−3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within “chemical accuracy” of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.« less

Light Helicopter Family Trade-Off Analysis. Volume 4. Appendix N

DTIC Science & Technology

1985-05-15

Figur«! N -V1I-9 through N -VII-U ahow th« futl flow CMp«rlsoas chac comt|>oad r.o th« powar r«qutr«««nt* thown by flguraa (J-VII-l through M-VII-4...HELICOPTER. FAMILY TRADE-OFF ANALYSIS APPENDIX N VOLUME IV ACN: 69396 • Copy l_Q] of 130 c:optea. 15 Nay 198S ~ .. 8 06 .0&1 OTIC ELECTE AU613...TITLE (- ..... do) I. TYPf ’!! ~POitT a PI!I’IOD COVI:IU!O LIGHT HELICOPTER FAMILY TRADE-OFF ANALYSIS, Fina t y Report, APPENDIX N , VOLUME IV of XI

Equilibrium and dynamic methods when comparing an English text and its Esperanto translation

NASA Astrophysics Data System (ADS)

Ausloos, M.

2008-11-01

A comparison of two English texts written by Lewis Carroll, one (Alice in Wonderland), also translated into Esperanto, the other (Through the Looking Glass) are discussed in order to observe whether natural and artificial languages significantly differ from each other. One dimensional time series like signals are constructed using only word frequencies (FTS) or word lengths (LTS). The data is studied through (i) a Zipf method for sorting out correlations in the FTS and (ii) a Grassberger-Procaccia (GP) technique based method for finding correlations in LTS. The methods correspond to an equilibrium and a dynamic approach respectively to human texts features. There are quantitative statistical differences between the original English text and its Esperanto translation, but the qualitative differences are very minutes. However different power laws are observed with characteristic exponents for the ranking properties, and the phase space attractor dimensionality. The Zipf exponent can take values much less than unity (∼0.50 or 0.30) depending on how a sentence is defined. This variety in exponents can be conjectured to be an intrinsic measure of the book style or purpose, rather than the language or author vocabulary richness, since a similar exponent is obtained whatever the text. Moreover the attractor dimension r is a simple function of the so called phase space dimension n, i.e., r=nλ, with λ=0.79. Such an exponent could also be conjectured to be a measure of the author style versatility, - here well preserved in the translation.

Trimodal interpretation of constraints for planning

NASA Technical Reports Server (NTRS)

Krieger, David; Brown, Richard

1987-01-01

Constraints are used in the CAMPS knowledge based planning system to represent those propositions that must be true for a plan to be acceptable. CAMPS introduces the make-mode for interpreting a constraint. Given an unsatisfied constraint, make evaluation mode suggests planning actions which, if taken, would result in a modified plan in which the constraint in question may be satisfied. These suggested planning actions, termed delta-tuples, are the raw material of intelligent plan repair. They are used both in debugging an almost-right plan and in replanning due to changing situations. Given a defective plan in which some set of constraints are violated, a problem solving strategy selects one or more constraints as a focus of attention. These selected constraints are evaluated in the make-mode to produce delta-tuples. The problem solving strategy then reviews the delta-tuples according to its application and problem-specific criteria to find the most acceptable change in terms of success likelihood and plan disruption. Finally, the problem solving strategy makes the suggested alteration to the plan and then rechecks constraints to find any unexpected consequences.

In-Network Processing of an Iceberg Join Query in Wireless Sensor Networks Based on 2-Way Fragment Semijoins

PubMed Central

Kang, Hyunchul

2015-01-01

We investigate the in-network processing of an iceberg join query in wireless sensor networks (WSNs). An iceberg join is a special type of join where only those joined tuples whose cardinality exceeds a certain threshold (called iceberg threshold) are qualified for the result. Processing such a join involves the value matching for the join predicate as well as the checking of the cardinality constraint for the iceberg threshold. In the previous scheme, the value matching is carried out as the main task for filtering non-joinable tuples while the iceberg threshold is treated as an additional constraint. We take an alternative approach, meeting the cardinality constraint first and matching values next. In this approach, with a logical fragmentation of the join operand relations on the aggregate counts of the joining attribute values, the optimal sequence of 2-way fragment semijoins is generated, where each fragment semijoin employs a Bloom filter as a synopsis of the joining attribute values. This sequence filters non-joinable tuples in an energy-efficient way in WSNs. Through implementation and a set of detailed experiments, we show that our alternative approach considerably outperforms the previous one. PMID:25774710

Arithmetic Data Cube as a Data Intensive Benchmark

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Shabano, Leonid

2003-01-01

Data movement across computational grids and across memory hierarchy of individual grid machines is known to be a limiting factor for application involving large data sets. In this paper we introduce the Data Cube Operator on an Arithmetic Data Set which we call Arithmetic Data Cube (ADC). We propose to use the ADC to benchmark grid capabilities to handle large distributed data sets. The ADC stresses all levels of grid memory by producing 2d views of an Arithmetic Data Set of d-tuples described by a small number of parameters. We control data intensity of the ADC by controlling the sizes of the views through choice of the tuple parameters.

Time is Money

NASA Astrophysics Data System (ADS)

Ausloos, Marcel; Vandewalle, Nicolas; Ivanova, Kristinka

Specialized topics on financial data analysis from a numerical and physical point of view are discussed when pertaining to the analysis of coherent and random sequences in financial fluctuations within (i) the extended detrended fluctuation analysis method, (ii) multi-affine analysis technique, (iii) mobile average intersection rules and distributions, (iv) sandpile avalanches models for crash prediction, (v) the (m,k)-Zipf method and (vi) the i-variability diagram technique for sorting out short range correlations. The most baffling result that needs further thought from mathematicians and physicists is recalled: the crossing of two mobile averages is an original method for measuring the "signal" roughness exponent, but why it is so is not understood up to now.

Performance Analysis of GaN Capping Layer Thickness on GaN/AlGaN/GaN High Electron Mobility Transistors.

PubMed

Sharma, N; Periasamy, C; Chaturvedi, N

2018-07-01

In this paper, we present an investigation of the impact of GaN capping layer and AlGaN layer thickness on the two-dimensional (2D)-electron mobility and the carrier concentration which was formed close to the AlGaN/GaN buffer layer for Al0.25Ga0.75N/GaN and GaN/Al0.25Ga0.75N/GaN heterostructures deposited on sapphire substrates. The results of our analysis clearly indicate that expanding the GaN capping layer thickness from 1 nm to 100 nm prompts an increment in the electron concentration at hetero interface. As consequence of which drain current was additionally increments with GaN cap layer thicknesses, and eventually saturates at approximately 1.85 A/mm for capping layer thickness greater than 40 nm. Interestingly, for the same structure, the 2D-electron mobility, decrease monotonically with GaN capping layer thickness, and saturate at approximately 830 cm2/Vs for capping layer thickness greater than 50 nm. A device with a GaN cap layer didn't exhibit gate leakage current. Furthermore, it was observed that the carrier concentration was first decrease 1.03 × 1019/cm3 to 6.65 × 1018/cm3 with AlGaN Layer thickness from 5 to 10 nm and after that it increases with the AlGaN layer thickness from 10 to 30 nm. The same trend was followed for electric field distributions. Electron mobility decreases monotonically with AlGaN layer thickness. Highest electron mobility 1354 cm2/Vs were recorded for the AlGaN layer thickness of 5 nm. Results obtained are in good agreement with published experimental data.

Logical definability and asymptotic growth in optimization and counting problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Compton, K.

1994-12-31

There has recently been a great deal of interest in the relationship between logical definability and NP-optimization problems. Let MS{sub n} (resp. MP{sub n}) be the class of problems to compute, for given a finite structure A, the maximum number of tuples {bar x} in A satisfying a {Sigma}{sub n} (resp. II{sub n}) formula {psi}({bar x}, {bar S}) as {bar S} ranges over predicates on A. Kolaitis and Thakur showed that the classes MS{sub n} and MP{sub n} collapse to a hierarchy of four levels. Papadimitriou and Yannakakis previously showed that problems in the two lowest levels MS{sub 0} andmore » MS{sub 1} (which they called Max Snp and Max Np) are approximable to within a contrast factor in polynomial time. Similarly, Saluja, Subrahmanyam, and Thakur defined SS{sub n} (resp. SP{sub n}) to be the class of problems to compute, for given a finite structure A, the number of tuples ({bar T}, {bar S}) satisfying a given {Sigma}{sub n} (resp. II{sub n}) formula {psi}({bar T}, {bar c}) in A. They showed that the classes SS{sub n} and SP{sub n} collapse to a hierarchy of five levels and that problems in the two lowest levels SS{sub 0} and SS{sub 1} have a fully polynomial time randomized approximation scheme. We define extended classes MSF{sub n}, MPF{sub n} SSF{sub n}, and SPF{sub n} by allowing formulae to contain predicates definable in a logic known as least fixpoint logic. The resulting hierarchies classes collapse to the same number of levels and problems in the bottom levels can be approximated as before, but now some problems descend from the highest levels in the original hierarchies to the lowest levels in the new hierarchies. We introduce a method characterizing rates of growth of average solution sizes thereby showing a number of important problems do not belong MSF{sub 1} and SSF{sub 1}. This method is related to limit laws for logics and the probabilistic method from combinatorics.« less

Microstructural analysis of Ti/Al/Ti/Au ohmic contacts to n-AlGaN/GaN

NASA Astrophysics Data System (ADS)

Chen, J.; Ivey, D. G.; Bardwell, J.; Liu, Y.; Tang, H.; Webb, J. B.

2002-05-01

To develop high quality AlGaN/GaN heterostructure field effect transistors for use in high power, high frequency, and high temperature applications, low resistance, thermal stable ohmic contacts with good surface morphology are essential. Low specific contact resistances have been achieved using an Au/Ti/Al/Ti contact: a minimum value of 6.33×10-6 Ω cm2 was attained after annealing at 700 °C for 30 s. Microstructural analysis using transmission electron microscopy indicated that there is significant interaction between the metallization components and the semiconductor during annealing. The optimum electrical properties correspond to a microstructure that consists of Au2Ti and TiAl layers as well as of a thin Ti-rich layer (~10 nm thick) at the metallization/AlGaN interface. Degradation of the contact occurred for annealing temperatures in excess of 750 °C, and was accompanied by decomposition of the AlGaN layer and formation of a Au-Ti-Al-Ga quaternary phase.

Reliability analysis of InGaN/GaN multi-quantum-well solar cells under thermal stress

NASA Astrophysics Data System (ADS)

Huang, Xuanqi; Fu, Houqiang; Chen, Hong; Lu, Zhijian; Baranowski, Izak; Montes, Jossue; Yang, Tsung-Han; Gunning, Brendan P.; Koleske, Dan; Zhao, Yuji

2017-12-01

We investigate the thermal stability of InGaN solar cells under thermal stress at elevated temperatures from 400 °C to 500 °C. High Resolution X-Ray Diffraction analysis reveals that material quality of InGaN/GaN did not degrade after thermal stress. The external quantum efficiency characteristics of solar cells were well-maintained at all temperatures, which demonstrates the thermal robustness of InGaN materials. Analysis of current density-voltage (J-V) curves shows that the degradation of conversion efficiency of solar cells is mainly caused by the decrease in open-circuit voltage (Voc), while short-circuit current (Jsc) and fill factor remain almost constant. The decrease in Voc after thermal stress is attributed to the compromised metal contacts. Transmission line method results further confirmed that p-type contacts became Schottky-like after thermal stress. The Arrhenius model was employed to estimate the failure lifetime of InGaN solar cells at different temperatures. These results suggest that while InGaN solar cells have high thermal stability, the degradation in the metal contact could be the major limiting factor for these devices under high temperature operation.

Familial 18 centromere variant resulting in difficulties in interpreting prenatal interphase FISH.

PubMed

Bourthoumieu, S; Esclaire, F; Terro, F; Brosset, P; Fiorenza, M; Aubard, V; Beguet, M; Yardin, C

2010-08-01

We report here on a familial case of centromeric heteromorphism of chromosome 18 detected by prenatal interphase fluorescence in situ hybridization (FISH) analysis transmitted by the mother to her fetus, and resulting in complete loss of one 18 signal. The prenatal diagnosis was performed by interphase FISH (AneuVysion probe set, and LSI DiGeorge 22q11.2 kit) because of the presence of an isolated fetal cardiac abnormality, and was first difficult to interpret: only one centromeric 18 signal was detectable on prenatal interphase nuclei, along with one signal for the Y and one for the X chromosome. The LSI DiGeorge 22q11.2 kit also showed the absence of one TUPLE 1 signal on all examined nuclei. In fact, the FISH performed on maternal buccal smear displayed the same absence of one chromosome 18 centromeric signal, combined with the presence of two TUPLE1 signals. All these results led to the diagnosis of an isolated 22q11.2 fetal microdeletion that was confirmed on metaphases spreads. This case illustrates once again that the locus specific (LSI) probes are more effective than the alpha centromeric probes for interphase analysis. The development of high-quality LSI probes for chromosomes 18, X and Y could avoid the misinterpretation of prenatal interphase FISH leading to numerous additional and expensive investigations. Copyright 2010 Elsevier Masson SAS. All rights reserved.

Do neural nets learn statistical laws behind natural language?

PubMed

Takahashi, Shuntaro; Tanaka-Ishii, Kumiko

2017-01-01

The performance of deep learning in natural language processing has been spectacular, but the reasons for this success remain unclear because of the inherent complexity of deep learning. This paper provides empirical evidence of its effectiveness and of a limitation of neural networks for language engineering. Precisely, we demonstrate that a neural language model based on long short-term memory (LSTM) effectively reproduces Zipf's law and Heaps' law, two representative statistical properties underlying natural language. We discuss the quality of reproducibility and the emergence of Zipf's law and Heaps' law as training progresses. We also point out that the neural language model has a limitation in reproducing long-range correlation, another statistical property of natural language. This understanding could provide a direction for improving the architectures of neural networks.

Analysis of reverse gate leakage mechanism of AlGaN/GaN HEMTs with N2 plasma surface treatment

NASA Astrophysics Data System (ADS)

Liu, Hui; Zhang, Zongjing; Luo, Weijun

2018-06-01

The mechanism of reverse gate leakage current of AlGaN/GaN HEMTs with two different surface treatment methods are studied by using C-V, temperature dependent I-V and theoretical analysis. At the lower reverse bias region (VR >- 3.5 V), the dominant leakage current mechanism of the device with N2 plasma surface treatment is the Poole-Frenkel emission current (PF), and Trap-Assisted Tunneling current (TAT) is the principal leakage current of the device which treated by HCl:H2O solution. At the higher reverse bias region (VR <- 3.5 V), both of the two samples show good agreement with the surface leakage mechanism. The leakage current of the device with N2 plasma surface treatment is one order of magnitude smaller than the device which treated by HCl:H2O solution. This is due to the recovery of Ga-N bond in N2 plasma surface treatment together with the reduction of the shallow traps in post-gate annealing (PGA) process. The measured results agree well with the theoretical calculations and demonstrate N2 plasma surface treatment can reduce the reverse leakage current of the AlGaN/GaN HEMTs.

Conformational analysis of some N,N-diethyl-2-[(4‧-substituted) phenylthio] acetamides

NASA Astrophysics Data System (ADS)

Vinhato, Elisângela; Olivato, Paulo R.; Zukerman-Schpector, Julio; Dal Colle, Maurizio

2013-11-01

The conformational analysis of some N,N-diethyl-2[(4‧-substituted)phenylthio]acetamides bearing the substituents OMe 1, Me 2, H 3, Cl 4, Br 5 and NO26, was performed by νCO IR analysis, along with B3LYP/6-311++G(d,p) and Polarisable Continuum Model (PCM) calculations, as well as NBO analysis for 1, 3, and 6 and X-ray diffraction for 4. The results of the calculations indicated the existence of two stable conformation pairs, i.e. gauche (anti; syn) (most stable) and cis (anti; syn) in the gas phase. The gauche conformers were less polar with respect to the cis ones for 1 and 3, but more polar for 6. The most intense IR carbonyl doublet component observed at the lower frequency can be ascribed to the gauche conformers g(anti; syn) for 3-6 in n-C6H14, which is in agreement with the gauche and cis relative stabilities and frequencies resulting from the PCM calculations. Similarly, the single IR band for 1 and 2 in n-hexane may be attributed to the gauche conformers. The PCM calculations compared well with the IR data for the compounds in solution, showing that there is a progressive increase of the cis/gauche population ratio as the solvent polarity increases. The NBO analysis indicated that the gauche(anti; syn) conformation in the gas phase was stabilized by the relevant LPS4 → πC 2dbnd O 1∗, πC 2dbnd O 1 → σC 3sbnd S 4∗ , σC 3sbnd S 4 → πC 2dbnd O 1∗, πC 2dbnd O 1∗ → σC 3sbnd S 4∗, and LPO1 →σ∗ C11sbnd H28 orbital interactions, which were absent in the cis(anti; syn) conformer. On the contrary, the cis conformer for derivatives 1, 3, and 6 were stabilized by the σC 3 -S 4∗ →σ∗ C2sbnd N5 orbital interaction (through bond coupling), along with the additional LPO1 →σ∗ S4sbnd C10 interaction for 6. Moreover, the electrostatic repulsion between the Cδ+sbnd Sδ- and Cδ+dbnd Oδ- dipoles (Repulsive Field Effect) contributed to both the larger destabilization and increase of the νCO frequency of the cis conformer with respect

Quantitative analysis of substituted N,N-dimethyl-tryptamines in the presence of natural type XII alkaloids.

PubMed

Ivanova, Bojidarka; Spiteller, Michael

2012-10-01

This paper reports the qualitative and quantitative analysis (QA) of mixtures of hallucinogens, N,N-dimethyltryptamine (DMT) (1), 5-methoxy- (la) and 5-hydroxy-N,N-dimethyltryptamine (1b) in the presence of beta-carbolines (indole alkaloids of type XII) ((2), (3) and (5)}. The validated electronic absorption spectroscopic (EAs) protocol achieved a concentration limit of detection (LOD) of 7.2.10(-7) mol/L {concentration limit of quantification (LOQ) of 24.10(-7) mol/L) using bands (lambda max within 260+/-0.23-262+/-0.33 nm. Metrology, including accuracy, measurement repeatability, measurement precision, trueness of measurement, and reproducibility of the measurements are presented using N,N-dimethyltryptamine (DMA) as standard. The analytical quantities of mixtures of alkaloids 4, 6 and 7 are: lambda max 317+/-0.45, 338+/-0.69 and 430+/-0.09 for 4 (LOD, 8.6.10(-7) mol/L; LOQ, 28.66(6), mol/L), as well as 528+/-0.75 nm for 6 and 7 (LOD, 8.2.10(-7) mol/L; LOQ, 27.33(3), mol/L), respectively. The partially validated protocols by high performance liquid chromatography (HPLC), electrospray ionization (ESI), mass spectrometry (MS), both in single and tandem operation (MS/MS) mode, as well as matrix/assisted laser desorption/ionization (MALDI) MS are elaborated. The Raman spectroscopic (RS) protocol for analysis of psychoactive substances, characterized by strong fluorescence RS profile was developed, with the detection limits being discussed. The known synergistic effect leading to increase the psychoactive and hallucinogenic properties and the reported acute poisoning cases from 1-7, make the present study emergent, since as well the current lack of analytical data and the herein metrology obtained contributed to the elaboration of highly selective and precise analytical protocols, which would be of interest in the field of criminal forensic analysis.

Sandia Unstructured Triangle Tabular Interpolation Package v 0.1 beta

DOE Office of Scientific and Technical Information (OSTI.GOV)

2013-09-24

The software interpolates tabular data, such as for equations of state, provided on an unstructured triangular grid. In particular, interpolation occurs in a two dimensional space by looking up the triangle in which the desired evaluation point resides and then performing a linear interpolation over the n-tuples associated with the nodes of the chosen triangle. The interface to the interpolation routines allows for automated conversion of units from those tabulated to the desired output units. when multiple tables are included in a data file, new tables may be generated by on-the-fly mixing of the provided tables

Supporting Uncertainty Reasoning in SIMulated Operators for Networks (SIMON) (Le support du raisonnement dans l’incertitude pour des operateurs simules dans un reseau)

DTIC Science & Technology

2005-12-01

moteur de simulation de l’Environnement Intégré de Modélisation de la Performance est utilisé de pair avec l’approche pour démontrer comment des...d’être utilisé dans les forces générées par ordinateur. Le travail ultérieur inclura plus d’essais, l’intégration avec les moteurs de simulateurs et...Aspects are reasoning units relevant to simulated tasks. Each Aspect schema is a 4-tuple: AspectSchema = <MA, WM, LM, CL>, where MA refers to meta

Investigation of Trap States in AlInN/AlN/GaN Heterostructures by Frequency-Dependent Admittance Analysis

NASA Astrophysics Data System (ADS)

Arslan, Engin; Bütün, Serkan; Şafak, Yasemin; Ozbay, Ekmel

2010-12-01

We present a systematic study on the admittance characterization of surface trap states in unpassivated and SiN x -passivated Al0.83In0.17N/AlN/GaN heterostructures. C- V and G/ ω- V measurements were carried out in the frequency range of 1 kHz to 1 MHz, and an equivalent circuit model was used to analyze the experimental data. A detailed analysis of the frequency-dependent capacitance and conductance data was performed, assuming models in which traps are located at the metal-AlInN surface. The density ( D t) and time constant ( τ t) of the surface trap states have been determined as a function of energy separation from the conduction-band edge ( E c - E t). The D st and τ st values of the surface trap states for the unpassivated samples were found to be D_{{st}} \\cong (4 - 13) × 10^{12} {eV}^{ - 1} {cm}^{ - 2} and τ st ≈ 3 μs to 7 μs, respectively. For the passivated sample, D st decreased to 1.5 × 10^{12} {eV}^{ - 1} {cm}^{ - 2} and τ st to 1.8 μs to 2 μs. The density of surface trap states in Al0.83In0.17N/AlN/GaN heterostructures decreased by approximately one order of magnitude with SiN x passivation, indicating that the SiN x insulator layer between the metal contact and the surface of the Al0.83In0.17N layer can passivate surface states.

Lexical Frequency Profiles and Zipf's Law

ERIC Educational Resources Information Center

Edwards, Roderick; Collins, Laura

2011-01-01

Laufer and Nation (1995) proposed that the Lexical Frequency Profile (LFP) can estimate the size of a second-language writer's productive vocabulary. Meara (2005) questioned the sensitivity and the reliability of LFPs for estimating vocabulary sizes, based on the results obtained from probabilistic simulations of LFPs. However, the underlying…

Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N'Dama.

PubMed

Kim, Soo-Jin; Ka, Sojeong; Ha, Jung-Woo; Kim, Jaemin; Yoo, DongAhn; Kim, Kwondo; Lee, Hak-Kyo; Lim, Dajeong; Cho, Seoae; Hanotte, Olivier; Mwai, Okeyo Ally; Dessie, Tadelle; Kemp, Stephen; Oh, Sung Jong; Kim, Heebal

2017-05-12

Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied. We performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N'Dama cattle. We analysed genetic variation patterns in N'Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N'Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N'Dama may engage in skeletal growth as well as immune systems. Our results imply that N'Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreover, this study offers significant insights into identifying genetic signatures for natural and artificial selection of diverse African cattle breeds.

Finite-size effects in transcript sequencing count distribution: its power-law correction necessarily precedes downstream normalization and comparative analysis.

PubMed

Wong, Wing-Cheong; Ng, Hong-Kiat; Tantoso, Erwin; Soong, Richie; Eisenhaber, Frank

2018-02-12

Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip's law, the observed distributions often deviate from a single power-law slope. In hindsight, while power-laws of critical phenomena are derived asymptotically under the conditions of infinite observations, real world observations are finite where the finite-size effects will set in to force a power-law distribution into an exponential decay and consequently, manifests as a curvature (i.e., varying exponent values) in a log-log plot. If transcript abundance is truly power-law distributed, the varying exponent signifies changing mathematical moments (e.g., mean, variance) and creates heteroskedasticity which compromises statistical rigor in analysis. The impact of this deviation from the asymptotic power-law on sequencing count data has never truly been examined and quantified. The anecdotal description of transcript abundance being almost Zipf's law-like distributed can be conceptualized as the imperfect mathematical rendition of the Pareto power-law distribution when subjected to the finite-size effects in the real world; This is regardless of the advancement in sequencing technology since sampling is finite in practice. Our conceptualization agrees well with our empirical analysis of two modern day NGS (Next-generation sequencing) datasets: an in-house generated dilution miRNA study of two gastric cancer cell lines (NUGC3 and AGS) and a publicly available spike-in miRNA data; Firstly, the finite-size effects causes the deviations of sequencing count data from Zipf's law and issues of reproducibility in sequencing experiments. Secondly, it manifests as heteroskedasticity among experimental replicates to bring about statistical woes. Surprisingly, a straightforward power-law correction that restores the distribution distortion to a single exponent value can dramatically reduce data heteroskedasticity to invoke an instant increase in

On splice site prediction using weight array models: a comparison of smoothing techniques

NASA Astrophysics Data System (ADS)

Taher, Leila; Meinicke, Peter; Morgenstern, Burkhard

2007-11-01

In most eukaryotic genes, protein-coding exons are separated by non-coding introns which are removed from the primary transcript by a process called "splicing". The positions where introns are cut and exons are spliced together are called "splice sites". Thus, computational prediction of splice sites is crucial for gene finding in eukaryotes. Weight array models are a powerful probabilistic approach to splice site detection. Parameters for these models are usually derived from m-tuple frequencies in trusted training data and subsequently smoothed to avoid zero probabilities. In this study we compare three different ways of parameter estimation for m-tuple frequencies, namely (a) non-smoothed probability estimation, (b) standard pseudo counts and (c) a Gaussian smoothing procedure that we recently developed.

Empowering Provenance in Data Integration

NASA Astrophysics Data System (ADS)

Kondylakis, Haridimos; Doerr, Martin; Plexousakis, Dimitris

The provenance of data has recently been recognized as central to the trust one places in data. This paper presents a novel framework in order to empower provenance in a mediator based data integration system. We use a simple mapping language for mapping schema constructs, between an ontology and relational sources, capable to carry provenance information. This language extends the traditional data exchange setting by translating our mapping specifications into source-to-target tuple generating dependencies (s-t tgds). Then we define formally the provenance information we want to retrieve i.e. annotation, source and tuple provenance. We provide three algorithms to retrieve provenance information using information stored on the mappings and the sources. We show the feasibility of our solution and the advantages of our framework.

Analysis of the conduction mechanism and dielectric properties of N, N', N" tris(4-methylphenyl)phosphoric triamide

NASA Astrophysics Data System (ADS)

Ali, H. A. M.

2016-03-01

The structure for the powder of N,N', N"-tris(4-methylphenyl)phosphoric triamide, TMP-TA, was characterized using X-ray diffraction (XRD) and differential thermal analysis (DTA) techniques. The ac conductivity and dielectric properties were measured in the frequency range of 42-105 Hz for the bulk TMP-TA in a pellet form at different temperatures. The frequency dependence of ac conductivity was expressed by a Jonscher's universal power law. The frequency exponent (s) was determined from the fitting of experimental data of ac conductivity. The correlated barrier hopping (CBH) model was found to be responsible for the ac conduction mechanism in TMP-TA. The activation energy was calculated from the temperature dependence of ac conductivity. The values of the density of states at the Fermi level were determined for different frequencies. The components of the electric modulus (M' and M") were calculated and used to estimate the relaxation time.

Purification and thermal analysis of perfluoro-n-alkanoic acids.

PubMed

Tsuji, Minami; Inoue, Tohru; Shibata, Osamu

2008-01-15

Purification of perfluoro-n-alkanoic acids (C(n)F(2n+1)COOH, n=7, 9, 11, 13, 15 and 17) was made by repeated recrystallizations from n-hexane/acetone mixed solvent, and their purity was found to be more than 99.5% by GC-MS, NMR, and elemental analysis. The thermal behaviors such as melting point and enthalpy change of fusion were investigated using differential scanning calorimetry (DSC). The melting point monotonously increased with increasing carbon number (n) of the acids, while the enthalpy change showed irregularity at n=14. The crystal structure of these acids was found to be dependent upon solvent used for recrystallization; that is, the acids recrystallized from the above solvent becomes more stable energetically, indicating their higher enthalpy change of fusion than that of the solidified acids from fused ones. The solid state was also found to vary depending upon the thermal history, indicating that a few crystal structures of the solid state are quite similar energetically. The melting points (T(m)) of perfluoro-n-alkanoic acids are higher than those of corresponding n-alkanoic acids, and the difference in T(m) increases with increasing carbon number in the acids.

The digital history of the anglophone vocabulary of psychology: An exploration using Zipfian methods.

PubMed

Benjafield, John G

2016-05-01

The digital humanities are being applied with increasing frequency to the analysis of historically important texts. In this study, the methods of G. K. Zipf are used to explore the digital history of the vocabulary of psychology. Zipf studied a great many phenomena, from word frequencies to city sizes, showing that they tend to have a characteristic distribution in which there are a few cases that occur very frequently and many more cases that occur very infrequently. We find that the number of new words and word senses that writers contribute to the vocabulary of psychology have such a Zipfian distribution. Moreover, those who make the most contributions, such as William James, tend also to invent new metaphorical senses of words rather than new words. By contrast, those who make the fewest contributions tend to invent entirely new words. The use of metaphor makes a text easier for a reader to understand. While the use of new words requires more effort on the part of the reader, it may lead to more precise understanding than does metaphor. On average, new words and word senses become a part of psychology's vocabulary in the time leading up to World War I, suggesting that psychology was "finding its language" (Danziger, 1997) during this period. (c) 2016 APA, all rights reserved).

Theoretical analysis of AlGaN/GaN resonant tunnelling diodes with step heterojunctions spacer and sub-quantum well

NASA Astrophysics Data System (ADS)

Liu, Y.; Gao, B.; Gong, M.

2017-06-01

In this paper, we proposed to use step heterojunctions emitter spacer (SHES) and InGaN sub-quantum well in AlGaN/GaN/AlGaN double barrier resonant tunnelling diodes (RTDs). Theoretical analysis of RTD with SHES and InGaN sub-quantum well was presented, which indicated that the negative differential resistance (NDR) characteristic was improved. And the simulation results, peak current density JP=82.67 mA/μm2, the peak-to-valley current ratio PVCR=3.38, and intrinsic negative differential resistance RN=-0.147Ω at room temperature, verified the improvement of NDR characteristic brought about by SHES and InGaN sub-quantum well. Both the theoretical analysis and simulation results showed that the device performance, especially the average oscillator output power presented great improvement and reached 2.77mW/μm2 magnitude. And the resistive cut-off frequency would benefit a lot from the relatively small RN as well. Our works provide an important alternative to the current approaches in designing new structure GaN based RTD for practical high frequency and high power applications.

Inferring Human Activity in Mobile Devices by Computing Multiple Contexts.

PubMed

Chen, Ruizhi; Chu, Tianxing; Liu, Keqiang; Liu, Jingbin; Chen, Yuwei

2015-08-28

This paper introduces a framework for inferring human activities in mobile devices by computing spatial contexts, temporal contexts, spatiotemporal contexts, and user contexts. A spatial context is a significant location that is defined as a geofence, which can be a node associated with a circle, or a polygon; a temporal context contains time-related information that can be e.g., a local time tag, a time difference between geographical locations, or a timespan; a spatiotemporal context is defined as a dwelling length at a particular spatial context; and a user context includes user-related information that can be the user's mobility contexts, environmental contexts, psychological contexts or social contexts. Using the measurements of the built-in sensors and radio signals in mobile devices, we can snapshot a contextual tuple for every second including aforementioned contexts. Giving a contextual tuple, the framework evaluates the posteriori probability of each candidate activity in real-time using a Naïve Bayes classifier. A large dataset containing 710,436 contextual tuples has been recorded for one week from an experiment carried out at Texas A&M University Corpus Christi with three participants. The test results demonstrate that the multi-context solution significantly outperforms the spatial-context-only solution. A classification accuracy of 61.7% is achieved for the spatial-context-only solution, while 88.8% is achieved for the multi-context solution.

Understanding N2O sources and sinks with laser based isotopic analysis

NASA Astrophysics Data System (ADS)

Mohn, Joachim; Harris, Eliza; Tuzson, Béla; Emmenegger, Lukas

2015-04-01

Nitrous oxide (N2O) is a potent greenhouse gas and the strongest ozone-destroying substance. The main emissions of N2O are linked to different microbial processes, therefore the sources are disperse and highly variable, complicating the development of effective mitigation strategies. Isotopic measurements have great potential to unravel spatial and temporal variations in sources, sinks and chemistry of N2O. Recent developments in quantum cascade laser spectroscopy (QCLAS) [1] allow both the intermolecular distribution of 15N substitutions ('site preference'; 15N14N16O versus 14N15N16O) and the oxygen isotopic composition (d18O) of N2O to be measured in real-time and at high precision of <0.2 ‰ [2]. Additionally, N2O isotopic analysis by QCLAS has demonstrated excellent compatibility to the standard technique isotope-ratio mass-spectrometry [3]. In a number of laboratory and pilot plant studies we investigated the isotopic signature of distinct microbial and abiotic N2O production and consumption pathways in soil and aqueous solution [e.g. 4]. Specific pathways were favoured by selection of the nitrogen substrates and process conditions and their isotopic signatures identified by real-time laser spectroscopic analysis. Results from our laboratory studies are in accordance with pure culture experiments and can therefore be applied to other ecosystems. Recently, high precision isotopic analysis at ambient N2O is also feasible by combining laser spectroscopy with automated preconcentration [5]. The field deployment was demonstrated by real-time monitoring isotopic composition of N2O emissions from an intensively managed grassland in central Switzerland for three months. The responses of the N2O isotopic signatures were analysed with respect to management events and weather influences [2]. In a follow-up project we intend to combine real-time N2O isotopic analysis at a tall tower in central Switzerland with atmospheric transport simulations and a biogeochemical model

Languages cool as they expand: Allometric scaling and the decreasing need for new words

NASA Astrophysics Data System (ADS)

Petersen, Alexander M.; Tenenbaum, Joel N.; Havlin, Shlomo; Stanley, H. Eugene; Perc, Matjaž

2012-12-01

We analyze the occurrence frequencies of over 15 million words recorded in millions of books published during the past two centuries in seven different languages. For all languages and chronological subsets of the data we confirm that two scaling regimes characterize the word frequency distributions, with only the more common words obeying the classic Zipf law. Using corpora of unprecedented size, we test the allometric scaling relation between the corpus size and the vocabulary size of growing languages to demonstrate a decreasing marginal need for new words, a feature that is likely related to the underlying correlations between words. We calculate the annual growth fluctuations of word use which has a decreasing trend as the corpus size increases, indicating a slowdown in linguistic evolution following language expansion. This ``cooling pattern'' forms the basis of a third statistical regularity, which unlike the Zipf and the Heaps law, is dynamical in nature.

Capital death in the world market

NASA Astrophysics Data System (ADS)

Avakian, Adam; Podobnik, Boris; Piskor, Manuela; Stanley, H. Eugene

2014-03-01

We study the gross domestic product (GDP) per capita together with the market capitalization (MCAP) per capita as two indicators of the effect of globalization. We find that g, the GDP per capita, as a function of m, the MCAP per capita, follows a power law with average exponent close to 1/3. In addition, the Zipf ranking approach confirms that the m for countries with initially lower values of m tends to grow more rapidly than for countries with initially larger values of m. If the trends over the past 20 years continue to hold in the future, then the Zipf ranking approach leads to the prediction that in about 50 years, all countries participating in globalization will have comparable values of their MCAP per capita. We call this economic state "capital death," in analogy to the physics state of "heat death" predicted by thermodynamic arguments.

The Non-Gaussian Nature of Bibliometric and Scientometric Distributions: A New Approach to Interpretation.

ERIC Educational Resources Information Center

Ivancheva, Ludmila E.

2001-01-01

Discusses the concept of the hyperbolic or skew distribution as a universal statistical law in information science and socioeconomic studies. Topics include Zipf's law; Stankov's universal law; non-Gaussian distributions; and why most bibliometric and scientometric laws reveal characters of non-Gaussian distribution. (Author/LRW)

CFD Analysis of Emissions for a Candidate N+3 Combustor

NASA Technical Reports Server (NTRS)

Ajmani, Kumud

2015-01-01

An effort was undertaken to analyze the performance of a model Lean-Direct Injection (LDI) combustor designed to meet emissions and performance goals for NASA's N+3 program. Computational predictions of Emissions Index (EINOx) and combustor exit temperature were obtained for operation at typical power conditions expected of a small-core, high pressure-ratio (greater than 50), high T3 inlet temperature (greater than 950K) N+3 combustor. Reacting-flow computations were performed with the National Combustion Code (NCC) for a model N+3 LDI combustor, which consisted of a nine-element LDI flame-tube derived from a previous generation (N+2) thirteen-element LDI design. A consistent approach to mesh-optimization, spraymodeling and kinetics-modeling was used, in order to leverage the lessons learned from previous N+2 flame-tube analysis with the NCC. The NCC predictions for the current, non-optimized N+3 combustor operating indicated a 74% increase in NOx emissions as compared to that of the emissions-optimized, parent N+2 LDI combustor.

CFD Analysis of Emissions for a Candidate N+3 Combustor

NASA Technical Reports Server (NTRS)

Ajmani, Kumud

2015-01-01

An effort was undertaken to analyze the performance of a model Lean-Direct Injection (LDI) combustor designed to meet emissions and performance goals for NASA's N+3 program. Computational predictions of Emissions Index (EINOx) and combustor exit temperature were obtained for operation at typical power conditions expected of a small-core, high pressure-ratio (greater than 50), high T3 inlet temperature (greater than 950K) N+3 combustor. Reacting-flow computations were performed with the National Combustion Code (NCC) for a model N+3 LDI combustor, which consisted of a nine-element LDI flame-tube derived from a previous generation (N+2) thirteen-element LDI design. A consistent approach to mesh-optimization, spray-modeling and kinetics-modeling was used, in order to leverage the lessons learned from previous N+2 flame-tube analysis with the NCC. The NCC predictions for the current, non-optimized N+3 combustor operating indicated a 74% increase in NOx emissions as compared to that of the emissions-optimized, parent N+2 LDI combustor.

Isotropic probability measures in infinite dimensional spaces: Inverse problems/prior information/stochastic inversion

NASA Technical Reports Server (NTRS)

Backus, George

1987-01-01

Let R be the real numbers, R(n) the linear space of all real n-tuples, and R(infinity) the linear space of all infinite real sequences x = (x sub 1, x sub 2,...). Let P sub n :R(infinity) approaches R(n) be the projection operator with P sub n (x) = (x sub 1,...,x sub n). Let p(infinity) be a probability measure on the smallest sigma-ring of subsets of R(infinity) which includes all of the cylinder sets P sub n(-1) (B sub n), where B sub n is an arbitrary Borel subset of R(n). Let p sub n be the marginal distribution of p(infinity) on R(n), so p sub n(B sub n) = p(infinity)(P sub n to the -1(B sub n)) for each B sub n. A measure on R(n) is isotropic if it is invariant under all orthogonal transformations of R(n). All members of the set of all isotropic probability distributions on R(n) are described. The result calls into question both stochastic inversion and Bayesian inference, as currently used in many geophysical inverse problems.

Analysis of N-acetylaminosugars by CE: a comparative derivatization study.

PubMed

Rustighi, Isabella; Campa, Cristiana; Rossi, Marco; Semeraro, Sabrina; Vetere, Amedeo; Gamini, Amelia

2009-08-01

N-linked or O-linked glycans derived from glycoprotein processing carry, an N-acetylglucosamine or an N-acetylgalactosamine respectively, at their reducing termini. The presence of the N-acetylamino group on C-2 of reducing sugar residues has been reported to hamper the derivatization reaction with a chromophore at the anomeric centre. In this paper N-acetyllactosamine, N-acetylglucosamine, N-acetylgalactosamine and several other neutral monosaccharides are coupled to three different dyes (4-aminobenzonitrile, 2-aminopyridine, 2-aminobenzoic acid (2-AA)) by reductive amination and analysed by CE with UV detection. The 2-AA derivatives showed the lowest concentration detection limits, varying approximately in the 2-3 muM range for the saccharides tested including the N-acetamido ones. The possibility to separate and detect with the same sensitivity ten 2-AA-labelled monosaccharides mainly found in mammalian or plant glycoproteins in a single CE run is highlighted. The analysis has been carried out in less than 25 min using the borate-complexation method in CZE mode. The influence of the strength of the acid used as catalyst in the chemical modification of the sugars with 2-AA is also shortly addressed.

Isotropic probability measures in infinite-dimensional spaces

NASA Technical Reports Server (NTRS)

Backus, George

1987-01-01

Let R be the real numbers, R(n) the linear space of all real n-tuples, and R(infinity) the linear space of all infinite real sequences x = (x sub 1, x sub 2,...). Let P sub in :R(infinity) approaches R(n) be the projection operator with P sub n (x) = (x sub 1,...,x sub n). Let p(infinity) be a probability measure on the smallest sigma-ring of subsets of R(infinity) which includes all of the cylinder sets P sub n(-1) (B sub n), where B sub n is an arbitrary Borel subset of R(n). Let p sub n be the marginal distribution of p(infinity) on R(n), so p sub n(B sub n) = p(infinity) (P sub n to the -1 (B sub n)) for each B sub n. A measure on R(n) is isotropic if it is invariant under all orthogonal transformations of R(n). All members of the set of all isotropic probability distributions on R(n) are described. The result calls into question both stochastic inversion and Bayesian inference, as currently used in many geophysical inverse problems.

Quantitative analysis of immobilized penicillinase using enzyme-modified AlGaN/GaN field-effect transistors.

PubMed

Müntze, Gesche Mareike; Baur, Barbara; Schäfer, Wladimir; Sasse, Alexander; Howgate, John; Röth, Kai; Eickhoff, Martin

2015-02-15

Penicillinase-modified AlGaN/GaN field-effect transistors (PenFETs) are utilized to systematically investigate the covalently immobilized enzyme penicillinase under different experimental conditions. We demonstrate quantitative evaluation of covalently immobilized penicillinase layers on pH-sensitive field-effect transistors (FETs) using an analytical kinetic PenFET model. This kinetic model is explicitly suited for devices with thin enzyme layers that are not diffusion-limited, as it is the case for the PenFETs discussed here. By means of the kinetic model it was possible to extract the Michaelis constant of covalently immobilized penicillinase as well as relative transport coefficients of the different species associated with the enzymatic reaction which, exempli gratia, give information about the permeability of the enzymatic layer. Based on this analysis we quantify the reproducibility and the stability of the analyzed PenFETs over the course of 33 days as well as the influence of pH and buffer concentration on the properties of the enzymatic layer. Thereby the stability measurements reveal a Michalis constant KM of (67 ± 13)μM while the chronological development of the relative transport coefficients suggests a detachment of physisorbed penicillinase during the first two weeks since production. Our results show that AlGaN/GaN PenFETs prepared by covalent immobilization of a penicillinase enzyme layer present a powerful tool for quantitative analysis of enzyme functionality. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast *

PubMed Central

Clauser, Karl R.; Shen, Hongying; Kamer, Kimberli J.; Wells, James A.

2017-01-01

The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by an N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here, we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that whereas presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved, including a length of ∼20–60 amino acids, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-terminus of mature proteins that follow the N-end rule from bacteria. As in yeast, ∼80% of mouse presequence cleavage sites match canonical motifs for three mitochondrial peptidases (MPP, Icp55, and Oct1), whereas the remainder do not match any known peptidase motifs. We show that mature mitochondrial proteins often exist with a spectrum of N-termini, consistent with a model of multiple cleavage events by MPP and Icp55. In addition to analysis of canonical targeting presequences, our N-terminal dataset allows the exploration of other cleavage events and provides support for polypeptide cleavage into two distinct enzymes (Hsd17b4), protein cleavages key for signaling (Oma1, Opa1, Htra2, Mavs, and Bcs2l13), and in several cases suggests novel protein isoforms (Scp2, Acadm, Adck3, Hsdl2, Dlst, and Ogdh). We present an integrated catalog of mammalian mitochondrial N-termini that can be used as a community resource to investigate individual proteins, to elucidate mechanisms of mammalian mitochondrial processing, and to allow researchers to engineer tags distally to the presequence cleavage. PMID:28122942

Languages cool as they expand: Allometric scaling and the decreasing need for new words

PubMed Central

Petersen, Alexander M.; Tenenbaum, Joel N.; Havlin, Shlomo; Stanley, H. Eugene; Perc, Matjaž

2012-01-01

We analyze the occurrence frequencies of over 15 million words recorded in millions of books published during the past two centuries in seven different languages. For all languages and chronological subsets of the data we confirm that two scaling regimes characterize the word frequency distributions, with only the more common words obeying the classic Zipf law. Using corpora of unprecedented size, we test the allometric scaling relation between the corpus size and the vocabulary size of growing languages to demonstrate a decreasing marginal need for new words, a feature that is likely related to the underlying correlations between words. We calculate the annual growth fluctuations of word use which has a decreasing trend as the corpus size increases, indicating a slowdown in linguistic evolution following language expansion. This “cooling pattern” forms the basis of a third statistical regularity, which unlike the Zipf and the Heaps law, is dynamical in nature. PMID:23230508

Modeling species-abundance relationships in multi-species collections

USGS Publications Warehouse

Peng, S.; Yin, Z.; Ren, H.; Guo, Q.

2003-01-01

Species-abundance relationship is one of the most fundamental aspects of community ecology. Since Motomura first developed the geometric series model to describe the feature of community structure, ecologists have developed many other models to fit the species-abundance data in communities. These models can be classified into empirical and theoretical ones, including (1) statistical models, i.e., negative binomial distribution (and its extension), log-series distribution (and its extension), geometric distribution, lognormal distribution, Poisson-lognormal distribution, (2) niche models, i.e., geometric series, broken stick, overlapping niche, particulate niche, random assortment, dominance pre-emption, dominance decay, random fraction, weighted random fraction, composite niche, Zipf or Zipf-Mandelbrot model, and (3) dynamic models describing community dynamics and restrictive function of environment on community. These models have different characteristics and fit species-abundance data in various communities or collections. Among them, log-series distribution, lognormal distribution, geometric series, and broken stick model have been most widely used.

Definition of (so MIScalled) ''Complexity'' as UTTER-SIMPLICITY!!! Versus Deviations From it as Complicatedness-Measure

NASA Astrophysics Data System (ADS)

Young, F.; Siegel, Edward Carl-Ludwig

2011-03-01

(so MIScalled) "complexity" with INHERENT BOTH SCALE-Invariance Symmetry-RESTORING, AND 1 / w (1.000..) "pink" Zipf-law Archimedes-HYPERBOLICITY INEVITABILITY power-spectrum power-law decay algebraicity. Their CONNECTION is via simple-calculus SCALE-Invariance Symmetry-RESTORING logarithm-function derivative: (d/ d ω) ln(ω) = 1 / ω , i.e. (d/ d ω) [SCALE-Invariance Symmetry-RESTORING](ω) = 1/ ω . Via Noether-theorem continuous-symmetries relation to conservation-laws: (d/ d ω) [inter-scale 4-current 4-div-ergence} = 0](ω) = 1 / ω . Hence (so MIScalled) "complexity" is information inter-scale conservation, in agreement with Anderson-Mandell [Fractals of Brain/Mind, G. Stamov ed.(1994)] experimental-psychology!!!], i.e. (so MIScalled) "complexity" is UTTER-SIMPLICITY!!! Versus COMPLICATEDNESS either PLUS (Additive) VS. TIMES (Multiplicative) COMPLICATIONS of various system-specifics. COMPLICATEDNESS-MEASURE DEVIATIONS FROM complexity's UTTER-SIMPLICITY!!!: EITHER [SCALE-Invariance Symmetry-BREAKING] MINUS [SCALE-Invariance Symmetry-RESTORING] via power-spectrum power-law algebraicity decays DIFFERENCES: ["red"-Pareto] MINUS ["pink"-Zipf Archimedes-HYPERBOLICITY INEVITABILITY]!!!

Evaluation on Collaborative Satisfaction for Project Management Team in Integrated Project Delivery Mode

NASA Astrophysics Data System (ADS)

Zhang, L.; Li, Y.; Wu, Q.

2013-05-01

Integrated Project Delivery (IPD) is a newly-developed project delivery approach for construction projects, and the level of collaboration of project management team is crucial to the success of its implementation. Existing research has shown that collaborative satisfaction is one of the key indicators of team collaboration. By reviewing the literature on team collaborative satisfaction and taking into consideration the characteristics of IPD projects, this paper summarizes the factors that influence collaborative satisfaction of IPD project management team. Based on these factors, this research develops a fuzzy linguistic method to effectively evaluate the level of team collaborative satisfaction, in which the authors adopted the 2-tuple linguistic variables and 2-tuple linguistic hybrid average operators to enhance the objectivity and accuracy of the evaluation. The paper demonstrates the practicality and effectiveness of the method through carrying out a case study with the method.

Modeling N Cycling during Succession after Forest Disturbance: an Analysis of N Mining and Retention Hypothesis

NASA Astrophysics Data System (ADS)

Zhou, Z.; Ollinger, S. V.; Ouimette, A.; Lovett, G. M.; Fuss, C. B.; Goodale, C. L.

2017-12-01

Dissolved inorganic nitrogen losses at the Hubbard Brook Experimental Forest (HBEF), New Hampshire, USA, have declined in recent decades, a pattern that counters expectations based on prevailing theory. An unbalanced ecosystem nitrogen (N) budget implies there is a missing component for N sink. Hypotheses to explain this discrepancy include increasing rates of denitrification and accumulation of N in mineral soil pools following N mining by plants. Here, we conducted a modeling analysis fused with field measurements of N cycling, specifically examining the hypothesis relevant to N mining and retention in mineral soils. We included simplified representations of both mechanisms, N mining and retention, in a revised ecosystem process model, PnET-SOM, to evaluate the dynamics of N cycling during succession after forest disturbance at the HBEF. The predicted N mining during the early succession was regulated by a metric representing a potential demand of extra soil N for large wood growth. The accumulation of nitrate in mineral soil pools was a function of the net aboveground biomass accumulation and soil N availability and parameterized based on field 15N tracer incubation data. The predicted patterns of forest N dynamics were consistent with observations. The addition of the new algorithms also improved the predicted DIN export in stream water with an R squared of 0.35 (P<0.01) aganist observations. Predicted mining processes had an average rate of 7.4 kgNha-1yr-1 and Predicted rates of N retention processes were 5.2 kgNha-1yr-1, both of which were in line with estimates only based on field data. The predicted trend of low DIN export could continue for another 70 years to pay back the mined N in mineral soils. Predicted ecosystem N balance showed that N gas loss could account for 14-46% of the total N deposition, the soil mining about 103% during the early succession, and soil retention about 35% at the current forest stage at the HBEF.

In situ X-ray diffraction analysis of (CF x) n batteries: signal extraction by multivariate analysis

DOE PAGES

Rodriguez, Mark A.; Keenan, Michael R.; Nagasubramanian, Ganesan

2007-11-10

In this study, (CF x) n cathode reaction during discharge has been investigated using in situ X-ray diffraction (XRD). Mathematical treatment of the in situ XRD data set was performed using multivariate curve resolution with alternating least squares (MCR–ALS), a technique of multivariate analysis. MCR–ALS analysis successfully separated the relatively weak XRD signal intensity due to the chemical reaction from the other inert cell component signals. The resulting dynamic reaction component revealed the loss of (CF x) n cathode signal together with the simultaneous appearance of LiF by-product intensity. Careful examination of the XRD data set revealed an additional dynamicmore » component which may be associated with the formation of an intermediate compound during the discharge process.« less

Sensitive and Structure-Informative N-Glycosylation Analysis by MALDI-MS; Ionization, Fragmentation, and Derivatization

PubMed Central

Nishikaze, Takashi

2017-01-01

Mass spectrometry (MS) has become an indispensable tool for analyzing post translational modifications of proteins, including N-glycosylated molecules. Because most glycosylation sites carry a multitude of glycans, referred to as “glycoforms,” the purpose of an N-glycosylation analysis is glycoform profiling and glycosylation site mapping. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has unique characteristics that are suited for the sensitive analysis of N-glycosylated products. However, the analysis is often hampered by the inherent physico-chemical properties of N-glycans. Glycans are highly hydrophilic in nature, and therefore tend to show low ion yields in both positive- and negative-ion modes. The labile nature and complicated branched structures involving various linkage isomers make structural characterization difficult. This review focuses on MALDI-MS-based approaches for enhancing analytical performance in N-glycosylation research. In particular, the following three topics are emphasized: (1) Labeling for enhancing the ion yields of glycans and glycopeptides, (2) Negative-ion fragmentation for less ambiguous elucidation of the branched structure of N-glycans, (3) Derivatization for the stabilization and linkage isomer discrimination of sialic acid residues. PMID:28794918

Targeted mass spectrometric analysis of N-terminally truncated isoforms generated via alternative translation initiation.

PubMed

Kobayashi, Ryuji; Patenia, Rebecca; Ashizawa, Satoshi; Vykoukal, Jody

2009-07-21

Alternative translation initiation is a mechanism whereby functionally altered proteins are produced from a single mRNA. Internal initiation of translation generates N-terminally truncated protein isoforms, but such isoforms observed in immunoblot analysis are often overlooked or dismissed as degradation products. We identified an N-terminally truncated isoform of human Dok-1 with N-terminal acetylation as seen in the wild-type. This Dok-1 isoform exhibited distinct perinuclear localization whereas the wild-type protein was distributed throughout the cytoplasm. Targeted analysis of blocked N-terminal peptides provides rapid identification of protein isoforms and could be widely applied for the general evaluation of perplexing immunoblot bands.

Tuple spaces in hardware for accelerated implicit routing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker, Zachary Kent; Tripp, Justin

2010-12-01

Organizing and optimizing data objects on networks with support for data migration and failing nodes is a complicated problem to handle as systems grow. The goal of this work is to demonstrate that high levels of speedup can be achieved by moving responsibility for finding, fetching, and staging data into an FPGA-based network card. We present a system for implicit routing of data via FPGA-based network cards. In this system, data structures are requested by name, and the network of FPGAs finds the data within the network and relays the structure to the requester. This is acheived through successive examinationmore » of hardware hash tables implemented in the FPGA. By avoiding software stacks between nodes, the data is quickly fetched entirely through FPGA-FPGA interaction. The performance of this system is orders of magnitude faster than software implementations due to the improved speed of the hash tables and lowered latency between the network nodes.« less

Impact of gate engineering in enhancement mode n++GaN/InAlN/AlN/GaN HEMTs

NASA Astrophysics Data System (ADS)

Adak, Sarosij; Swain, Sanjit Kumar; Rahaman, Hafizur; Sarkar, Chandan Kumar

2016-12-01

This paper illustrate the effect of gate material engineering on the performance of enhancement mode n++GaN/InAlN/AlN/GaN high electron mobility transistors (HEMTs). A comparative analysis of key device parameters is discussed for the Triple Material Gate (TMG), Dual Material Gate (DMG) and the Single Material Gate (SMG) structure HEMTs by considering the same device dimensions. The simulation results shows that an significant improvement is noticed in the key analysis parameters such as drain current (Id), transconductance (gm), cut off frequency (fT), RF current gain, maximum cut off frequency (fmax) and RF power gain of the gate material engineered devices with respect to SMG normally off n++GaN/InAlN/AlN/GaN HEMTs. This improvement is due to the existence of the perceivable step in the surface potential along the channel which successfully screens the drain potential variation in the source side of the channel for the gate engineering devices. The analysis suggested that the proposed TMG and DMG engineered structure enhancement mode n++GaN/InAlN/AlN/GaN HEMTs can be considered as a potential device for future high speed, microwave and digital application.

Rescuing Computerized Testing by Breaking Zipf's Law.

ERIC Educational Resources Information Center

Wainer, Howard

2000-01-01

Suggests that because of the nonlinear relationship between item usage and item security, the problems of test security posed by continuous administration of standardized tests cannot be resolved merely by increasing the size of the item pool. Offers alternative strategies to overcome these problems, distributing test items so as to avoid the…

Simulation based comparative analysis of photoresponse in front- and back-illuminated GaN P-I-N ultraviolet photodetectors

NASA Astrophysics Data System (ADS)

Wang, Jun; Guo, Jin; Xie, Feng; Wang, Guosheng; Wu, Haoran; Song, Man; Yi, Yuanyuan

2016-10-01

This paper presents the comparative analysis of influence of doping level and doping profile of the active region on zero bias photoresponse characteristics of GaN-based p-i-n ultraviolet (UV) photodetectors operating at front- and back-illuminated. A two dimensional physically-based computer simulation of GaN-based p-i-n UV photodetectors is presented. We implemented GaN material properties and physical models taken from the literature. It is shown that absorption layer doping profile has notable impacts on the photoresponse of the device. Especially, the effect of doping concentration and distribution of the absorption layer on photoresponse is discussed in detail. In the case of front illumination, comparative to uniform n-type doping, the device with n-type Gaussian doping profiles at absorption layer has higher responsivity. Comparative to front illumination, back illuminated detector with p-type doping profiles at absorption layer has higher maximum photoresponse, while the Gaussian doping profiles have a weaker ability to enhance the device responsivity. It is demonstrated that electric field distribution, mobility degradation, and recombinations are jointly responsible for the variance of photoresponse. Our work enriches the understanding and utilization of GaN based p-i-n UV photodetectors.

Global site-specific analysis of glycoprotein N-glycan processing.

PubMed

Cao, Liwei; Diedrich, Jolene K; Ma, Yuanhui; Wang, Nianshuang; Pauthner, Matthias; Park, Sung-Kyu Robin; Delahunty, Claire M; McLellan, Jason S; Burton, Dennis R; Yates, John R; Paulson, James C

2018-06-01

N-glycans contribute to the folding, stability and functions of the proteins they decorate. They are produced by transfer of the glycan precursor to the sequon Asn-X-Thr/Ser, followed by enzymatic trimming to a high-mannose-type core and sequential addition of monosaccharides to generate complex-type and hybrid glycans. This process, mediated by the concerted action of multiple enzymes, produces a mixture of related glycoforms at each glycosite, making analysis of glycosylation difficult. To address this analytical challenge, we developed a robust semiquantitative mass spectrometry (MS)-based method that determines the degree of glycan occupancy at each glycosite and the proportion of N-glycans processed from high-mannose type to complex type. It is applicable to virtually any glycoprotein, and a complete analysis can be conducted with 30 μg of protein. Here, we provide a detailed description of the method that includes procedures for (i) proteolytic digestion of glycoprotein(s) with specific and nonspecific proteases; (ii) denaturation of proteases by heating; (iii) sequential treatment of the glycopeptide mixture with two endoglycosidases, Endo H and PNGase F, to create unique mass signatures for the three glycosylation states; (iv) LC-MS/MS analysis; and (v) data analysis for identification and quantitation of peptides for the three glycosylation states. Full coverage of site-specific glycosylation of glycoproteins is achieved, with up to thousands of high-confidence spectra hits for each glycosite. The protocol can be performed by an experienced technician or student/postdoc with basic skills for proteomics experiments and takes ∼7 d to complete.

Quantum catastrophes: a case study

NASA Astrophysics Data System (ADS)

Znojil, Miloslav

2012-11-01

The bound-state spectrum of a Hamiltonian H is assumed real in a non-empty domain D of physical values of parameters. This means that for these parameters, H may be called crypto-Hermitian, i.e. made Hermitian via an ad hoc choice of the inner product in the physical Hilbert space of quantum bound states (i.e. via an ad hoc construction of the operator Θ called the metric). The name quantum catastrophe is then assigned to the N-tuple-exceptional-point crossing, i.e. to the scenario in which we leave the domain D along such a path that at the boundary of D, an N-plet of bound-state energies degenerates and, subsequently, complexifies. At any fixed N ⩾ 2, this process is simulated via an N × N benchmark effective matrix Hamiltonian H. It is being assigned such a closed-form metric which is made unique via an N-extrapolation-friendliness requirement. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Quantum physics with non-Hermitian operators’.

Whole-lesion apparent diffusion coefficient histogram analysis: significance in T and N staging of gastric cancers.

PubMed

Liu, Song; Zhang, Yujuan; Chen, Ling; Guan, Wenxian; Guan, Yue; Ge, Yun; He, Jian; Zhou, Zhengyang

2017-10-02

Whole-lesion apparent diffusion coefficient (ADC) histogram analysis has been introduced and proved effective in assessment of multiple tumors. However, the application of whole-volume ADC histogram analysis in gastrointestinal tumors has just started and never been reported in T and N staging of gastric cancers. Eighty patients with pathologically confirmed gastric carcinomas underwent diffusion weighted (DW) magnetic resonance imaging before surgery prospectively. Whole-lesion ADC histogram analysis was performed by two radiologists independently. The differences of ADC histogram parameters among different T and N stages were compared with independent-samples Kruskal-Wallis test. Receiver operating characteristic (ROC) analysis was performed to evaluate the performance of ADC histogram parameters in differentiating particular T or N stages of gastric cancers. There were significant differences of all the ADC histogram parameters for gastric cancers at different T (except ADC min and ADC max ) and N (except ADC max ) stages. Most ADC histogram parameters differed significantly between T1 vs T3, T1 vs T4, T2 vs T4, N0 vs N1, N0 vs N3, and some parameters (ADC 5% , ADC 10% , ADC min ) differed significantly between N0 vs N2, N2 vs N3 (all P < 0.05). Most parameters except ADC max performed well in differentiating different T and N stages of gastric cancers. Especially for identifying patients with and without lymph node metastasis, the ADC 10% yielded the largest area under the ROC curve of 0.794 (95% confidence interval, 0.677-0.911). All the parameters except ADC max showed excellent inter-observer agreement with intra-class correlation coefficients higher than 0.800. Whole-volume ADC histogram parameters held great potential in differentiating different T and N stages of gastric cancers preoperatively.

Cl⋯N weak interactions. Conformational analysis of imidazol-2-ylum heterocycles bearing N-β-chloroethyl and N-vinyl pendant groups

NASA Astrophysics Data System (ADS)

Rodríguez-López, Germán; Montes-Tolentino, Pedro; Sánchez-Ruiz, Sonia; Villaseñor-Granados, Tayde Osvaldo; Flores-Parra, Angelina

2017-11-01

Enantiomerically pure and racemic mixtures of β-chloroethylamines hydrochlorides with one and two stereogenic centres were used to synthesise 1,4-dialkyl-1,3-diimines, which in turn gave place to a series of imidazolium chlorides and tetraphenylborates bearing pendant N-β-chloroethyl substituents (sbnd CHEt-CH2Cl; sbnd CHMe-CHPhCl). Stereoselective dehydrochlorination of imidazolium compounds afforded in good yield the corresponding heterocycles bearing N-vinyl groups (-CEt=CH2; -CMe=CHPh). The volume of the N-substituents provides a steric screening of the cationic ring. The structure of the new compounds was determined by IR, mass spectra, NMR and X-ray diffraction analyses as well as DFT calculations of the optimized geometries. Uncommon stabilising intramolecular Cl⋯N weak interactions are described, together with H⋯Cl and H···π hydrogen bonds. The existence of the non-covalent weak intramolecular bonds was deduced from the X-ray diffraction analysis and confirmed by calculations of the electrostatic potential, electronic density distributions and the maps of the Laplacian functions of the electronic density.

N,N-Dimethyltryptamine and dichloromethane: rearrangement of quaternary ammonium salt product during GC-EI and CI-MS-MS analysis.

PubMed

Brandt, Simon D; Martins, Cláudia P B; Freeman, Sally; Dempster, Nicola; Wainwright, Mark; Riby, Philip G; Alder, John F

2008-05-12

N,N-Dimethyltryptamine (DMT) 1 is a simple tryptamine derivative with powerful psychoactive properties. It is abundant in nature and easily accessible through a variety of synthetic routes. Most work-up procedures require the use of organic solvents and halogenated representatives are often employed. DMT was found to be reactive towards dichloromethane, either during work-up or long term storage therein, which led to the formation of the quaternary ammonium salt N-chloromethyl-DMT chloride 2. Analysis of this side-product by gas chromatography ion trap mass spectrometry (GC-MS), both in electron and chemical ionisation tandem MS modes, gave only degradation products. For example, 2 could not be detected but appeared to have rearranged to 3-(2-chloroethyl)indole 3 and 2-methyltetrahydro-beta-carboline 4, whereas HPLC analysis enabled the detection of 2. GC-MS is a standard tool for the fingerprinting of drug products. The identification of a particular synthetic route is based on the analysis of impurities, provided these side products can be established to be route-specific. The in situ detection of both 3 and 4 within a DMT sample may have led to erroneous conclusions with regards to the identification of the synthetic route.

In vivo analysis of NH4+ transport and central N-metabolism of Saccharomyces cerevisiae under aerobic N-limited conditions.

PubMed

Cueto-Rojas, H F; Maleki Seifar, R; Ten Pierick, A; van Helmond, W; Pieterse M, M; Heijnen, J J; Wahl, S A

2016-09-16

Ammonium is the most common N-source for yeast fermentations. Although, its transport and assimilation mechanisms are well documented, there have been only few attempts to measure the in vivo intracellular concentration of ammonium and assess its impact on gene expression. Using an isotope dilution mass spectrometry (IDMS)-based method we were able to measure the intracellular ammonium concentration in N-limited aerobic chemostat cultivations using three different N-sources (ammonium, urea and glutamate) at the same growth rate (0.05 h -1 ). The experimental results suggest that, at this growth rate, a similar concentration of intracellular ammonium, about 3.6 mmol NH 4 + /L IC , is required to supply the reactions in the central N-metabolism independent of the N-source. Based on the experimental results and different assumptions, the vacuolar and cytosolic ammonium concentrations were estimated. Furthermore, we identified a futile cycle caused by NH 3 leakage to the extracellular space, which can cost up to 30% of the ATP production of the cell under N-limited conditions, and a futile redox cycle between reactions Gdh1 and Gdh2. Finally, using shotgun proteomics with labeled reference-relative protein expression, differences between the various environmental conditions were identified and correlated with previously identified N-compound sensing mechanisms. In our work, we study central N-metabolism using quantitative approaches. First, intracellular ammonium was measured under different N-sources. The results suggest that Saccharomyces cerevisiae cells keep a constant NH 4 + concentration (around 3 mmol NH 4 + /L IC ), independent of the applied nitrogen source. We hypothesize that this amount of intracellular ammonium is required to obtain sufficient thermodynamic driving force.Furthermore, our calculations based on thermodynamic analysis of the transport mechanisms of ammonium suggest that ammonium is not equally distributed, indicating a high degree of

Symplocin A, a Linear Peptide from the Bahamian Cyanobacterium Symploca sp. Configurational Analysis of N,N-Dimethylamino Acids by Chiral-Phase HPLC of Naphthacyl Esters†

PubMed Central

Molinski, Tadeusz F.; Reynolds, Kirk A.; Morinaka, Brandon I.

2012-01-01

The absolute stereostructures of the components of symplocin A (3), a new N,N-dimethyl-terminated peptide from the Bahamian cyanobacterium, Symploca sp., were assigned from spectroscopic analysis, including MS and 2D NMR and Marfey’s analysis. The complete absolute configuration of symplocin A, including the unexpected D-configurations of the terminal N,N-dimethylisoleucine and valic acid residues, were assigned by chiral-phase HPLC of the corresponding 2-naphthacyl esters, a highly sensitive, complementary strategy for assignment of N-blocked peptide residues where Marfey’s method is ineffectual, or other methods fall short. Symplocin A exhibited potent activity as an inhibitor of cathepsin E (IC50 300 pM). PMID:22360587

An Efficient Conflict Detection Algorithm for Packet Filters

NASA Astrophysics Data System (ADS)

Lee, Chun-Liang; Lin, Guan-Yu; Chen, Yaw-Chung

Packet classification is essential for supporting advanced network services such as firewalls, quality-of-service (QoS), virtual private networks (VPN), and policy-based routing. The rules that routers use to classify packets are called packet filters. If two or more filters overlap, a conflict occurs and leads to ambiguity in packet classification. This study proposes an algorithm that can efficiently detect and resolve filter conflicts using tuple based search. The time complexity of the proposed algorithm is O(nW+s), and the space complexity is O(nW), where n is the number of filters, W is the number of bits in a header field, and s is the number of conflicts. This study uses the synthetic filter databases generated by ClassBench to evaluate the proposed algorithm. Simulation results show that the proposed algorithm can achieve better performance than existing conflict detection algorithms both in time and space, particularly for databases with large numbers of conflicts.

Strong-coupling analysis of two-dimensional O({ital N}) {sigma} models with {ital N}{le}2 on square, triangular, and honeycomb lattices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campostrini, M.; Pelissetto, A.; Rossi, P.

1996-09-01

The critical behavior of two-dimensional (2D) O({ital N}) {sigma} models with {ital N}{le}2 on square, triangular, and honeycomb lattices is investigated by an analysis of the strong-coupling expansion of the two-point fundamental Green{close_quote}s function {ital G}({ital x}), calculated up to 21st order on the square lattice, 15th order on the triangular lattice, and 30th order on the honeycomb lattice. For {ital N}{lt}2 the critical behavior is of power-law type, and the exponents {gamma} and {nu} extracted from our strong-coupling analysis confirm exact results derived assuming universality with solvable solid-on-solid models. At {ital N}=2, i.e., for the 2D {ital XY} model,more » the results from all lattices considered are consistent with the Kosterlitz-Thouless exponential approach to criticality, characterized by an exponent {sigma}=1/2, and with universality. The value {sigma}=1/2 is confirmed within an uncertainty of few percent. The prediction {eta}=1/4 is also roughly verified. For various values of {ital N}{le}2, we determine some ratios of amplitudes concerning the two-point function {ital G}({ital x}) in the critical limit of the symmetric phase. This analysis shows that the low-momentum behavior of {ital G}({ital x}) in the critical region is essentially Gaussian at all values of {ital N}{le}2. Exact results for the long-distance behavior of {ital G}({ital x}) when {ital N}=1 (Ising model in the strong-coupling phase) confirm this statement. {copyright} {ital 1996 The American Physical Society.}« less

RBS Depth Profiling Analysis of (Ti, Al)N/MoN and CrN/MoN Multilayers.

PubMed

Han, Bin; Wang, Zesong; Devi, Neena; Kondamareddy, K K; Wang, Zhenguo; Li, Na; Zuo, Wenbin; Fu, Dejun; Liu, Chuansheng

2017-12-01

(Ti, Al)N/MoN and CrN/MoN multilayered films were synthesized on Si (100) surface by multi-cathodic arc ion plating system with various bilayer periods. The elemental composition and depth profiling of the films were investigated by Rutherford backscattering spectroscopy (RBS) using 2.42 and 1.52 MeV Li 2+ ion beams and different incident angles (0°, 15°, 37°, and 53°). The microstructures of (Ti, Al)N/MoN multilayered films were evaluated by X-ray diffraction. The multilayer periods and thickness of the multilayered films were characterized by scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HR-TEM) and then compared with RBS results.

Dual element ((15)N/(14)N, (13)C/(12)C) isotope analysis of glyphosate and AMPA by derivatization-gas chromatography isotope ratio mass spectrometry (GC/IRMS) combined with LC/IRMS.

PubMed

Mogusu, Emmanuel O; Wolbert, J Benjamin; Kujawinski, Dorothea M; Jochmann, Maik A; Elsner, Martin

2015-07-01

To assess sources and degradation of the herbicide glyphosate [N-(phosphonomethyl) glycine] and its metabolite AMPA (aminomethylphosphonic acid), concentration measurements are often inconclusive and even (13)C/(12)C analysis alone may give limited information. To advance isotope ratio analysis of an additional element, we present compound-specific (15)N/(14)N analysis of glyphosate and AMPA by a two step derivatization in combination with gas chromatography/isotope ratio mass spectrometry (GC/IRMS). The N-H group was derivatized with isopropyl chloroformate (iso-PCF), and remaining acidic groups were subsequently methylated with trimethylsilyldiazomethane (TMSD). Iso-PCF treatment at pH <10 gave too low (15)N/(14)N ratios indicating an incomplete derivatization; in contrast, too high (15)N/(14)N ratios at pH >10 indicated decomposition of the derivative. At pH 10, and with an excess of iso-PCF by 10-24, greatest yields and accurate (15)N/(14)N ratios were obtained (deviation from elemental analyzer-IRMS: -0.2 ± 0.9% for glyphosate; -0.4 ± 0.7% for AMPA). Limits for accurate δ(15)N analysis of glyphosate and AMPA were 150 and 250 ng injected, respectively. A combination of δ(15)N and δ(13)C analysis by liquid chromatography/isotope ratio mass spectrometry (LC/IRMS) (1) enabled an improved distinction of commercial glyphosate products and (2) showed that glyphosate isotope values during degradation by MnO2 clearly fell outside the commercial product range. This highlights the potential of combined carbon and nitrogen isotopes analysis to trace sources and degradation of glyphosate.

A Meta-Analysis of the Prevalence of Influenza A H5N1 and H7N9 Infection in Birds.

PubMed

Bui, C; Rahman, B; Heywood, A E; MacIntyre, C R

2017-06-01

Despite a much higher rate of human influenza A (H7N9) infection compared to influenza A (H5N1), and the assumption that birds are the source of human infection, detection rates of H7N9 in birds are lower than those of H5N1. This raises a question about the role of birds in the spread and transmission of H7N9 to humans. We conducted a meta-analysis of overall prevalence of H5N1 and H7N9 in different bird populations (domestic poultry, wild birds) and different environments (live bird markets, commercial poultry farms, wild habitats). The electronic database, Scopus, was searched for published papers, and Google was searched for country surveillance reports. A random effect meta-analysis model was used to produce pooled estimates of the prevalence of H5N1 and H7N9 for various subcategories. A random effects logistic regression model was used to compare prevalence rates between H5N1 and H7N9. Both viruses have low prevalence across all bird populations. Significant differences in prevalence rates were observed in domestic birds, farm settings, for pathogen and antibody testing, and during routine surveillance. Random effects logistic regression analyses show that among domestic birds, the prevalence of H5N1 is 47.48 (95% CI: 17.15-133.13, P < 0.001) times higher than H7N9. In routine surveillance (where surveillance was not conducted in response to human infections or bird outbreaks), the prevalence of H5N1 is still higher than H7N9 with an OR of 43.02 (95% CI: 16.60-111.53, P < 0.001). H7N9 in humans has occurred at a rate approximately four times higher than H5N1, and for both infections, birds are postulated to be the source. Much lower rates of H7N9 in birds compared to H5N1 raise doubts about birds as the sole source of high rates of human H7N9 infection. Other sources of transmission of H7N9 need to be considered and explored. © 2016 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

Compression as a Universal Principle of Animal Behavior

ERIC Educational Resources Information Center

Ferrer-i-Cancho, Ramon; Hernández-Fernández, Antoni; Lusseau, David; Agoramoorthy, Govindasamy; Hsu, Minna J.; Semple, Stuart

2013-01-01

A key aim in biology and psychology is to identify fundamental principles underpinning the behavior of animals, including humans. Analyses of human language and the behavior of a range of non-human animal species have provided evidence for a common pattern underlying diverse behavioral phenomena: Words follow Zipf's law of brevity (the…

Between disorder and order: A case study of power law

NASA Astrophysics Data System (ADS)

Cao, Yong; Zhao, Youjie; Yue, Xiaoguang; Xiong, Fei; Sun, Yongke; He, Xin; Wang, Lichao

2016-08-01

Power law is an important feature of phenomena in long memory behaviors. Zipf ever found power law in the distribution of the word frequencies. In physics, the terms order and disorder are Thermodynamic or statistical physics concepts originally and a lot of research work has focused on self-organization of the disorder ingredients of simple physical systems. It is interesting what make disorder-order transition. We devise an experiment-based method about random symbolic sequences to research regular pattern between disorder and order. The experiment results reveal power law is indeed an important regularity in transition from disorder to order. About these results the preliminary study and analysis has been done to explain the reasons.

Methods, apparatuses, and computer-readable media for projectional morphological analysis of N-dimensional signals

DOEpatents

Glazoff, Michael V.; Gering, Kevin L.; Garnier, John E.; Rashkeev, Sergey N.; Pyt'ev, Yuri Petrovich

2016-05-17

Embodiments discussed herein in the form of methods, systems, and computer-readable media deal with the application of advanced "projectional" morphological algorithms for solving a broad range of problems. In a method of performing projectional morphological analysis, an N-dimensional input signal is supplied. At least one N-dimensional form indicative of at least one feature in the N-dimensional input signal is identified. The N-dimensional input signal is filtered relative to the at least one N-dimensional form and an N-dimensional output signal is generated indicating results of the filtering at least as differences in the N-dimensional input signal relative to the at least one N-dimensional form.

Benchmarking Memory Performance with the Data Cube Operator

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Shabanov, Leonid V.

2004-01-01

Data movement across a computer memory hierarchy and across computational grids is known to be a limiting factor for applications processing large data sets. We use the Data Cube Operator on an Arithmetic Data Set, called ADC, to benchmark capabilities of computers and of computational grids to handle large distributed data sets. We present a prototype implementation of a parallel algorithm for computation of the operatol: The algorithm follows a known approach for computing views from the smallest parent. The ADC stresses all levels of grid memory and storage by producing some of 2d views of an Arithmetic Data Set of d-tuples described by a small number of integers. We control data intensity of the ADC by selecting the tuple parameters, the sizes of the views, and the number of realized views. Benchmarking results of memory performance of a number of computer architectures and of a small computational grid are presented.

Dynamic gene expression analysis in a H1N1 influenza virus mouse pneumonia model.

PubMed

Bao, Yanyan; Gao, Yingjie; Shi, Yujing; Cui, Xiaolan

2017-06-01

H1N1, a major pathogenic subtype of influenza A virus, causes a respiratory infection in humans and livestock that can range from a mild infection to more severe pneumonia associated with acute respiratory distress syndrome. Understanding the dynamic changes in the genome and the related functional changes induced by H1N1 influenza virus infection is essential to elucidating the pathogenesis of this virus and thereby determining strategies to prevent future outbreaks. In this study, we filtered the significantly expressed genes in mouse pneumonia using mRNA microarray analysis. Using STC analysis, seven significant gene clusters were revealed, and using STC-GO analysis, we explored the significant functions of these seven gene clusters. The results revealed GOs related to H1N1 virus-induced inflammatory and immune functions, including innate immune response, inflammatory response, specific immune response, and cellular response to interferon-beta. Furthermore, the dynamic regulation relationships of the key genes in mouse pneumonia were revealed by dynamic gene network analysis, and the most important genes were filtered, including Dhx58, Cxcl10, Cxcl11, Zbp1, Ifit1, Ifih1, Trim25, Mx2, Oas2, Cd274, Irgm1, and Irf7. These results suggested that during mouse pneumonia, changes in the expression of gene clusters and the complex interactions among genes lead to significant changes in function. Dynamic gene expression analysis revealed key genes that performed important functions. These results are a prelude to advancements in mouse H1N1 influenza virus infection biology, as well as the use of mice as a model organism for human H1N1 influenza virus infection studies.

Functional and bioinformatics analysis of an exopolysaccharide-related gene (epsN) from Lactobacillus kefiranofaciens ZW3.

PubMed

Wang, Jingrui; Tang, Wei; Zheng, Yongna; Xing, Zhuqing; Wang, Yanping

2016-09-01

A novel lactic acid bacteria strain Lactobacillus kefiranofaciens ZW3 exhibited the characteristics of high production of exopolysaccharide (EPS). The epsN gene, located in the eps gene cluster of this strain, is associated with EPS biosynthesis. Bioinformatics analysis of this gene was performed. The conserved domain analysis showed that the EpsN protein contained MATE-Wzx-like domains. Then the epsN gene was amplified to construct the recombinant expression vector pMG36e-epsN. The results showed that the EPS yields of the recombinants were significantly improved. By determining the yields of EPS and intracellular polysaccharide, it was considered that epsN gene could play its Wzx flippase role in the EPS biosynthesis. This is the first time to prove the effect of EpsN on L. kefiranofaciens EPS biosynthesis and further prove its functional property.

The convergence of complete active space self-consistent-field configuration interaction including all single and double excitation energies to the complete basis set limit

NASA Astrophysics Data System (ADS)

Petersson, George A.; Malick, David K.; Frisch, Michael J.; Braunstein, Matthew

2006-07-01

Examination of the convergence of full valence complete active space self-consistent-field configuration interaction including all single and double excitation (CASSCF-CISD) energies with expansion of the one-electron basis set reveals a pattern very similar to the convergence of single determinant energies. Calculations on the lowest four singlet states and the lowest four triplet states of N2 with the sequence of n-tuple-ζ augmented polarized (nZaP) basis sets (n =2, 3, 4, 5, and 6) are used to establish the complete basis set limits. Full configuration-interaction (CI) and core electron contributions must be included for very accurate potential energy surfaces. However, a simple extrapolation scheme that has no adjustable parameters and requires nothing more demanding than CAS(10e -,8orb)-CISD/3ZaP calculations gives the Re, ωe, ωeXe, Te, and De for these eight states with rms errors of 0.0006Å, 4.43cm-1, 0.35cm-1, 0.063eV, and 0.018eV, respectively.

Pulse-chase Analysis of N-linked Sugar Chains from Glycoproteins in Mammalian Cells

PubMed Central

Avezov, Edward; Ron, Efrat; Izenshtein, Yana; Adan, Yosef; Lederkremer, Gerardo Z.

2010-01-01

Attachment of the Glc3Man9GlcNAc2 precursor oligosaccharide to nascent polypeptides in the ER is a common modification for secretory proteins. Although this modification was implicated in several biological processes, additional aspects of its function are emerging, with recent evidence of its role in the production of signals for glycoprotein quality control and trafficking. Thus, phenomena related to N-linked glycans and their processing are being intensively investigated. Methods that have been recently developed for proteomic analysis have greatly improved the characterization of glycoprotein N-linked glycans. Nevertheless, they do not provide insight into the dynamics of the sugar chain processing involved. For this, labeling and pulse-chase analysis protocols are used that are usually complex and give very low yields. We describe here a simple method for the isolation and analysis of metabolically labeled N-linked oligosaccharides. The protocol is based on labeling of cells with [2-3H] mannose, denaturing lysis and enzymatic release of the oligosaccharides from either a specifically immunoprecipitated protein of interest or from the general glycoprotein pool by sequential treatments with endo H and N-glycosidase F, followed by molecular filtration (Amicon). In this method the isolated oligosaccharides serve as an input for HPLC analysis, which allows discrimination between various glycan structures according to the number of monosaccharide units comprising them, with a resolution of a single monosaccharide. Using this method we were able to study high mannose N-linked oligosaccharide profiles of total cell glycoproteins after pulse-chase in normal conditions and under proteasome inhibition. These profiles were compared to those obtained from an immunoprecipitated ER-associated degradation (ERAD) substrate. Our results suggest that most NIH 3T3 cellular glycoproteins are relatively stable and that most of their oligosaccharides are trimmed to Man9-8GlcNAc2. In

Pulse-chase analysis of N-linked sugar chains from glycoproteins in mammalian cells.

PubMed

Avezov, Edward; Ron, Efrat; Izenshtein, Yana; Adan, Yosef; Lederkremer, Gerardo Z

2010-04-27

Attachment of the Glc3Man9GlcNAc2 precursor oligosaccharide to nascent polypeptides in the ER is a common modification for secretory proteins. Although this modification was implicated in several biological processes, additional aspects of its function are emerging, with recent evidence of its role in the production of signals for glycoprotein quality control and trafficking. Thus, phenomena related to N-linked glycans and their processing are being intensively investigated. Methods that have been recently developed for proteomic analysis have greatly improved the characterization of glycoprotein N-linked glycans. Nevertheless, they do not provide insight into the dynamics of the sugar chain processing involved. For this, labeling and pulse-chase analysis protocols are used that are usually complex and give very low yields. We describe here a simple method for the isolation and analysis of metabolically labeled N-linked oligosaccharides. The protocol is based on labeling of cells with [2-(3)H] mannose, denaturing lysis and enzymatic release of the oligosaccharides from either a specifically immunoprecipitated protein of interest or from the general glycoprotein pool by sequential treatments with endo H and N-glycosidase F, followed by molecular filtration (Amicon). In this method the isolated oligosaccharides serve as an input for HPLC analysis, which allows discrimination between various glycan structures according to the number of monosaccharide units comprising them, with a resolution of a single monosaccharide. Using this method we were able to study high mannose N-linked oligosaccharide profiles of total cell glycoproteins after pulse-chase in normal conditions and under proteasome inhibition. These profiles were compared to those obtained from an immunoprecipitated ER-associated degradation (ERAD) substrate. Our results suggest that most NIH 3T3 cellular glycoproteins are relatively stable and that most of their oligosaccharides are trimmed to Man9-8GlcNAc2

N-Acetylcysteine in depressive symptoms and functionality: a systematic review and meta-analysis.

PubMed

Fernandes, Brisa S; Dean, Olivia M; Dodd, Seetal; Malhi, Gin S; Berk, Michael

2016-04-01

To assess the utility of N-acetylcysteine administration for depressive symptoms in subjects with psychiatric conditions using a systematic review and meta-analysis. A computerized literature search was conducted in MEDLINE, Embase, the Cochrane Library, SciELO, PsycINFO, Scopus, and Web of Knowledge. No year or country restrictions were used. The Boolean terms used for the electronic database search were (NAC OR N-acetylcysteine OR acetylcysteine) AND (depression OR depressive OR depressed) AND (trial). The last search was performed in November 2014. The literature was searched for double-blind, randomized, placebo-controlled trials using N-acetylcysteine for depressive symptoms regardless of the main psychiatric condition. Using keywords and cross-referenced bibliographies, 38 studies were identified and examined in depth. Of those, 33 articles were rejected because inclusion criteria were not met. Finally, 5 studies were included. Data were extracted independently by 2 investigators. The primary outcome measure was change in depressive symptoms. Functionality, quality of life, and manic and anxiety symptoms were also examined. A full review and meta-analysis were performed. Standardized mean differences (SMDs) and odds ratios (ORs) with 95% CIs were calculated. Five studies fulfilled our inclusion criteria for the meta-analysis, providing data on 574 participants, of whom 291 were randomized to receive N-acetylcysteine and 283 to placebo. The follow-up varied from 12 to 24 weeks. Two studies included subjects with bipolar disorder and current depressive symptoms, 1 included subjects with MDD in a current depressive episode, and 2 included subjects with depressive symptoms in the context of other psychiatric conditions (1 trichotillomania and 1 heavy smoking). Treatment with N-acetylcysteine improved depressive symptoms as assessed by Montgomery-Asberg Depression Rating Scale and Hamilton Depression Rating Scale when compared to placebo (SMD = 0.37; 95% CI = 0

Simple and Robust N-Glycan Analysis Based on Improved 2-Aminobenzoic Acid Labeling for Recombinant Therapeutic Glycoproteins.

PubMed

Jeong, Yeong Ran; Kim, Sun Young; Park, Young Sam; Lee, Gyun Min

2018-03-21

N-glycans of therapeutic glycoproteins are critical quality attributes that should be monitored throughout all stages of biopharmaceutical development. To reduce both the time for sample preparation and the variations in analytical results, we have developed an N-glycan analysis method that includes improved 2-aminobenzoic acid (2-AA) labeling to easily remove deglycosylated proteins. Using this analytical method, 15 major 2-AA-labeled N-glycans of Enbrel ® were separated into single peaks in hydrophilic interaction chromatography mode and therefore could be quantitated. 2-AA-labeled N-glycans were also highly compatible with in-line quadrupole time-of-flight mass spectrometry (MS) for structural identification. The structures of 15 major and 18 minor N-glycans were identified from their mass values determined by quadrupole time-of-flight MS. Furthermore, the structures of 14 major N-glycans were confirmed by interpreting the MS/MS data of each N-glycan. This analytical method was also successfully applied to neutral N-glycans of Humira ® and highly sialylated N-glycans of NESP ® . Furthermore, the analysis data of Enbrel ® that were accumulated for 2.5 years demonstrated the high-level consistency of this analytical method. Taken together, the results show that a wide repertoire of N-glycans of therapeutic glycoproteins can be analyzed with high efficiency and consistency using the improved 2-AA labeling-based N-glycan analysis method. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

nSTAT: Open-Source Neural Spike Train Analysis Toolbox for Matlab

PubMed Central

Cajigas, I.; Malik, W.Q.; Brown, E.N.

2012-01-01

Over the last decade there has been a tremendous advance in the analytical tools available to neuroscientists to understand and model neural function. In particular, the point process - Generalized Linear Model (PPGLM) framework has been applied successfully to problems ranging from neuro-endocrine physiology to neural decoding. However, the lack of freely distributed software implementations of published PP-GLM algorithms together with problem-specific modifications required for their use, limit wide application of these techniques. In an effort to make existing PP-GLM methods more accessible to the neuroscience community, we have developed nSTAT – an open source neural spike train analysis toolbox for Matlab®. By adopting an Object-Oriented Programming (OOP) approach, nSTAT allows users to easily manipulate data by performing operations on objects that have an intuitive connection to the experiment (spike trains, covariates, etc.), rather than by dealing with data in vector/matrix form. The algorithms implemented within nSTAT address a number of common problems including computation of peri-stimulus time histograms, quantification of the temporal response properties of neurons, and characterization of neural plasticity within and across trials. nSTAT provides a starting point for exploratory data analysis, allows for simple and systematic building and testing of point process models, and for decoding of stimulus variables based on point process models of neural function. By providing an open-source toolbox, we hope to establish a platform that can be easily used, modified, and extended by the scientific community to address limitations of current techniques and to extend available techniques to more complex problems. PMID:22981419

Analysis of polychlorinated n-alkanes in environmental samples.

PubMed

Santos, F J; Parera, J; Galceran, M T

2006-10-01

Polychlorinated n-alkanes (PCAs), also known as chlorinated paraffins (CPs), are highly complex technical mixtures that contain a huge number of structural isomers, theoretically more than 10,000 diastereomers and enantiomers. As a consequence of their persistence, tendency to bioaccumulation, and widespread and unrestricted use, PCAs have been found in aquatic and terrestrial food webs, even in rural and remote areas. Recently, these compounds have been included in regulatory programs of several international organizations, including the US Environmental Protection Agency and the European Union. Consequently, there is a growing demand for reliable methods with which to analyze PCAs in environmental samples. Here, we review current trends and recent developments in the analysis of PCAs in environmental samples such as air, water, sediment, and biota. Practical aspects of sample preparation, chromatographic separation, and detection are covered, with special emphasis placed on analysis of PCAs using gas chromatography-mass spectrometry. The advantages and limitations of these techniques as well as recent improvements in quantification procedures are discussed.

Thermodynamic analysis of vapor-phase epitaxial growth of GaAsN on Ge

NASA Astrophysics Data System (ADS)

Kawano, Jun; Kangawa, Yoshihiro; Ito, Tomonori; Kakimoto, Koichi; Koukitu, Akinori

2012-03-01

In this paper, we use thermodynamic analysis to determine how the nitrogen (N) ratio in the source gases affects the solid composition of coherently grown GaAs1-xNx(x˜0.03). The source gases for Ga, As, and N are trimethylgallium ((CH3)3Ga), arsine (AsH3), and ammonia (NH3), respectively. The growth occurs on a Ge substrate, and the analysis includes the stress from the substrate-crystal lattice mismatch. Calculation results indicate that to have just a few percent N incorporation into the grown solid, the V/III ratio in the source gases should be several thousands and the input-gas partial-pressure ratio NH3/(NH3+AsH3) should exceed 0.99. We also find that the lattice mismatch stress from the Ge substrate increases the V/III source-gas ratio required for stable growth, whereas an increase in input Ga partial pressure ratio has the opposite effect.

Statistical physics in foreign exchange currency and stock markets

NASA Astrophysics Data System (ADS)

Ausloos, M.

2000-09-01

Problems in economy and finance have attracted the interest of statistical physicists all over the world. Fundamental problems pertain to the existence or not of long-, medium- or/and short-range power-law correlations in various economic systems, to the presence of financial cycles and on economic considerations, including economic policy. A method like the detrended fluctuation analysis is recalled emphasizing its value in sorting out correlation ranges, thereby leading to predictability at short horizon. The ( m, k)-Zipf method is presented for sorting out short-range correlations in the sign and amplitude of the fluctuations. A well-known financial analysis technique, the so-called moving average, is shown to raise questions to physicists about fractional Brownian motion properties. Among spectacular results, the possibility of crash predictions has been demonstrated through the log-periodicity of financial index oscillations.

Phylogenetic Diversity and Genotypical Complexity of H9N2 Influenza A Viruses Revealed by Genomic Sequence Analysis

PubMed Central

Dong, Guoying; Luo, Jing; Zhang, Hong; Wang, Chengmin; Duan, Mingxing; Deliberto, Thomas Jude; Nolte, Dale Louis; Ji, Guangju; He, Hongxuan

2011-01-01

H9N2 influenza A viruses have become established worldwide in terrestrial poultry and wild birds, and are occasionally transmitted to mammals including humans and pigs. To comprehensively elucidate the genetic and evolutionary characteristics of H9N2 influenza viruses, we performed a large-scale sequence analysis of 571 viral genomes from the NCBI Influenza Virus Resource Database, representing the spectrum of H9N2 influenza viruses isolated from 1966 to 2009. Our study provides a panoramic framework for better understanding the genesis and evolution of H9N2 influenza viruses, and for describing the history of H9N2 viruses circulating in diverse hosts. Panorama phylogenetic analysis of the eight viral gene segments revealed the complexity and diversity of H9N2 influenza viruses. The 571 H9N2 viral genomes were classified into 74 separate lineages, which had marked host and geographical differences in phylogeny. Panorama genotypical analysis also revealed that H9N2 viruses include at least 98 genotypes, which were further divided according to their HA lineages into seven series (A–G). Phylogenetic analysis of the internal genes showed that H9N2 viruses are closely related to H3, H4, H5, H7, H10, and H14 subtype influenza viruses. Our results indicate that H9N2 viruses have undergone extensive reassortments to generate multiple reassortants and genotypes, suggesting that the continued circulation of multiple genotypical H9N2 viruses throughout the world in diverse hosts has the potential to cause future influenza outbreaks in poultry and epidemics in humans. We propose a nomenclature system for identifying and unifying all lineages and genotypes of H9N2 influenza viruses in order to facilitate international communication on the evolution, ecology and epidemiology of H9N2 influenza viruses. PMID:21386964

Parental Relationships, Autonomy, and Identity Processes of High School Students

ERIC Educational Resources Information Center

Mullis, Ronald L.; Graf, Shruti Chatterjee; Mullis, Ann K.

2009-01-01

To examine the interrelations among parental relationships, emotional autonomy, and identity statuses, the authors asked 234 (105 male, 129 female) high school students to complete the Parental Bonding Scale (G. Parker, H. Tupling, & L. B. Brown, 1979), Emotional Autonomy Scale (L. D. Steinberg & S. B. Silverberg, 1986), and Extended Objective…

Focused glycomic analysis of the N-linked glycan biosynthetic pathway in ovarian cancer

PubMed Central

Abbott, Karen L.; Nairn, Alison V.; Hall, Erica M.; Horton, Marc B.; McDonald, John F.; Moremen, Kelley W.; Dinulescu, Daniela M.; Pierce, Michael

2014-01-01

Epithelial ovarian cancer is the deadliest female reproductive tract malignancy in Western countries. Less than 25% of cases are diagnosed when the cancer is confined, however, pointing to the critical need for early diagnostics for ovarian cancer. Identifying the changes that occur in the glycome of ovarian cancer cells may provide an avenue to develop a new generation of potential biomarkers for early detection of this disease. We performed a glycotranscriptomic analysis of endometrioid ovarian carcinoma using human tissue, as well as a newly developed mouse model that mimics this disease. Our results show that the N-linked glycans expressed in both non-diseased mouse and human ovarian tissues are similar; moreover, malignant changes in the expression of N-linked glycans in both mouse and human endometrioid ovarian carcinoma are qualitatively similar. Lectin reactivity was used as a means for rapid validation of glycan structural changes in the carcinomas that were predicted by the glycotranscriptome analysis. Among several changes in glycan expression noted, the increase of bisected N-linked glycans and the transcripts of the enzyme responsible for its biosynthesis, GnT-III, was the most significant. This study provides evidence that glycotranscriptome analysis can be an important tool in identifying potential cancer biomarkers. PMID:18690643

Spectroscopic investigation (FT-IR, FT-Raman), HOMO-LUMO, NBO, and molecular docking analysis of N-ethyl-N-nitrosourea, a potential anticancer agent

NASA Astrophysics Data System (ADS)

Singh, Priyanka; Islam, S. S.; Ahmad, Hilal; Prabaharan, A.

2018-02-01

Nitrosourea plays an important role in the treatment of cancer. N-ethyl-N-nitrosourea, also known as ENU, (chemical formula C3H7N3O2), is a highly potent mutagen. The chemical is an alkylating agent and acts by transferring the ethyl group of ENU to nucleobases (usually thymine) in nucleic acids. The molecular structure of N-ethyl-N-nitrosourea has been elucidated using experimental (FT-IR and FT-Raman) and theoretical (DFT) techniques. APT charges, Mulliken atomic charges, Natural bond orbital, Electrostatic potential, HOMO-LUMO and AIM analysis were performed to identify the reactive sites and charge transfer interactions. Furthermore, to evaluate the anticancer activity of ENU molecular docking studies were carried out against 2JIU protein.

Tribological Testing, Analysis and Characterization of D.C. Magnetron Sputtered Ti-Nb-N Thin Film Coatings on Stainless Steel

NASA Astrophysics Data System (ADS)

Joshi, Prathmesh

To enhance the surface properties of stainless steel, the substrate was coated with a 1μm thick coating of Ti-Nb-N by reactive DC magnetron sputtering at different N2 flow rates, substrate biasing and Nb-Ti ratio. The characterization of the coated samples was performed by the following techniques: hardness by Knoop micro-hardness tester, phase analysis by X-ray Diffraction (XRD), compositional analysis by Energy Dispersive X-ray Spectroscopy (EDS) and adhesion by scratch test. The tribology testing was performed on linearly reciprocating ball-on-plate wear testing machine and wear depth and wear volume were evaluated by white light interferometer. The micro-hardness test yielded appreciable enhancement in the surface hardness with the highest value being 1450 HK. Presence of three prominent phases namely NbN, Nb2N3 and TiN resulted from the XRD analysis. EDS analysis revealed the presence of Ti, Nb and Nitrogen. Adhesion was evaluated on the basis of critical loads for cohesive (Lc1) and adhesive (Lc2) failures with values varying between 7-12 N and 16-25 N respectively, during scratch test for coatings on SS substrates.

Compositional and strain analysis of In(Ga)N/GaN short period superlattices

NASA Astrophysics Data System (ADS)

Dimitrakopulos, G. P.; Vasileiadis, I. G.; Bazioti, C.; Smalc-Koziorowska, J.; Kret, S.; Dimakis, E.; Florini, N.; Kehagias, Th.; Suski, T.; Karakostas, Th.; Moustakas, T. D.; Komninou, Ph.

2018-01-01

Extensive high resolution transmission and scanning transmission electron microscopy observations were performed in In(Ga)N/GaN multi-quantum well short period superlattices comprising two-dimensional quantum wells (QWs) of nominal thicknesses 1, 2, and 4 monolayers (MLs) in order to obtain a correlation between their average composition, geometry, and strain. The high angle annular dark field Z-contrast observations were quantified for such layers, regarding the indium content of the QWs, and were correlated to their strain state using peak finding and geometrical phase analysis. Image simulations taking into thorough account the experimental imaging conditions were employed in order to associate the observed Z-contrast to the indium content. Energetically relaxed supercells calculated with a Tersoff empirical interatomic potential were used as the input for such simulations. We found a deviation from the tetragonal distortion prescribed by continuum elasticity for thin films, i.e., the strain in the relaxed cells was lower than expected for the case of 1 ML QWs. In all samples, the QW thickness and strain were confined in up to 2 ML with possible indium enrichment of the immediately abutting MLs. The average composition of the QWs was quantified in the form of alloy content.

Efficacy of N-Acetylcysteine in Idiopathic Pulmonary Fibrosis: A Systematic Review and Meta-Analysis.

PubMed

Sun, Tong; Liu, Jing; Zhao, De Wei

2016-05-01

There are a number of conflicting reports describing the clinical outcomes of using N-acetylcysteine for the treatment of idiopathic pulmonary fibrosis. We have, therefore, performed a meta-analysis to evaluate the efficacy of N-acetylcysteine, compared with control, for the treatment of idiopathic pulmonary fibrosis.Original controlled clinical trials evaluating the efficacy of N-acetylcysteine for the treatment of idiopathic pulmonary fibrosis were included in the analysis. Searches for relevant articles were carried out in July 2014 by 2 independent researchers using PubMed, Embase, Cochrane Central, and Google Scholar. Change in forced vital capacity, change in percentage of predicted vital capacity, change in percentage of predicted carbon monoxide diffusing capacity, changes in 6 minutes walking test distance, rate of adverse events, and rate of death were expressed as outcomes using RevMan 5.0.1.Five trials, with a total of 564 patients, were included in this meta-analysis. The meta-analysis showed that the control group had significant decreases in percentage of predicted vital capacity (standardized mean difference [SMD] = 0.37; 95% confidence interval [CI]: 0.13 to -0.62; P = 0.003) and 6 minutes walking test distance (SMD = 0.25; 95% CI: 0.02-0.48; P = 0.04). There were no statistically significant differences in forced vital capacity (SMD = 0.07; 95% CI: -0.13-0.27; P = 0.52), percentage of predicted carbon monoxide diffusing capacity (SMD = 0.12; 95% CI: -0.06-0.30; P = 0.18), rates of adverse events (odd ratio = 4.50; 95% CI: 0.19-106.41; P = 0.35), or death rates (odd ratio = 1.79; 95% CI: 0.3-5.12; P = 0.28) between the N-acetylcysteine group and the control group.N-Acetylcysteine was found to have a significant effect only on decreases in percentage of predicted vital capacity and 6 minutes walking test distance. N-acetylcysteine showed no beneficial effect on changes in forced vital capacity

Analysis of the aac(3)-VIa gene encoding a novel 3-N-acetyltransferase.

PubMed Central

Rather, P N; Mann, P A; Mierzwa, R; Hare, R S; Miller, G H; Shaw, K J

1993-01-01

Biochemical analysis (G. A. Papanicolaou, R. S. Hare, R. Mierzwa, and G. H. Miller, abstr. 152, Program Abstr. 29th Intersci. Conf. Antimicrob. Agents Chemother., 1989) demonstrated the presence of a novel 3-N-acetyltransferase in Enterobacter cloacae 88020217. This organism was resistant to gentamicin, and the MIC of 2'-N-ethylnetilmicin for it was fourfold lower than that of 6'-N-ethylnetilmicin, a resistance pattern which suggested 2'-acetylating activity. However, high-pressure liquid chromatography analysis demonstrated that the enzyme acetylated sisomicin in the 3 position. We have cloned the structural gene for this enzyme from a large (> 70-kb) conjugative plasmid present in E. cloacae. Subcloning experiments have localized the aac(3)-VIa gene to a 2.1-kb Sau3A fragment. The deduced AAC(3)-VIa protein showed 48% amino acid identity to the AAC(3)-IIa protein and 39% identity to the AAC(3)-VII protein. Examination of the 5'-flanking sequences demonstrated that the aac(3)-VIa gene was located 167 bp downstream of the aadA1 gene and was present in an integron. In addition, the aac(3)-VIa gene is also downstream of a 59-base element often seen in an integron environment. Primer extension analysis has identified a promoter for the aac(3)-VIa gene downstream of both the aadA1 gene and a 59-base element. Images PMID:8257126

Phylogenetic and molecular analysis of highly pathogenic avian influenza H5N8 and H5N5 viruses detected in Poland in 2016-2017.

PubMed

Świętoń, Edyta; Śmietanka, Krzysztof

2018-06-19

Sixty-five poultry outbreaks and sixty-eight events in wild birds were reported during the highly pathogenic H5N8/H5N5 avian influenza epidemic in Poland in 2016-2017. The analysis of all gene segment sequences of selected strains revealed cocirculation of at least four different genome configurations (genotypes) generated through reassortment of clade 2.3.4.4 H5N8 viruses detected in Russia and China in mid-2016. The geographical and temporal distribution of three H5N8 genotypes indicates separate introductions. Additionally, an H5N5 virus with a different gene configuration was detected in wild birds. The compilation of the results with those from studies on the virus' diversity in Germany, Italy and the Netherlands revealed that Europe was affected by at least eight different H5N8/H5N5 reassortants. Analysis of the HA gene sequence of a larger subset of samples showed its diversification corresponding to the genotype classification. The close relationship between poultry and wild bird strains from the same locations observed in several cases points to wild birds as the primary source of the outbreaks in poultry. © 2018 Blackwell Verlag GmbH.

A peptide N-terminal protection strategy for comprehensive glycoproteome analysis using hydrazide chemistry based method

PubMed Central

Huang, Junfeng; Qin, Hongqiang; Sun, Zhen; Huang, Guang; Mao, Jiawei; Cheng, Kai; Zhang, Zhang; Wan, Hao; Yao, Yating; Dong, Jing; Zhu, Jun; Wang, Fangjun; Ye, Mingliang; Zou, Hanfa

2015-01-01

Enrichment of glycopeptides by hydrazide chemistry (HC) is a popular method for glycoproteomics analysis. However, possible side reactions of peptide backbones during the glycan oxidation in this method have not been comprehensively studied. Here, we developed a proteomics approach to locate such side reactions and found several types of the side reactions that could seriously compromise the performance of glycoproteomics analysis. Particularly, the HC method failed to identify N-terminal Ser/Thr glycopeptides because the oxidation of vicinal amino alcohol on these peptides generates aldehyde groups and after they are covalently coupled to HC beads, these peptides cannot be released by PNGase F for identification. To overcome this drawback, we apply a peptide N-terminal protection strategy in which primary amine groups on peptides are chemically blocked via dimethyl labeling, thus the vicinal amino alcohols on peptide N-termini are eliminated. Our results showed that this strategy successfully prevented the oxidation of peptide N-termini and significantly improved the coverage of glycoproteome. PMID:25959593

Analysis of electronic parameters and frequency-dependent properties of Au/NiO/ n-GaN heterojunctions

NASA Astrophysics Data System (ADS)

Reddy, Varra Niteesh; Padma, R.; Gunasekhar, K. R.

2018-01-01

The electrical and frequency-dependent properties of ten Au/NiO/ n-GaN heterojunctions fabricated with similar conditions are assessed by I-V, C-V, and G-V measurement methods. In addition, C-f and G-f measurements are conducted in the frequency range of 1 kHz-1 MHz. The electronic parameters are changed from junction to junction even if they are fabricated in the similar way. The calculated barrier height and ideality factor values are fitted by the Gaussian distribution function. Statistical analysis of the data provides the mean barrier height and ideality factor values of 0.84 eV and 2.70 for the heterojunction. Besides, the mean barrier height ( V b), donor concentration ( N d), space charge layer width ( W D), and Fermi level ( E F) are determined from the C-V data and the corresponding values are 1.30 eV, 2.00 × 1017 cm-3, 8.222 × 10-6 cm, and 0.018 eV, respectively. The interface state density ( N SS) and relaxation time (τ) are assessed from C-f and G-f measurements. Moreover, the dielectric constant ( ɛ'), dielectric loss ( ɛ″), tangent loss (tan δ), and electrical conductivity ( σ ac) are determined from C-f and G-f data in the frequency range of 1 kHz-1 MHz with various biases (0.1-0.6 V). ɛ' and ɛ″ are decreased with increasing frequency.

Multidimensional entropic uncertainty relation based on a commutator matrix in position and momentum spaces

NASA Astrophysics Data System (ADS)

Hertz, Anaelle; Vanbever, Luc; Cerf, Nicolas J.

2018-01-01

The uncertainty relation for continuous variables due to Byałinicki-Birula and Mycielski [I. Białynicki-Birula and J. Mycielski, Commun. Math. Phys. 44, 129 (1975), 10.1007/BF01608825] expresses the complementarity between two n -tuples of canonically conjugate variables (x1,x2,...,xn) and (p1,p2,...,pn) in terms of Shannon differential entropy. Here we consider the generalization to variables that are not canonically conjugate and derive an entropic uncertainty relation expressing the balance between any two n -variable Gaussian projective measurements. The bound on entropies is expressed in terms of the determinant of a matrix of commutators between the measured variables. This uncertainty relation also captures the complementarity between any two incompatible linear canonical transforms, the bound being written in terms of the corresponding symplectic matrices in phase space. Finally, we extend this uncertainty relation to Rényi entropies and also prove a covariance-based uncertainty relation which generalizes the Robertson relation.

Fully Automated Sample Preparation for Ultrafast N-Glycosylation Analysis of Antibody Therapeutics.

PubMed

Szigeti, Marton; Lew, Clarence; Roby, Keith; Guttman, Andras

2016-04-01

There is a growing demand in the biopharmaceutical industry for high-throughput, large-scale N-glycosylation profiling of therapeutic antibodies in all phases of product development, but especially during clone selection when hundreds of samples should be analyzed in a short period of time to assure their glycosylation-based biological activity. Our group has recently developed a magnetic bead-based protocol for N-glycosylation analysis of glycoproteins to alleviate the hard-to-automate centrifugation and vacuum-centrifugation steps of the currently used protocols. Glycan release, fluorophore labeling, and cleanup were all optimized, resulting in a <4 h magnetic bead-based process with excellent yield and good repeatability. This article demonstrates the next level of this work by automating all steps of the optimized magnetic bead-based protocol from endoglycosidase digestion, through fluorophore labeling and cleanup with high-throughput sample processing in 96-well plate format, using an automated laboratory workstation. Capillary electrophoresis analysis of the fluorophore-labeled glycans was also optimized for rapid (<3 min) separation to accommodate the high-throughput processing of the automated sample preparation workflow. Ultrafast N-glycosylation analyses of several commercially relevant antibody therapeutics are also shown and compared to their biosimilar counterparts, addressing the biological significance of the differences. © 2015 Society for Laboratory Automation and Screening.

Functional analysis of the Helicobacter pullorum N-linked protein glycosylation system.

PubMed

Jervis, Adrian J; Wood, Alison G; Cain, Joel A; Butler, Jonathan A; Frost, Helen; Lord, Elizabeth; Langdon, Rebecca; Cordwell, Stuart J; Wren, Brendan W; Linton, Dennis

2018-04-01

N-linked protein glycosylation systems operate in species from all three domains of life. The model bacterial N-linked glycosylation system from Campylobacter jejuni is encoded by pgl genes present at a single chromosomal locus. This gene cluster includes the pglB oligosaccharyltransferase responsible for transfer of glycan from lipid carrier to protein. Although all genomes from species of the Campylobacter genus contain a pgl locus, among the related Helicobacter genus only three evolutionarily related species (H. pullorum, H. canadensis and H. winghamensis) potentially encode N-linked protein glycosylation systems. Helicobacter putative pgl genes are scattered in five chromosomal loci and include two putative oligosaccharyltransferase-encoding pglB genes per genome. We have previously demonstrated the in vitro N-linked glycosylation activity of H. pullorum resulting in transfer of a pentasaccharide to a peptide at asparagine within the sequon (D/E)XNXS/T. In this study, we identified the first H. pullorum N-linked glycoprotein, termed HgpA. Production of histidine-tagged HgpA in the background of insertional knockout mutants of H. pullorum pgl/wbp genes followed by analysis of HgpA glycan structures demonstrated the role of individual gene products in the PglB1-dependent N-linked protein glycosylation pathway. Glycopeptide purification by zwitterionic-hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry identified six glycosites from five H. pullorum proteins, which was consistent with proteins reactive with a polyclonal antiserum generated against glycosylated HgpA. This study demonstrates functioning of a H. pullorum N-linked general protein glycosylation system.

Nonreductive chemical release of intact N-glycans for subsequent labeling and analysis by mass spectrometry.

PubMed

Yuan, Jiangbei; Wang, Chengjian; Sun, Yujiao; Huang, Linjuan; Wang, Zhongfu

2014-10-01

A novel strategy is proposed, using cost-saving chemical reactions to generate intact free reducing N-glycans and their fluorescent derivatives from glycoproteins for subsequent analysis. N-Glycans without core α-1,3-linked fucose are released in reducing form by selective hydrolysis of the N-type carbohydrate-peptide bond of glycoproteins under a set of optimized mild alkaline conditions and are comparable to those released by commonly used peptide-N-glycosidase (PNGase) F in terms of yield without any detectable side reaction (peeling or deacetylation). The obtained reducing glycans can be routinely derivatized with 2-aminobenzoic acid (2-AA), 1-phenyl-3-methyl-5-pyrazolone (PMP), and potentially some other fluorescent reagents for comprehensive analysis. Alternatively, the core α-1,3-fucosylated N-glycans are released in mild alkaline medium and derivatized with PMP in situ, and their yields are comparable to those obtained using commonly used PNGase A without conspicuous peeling reaction or any detectable deacetylation. Using this new technique, the N-glycans of a series of purified glycoproteins and complex biological samples were successfully released and analyzed by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS), demonstrating its general applicability to glycomic studies. Copyright © 2014 Elsevier Inc. All rights reserved.

Randomness versus specifics for word-frequency distributions

NASA Astrophysics Data System (ADS)

Yan, Xiaoyong; Minnhagen, Petter

2016-02-01

The text-length-dependence of real word-frequency distributions can be connected to the general properties of a random book. It is pointed out that this finding has strong implications, when deciding between two conceptually different views on word-frequency distributions, i.e. the specific 'Zipf's-view' and the non-specific 'Randomness-view', as is discussed. It is also noticed that the text-length transformation of a random book does have an exact scaling property precisely for the power-law index γ = 1, as opposed to the Zipf's exponent γ = 2 and the implication of this exact scaling property is discussed. However a real text has γ > 1 and as a consequence γ increases when shortening a real text. The connections to the predictions from the RGF (Random Group Formation) and to the infinite length-limit of a meta-book are also discussed. The difference between 'curve-fitting' and 'predicting' word-frequency distributions is stressed. It is pointed out that the question of randomness versus specifics for the distribution of outcomes in case of sufficiently complex systems has a much wider relevance than just the word-frequency example analyzed in the present work.

N-tert-butylmethanimine N-oxide is an efficient spin-trapping probe for EPR analysis of glutathione thiyl radical

PubMed Central

Scott, Melanie J.; Billiar, Timothy R.; Stoyanovsky, Detcho A.

2016-01-01

The electron spin resonance (EPR) spin-trapping technique allows detection of radical species with nanosecond half-lives. This technique is based on the high rates of addition of radicals to nitrones or nitroso compounds (spin traps; STs). The paramagnetic nitroxides (spin-adducts) formed as a result of reactions between STs and radical species are relatively stable compounds whose EPR spectra represent “structural fingerprints” of the parent radical species. Herein we report a novel protocol for the synthesis of N-tert-butylmethanimine N-oxide (EBN), which is the simplest nitrone containing an α-H and a tertiary α′-C atom. We present EPR spin-trapping proof that: (i) EBN is an efficient probe for the analysis of glutathione thiyl radical (GS•); (ii) β-cyclodextrins increase the kinetic stability of the spin-adduct EBN/•SG; and (iii) in aqueous solutions, EBN does not react with superoxide anion radical (O2−•) to form EBN/•OOH to any significant extent. The data presented complement previous studies within the context of synthetic accessibility to EBN and efficient spin-trapping analysis of GS•. PMID:27941944

Analysis of the auger recombination rate in P+N-n-N-N HgCdTe detectors for HOT applications

NASA Astrophysics Data System (ADS)

Schuster, J.; Tennant, W. E.; Bellotti, E.; Wijewarnasuriya, P. S.

2016-05-01

Infrared (IR) photon detectors must be cryogenically cooled to provide the highest possible performance, usually to temperatures at or below ~ 150K. Such low operating temperatures (Top) impose very stringent requirements on cryogenic coolers. As such, there is a constant push in the industry to engineer new detector architectures that operate at higher temperatures, so called higher operating temperature (HOT) detectors. The ultimate goal for HOT detectors is room temperature operation. While this is not currently possibly for photon detectors, significant increases in Top are nonetheless beneficial in terms of reduced size, weight, power and cost (SWAP-C). The most common HgCdTe IR detector architecture is the P+n heterostructure photodiode (where a capital letter indicates a wide band gap relative to the active layer or "AL"). A variant of this architecture, the P+N-n-N-N heterostructure photodiode, should have a near identical photo-response to the P+n heterostructure, but with significantly lower dark diffusion current. The P+N-n-N-N heterostructure utilizes a very low doped AL, surrounded on both sides by wide-gap layers. The low doping in the AL, allows the AL to be fully depleted, which drastically reduces the Auger recombination rate in that layer. Minimizing the Auger recombination rate reduces the intrinsic dark diffusion current, thereby increasing Top. Note when we use the term "recombination rate" for photodiodes, we are actually referring to the net generation and recombination of minority carriers (and corresponding dark currents) by the Auger process. For these benefits to be realized, these devices must be intrinsically limited and well passivated. The focus of this proceeding is on studying the fundamental physics of the intrinsic dark currents in ideal P+N-n-N-N heterostructures, namely Auger recombination. Due to the complexity of these devices, specifically the presence of multiple heterojunctions, numerical device modeling techniques must be

High Performance Active Database Management on a Shared-Nothing Parallel Processor

DTIC Science & Technology

1998-05-01

either stored or virtual. A stored node is like a materialized view. It actually contains the specified tuples. A virtual node is like a real view...90292-6695 DL-5 COLUMBIA UNIV/DEPT COMPUTER SCIENCi ATTN: OR GAIL £. KAISER 450 COMPUTER SCIENCE 3LDG 500 WEST 12ÖTH STRSET NEW YORK NY 10027

Releasing N-glycan from peptide N-terminus by N-terminal succinylation assisted enzymatic deglycosylation.

PubMed

Weng, Yejing; Sui, Zhigang; Jiang, Hao; Shan, Yichu; Chen, Lingfan; Zhang, Shen; Zhang, Lihua; Zhang, Yukui

2015-04-22

Due to the important roles of N-glycoproteins in various biological processes, the global N-glycoproteome analysis has been paid much attention. However, by current strategies for N-glycoproteome profiling, peptides with glycosylated Asn at N-terminus (PGANs), generated by protease digestion, could hardly be identified, due to the poor deglycosylation capacity by enzymes. However, theoretically, PGANs occupy 10% of N-glycopeptides in the typical tryptic digests. Therefore, in this study, we developed a novel strategy to identify PGANs by releasing N-glycans through the N-terminal site-selective succinylation assisted enzymatic deglycosylation. The obtained PGANs information is beneficial to not only achieve the deep coverage analysis of glycoproteomes, but also discover the new biological functions of such modification.

Paradise: A Parallel Information System for EOSDIS

NASA Technical Reports Server (NTRS)

DeWitt, David

1996-01-01

The Paradise project was begun-in 1993 in order to explore the application of the parallel and object-oriented database system technology developed as a part of the Gamma, Exodus. and Shore projects to the design and development of a scaleable, geo-spatial database system for storing both massive spatial and satellite image data sets. Paradise is based on an object-relational data model. In addition to the standard attribute types such as integers, floats, strings and time, Paradise also provides a set of and multimedia data types, designed to facilitate the storage and querying of complex spatial and multimedia data sets. An individual tuple can contain any combination of this rich set of data types. For example, in the EOSDIS context, a tuple might mix terrain and map data for an area along with the latest satellite weather photo of the area. The use of a geo-spatial metaphor simplifies the task of fusing disparate forms of data from multiple data sources including text, image, map, and video data sets.

Optical model potential analysis of n ¯ A and n A interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Teck-Ghee; Wong, Cheuk-Yin

In this study, we use a momentum-dependent optical model potential to analyze the annihilation cross sections of the antineutronmore » $$\\overline{n}$$ on C, Al, Fe, Cu, Ag, Sn, and Pb nuclei for projectile momenta p lab ≲ 500 MeV / c . We obtain a good description of annihilation cross section data of Barbina et al. [Nucl. Phys. A 612, 346 (1997)] and of Astrua et al. [Nucl. Phys. A 697, 209 (2002)] which exhibit an interesting dependence of the cross sections on p lab as well as on the target mass number A. We also obtain the neutron (n) nonelastic reaction cross sections for the same targets. Comparing the $nA$ reaction cross sections σ$$nA\\atop{rec}$$ to the $$\\overline{n}A$$ annihilation cross sections σ $$\\overline{n}A$$ ann, we find that σ $$\\overline{n}A$$ ann is significantly larger than σ$$nA\\atop{rec}$$, that is, theσ $$\\overline{n}A$$ ann / σ$$nA\\atop{rec}$$ cross section ratio lies between the values of about 1.5 to 4.0 in the momentum region where comparison is possible. The dependence of the $$\\overline{n}$$ annihilation cross section on the projectile charge is also examined in comparison with the antiproton $$\\overline{p}$$. Here we predict the $$\\overline{p}A$$ annihilation cross section on the simplest assumption that both $$\\overline{p}A$$ and $$\\overline{n}A$$ interactions have the same nuclear part of the optical potential but differ only in the electrostatic Coulomb interaction. Finally, deviation from a such simple model extrapolation in measurements will provide new information on the difference between $$\\overline{n}A$$ and $$\\overline{p}A$$ potentials.« less

Optical model potential analysis of n ¯ A and n A interactions

DOE PAGES

Lee, Teck-Ghee; Wong, Cheuk-Yin

2018-05-25

In this study, we use a momentum-dependent optical model potential to analyze the annihilation cross sections of the antineutronmore » $$\\overline{n}$$ on C, Al, Fe, Cu, Ag, Sn, and Pb nuclei for projectile momenta p lab ≲ 500 MeV / c . We obtain a good description of annihilation cross section data of Barbina et al. [Nucl. Phys. A 612, 346 (1997)] and of Astrua et al. [Nucl. Phys. A 697, 209 (2002)] which exhibit an interesting dependence of the cross sections on p lab as well as on the target mass number A. We also obtain the neutron (n) nonelastic reaction cross sections for the same targets. Comparing the $nA$ reaction cross sections σ$$nA\\atop{rec}$$ to the $$\\overline{n}A$$ annihilation cross sections σ $$\\overline{n}A$$ ann, we find that σ $$\\overline{n}A$$ ann is significantly larger than σ$$nA\\atop{rec}$$, that is, theσ $$\\overline{n}A$$ ann / σ$$nA\\atop{rec}$$ cross section ratio lies between the values of about 1.5 to 4.0 in the momentum region where comparison is possible. The dependence of the $$\\overline{n}$$ annihilation cross section on the projectile charge is also examined in comparison with the antiproton $$\\overline{p}$$. Here we predict the $$\\overline{p}A$$ annihilation cross section on the simplest assumption that both $$\\overline{p}A$$ and $$\\overline{n}A$$ interactions have the same nuclear part of the optical potential but differ only in the electrostatic Coulomb interaction. Finally, deviation from a such simple model extrapolation in measurements will provide new information on the difference between $$\\overline{n}A$$ and $$\\overline{p}A$$ potentials.« less

Detailed product analysis during the low temperature oxidation of n-butane

PubMed Central

Herbinet, Olivier; Battin-Leclerc, Frédérique; Bax, Sarah; Le Gall, Hervé; Glaude, Pierre-Alexandre; Fournet, René; Zhou, Zhongyue; Deng, Liulin; Guo, Huijun; Xie, Mingfeng; Qi, Fei

2013-01-01

The products obtained from the low-temperature oxidation of n-butane in a jet-stirred reactor (JSR) have been analysed using two methods: gas chromatography analysis of the outlet gas and reflectron time-of-flight mass spectrometry. The mass spectrometer was combined with tunable synchrotron vacuum ultraviolet photoionization and coupled with a JSR via a molecular-beam sampling system. Experiments were performed under quasi-atmospheric pressure, for temperatures between 550 and 800 K, at a mean residence time of 6s and with a stoichiometric n-butane/oxygen/argon mixture (composition = 4/26/70 in mol %). 36 reaction products have been quantified, including addition to the usual oxidation products, acetic acid, hydrogen peroxide, C1, C2 and C4 alkylhydroperoxides and C4 ketohydroperoxides. Evidence of the possible formation of products (dihydrofuranes, furanones) derived from cyclic ethers has also been found. The performance of a detailed kinetic model of the literature has been assessed with the simulation of the formation of this extended range of species. These simulations have also allowed the analysis of possible pathways for the formation of some obtained products. PMID:21031192

A Study of the γ-Radiolysis of N,N-Didodecyl-N',N'-Dioctyldiglycolamide Using UHPLC-ESI-MS Analysis

DOE PAGES

Roscioli-Johnson, Kristyn M.; Zarzana, Christopher A.; Groenewold, Gary S.; ...

2016-07-12

In this paper, solutions of N,N-didodecyl-N',N'-dioctyldiglycolamide in n-dodecane were subjected to γ-irradiation in the presence and absence of both an aqueous nitric acid phase and air sparging. The solutions were analyzed using ultra-high-performance liquid chromatography-electrospray ionization-mass spectrometry (UHPLC-ESI-MS) to determine the rates of radiolytic decay of the extractant as well as to identify radiolysis products. The DGA concentration decreased exponentially with increasing dose, and the measured degradation rate constants were uninfluenced by the presence or absence of acidic aqueous phase, or by air sparging. Finally, the identified radiolysis products suggest that the bonds most vulnerable to radiolytic attack are thosemore » in the diglycolamide center of these molecules and not in the side chains.« less

High-performance liquid chromatographic analysis of as-synthesised N,N'-dimethylformamide-stabilised gold nanoclusters product

NASA Astrophysics Data System (ADS)

Xie, Shunping; Paau, Man Chin; Zhang, Yan; Shuang, Shaomin; Chan, Wan; Choi, Martin M. F.

2012-08-01

Reverse-phase high-performance liquid chromatographic (RP-HPLC) separation and analysis of polydisperse water-soluble gold nanoclusters (AuNCs) stabilised with N,N'-dimethylformamide (DMF) were investigated. Under optimal elution gradient conditions, the separation of DMF-AuNCs was monitored by absorption and fluorescence spectroscopy. The UV-vis spectral characteristics of the separated DMF-AuNCs have been captured and they do not possess distinct surface plasmon resonance bands, indicating that all DMF-AuNCs are small AuNCs. The photoluminescence emission spectra of the separated DMF-AuNCs are in the blue-light region. Moreover, cationic DMF-AuNCs are for the first time identified by ion chromatography. Our proposed RP-HPLC methodology has been successfully applied to separate AuNCs of various Au atoms as well as DMF-stabilised ligands. Finally, the composition of the separated DMF-AuNCs was confirmed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and electrospray ionisation mass spectrometry, proving that the as-synthesised DMF-AuNCs product consists of Au10+, Au10, Au11, Au12, Au13, and Au14 NCs stabilised with various numbers of DMF ligands.Reverse-phase high-performance liquid chromatographic (RP-HPLC) separation and analysis of polydisperse water-soluble gold nanoclusters (AuNCs) stabilised with N,N'-dimethylformamide (DMF) were investigated. Under optimal elution gradient conditions, the separation of DMF-AuNCs was monitored by absorption and fluorescence spectroscopy. The UV-vis spectral characteristics of the separated DMF-AuNCs have been captured and they do not possess distinct surface plasmon resonance bands, indicating that all DMF-AuNCs are small AuNCs. The photoluminescence emission spectra of the separated DMF-AuNCs are in the blue-light region. Moreover, cationic DMF-AuNCs are for the first time identified by ion chromatography. Our proposed RP-HPLC methodology has been successfully applied to separate AuNCs of

Multiscale volatility duration characteristics on financial multi-continuum percolation dynamics

NASA Astrophysics Data System (ADS)

Wang, Min; Wang, Jun

A random stock price model based on the multi-continuum percolation system is developed to investigate the nonlinear dynamics of stock price volatility duration, in an attempt to explain various statistical facts found in financial data, and have a deeper understanding of mechanisms in the financial market. The continuum percolation system is usually referred to be a random coverage process or a Boolean model, it is a member of a class of statistical physics systems. In this paper, the multi-continuum percolation (with different values of radius) is employed to model and reproduce the dispersal of information among the investors. To testify the rationality of the proposed model, the nonlinear analyses of return volatility duration series are preformed by multifractal detrending moving average analysis and Zipf analysis. The comparison empirical results indicate the similar nonlinear behaviors for the proposed model and the actual Chinese stock market.

Synchrotron radiation x-ray topography and defect selective etching analysis of threading dislocations in GaN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sintonen, Sakari, E-mail: sakari.sintonen@aalto.fi; Suihkonen, Sami; Jussila, Henri

2014-08-28

The crystal quality of bulk GaN crystals is continuously improving due to advances in GaN growth techniques. Defect characterization of the GaN substrates by conventional methods is impeded by the very low dislocation density and a large scale defect analysis method is needed. White beam synchrotron radiation x-ray topography (SR-XRT) is a rapid and non-destructive technique for dislocation analysis on a large scale. In this study, the defect structure of an ammonothermal c-plane GaN substrate was recorded using SR-XRT and the image contrast caused by the dislocation induced microstrain was simulated. The simulations and experimental observations agree excellently and themore » SR-XRT image contrasts of mixed and screw dislocations were determined. Apart from a few exceptions, defect selective etching measurements were shown to correspond one to one with the SR-XRT results.« less

Hydrogen loss during N-15 nuclear reaction analysis of high strength steel

NASA Astrophysics Data System (ADS)

Larochelle, J. S.; Désilets-Benoit, A.; Borduas, G.; Laliberté-Riverin, S.; Roorda, S.; Brochu, M.

2017-10-01

High strength steel samples were analysed by N-15 nuclear reaction analysis in order to detect hydrogen that may have been introduced by electroplating process. The NRA signal decreased during exposure of the ion beam and residual gas analysis showed that the gas was desorbed by the beam interaction. The variable hydrogen signal could be well described as the sum of a constant concentration and a fraction susceptible to second order desorption. A mechanically polished bevel allowed measurements to be extended to a depth of 0.2 mm.

Nuclear reaction analysis for H, Li, Be, B, C, N, O and F with an RBS check

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lanford, W. A.; Parenti, M.; Nordell, B. J.

2015-11-12

In this paper, 15N nuclear reaction analysis (NRA) for H is combined with 1.2 MeV deuteron (D) NRA which provides a simultaneous analysis for Li, Be, B, C, N, O and F. The energy dependence of the D NRA has been measured and used to correct for the D energy loss in film being analyzed. A 2 MeV He RBS measurement is made. Film composition is determined by a self-consistent analysis of the light element NRA data combined with an RBS analysis for heavy elements. This composition is used to simulate, with no adjustable parameters, the complete RBS spectrum. Finally,more » comparison of this simulated RBS spectrum with the measured spectrum provides a powerful check of the analysis.« less

Analysis of the coexisting pathways for NO and N2O formation in Chernozem using the (15)N-tracer SimKIM-Advanced model.

PubMed

Stange, Claus Florian; Spott, Oliver; Russow, Rolf

2013-01-01

The nitrogen (N) cycle consists of a variety of microbial processes. These processes often occur simultaneously in soils, but respond differently to local environmental conditions due to process-specific biochemical restrictions (e.g. oxygen levels). Hence, soil nitrogen cycling (e.g. soil N gas production through nitrification and denitrification) is individually affected through these processes, resulting in the complex and highly dynamic behaviour of total soil N turnover. The development and application of methods that facilitate the quantification of individual contributions of coexisting processes is a fundamental prerequisite for (i) understanding the dynamics of soil N turnover and (ii) implementing these processes in ecosystem models. To explain the unexpected results of the triplet tracer experiment (TTE) of Russow et al. (Role of nitrite and nitric oxide in the processes of nitrification and denitrification in soil: results from (15)N tracer experiments. Soil Biol Biochem. 2009;41:785-795) the existing SimKIM model was extended to the SimKIM-Advanced model through the addition of three separate nitrite subpools associated with ammonia oxidation, oxidation of organic nitrogen (Norg), and denitrification, respectively. For the TTE, individual treatments with (15)N ammonium, (15)N nitrate, and (15)N nitrite were conducted under oxic, hypoxic, and anoxic conditions, respectively, to clarify the role of nitric oxide as a denitrification intermediate during N2O formation. Using a split nitrite pool, this analysis model explains the observed differences in the (15)N enrichments in nitric oxide (NO) and nitrous oxide (N2O) which occurred in dependence on different oxygen concentrations. The change from oxic over hypoxic to anoxic conditions only marginally increased the NO and N2O release rates (1.3-fold). The analysis using the model revealed that, under oxic and hypoxic conditions, Norg-based N2O production was the dominant pathway, contributing to 90 and 50�

Phase Diagrams of the n-Decane- n-Hexadecane-Cyclododecane, n-Decane-Cyclododecane, and n-Hexadecane-Cyclododecane Systems

NASA Astrophysics Data System (ADS)

Shamitov, A. A.; Garkushin, I. K.; Kolyado, A. V.; Petrov, E. P.

2018-02-01

The n-decane- n-hexadecane-cyclododecane, n-decane-cyclododecane, and n-hexadecane-cyclododecane systems are studied by means of low-temperature differential thermal analysis using a differential scanning heat flow calorimeter. It is noted that all studied systems belong to the eutectic type. It is concluded that in the n-decane- n-hexadecane-cyclododecane system, the eutectic composition contains 85.0 wt % n-C10H22, 4.0 wt % n-C16H34, and 11.0 wt % C12H24. It has a melting point of -35.0°C.

N-linked (N-) glycoproteomics of urinary exosomes. [Corrected].

PubMed

Saraswat, Mayank; Joenväära, Sakari; Musante, Luca; Peltoniemi, Hannu; Holthofer, Harry; Renkonen, Risto

2015-02-01

Epithelial cells lining the urinary tract secrete urinary exosomes (40-100 nm) that can be targeted to specific cells modulating their functionality. One potential targeting mechanism is adhesion between vesicle surface glycoproteins and target cells. This makes the glycopeptide analysis of exosomes important. Exosomes reflect the physiological state of the parent cells; therefore, they are a good source of biomarkers for urological and other diseases. Moreover, the urine collection is easy and noninvasive and urinary exosomes give information about renal and systemic organ systems. Accordingly, multiple studies on proteomic characterization of urinary exosomes in health and disease have been published. However, no systematic analysis of their glycoproteomic profile has been carried out to date, whereas a conserved glycan signature has been found for exosomes from urine and other sources including T cell lines and human milk. Here, we have enriched and identified the N-glycopeptides from these vesicles. These enriched N-glycopeptides were solved for their peptide sequence, glycan composition, structure, and glycosylation site using collision-induced dissociation MS/MS (CID-tandem MS) data interpreted by a publicly available software GlycopeptideId. Released glycans from the same sample was also analyzed with MALDI-MS. We have identified the N-glycoproteome of urinary exosomes. In total 126 N-glycopeptides from 51 N-glycosylation sites belonging to 37 glycoproteins were found in our results. The peptide sequences of these N-glycopeptides were identified unambiguously and their glycan composition (for 125 N-glycopeptides) and structures (for 87 N-glycopeptides) were proposed. A corresponding glycomic analysis with released N-glycans was also performed. We identified 66 unique nonmodified N-glycan compositions and in addition 13 sulfated/phosphorylated glycans were also found. This is the first systematic analysis of N-glycoproteome of urinary exosomes. © 2015 by The

Analysis of InxGa1-xN/Si p-n heterojunction solar cells and the effects of spontaneous and piezoelectric polarization charges

NASA Astrophysics Data System (ADS)

Zheng, Yangdong; Mihara, Akihiro; Yamamoto, Akio

2013-10-01

The band structures, current-voltage characteristics under solar illumination, and photovoltaic (PV) properties of InxGa1-xN/Si p-n heterojunction solar cells (SCs), as well as the effects of spontaneous and piezoelectric polarization (Psp-PPZ) induced charges are investigated theoretically and numerically. We find that the energy peaks on the conduction and valence bands could exponentially reduce the diffusion currents and photocurrents, thus profoundly affect the PV properties of the SCs. Except for large values, the Psp-PPZ induced interface charges have little influence on the band structures and the PV properties. These results should be useful in analysis and design for multijunction tandem InxGa1-xN/Si SC devices.

Simulation and analysis of the absorption enhancement in p-i-n InGaN/GaN solar cell using photonic crystal light trapping structures

NASA Astrophysics Data System (ADS)

Gupta, Nikhil Deep; Janyani, Vijay

2016-10-01

The structure of p-i-n InGaN/GaN based solar cell having a photonic crystal (PhC)-based light trapping structure (LTS) at the top assisted by the planar metallic (aluminum) back reflector (BR) is proposed. We propose two different designs for efficiency enhancement: in one we keep the PhC structure etching depth extending from the top antireflective coating (ARC) of indium tin oxide (ITO) up to the p-GaN layer (which is beneath the ITO and above the active layer), whereas in the other design, the PhC LTS etching depth has been extended up to the InxGa1-xN absorbing layer, starting from the top ITO layer. The theoretical optical simulation studies and optimization of the required parameters of the structure, which help to investigate and demonstrate the effectiveness of the LTS in the efficiency enhancement of the structure, are presented. The work also demonstrates the Lambertian light trapping limits for the practical indium concentrations in a InxGa1-xN active layer cell. The paper also presents the comparison between the proposed designs and compares their results with that of a planar reference cell. The studies are carried out for various indium concentrations. The results indicate considerable enhancement in the efficiency due to the PhC LTS, mainly because of better coupling, low reflectance, and diffraction capability of the proposed LTS, although it is still under the Lambertian limits. The performance evaluation of the proposed structure with respect to the angle of incident light has also been done, indicating improved performance. The parameters have been optimized and calculated by means of rigorous coupled wave analysis (RCWA) method.

Analysis of high-efficiency widely-tunable N-resonances in Cs vapor

NASA Astrophysics Data System (ADS)

Krasteva, A.; Gateva, S.; Tzvetkov, S.; Ghosh, P. N.; Sargsyan, A.; Cartaleva, S.

2018-03-01

The narrow-band coherent N-type resonance, promising for the development of advanced atomic clocks, can be considered as a type of three-photon resonance, where a two-photon Raman excitation is combined with a resonant optical pumping field. In this communication, we present an experimental study and a theoretical analysis related to three-photon, bi-chromatic excitation of Cs atomic vapor contained in an 8-mm long cell with 20 Torr of neon. If a coupling laser is fixed at a frequency that is lower by several GHz than the position of the absorption profile of the Fg = 4 set of transitions, and a probe laser is tuned over the D2 line (λ = 852 nm), a narrow high-contrast enhanced absorption N-resonance will be observed in the probe light profile, superimposed on the absorption profile of the Fg = 4 set of transitions. We present theoretical modeling aimed to clarify the processes behind the efficiency of the N-resonance preparation for different frequency positions of the coupling laser within the D2 line of Cs.

Progress in the analysis and interpretation of N2O isotopes: Potential and future challenges

NASA Astrophysics Data System (ADS)

Mohn, Joachim; Tuzson, Béla; Zellweger, Christoph; Harris, Eliza; Ibraim, Erkan; Yu, Longfei; Emmenegger, Lukas

2017-04-01

In recent years, research on nitrous oxide (N2O) stable isotopes has significantly advanced, addressing an increasing number of research questions in biogeochemical and atmospheric sciences [1]. An important milestone was the development of quantum cascade laser based spectroscopic devices [2], which are inherently specific for structural isomers (15N14N16O vs. 14N15N16O) and capable to collect real-time data with high temporal resolution, complementary to the well-established isotope-ratio mass-spectrometry (IRMS) method. In combination with automated preconcentration, optical isotope ratio spectroscopy (OIRS) has been applied to disentangle source processes in suburban, rural and pristine environments [e.g. 3, 4]. Within the European Metrology Research Programme (EMRP) ENV52 project "Metrology for high-impact greenhouse gases (HIGHGAS)", the quality of N2O stable isotope analysis by OIRS, the comparability between laboratories, and the traceability to the international isotope ratio scales have been addressed. An inter-laboratory comparison between eleven IRMS and OIRS laboratories, organised within HIGHGAS, indicated limited comparability for 15N site preference, i.e. the difference between 15N abundance in central (N*NO) and end (*NNO) position [5]. In addition, the accuracy of the NH4NO3 decomposition reaction, which provides the link between 15N site preference and the international 15N/14N scale, was found to be limited by non-quantitative NH4NO3 decomposition in combination with substantially different isotope enrichment factors for both nitrogen atoms [6]. Results of the HIGHGAS project indicate that the following research tasks have to be completed to foster research on N2O isotopes: 1) develop improved techniques to link the 15N and 18O abundance and the 15N site preference in N2O to the international stable isotope ratio scales; 2) provide N2O reference materials, pure and diluted in an air matrix, to improve inter-laboratory compatibility. These tasks

Mass Spectrometric Analysis of the Cell Surface N-Glycoproteome by Combining Metabolic Labeling and Click Chemistry

NASA Astrophysics Data System (ADS)

Smeekens, Johanna M.; Chen, Weixuan; Wu, Ronghu

2015-04-01

Cell surface N-glycoproteins play extraordinarily important roles in cell-cell communication, cell-matrix interactions, and cellular response to environmental cues. Global analysis is exceptionally challenging because many N-glycoproteins are present at low abundances and effective separation is difficult to achieve. Here, we have developed a novel strategy integrating metabolic labeling, copper-free click chemistry, and mass spectrometry (MS)-based proteomics methods to analyze cell surface N-glycoproteins comprehensively and site-specifically. A sugar analog containing an azido group, N-azidoacetylgalactosamine, was fed to cells to label glycoproteins. Glycoproteins with the functional group on the cell surface were then bound to dibenzocyclooctyne-sulfo-biotin via copper-free click chemistry under physiological conditions. After protein extraction and digestion, glycopeptides with the biotin tag were enriched by NeutrAvidin conjugated beads. Enriched glycopeptides were deglycosylated with peptide- N-glycosidase F in heavy-oxygen water, and in the process of glycan removal, asparagine was converted to aspartic acid and tagged with 18O for MS analysis. With this strategy, 144 unique N-glycopeptides containing 152 N-glycosylation sites were identified in 110 proteins in HEK293T cells. As expected, 95% of identified glycoproteins were membrane proteins, which were highly enriched. Many sites were located on important receptors, transporters, and cluster of differentiation proteins. The experimental results demonstrated that the current method is very effective for the comprehensive and site-specific identification of the cell surface N-glycoproteome and can be extensively applied to other cell surface protein studies.

N-3 polyunsaturated fatty acids intake and risk of colorectal cancer: meta-analysis of prospective studies.

PubMed

Chen, Guo-Chong; Qin, Li-Qiang; Lu, Da-Bing; Han, Tie-Mei; Zheng, Yan; Xu, Guo-Zhang; Wang, Xiao-Huai

2015-01-01

Growing body of laboratory evidence supports the beneficial effects of n-3 polyunsaturated fatty acids (PUFAs) on colorectal cancer (CRC) prevention. Epidemiologic studies investigating the relationship between n-3 PUFAs intake and risk of CRC, however, have been inconsistent. We aimed to clarify the relation by conducting a meta-analysis of prospective studies. Eligible studies were identified by searching PubMed database and by carefully reviewing bibliographies of retrieved publications. Summary relative risks (RRs) with their 95 % confidence intervals (CIs) were computed with a random-effects model. Subgroup, meta-regression, and dose-response analyses were performed to explore potential sources of heterogeneity. A total of 14 prospective studies involving 8,775 cancer cases were included in the final analysis. Overall, total n-3 or marine PUFAs intake was not associated with risk of CRC (RR 0.99 and 1.00). However, there was a trend toward reduced risk of proximal colon cancer (total n-3 PUFAs: RR 0.83, 95 % CI 0.66-1.05; marine PUFAs: RR 0.81, 95 % CI 0.59-1.10) and a significant increased risk of distal colon cancer (total n-3 PUFAs: RR 1.26, 95 % CI 1.06-1.50; marine PUFAs: RR 1.38, 95 % CI 1.11-1.71). Furthermore, marine PUFAs intake accessed longer before diagnosis was associated 21 % reduced risk of CRC (RR 0.79, 95 % CI 0.63-1.00). Overall, this meta-analysis finds no relation between n-3 PUFAs intake and risk of CRC. The observed subsite heterogeneity within colon cancer and the possible effect modification by latency time merit further studies.

R-Matrix Analysis of the 13C(α,n)16O Reaction

NASA Astrophysics Data System (ADS)

Kock, Arthur; Rogachev, Grigory

2015-10-01

The 13C(α,n)16O reaction plays a crucial role in the main s-process occurring in low-mass thermally-pulsing asymptotic giant branch (TP-AGB) stars, which produces about half of all nuclei heavier than iron. However, direct measurements of this reaction cross section near the Gamow-peak energy are currently not possible due to very small reaction cross sections. Additionally, available cross-section data at higher energy have some inconsistencies, leading to significant uncertainties in low energy extrapolations. A global R-matrix fit was conducted, using all available data for the 13C(α,n)16O, 13C(α, α)13C, and 16O(n,n)16O reactions. Of particular importance was the inclusion of the fixed ANC for the 1 / 2 + state at 6 . 356 MeV in 17O, which was measured recently using the sub-Coulomb α-transfer reaction, as well as the new 13C+ α elastic-scattering data measured in the low-energy region 1 . 6 - 3 . 8 MeV. Important constraining information on various resonances was found, and the uncertainty for the astrophysical 13C(α,n)16O reaction rate was dramatically reduced. Much work on the analysis was done by A. K. Nurmukhanbetova from National Laboratory Astana in Astana, Kazakhstan.

Risks on N-acetyltransferase 2 and bladder cancer: a meta-analysis.

PubMed

Zhu, Zongheng; Zhang, Jinshan; Jiang, Wei; Zhang, Xianjue; Li, Youkong; Xu, Xiaoming

2015-01-01

It is known that bladder cancer disease is closely related to aromatic amine compounds, which could cause cancer by regulating of N-acetylation and N-acetyltransferase 1 and 2 (NAT1 and NAT2). The NAT2 slowed acetylation and would increase the risk of bladder cancer, with tobacco smoke being regarded as a risk factor for this increased risk. However, the relationship between NAT2 slow acetylation and bladder cancer is still debatable at present. This study aims to explore preliminarily correlation of NAT2 slow acetylation and the risk of bladder cancer. The articles were searched from PubMed, Cochran, McGrane English databases, CBM, CNKI, and other databases. The extraction of bladder cancer patients and a control group related with the NAT2 gene were detected by the state, and the referenced articles and publications were also used for data retrieval. Using a random effects model, the model assumes that the studies included in the analysis cases belong to the overall population in the study of random sampling, and considering the variables within and between studies. Data were analyzed using STATA Version 6.0 software, using the META module. According to the inclusion and exclusion criteria of the literature study, 20 independent studies are included in this meta-analysis. The results showed that the individual differences of bladder cancer susceptibility might be part of the metabolism of carcinogens. Slow acetylation status of bladder cancer associated with the pooled odds ratio was 1.31 (95% confidence interval: 1.11-1.55). The status of NAT2 slow N-acetylation is associated with bladder cancer risks, and may increase the risk of bladder cancer.

Molecular Design, Structural Analysis and Antifungal Activity of Derivatives of Peptide CGA-N46.

PubMed

Li, Rui-Fang; Lu, Zhi-Fang; Sun, Ya-Nan; Chen, Shi-Hua; Yi, Yan-Jie; Zhang, Hui-Ru; Yang, Shuo-Ye; Yu, Guang-Hai; Huang, Liang; Li, Chao-Nan

2016-09-01

Chromogranin A (CGA)-N46, a derived peptide of human chromogranin A, has antifungal activity. To further research the active domain of CGA-N46, a series of derivatives were designed by successively deleting amino acid from both terminus of CGA-N46, and the amino acid sequence of each derivative was analyzed by bioinformatic software. Based on the predicted physicochemical properties of the peptides, including half-life time in mammalian reticulocytes (in vitro), yeast (in vivo) and E. coli (in vivo), instability index, aliphatic index and grand average of hydropathicity (GRAVY), the secondary structure, net charge, the distribution of hydrophobic residues and hydrophilic residues, the final derivatives CGA-N15, CGA-N16, CGA-N12 and CGA-N8 were synthesized by solid-phase peptide synthesis. The results of bioinformatic analysis showed that CGA-N46 and its derivatives were α-helix, neutral or weak positive charge, hydrophilic, and CGA-N12 and CGA-N8 were more stable than the other derivatives. The results of circular dichroism confirmed that CGA-N46 and its derived peptides displayed α-helical structure in an aqueous solution and 30 mM sodium dodecylsulfate, but α-helical contents decreased in hydrophobic lipid vesicles. CGA-N15, CGA-N16, CGA-N12 and CGA-N8 had higher antifungal activities than their mother peptide CGA-N46. Among of the derived peptides, CGA-N12 showed the least hemolytic activity. In conclusion, we have successfully identified the active domain of CGA-N46 with strong antifungal activity and weak hemolytic activity, which provides the possibility to develop a new class of antibiotics.

First-principles and thermodynamic analysis of trimethylgallium (TMG) decomposition during MOVPE growth of GaN

NASA Astrophysics Data System (ADS)

Sekiguchi, K.; Shirakawa, H.; Yamamoto, Y.; Araidai, M.; Kangawa, Y.; Kakimoto, K.; Shiraishi, K.

2017-06-01

We analyzed the decomposition mechanisms of trimethylgallium (TMG) used for the gallium source of GaN fabrication based on first-principles calculations and thermodynamic analysis. We considered two conditions. One condition is under the total pressure of 1 atm and the other one is under metal organic vapor phase epitaxy (MOVPE) growth of GaN. Our calculated results show that H2 is indispensable for TMG decomposition under both conditions. In GaN MOVPE, TMG with H2 spontaneously decomposes into Ga(CH3) and Ga(CH3) decomposes into Ga atom gas when temperature is higher than 440 K. From these calculations, we confirmed that TMG surely becomes Ga atom gas near the GaN substrate surfaces.

Refinement Types ML

DTIC Science & Technology

1994-03-16

105 2.10 Decidability ........ ................................ 116 3 Declaring Refinements of Recursive Data Types 165 3.1...However, when we introduce polymorphic constructors in Chapter 5, tuples will become a polymorphic data type very similar to other polymorphic data types...terminate. 0 Chapter 3 Declaring Refinements of Recursive Data Types 3.1 Introduction The previous chapter defined refinement type inference in terms of

Scenario analysis of fertilizer management practices for N2O mitigation from corn systems in Canada.

PubMed

Abalos, Diego; Smith, Ward N; Grant, Brian B; Drury, Craig F; MacKell, Sarah; Wagner-Riddle, Claudia

2016-12-15

Effective management of nitrogen (N) fertilizer application by farmers provides great potential for reducing emissions of the potent greenhouse gas nitrous oxide (N 2 O). However, such potential is rarely achieved because our understanding of what practices (or combination of practices) lead to N 2 O reductions without compromising crop yields remains far from complete. Using scenario analysis with the process-based model DNDC, this study explored the effects of nine fertilizer practices on N 2 O emissions and crop yields from two corn production systems in Canada. The scenarios differed in: timing of fertilizer application, fertilizer rate, number of applications, fertilizer type, method of application and use of nitrification/urease inhibitors. Statistical analysis showed that during the initial calibration and validation stages the simulated results had no significant total error or bias compared to measured values, yet grain yield estimations warrant further model improvement. Sidedress fertilizer applications reduced yield-scaled N 2 O emissions by c. 60% compared to fall fertilization. Nitrification inhibitors further reduced yield-scaled N 2 O emissions by c. 10%; urease inhibitors had no effect on either N 2 O emissions or crop productivity. The combined adoption of split fertilizer application with inhibitors at a rate 10% lower than the conventional application rate (i.e. 150kgNha -1 ) was successful, but the benefits were lower than those achieved with single fertilization at sidedress. Our study provides a comprehensive assessment of fertilizer management practices that enables policy development regarding N 2 O mitigation from agricultural soils in Canada. Copyright © 2016 Elsevier B.V. All rights reserved.

Halogenated solvent interactions with N,N-dimethyltryptamine: formation of quaternary ammonium salts and their artificially induced rearrangements during analysis.

PubMed

Brandt, Simon D; Martins, Cláudia P B; Freeman, Sally; Dempster, Nicola; Riby, Philip G; Gartz, Jochen; Alder, John F

2008-07-04

The psychoactive properties of N,N-dimethyltryptamine (DMT) 1a are known to induce altered states of consciousness in humans. This particular attribute attracts great interest from a variety of scientific and also clandestine communities. Our recent research has confirmed that DMT reacts with dichloromethane (DCM), either as a result of work-up or storage to give a quaternary N-chloromethyl ammonium salt 2a. Furthermore, this was observed to undergo rearrangement during analysis using gas chromatography-mass spectrometry (GC-MS) with products including 3-(2-chloroethyl)indole 3 and 2-methyltetrahydro-beta-carboline 4 (2-Me-THBC). This study further investigates this so far unexplored area of solvent interactions by the exposure of DMT to other halogenated solvents including dibromomethane and 1,2-dichloroethane (DCE). The N-bromomethyl- and N-chloroethyl quaternary ammonium derivatives were subsequently characterised by ion trap GC-MS in electron and chemical ionisation tandem MS mode and by NMR spectroscopy. The DCE-derived derivative formed at least six rearrangement products in the total ion chromatogram. Identification of mass spectrometry generated by-products was verified by conventional or microwave-accelerated synthesis. The use of deuterated DCM and deuterated DMT 1b provided insights into the mechanism of the rearrangements. The presence of potentially characteristic marker molecules may allow the identification of solvents used during the manufacture of controlled substances, which is often neglected since these are considered inert.

When the Sun's Away, N2O5 Comes Out to Play: An Updated Analysis of Ambient N2O5 Heterogeneous Chemistry

NASA Astrophysics Data System (ADS)

McDuffie, E. E.; Brown, S. S.

2017-12-01

The heterogeneous chemistry of N2O5 impacts the budget of tropospheric oxidants, which directly controls air quality at Earth's surface. The reaction between gas-phase N2O5 and aerosol particles occurs largely at night, and is therefore more important during the less-intensively-studied winter season. Though N2O5-aerosol interactions are vital for the accurate understanding and simulation of tropospheric chemistry and air quality, many uncertainties persist in our understanding of how various environmental factors influence the reaction rate and probability. Quantitative and accurate evaluation of these factors directly improves the predictive capabilities of atmospheric models, used to inform mitigation strategies for wintertime air pollution. In an update to last year's presentation, The Wintertime Fate of N2O5: Observations and Box Model Analysis for the 2015 WINTER Aircraft Campaign, this presentation will focus on recent field results regarding new information about N2O5 heterogeneous chemistry and future research directions.

The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum).

PubMed

Evens, Nicholas P; Buchner, Peter; Williams, Lorraine E; Hawkesford, Malcolm J

2017-10-01

Understanding the molecular basis of zinc (Zn) uptake and transport in staple cereal crops is critical for improving both Zn content and tolerance to low-Zn soils. This study demonstrates the importance of group F bZIP transcription factors and ZIP transporters in responses to Zn deficiency in wheat (Triticum aestivum). Seven group F TabZIP genes and 14 ZIPs with homeologs were identified in hexaploid wheat. Promoter analysis revealed the presence of Zn-deficiency-response elements (ZDREs) in a number of the ZIPs. Functional complementation of the zrt1/zrt2 yeast mutant by TaZIP3, -6, -7, -9 and -13 supported an ability to transport Zn. Group F TabZIPs contain the group-defining cysteine-histidine-rich motifs, which are the predicted binding site of Zn 2+ in the Zn-deficiency response. Conservation of these motifs varied between the TabZIPs suggesting that individual TabZIPs may have specific roles in the wheat Zn-homeostatic network. Increased expression in response to low Zn levels was observed for several of the wheat ZIPs and bZIPs; this varied temporally and spatially suggesting specific functions in the response mechanism. The ability of the group F TabZIPs to bind to specific ZDREs in the promoters of TaZIPs indicates a conserved mechanism in monocots and dicots in responding to Zn deficiency. In support of this, TabZIPF1-7DL and TabZIPF4-7AL afforded a strong level of rescue to the Arabidopsis hypersensitive bzip19 bzip23 double mutant under Zn deficiency. These results provide a greater understanding of Zn-homeostatic mechanisms in wheat, demonstrating an expanded repertoire of group F bZIP transcription factors, adding to the complexity of Zn homeostasis. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

ND 2 AV: N-dimensional data analysis and visualization analysis for the National Ignition Campaign

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bremer, Peer -Timo; Maljovec, Dan; Saha, Avishek

Here, one of the biggest challenges in high-energy physics is to analyze a complex mix of experimental and simulation data to gain new insights into the underlying physics. Currently, this analysis relies primarily on the intuition of trained experts often using nothing more sophisticated than default scatter plots. Many advanced analysis techniques are not easily accessible to scientists and not flexible enough to explore the potentially interesting hypotheses in an intuitive manner. Furthermore, results from individual techniques are often difficult to integrate, leading to a confusing patchwork of analysis snippets too cumbersome for data exploration. This paper presents a case study on how a combination of techniques from statistics, machine learning, topology, and visualization can have a significant impact in the field of inertial confinement fusion. We present themore » $$\\mathrm{ND}^2\\mathrm{AV}$$: N-dimensional data analysis and visualization framework, a user-friendly tool aimed at exploiting the intuition and current workflow of the target users. The system integrates traditional analysis approaches such as dimension reduction and clustering with state-of-the-art techniques such as neighborhood graphs and topological analysis, and custom capabilities such as defining combined metrics on the fly. All components are linked into an interactive environment that enables an intuitive exploration of a wide variety of hypotheses while relating the results to concepts familiar to the users, such as scatter plots. $$\\mathrm{ND}^2\\mathrm{AV}$$ uses a modular design providing easy extensibility and customization for different applications. $$\\mathrm{ND}^2\\mathrm{AV}$$ is being actively used in the National Ignition Campaign and has already led to a number of unexpected discoveries.« less

ND 2 AV: N-dimensional data analysis and visualization analysis for the National Ignition Campaign

DOE PAGES

Bremer, Peer -Timo; Maljovec, Dan; Saha, Avishek; ...

2015-07-01

Here, one of the biggest challenges in high-energy physics is to analyze a complex mix of experimental and simulation data to gain new insights into the underlying physics. Currently, this analysis relies primarily on the intuition of trained experts often using nothing more sophisticated than default scatter plots. Many advanced analysis techniques are not easily accessible to scientists and not flexible enough to explore the potentially interesting hypotheses in an intuitive manner. Furthermore, results from individual techniques are often difficult to integrate, leading to a confusing patchwork of analysis snippets too cumbersome for data exploration. This paper presents a case study on how a combination of techniques from statistics, machine learning, topology, and visualization can have a significant impact in the field of inertial confinement fusion. We present themore » $$\\mathrm{ND}^2\\mathrm{AV}$$: N-dimensional data analysis and visualization framework, a user-friendly tool aimed at exploiting the intuition and current workflow of the target users. The system integrates traditional analysis approaches such as dimension reduction and clustering with state-of-the-art techniques such as neighborhood graphs and topological analysis, and custom capabilities such as defining combined metrics on the fly. All components are linked into an interactive environment that enables an intuitive exploration of a wide variety of hypotheses while relating the results to concepts familiar to the users, such as scatter plots. $$\\mathrm{ND}^2\\mathrm{AV}$$ uses a modular design providing easy extensibility and customization for different applications. $$\\mathrm{ND}^2\\mathrm{AV}$$ is being actively used in the National Ignition Campaign and has already led to a number of unexpected discoveries.« less

Analysis of GaN Damage Induced by Cl2/SiCl4/Ar Plasma

NASA Astrophysics Data System (ADS)

Minami, Masaki; Tomiya, Shigetaka; Ishikawa, Kenji; Matsumoto, Ryosuke; Chen, Shang; Fukasawa, Masanaga; Uesawa, Fumikatsu; Sekine, Makoto; Hori, Masaru; Tatsumi, Tetsuya

2011-08-01

GaN-based optical devices are fabricated using a GaN/InGaN/GaN sandwiched structure. The effect of radicals, ions, and UV light on the GaN optical properties during Cl2/SiCl4/Ar plasma etching was evaluated using photoluminescence (PL) analysis. The samples were exposed to plasma (radicals, ions, and UV light) using an inductively coupled plasma (ICP) etching system and a plasma ion beam apparatus that can separate the effects of UV and ions both with and without covering the SiO2 window on the surface. Etching damage in an InGaN single quantum well (SQW) was formed by exposing the sample to plasma. The damage, which decreases PL emission intensity, was generated not only by ion beam irradiation but also by UV light irradiation. PL intensity decreased when the thickness of the upper GaN layer was etched to less than 60 nm. In addition, simultaneous irradiation of UV light and ions slightly increased the degree of damage. There seems to be a synergistic effect between the UV light and the ions. For high-quality GaN-based optoelectronics and power devices, UV light must be controlled during etching processes in addition to the etching profile, selectivity, and ion bombardment damage.

Beyond Word Frequency: Bursts, Lulls, and Scaling in the Temporal Distributions of Words

PubMed Central

Altmann, Eduardo G.; Pierrehumbert, Janet B.; Motter, Adilson E.

2009-01-01

Background Zipf's discovery that word frequency distributions obey a power law established parallels between biological and physical processes, and language, laying the groundwork for a complex systems perspective on human communication. More recent research has also identified scaling regularities in the dynamics underlying the successive occurrences of events, suggesting the possibility of similar findings for language as well. Methodology/Principal Findings By considering frequent words in USENET discussion groups and in disparate databases where the language has different levels of formality, here we show that the distributions of distances between successive occurrences of the same word display bursty deviations from a Poisson process and are well characterized by a stretched exponential (Weibull) scaling. The extent of this deviation depends strongly on semantic type – a measure of the logicality of each word – and less strongly on frequency. We develop a generative model of this behavior that fully determines the dynamics of word usage. Conclusions/Significance Recurrence patterns of words are well described by a stretched exponential distribution of recurrence times, an empirical scaling that cannot be anticipated from Zipf's law. Because the use of words provides a uniquely precise and powerful lens on human thought and activity, our findings also have implications for other overt manifestations of collective human dynamics. PMID:19907645

Statistics of Language Morphology Change: From Biconsonantal Hunters to Triconsonantal Farmers

PubMed Central

Agmon, Noam; Bloch, Yigal

2013-01-01

Linguistic evolution mirrors cultural evolution, of which one of the most decisive steps was the "agricultural revolution" that occurred 11,000 years ago in W. Asia. Traditional comparative historical linguistics becomes inaccurate for time depths greater than, say, 10 kyr. Therefore it is difficult to determine whether decisive events in human prehistory have had an observable impact on human language. Here we supplement the traditional methodology with independent statistical measures showing that following the transition to agriculture, languages of W. Asia underwent a transition from biconsonantal (2c) to triconsonantal (3c) morphology. Two independent proofs for this are provided. Firstly the reconstructed Proto-Semitic fire and hunting lexicons are predominantly 2c, whereas the farming lexicon is almost exclusively 3c in structure. Secondly, while Biblical verbs show the usual Zipf exponent of about 1, their 2c subset exhibits a larger exponent. After the 2c > 3c transition, this could arise from a faster decay in the frequency of use of the less common 2c verbs. Using an established frequency-dependent word replacement rate, we calculate that the observed increase in the Zipf exponent has occurred over the 7,500 years predating Biblical Hebrew namely, starting with the transition to agriculture. PMID:24367613

Understanding scaling through history-dependent processes with collapsing sample space.

PubMed

Corominas-Murtra, Bernat; Hanel, Rudolf; Thurner, Stefan

2015-04-28

History-dependent processes are ubiquitous in natural and social systems. Many such stochastic processes, especially those that are associated with complex systems, become more constrained as they unfold, meaning that their sample space, or their set of possible outcomes, reduces as they age. We demonstrate that these sample-space-reducing (SSR) processes necessarily lead to Zipf's law in the rank distributions of their outcomes. We show that by adding noise to SSR processes the corresponding rank distributions remain exact power laws, p(x) ~ x(-λ), where the exponent directly corresponds to the mixing ratio of the SSR process and noise. This allows us to give a precise meaning to the scaling exponent in terms of the degree to which a given process reduces its sample space as it unfolds. Noisy SSR processes further allow us to explain a wide range of scaling exponents in frequency distributions ranging from α = 2 to ∞. We discuss several applications showing how SSR processes can be used to understand Zipf's law in word frequencies, and how they are related to diffusion processes in directed networks, or aging processes such as in fragmentation processes. SSR processes provide a new alternative to understand the origin of scaling in complex systems without the recourse to multiplicative, preferential, or self-organized critical processes.

Definition of (so MIScalled) ``Complexity" as UTTER-SIMPLICITY!!!(sMciUS!!!) Versus Deviations From( sMciUS!!!): ``COMPLICATEDNESS" Definition(s) and MEASURE(S)!!!

NASA Astrophysics Data System (ADS)

Young, F.; Siegel, E.

2010-03-01

(so MIScalled) ``complexity''(sMc) associated BOTH SCALE- INVARIANCE Symmetry-RESTORING(S-I S-R) [vs. S-I S-B!!!], AND X (w) P(w ) 1/w^(1.000...) ``pink''/Zipf/Archimedes-HYPERBOLICITY INEVITABILITY CONNECTION is by simple-calculus SISR's logarithm- function derivative: (d/dw)ln(w)=1/w=1/w^(1.000...), hence: (d/dw) [SISR](w)=1/w=1/w^(1.000...)=(via Noether-theorem relating continuous-(SISR)-symmetries to conservation-laws)=(d/dw)[4-DIV (J(INTER-SCALE)=0](w)=1/w =1/w^(1.000...). Hence sMc is information inter-scale conservation [as Anderson-Mandell, Fractals of Brain; Fractals of Mind(1994)-experimental- psychology!!!], i.e. sMciUS!!!, VERSUS ``COMPLICATEDNESS", is sMcciUS!!!: EITHER: PLUS (Additive: Murphy's-law absence) OR TIMES (Multiplicative: Murphy's-law dominance) various disparate system-specificity ``COMPLICATIONS". ``COMPLICATEDNESS" MEASURES: DEVIATIONS FROM sMciUS!!!: EITHER [S-I S-B] MINUS [S- I S-R] AND/OR [``red"/Pareto X(w) P(w) 1/w^(#=/=1.000...)] MINUS [X(w) P(w) 1/w^(1.000...) ``pink"/Zipf/Archimedes-HYPERBOLICITY INEVITABILITY] = [1/w^(#=/=1.000...)] MINUS [1/w^(1.000...)]; almost but not exactly a fractals Hurst-exponent-like [# - 1.000...]!!!

Thermodynamic analysis of trimethylgallium decomposition during GaN metal organic vapor phase epitaxy

NASA Astrophysics Data System (ADS)

Sekiguchi, Kazuki; Shirakawa, Hiroki; Chokawa, Kenta; Araidai, Masaaki; Kangawa, Yoshihiro; Kakimoto, Koichi; Shiraishi, Kenji

2018-04-01

We analyzed the decomposition of Ga(CH3)3 (TMG) during the metal organic vapor phase epitaxy (MOVPE) of GaN on the basis of first-principles calculations and thermodynamic analysis. We performed activation energy calculations of TMG decomposition and determined the main reaction processes of TMG during GaN MOVPE. We found that TMG reacts with the H2 carrier gas and that (CH3)2GaH is generated after the desorption of the methyl group. Next, (CH3)2GaH decomposes into (CH3)GaH2 and this decomposes into GaH3. Finally, GaH3 becomes GaH. In the MOVPE growth of GaN, TMG decomposes into GaH by the successive desorption of its methyl groups. The results presented here concur with recent high-resolution mass spectroscopy results.

Tool independence for the Web Accessibility Quantitative Metric.

PubMed

Vigo, Markel; Brajnik, Giorgio; Arrue, Myriam; Abascal, Julio

2009-07-01

The Web Accessibility Quantitative Metric (WAQM) aims at accurately measuring the accessibility of web pages. One of the main features of WAQM among others is that it is evaluation tool independent for ranking and accessibility monitoring scenarios. This article proposes a method to attain evaluation tool independence for all foreseeable scenarios. After demonstrating that homepages have a more similar error profile than any other web page in a given web site, 15 homepages were measured with 10,000 different values of WAQM parameters using EvalAccess and LIFT, two automatic evaluation tools for accessibility. A similar procedure was followed with random pages and with several test files obtaining several tuples that minimise the difference between both tools. One thousand four hundred forty-nine web pages from 15 web sites were measured with these tuples and those values that minimised the difference between the tools were selected. Once the WAQM was tuned, the accessibility of 15 web sites was measured with two metrics for web sites, concluding that even if similar values can be produced, obtaining the same scores is undesirable since evaluation tools behave in a different way.

Architecture for interoperable software in biology.

PubMed

Bare, James Christopher; Baliga, Nitin S

2014-07-01

Understanding biological complexity demands a combination of high-throughput data and interdisciplinary skills. One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment. To this end, simple flexible strategies are needed for interconnecting heterogeneous software tools and enabling data exchange between them. Drawing on our own work and that of others, we present several strategies for interoperability and their consequences, in particular, a set of simple data structures--list, matrix, network, table and tuple--that have proven sufficient to achieve a high degree of interoperability. We provide a few guidelines for the development of future software that will function as part of an interoperable community of software tools for biological data analysis and visualization. © The Author 2012. Published by Oxford University Press.

Thermodynamic Analysis of Coherently Grown GaAsN/Ge: Effects of Different Gaseous Sources

NASA Astrophysics Data System (ADS)

Kawano, Jun; Kangawa, Yoshihiro; Yayama, Tomoe; Kakimoto, Koichi; Koukitu, Akinori

2013-04-01

Thermodynamic analysis of coherently grown GaAs1-xNx on Ge with low N content was performed to determine the relationship between solid composition and growth conditions. In this study, a new algorithm for the simulation code, which is applicable to wider combinations of gaseous sources than the traditional algorithm, was developed to determine the influence of different gaseous sources on N incorporation. Using this code, here we successfully compared two cases: one is a system using trimethylgallium (TMG), AsH3, and NH3, and the other uses dimethylhydrazine (DMHy) instead of NH3. It was found that the optimal N/As ratio of input gas in the system using DMHy was much lower than that using NH3. This shows that the newly developed algorithm could be a useful tool for analyzing the N incorporation during the vapor growth of GaAs1-xNx.

Genome-Wide Analysis of Evolutionary Markers of Human Influenza A(H1N1)pdm09 and A(H3N2) Viruses May Guide Selection of Vaccine Strain Candidates.

PubMed

Belanov, Sergei S; Bychkov, Dmitrii; Benner, Christian; Ripatti, Samuli; Ojala, Teija; Kankainen, Matti; Kai Lee, Hong; Wei-Tze Tang, Julian; Kainov, Denis E

2015-11-27

Here we analyzed whole-genome sequences of 3,969 influenza A(H1N1)pdm09 and 4,774 A(H3N2) strains that circulated during 2009-2015 in the world. The analysis revealed changes at 481 and 533 amino acid sites in proteins of influenza A(H1N1)pdm09 and A(H3N2) strains, respectively. Many of these changes were introduced as a result of random drift. However, there were 61 and 68 changes that were present in relatively large number of A(H1N1)pdm09 and A(H3N2) strains, respectively, that circulated during relatively long time. We named these amino acid substitutions evolutionary markers, as they seemed to contain valuable information regarding the viral evolution. Interestingly, influenza A(H1N1)pdm09 and A(H3N2) viruses acquired non-overlapping sets of evolutionary markers. We next analyzed these characteristic markers in vaccine strains recommended by the World Health Organization for the past five years. Our analysis revealed that vaccine strains carried only few evolutionary markers at antigenic sites of viral hemagglutinin (HA) and neuraminidase (NA). The absence of these markers at antigenic sites could affect the recognition of HA and NA by human antibodies generated in response to vaccinations. This could, in part, explain moderate efficacy of influenza vaccines during 2009-2014. Finally, we identified influenza A(H1N1)pdm09 and A(H3N2) strains, which contain all the evolutionary markers of influenza A strains circulated in 2015, and which could be used as vaccine candidates for the 2015/2016 season. Thus, genome-wide analysis of evolutionary markers of influenza A(H1N1)pdm09 and A(H3N2) viruses may guide selection of vaccine strain candidates. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Quantitative effects of composting state variables on C/N ratio through GA-aided multivariate analysis.

PubMed

Sun, Wei; Huang, Guo H; Zeng, Guangming; Qin, Xiaosheng; Yu, Hui

2011-03-01

It is widely known that variation of the C/N ratio is dependent on many state variables during composting processes. This study attempted to develop a genetic algorithm aided stepwise cluster analysis (GASCA) method to describe the nonlinear relationships between the selected state variables and the C/N ratio in food waste composting. The experimental data from six bench-scale composting reactors were used to demonstrate the applicability of GASCA. Within the GASCA framework, GA searched optimal sets of both specified state variables and SCA's internal parameters; SCA established statistical nonlinear relationships between state variables and the C/N ratio; to avoid unnecessary and time-consuming calculation, a proxy table was introduced to save around 70% computational efforts. The obtained GASCA cluster trees had smaller sizes and higher prediction accuracy than the conventional SCA trees. Based on the optimal GASCA tree, the effects of the GA-selected state variables on the C/N ratio were ranged in a descending order as: NH₄+-N concentration>Moisture content>Ash Content>Mean Temperature>Mesophilic bacteria biomass. Such a rank implied that the variation of ammonium nitrogen concentration, the associated temperature and the moisture conditions, the total loss of both organic matters and available mineral constituents, and the mesophilic bacteria activity, were critical factors affecting the C/N ratio during the investigated food waste composting. This first application of GASCA to composting modelling indicated that more direct search algorithms could be coupled with SCA or other multivariate analysis methods to analyze complicated relationships during composting and many other environmental processes. Copyright © 2010 Elsevier B.V. All rights reserved.

Analytical solution of a stochastic model of risk spreading with global coupling

NASA Astrophysics Data System (ADS)

Morita, Satoru; Yoshimura, Jin

2013-11-01

We study a stochastic matrix model to understand the mechanics of risk spreading (or bet hedging) by dispersion. Up to now, this model has been mostly dealt with numerically, except for the well-mixed case. Here, we present an analytical result that shows that optimal dispersion leads to Zipf's law. Moreover, we found that the arithmetic ensemble average of the total growth rate converges to the geometric one, because the sample size is finite.

Kansas environmental and resource study: A Great Plains model. [land use, image enhancement, winter wheat, agriculture, water resources, and pattern recognition

NASA Technical Reports Server (NTRS)

Haralick, R. M.; Kanemasu, E. T.; Morain, S. A.; Yarger, H. L.; Ulaby, F. T.; Davis, J. C. (Principal Investigator); Bosley, R. J.; Williams, D. L.; Mccauley, J. R.; Mcnaughton, J. L.

1973-01-01

The author has identified the following significant results. Improvement in the land use classification accuracy of ERTS-1 MSS multi-images over Kansas can be made using two distances between neighboring grey tone N-tuples instead of one distance. Much more information is contained texturally than spectrally on the Kansas image. Ground truth measurements indicate that reflectance ratios of the 545 and 655 nm wavebands provide an index of plant development and possibly physiological stress. Preliminary analysis of MSS 4 and 5 channels substantiate the ground truth interpretation. Results of the land use mapping experiment indicate that ERTS-1 imagery has major potential in regionalization. The ways in which land is utilized within these regions may then be studied more effectively than if no adequate regionalization is available. A model for estimating wheat yield per acre has been applied to acreage estimates derived from ERTS-1 imagery to project the 1973 wheat yields for a ten county area in southwest Kansas. The results are within 3% of the preharvest estimates for the same area prepared by the USDA. Visual identification of winter wheat is readily achieved by using a temporal sequence of images. Identification can be improve by stratifying the project area into subregions having more or less homogeneous agricultural practices and crop mixes.

Optical model potential analysis of n ¯A and n A interactions

NASA Astrophysics Data System (ADS)

Lee, Teck-Ghee; Wong, Cheuk-Yin

2018-05-01

We use a momentum-dependent optical model potential to analyze the annihilation cross sections of the antineutron n ¯ on C, Al, Fe, Cu, Ag, Sn, and Pb nuclei for projectile momenta plab ≲500 MeV /c . We obtain a good description of annihilation cross section data of Barbina et al. [Nucl. Phys. A 612, 346 (1997), 10.1016/S0375-9474(96)00331-4] and of Astrua et al. [Nucl. Phys. A 697, 209 (2002), 10.1016/S0375-9474(01)01252-0] which exhibit an interesting dependence of the cross sections on plab as well as on the target mass number A . We also obtain the neutron (n ) nonelastic reaction cross sections for the same targets. Comparing the n A reaction cross sections σrecn A to the n ¯A annihilation cross sections σannn ¯A, we find that σannn ¯A is significantly larger than σrecn A, that is, the σannn ¯A/σrecn A cross section ratio lies between the values of about 1.5 to 4.0 in the momentum region where comparison is possible. The dependence of the n ¯ annihilation cross section on the projectile charge is also examined in comparison with the antiproton p ¯. Here we predict the p ¯A annihilation cross section on the simplest assumption that both p ¯A and n ¯A interactions have the same nuclear part of the optical potential but differ only in the electrostatic Coulomb interaction. Deviation from a such simple model extrapolation in measurements will provide new information on the difference between n ¯A and p ¯A potentials.

Nitrogen Cycle Evaluation (NiCE) Chip for the Simultaneous Analysis of Multiple N-Cycle Associated Genes.

PubMed

Oshiki, Mamoru; Segawa, Takahiro; Ishii, Satoshi

2018-02-02

Various microorganisms play key roles in the Nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR-amplicon sequencing of the N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible in the N transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive especially when we analyze multiple samples and try to detect N cycle functional genes present at relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named as N cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine abundance and diversity of N cycle functional genes in wastewater samples. Although non-specific amplification was detected on the NiCE chip, this could be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples. Importance. We report a novel approach, namely Nitrogen Cycle Evaluation (NiCE) chip by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess diversities of the N cycle functional genes. The NiCE chip technology is applicable to analyze the temporal dynamics of the N cycle gene

Combining Spatial-Temporal and Phylogenetic Analysis Approaches for Improved Understanding on Global H5N1 Transmission

PubMed Central

Liang, Lu; Xu, Bing; Chen, Yanlei; Liu, Yang; Cao, Wuchun; Fang, Liqun; Feng, Limin; Goodchild, Michael F.; Gong, Peng

2010-01-01

Background Since late 2003, the highly pathogenic influenza A H5N1 had initiated several outbreak waves that swept across the Eurasia and Africa continents. Getting prepared for reassortment or mutation of H5N1 viruses has become a global priority. Although the spreading mechanism of H5N1 has been studied from different perspectives, its main transmission agents and spread route problems remain unsolved. Methodology/Principal Findings Based on a compilation of the time and location of global H5N1 outbreaks from November 2003 to December 2006, we report an interdisciplinary effort that combines the geospatial informatics approach with a bioinformatics approach to form an improved understanding on the transmission mechanisms of H5N1 virus. Through a spherical coordinate based analysis, which is not conventionally done in geographical analyses, we reveal obvious spatial and temporal clusters of global H5N1 cases on different scales, which we consider to be associated with two different transmission modes of H5N1 viruses. Then through an interdisciplinary study of both geographic and phylogenetic analysis, we obtain a H5N1 spreading route map. Our results provide insight on competing hypotheses as to which avian hosts are responsible for the spread of H5N1. Conclusions/Significance We found that although South China and Southeast Asia may be the virus pool of avian flu, East Siberia may be the source of the H5N1 epidemic. The concentration of migratory birds from different places increases the possibility of gene mutation. Special attention should be paid to East Siberia, Middle Siberia and South China for improved surveillance of H5N1 viruses and monitoring of migratory birds. PMID:21042591

Natural bond orbital analysis, electronic structure and vibrational spectral analysis of N-(4-hydroxyl phenyl) acetamide: A density functional theory

NASA Astrophysics Data System (ADS)

Govindasamy, P.; Gunasekaran, S.; Ramkumaar, G. R.

2014-09-01

The Fourier transform infrared (FT-IR) and FT-Raman spectra of N-(4-hydroxy phenyl) acetamide (N4HPA) of painkiller agent were recorded in the region 4000-450 cm-1 and 4000-50 cm-1 respectively. Density functional theory (DFT) has been used to calculate the optimized geometrical parameter, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations at DFT/B3LYP level with 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p) and 6-311++G(d,p) basis sets. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using Vibrational energy distribution analysis (VEDA 4) program. The oscillator’s strength calculated by TD-DFT and N4HPA is approach complement with the experimental findings. The NMR chemical shifts 13C and 1H were recorded and calculated using the gauge independent atomic orbital (GIAO) method. The molecular electrostatic potential (MESP) and electron density surfaces of the molecule were constructed. The Natural charges and intermolecular contacts have been interpreted using Natural Bond orbital (NBO) analysis the HOMO-LUMO energy gap has been calculated. The thermodynamic properties like entropy, heat capacity and zero vibrational energy have been calculated.

Ion Mobility-Mass Spectrometry Analysis of Serum N-linked Glycans from Esophageal Adenocarcinoma Phenotypes

PubMed Central

Gaye, M. M.; Valentine, S. J.; Hu, Y.; Mirjankar, N.; Hammoud, Z. T.; Mechref, Y.; Lavine, B. K.; Clemmer, D. E.

2012-01-01

Three disease phenotypes, Barrett’s esophagus (BE), high-grade dysplasia (HGD), esophageal adenocarcinoma (EAC), and a set of normal control (NC) serum samples are examined using a combination of ion mobility spectrometry (IMS), mass spectrometry (MS) and principal component analysis (PCA) techniques. Samples from a total of 136 individuals were examined, including: 7 characterized as BE, 12 as HGD, 56 as EAC and 61 as NC. In typical datasets it was possible to assign ~20 to 30 glycan ions based on MS measurements. Ion mobility distributions for these ions show multiple features. In some cases, such as the [S1H5N4+3Na]3+ and [S1F1H5N4+3Na]3+ glycan ions, the ratio of intensities of high-mobility features to low-mobility features vary significantly for different groups. The degree to which such variations in mobility profiles can be used to distinguish phenotypes is evaluated for eleven N-linked glycan ions. An outlier analysis on each sample class followed by an unsupervised PCA using a genetic algorithm for pattern recognition reveals that EAC samples are separated from NC samples based on 46 features originating from the 11-glycan composite IMS distribution. PMID:23126309

Theoretical analysis of nBn infrared photodetectors

NASA Astrophysics Data System (ADS)

Ting, David Z.; Soibel, Alexander; Khoshakhlagh, Arezou; Gunapala, Sarath D.

2017-09-01

The depletion and surface leakage dark current suppression properties of unipolar barrier device architectures such as the nBn have been highly beneficial for III-V semiconductor-based infrared detectors. Using a one-dimensional drift-diffusion model, we theoretically examine the effects of contact doping, minority carrier lifetime, and absorber doping on the dark current characteristics of nBn detectors to explore some basic aspects of their operation. We found that in a properly designed nBn detector with highly doped excluding contacts the minority carriers are extracted to nonequilibrium levels under reverse bias in the same manner as the high operating temperature (HOT) detector structure. Longer absorber Shockley-Read-Hall (SRH) lifetimes result in lower diffusion and depletion dark currents. Higher absorber doping can also lead to lower diffusion and depletion dark currents, but the benefit should be weighted against the possibility of reduced diffusion length due to shortened SRH lifetime. We also briefly examined nBn structures with unintended minority carrier blocking barriers due to excessive n-doping in the unipolar electron barrier, or due to a positive valence band offset between the barrier and the absorber. Both types of hole blocking structures lead to higher turn-on bias, although barrier n-doping could help suppress depletion dark current.

National Computer Security Conference (15th) held in Baltimore, Maryland on October 13-16, 1992. Volume 2: Proceedings

DTIC Science & Technology

1992-10-16

the DNA Fingerprint Laboratory. The Los Angeles Police Department and its former Chief, Daryl Gates for permitting a secret unit, the ...authorized to change information in. Conclusions Where angels fear .... Of all the reasons for compartmentation for which the level of evaluation...database, and a security label attribute is associated with data in each tuple in a relation. The range and distribution of security levels may

Knowledge Base Refinement as Improving an Incorrect and Incomplete Domain Theory

DTIC Science & Technology

1990-04-01

Ginsberg et al., 1985), and RL (Fu and Buchanan, 1985), which perform empirical induction over a library of test cases. This chapter describes a new...state knowledge. Examples of high-level goals are: to test a hypothesis, to differentiate between several plausible hypotheses, to ask a clarifying...one tuple when we Group Hypotheses Test Hypothesis Applyrule Findout Strategy Metarule Strategy Metarule Strategy Metarule Strategy Metarule goal(group

[Analysis of microdeletions in 22q11 in Colombian patients with congenital heart disease].

PubMed

Salazar, Marleny; Villalba, Guiovanny; Mateus, Heidi; Villegas, Victoria; Fonseca, Dora; Núñez, Federico; Caicedo, Víctor; Pachón, Sonia; Bernal, Jaime E

2011-12-01

Cardiac defects are the most frequent congenital malformations, with an incidence estimated between 4 and 12 per 1000 newborns. Their etiology is multifactorial and might be attributed to genetic predispositions and environmental factors. Since 1990 these types of pathologies have been associated with 22q11 microdeletion. In this study, the frequency of microdeletion 22q11 was determined in 61 patients with non-syndromic congenital heart disease. DNA was extracted from peripheral blood and TUPLE1 and STR D10S2198 genes were amplified by multiplex PCR and visualized in agarose gels. Gene content was quantified by densitometry. Three patients were found with microdeletion 22q11, representing a 4.9% frequency. This microdeletion was associated with two cases of Tetralogy of Fallot and a third case with atrial septal defect (ASD). In conclusion, the frequency for microdeletion 22q11 in the population analyzed was 4.9%. The cases that presented Teratology of Fallot had a frequency for this microdeletion of 7.4% and for ASD of 11.1%.

Characterization and production and consumption processes of N2O emitted from temperate agricultural soils determined via isotopomer ratio analysis

NASA Astrophysics Data System (ADS)

Toyoda, Sakae; Yano, Midori; Nishimura, Sei-Ichi; Akiyama, Hiroko; Hayakawa, Atsushi; Koba, Keisuke; Sudo, Shigeto; Yagi, Kazuyuki; Makabe, Akiko; Tobari, Yoshifumi; Ogawa, Nanako O.; Ohkouchi, Naohiko; Yamada, Keita; Yoshida, Naohiro

2011-06-01

Isotopomer ratios of N2O (bulk nitrogen and oxygen isotope ratios, δ15Nbulk and δ18O, and intramolecular 15N site preference, SP) are useful parameters that characterize sources of this greenhouse gas and also provide insight into production and consumption mechanisms. We measured isotopomer ratios of N2O emitted from typical Japanese agricultural soils (Fluvisols and Andisols) planted with rice, wheat, soybean, and vegetables, and treated with synthetic (urea or ammonium) and organic (poultry manure) fertilizers. The results were analyzed using a previously reported isotopomeric N2O signature produced by nitrifying/denitrifying bacteria and a characteristic relationship between δ15Nbulk and SP during N2O reduction by denitrifying bacteria. Relative contributions from nitrification (hydroxylamine oxidation) and denitrification (nitrite reduction) to gross N2O production deduced from the analysis depended on soil type and fertilizer. The contribution from nitrification was relatively high (40%-70%) in Andisols amended with synthetic ammonium fertilizer, while denitrification was dominant (50%-90%) in the same soils amended with poultry manure during the period when N2O production occurred in the surface layer. This information on production processes is in accordance with that obtained from flux/concentration analysis of N2O and soil inorganic nitrogen. However, isotopomer analysis further revealed that partial reduction of N2O was pronounced in high-bulk density, alluvial soil (Fluvisol) compared to low-bulk density, volcanic ash soil (Andisol), and that the observed difference in N2O flux between normal and pelleted manure could have resulted from a similar mechanism with different rates of gross production and gross consumption. The isotopomeric analysis is based on data from pure culture bacteria and would be improved by further studies on in situ biological processes in soils including those by fungi. When flux/concentration-weighted average isotopomer

N- and O-glycosylation Analysis of Human C1-inhibitor Reveals Extensive Mucin-type O-Glycosylation.

PubMed

Stavenhagen, Kathrin; Kayili, H Mehmet; Holst, Stephanie; Koeleman, Carolien A M; Engel, Ruchira; Wouters, Diana; Zeerleder, Sacha; Salih, Bekir; Wuhrer, Manfred

2018-06-01

Human C1-inhibitor (C1-Inh) is a serine protease inhibitor and the major regulator of the contact activation pathway as well as the classical and lectin complement pathways. It is known to be a highly glycosylated plasma glycoprotein. However, both the structural features and biological role of C1-Inh glycosylation are largely unknown. Here, we performed for the first time an in-depth site-specific N - and O -glycosylation analysis of C1-Inh combining various mass spectrometric approaches, including C18-porous graphitized carbon (PGC)-LC-ESI-QTOF-MS/MS applying stepping-energy collision-induced dissociation (CID) and electron-transfer dissociation (ETD). Various proteases were applied, partly in combination with PNGase F and exoglycosidase treatment, in order to analyze the (glyco)peptides. The analysis revealed an extensively O -glycosylated N-terminal region. Five novel and five known O -glycosylation sites were identified, carrying mainly core1-type O -glycans. In addition, we detected a heavily O -glycosylated portion spanning from Thr 82 -Ser 121 with up to 16 O -glycans attached. Likewise, all known six N -glycosylation sites were covered and confirmed by this site-specific glycosylation analysis. The glycoforms were in accordance with results on released N -glycans by MALDI-TOF/TOF-MS/MS. The comprehensive characterization of C1-Inh glycosylation described in this study will form the basis for further functional studies on the role of these glycan modifications. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Prognostic factors and relative risk for survival in N1-3 oral squamous cell carcinoma: a multivariate analysis using Cox's hazard model.

PubMed

Noguchi, M; Kido, Y; Kubota, H; Kinjo, H; Kohama, G

1999-12-01

The records of 136 patients with N1-3 oral squamous cell carcinoma treated by surgery were investigated retrospectively, with the aim of finding out which factors were predictive of survival on multivariate analysis. Four independent factors significantly influenced survival in the following order: pN stage; T stage; histological grade; and N stage. The most significant was pN stage, the five-year survival for patients with pN0 being 91% and for patients with pN1-3 41%. A further study was carried out on the 80 patients with pN1-3 to find out their prognostic factors for survival and the independent factors identified by multivariate analysis were T stage and presence or absence of extracapsular spread to metastatic lymph nodes.

Systematic R -matrix analysis of the 13C(p ,γ )14N capture reaction

NASA Astrophysics Data System (ADS)

Chakraborty, Suprita; deBoer, Richard; Mukherjee, Avijit; Roy, Subinit

2015-04-01

Background: The proton capture reaction 13C(p ,γ )14N is an important reaction in the CNO cycle during hydrogen burning in stars with mass greater than the mass of the Sun. It also occurs in astrophysical sites such as red giant stars: the asymptotic giant branch (AGB) stars. The low energy astrophysical S factor of this reaction is dominated by a resonance state at an excitation energy of around 8.06 MeV (Jπ=1-,T =1 ) in 14N. The other significant contributions come from the low energy tail of the broad resonance with Jπ=0-,T =1 at an excitation of 8.78 MeV and the direct capture process. Purpose: Measurements of the low energy astrophysical S factor of the radiative capture reaction 13C(p ,γ )14N reported extrapolated values of S (0 ) that differ by about 30 % . Subsequent R -matrix analysis and potential model calculations also yielded significantly different values for S (0 ) . The present work intends to look into the discrepancy through a detailed R -matrix analysis with emphasis on the associated uncertainties. Method: A systematic reanalysis of the available decay data following the capture to the Jπ=1-,T =1 resonance state of 14N around 8.06 MeV excitation had been performed within the framework of the R -matrix method. A simultaneous analysis of the 13C(p ,p0 ) data, measured over a similar energy range, was carried out with the capture data. The data for the ground state decay of the broad resonance state (Jπ=0-,T =1 ) around 8.78 MeV excitations was included as well. The external capture model along with the background poles to simulate the internal capture contribution were used to estimate the direct capture contribution. The asymptotic normalization constants (ANCs) for all states were extracted from the capture data. The multichannel, multilevel R -matrix code azure2 was used for the calculation. Results: The values of the astrophysical S factor at zero relative energy, resulting from the present analysis, are found to be consistent within the

Systematic analysis of inelastic α scattering off self-conjugate A =4 n nuclei

NASA Astrophysics Data System (ADS)

Adachi, S.; Kawabata, T.; Minomo, K.; Kadoya, T.; Yokota, N.; Akimune, H.; Baba, T.; Fujimura, H.; Fujiwara, M.; Funaki, Y.; Furuno, T.; Hashimoto, T.; Hatanaka, K.; Inaba, K.; Ishii, Y.; Itoh, M.; Iwamoto, C.; Kawase, K.; Maeda, Y.; Matsubara, H.; Matsuda, Y.; Matsuno, H.; Morimoto, T.; Morita, H.; Murata, M.; Nanamura, T.; Ou, I.; Sakaguchi, S.; Sasamoto, Y.; Sawada, R.; Shimizu, Y.; Suda, K.; Tamii, A.; Tameshige, Y.; Tsumura, M.; Uchida, M.; Uesaka, T.; Yoshida, H. P.; Yoshida, S.

2018-01-01

We systematically measured the differential cross sections of inelastic α scattering off self-conjugate A =4 n nuclei at two incident energies Eα=130 MeV and 386 MeV at Research Center for Nuclear Physics, Osaka University. The measured cross sections were analyzed by the distorted-wave Born-approximation (DWBA) calculation using the single-folding potentials, which are obtained by folding macroscopic transition densities with the phenomenological α N interaction. The DWBA calculation with the density-dependent α N interaction systematically overestimates the cross sections for the Δ L =0 transitions. However, the DWBA calculation using the density-independent α N interaction reasonably well describes all the transitions with Δ L =0 -4. We examined uncertainties in the present DWBA calculation stemming from the macroscopic transition densities, distorting potentials, phenomenological α N interaction, and coupled channel effects in 12C. It was found that the DWBA calculation is not sensitive to details of the transition densities nor the distorting potentials, and the phenomenological density-independent α N interaction gives reasonable results. The coupled-channel effects are negligibly small for the 21+ and 31- states in 12C, but not for the 02+ state. However, the DWBA calculation using the density-independent interaction at Eα=386 MeV is still reasonable even for the 02+ state. We concluded that the macroscopic DWBA calculations using the density-independent interaction are reliably applicable to the analysis of inelastic α scattering at Eα˜100 MeV /u .

Electron microscopic analysis and structural characterization of novel NADP(H)-containing methanol: N,N'-dimethyl-4-nitrosoaniline oxidoreductases from the gram-positive methylotrophic bacteria Amycolatopsis methanolica and Mycobacterium gastri MB19.

PubMed Central

Bystrykh, L V; Vonck, J; van Bruggen, E F; van Beeumen, J; Samyn, B; Govorukhina, N I; Arfman, N; Duine, J A; Dijkhuizen, L

1993-01-01

The quaternary protein structure of two methanol:N,N'-dimethyl-4-nitrosoaniline (NDMA) oxidoreductases purified from Amycolatopsis methanolica and Mycobacterium gastri MB19 was analyzed by electron microscopy and image processing. The enzymes are decameric proteins (displaying fivefold symmetry) with estimated molecular masses of 490 to 500 kDa based on their subunit molecular masses of 49 to 50 kDa. Both methanol:NDMA oxidoreductases possess a tightly but noncovalently bound NADP(H) cofactor at an NADPH-to-subunit molar ratio of 0.7. These cofactors are redox active toward alcohol and aldehyde substrates. Both enzymes contain significant amounts of Zn2+ and Mg2+ ions. The primary amino acid sequences of the A. methanolica and M. gastri MB19 methanol:NDMA oxidoreductases share a high degree of identity, as indicated by N-terminal sequence analysis (63% identity among the first 27 N-terminal amino acids), internal peptide sequence analysis, and overall amino acid composition. The amino acid sequence analysis also revealed significant similarity to a decameric methanol dehydrogenase of Bacillus methanolicus C1. Images PMID:8449887

Phylogenetic analysis of H9N2 avian influenza viruses in Afghanistan (2016-2017).

PubMed

Hosseini, Hossein; Ghalyanchilangeroudi, Arash; Fallah Mehrabadi, Mohammad Hossein; Sediqian, Mohammad Saeed; Shayeganmehr, Arzhang; Ghafouri, Seyed Ali; Maghsoudloo, Hossein; Abdollahi, Hamed; Farahani, Reza Kh

2017-10-01

Avian influenza A virus (AIV) subtype H9N2 is the most prevalent subtype found in terrestrial poultry throughout Eurasia and has been isolated from poultry outbreaks worldwide. Tracheal tissue specimens from 100 commercial broiler flocks in Afghanistan were collected between 2016 and 2017. After real-time RT-PCR, AI-positive samples were further characterized. A part of the HA gene was amplified using RT-PCR and sequenced. The results of real-time RT-PCR showed that 40 percent of the flocks were AI positive. Phylogenetic studies showed that these H9N2 AIVs grouped within the Eurasian-lineage G1 AIVs and had a correlation with H9N2 AIV circulating in the poultry population of the neighboring countries over the past decade. Analysis of the amino acid sequence of HA revealed that the detected H9N2 viruses possessed molecular profiles suggestive of low pathogenicity and specificity for the avian-like SAα2,3 receptor, demonstrating their specificity for and adaptation to domestic poultry. The results of the current study provide great insights into H9N2 viruses circulating in Afghanistan's poultry industry and demonstrate the necessity of planning an applied policy aimed at controlling and managing H9N2 infection in Afghan poultry.

Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase.

PubMed

Kaur, Gurmeet; Subramanian, Srikrishna

2017-10-18

Threonine synthase (TS) catalyzes the terminal reaction in the biosynthetic pathway of threonine and requires pyridoxal phosphate as a cofactor. TSs share a common catalytic domain with other fold type II PALP dependent enzymes. TSs are broadly grouped into two classes based on their sequence, quaternary structure, and enzyme regulation. We report the presence of a novel zinc ribbon domain in the N-terminal region preceding the catalytic core in TS. The zinc ribbon domain is present in TSs belonging to both classes. Our sequence analysis reveals that archaeal TSs possess all zinc chelating residues to bind a metal ion that are lacking in the structurally characterized homologs. Phylogenetic analysis suggests that TSs with an N-terminal zinc ribbon likely represents the ancestral state of the enzyme while TSs without a zinc ribbon must have diverged later in specific lineages. The zinc ribbon and its N- and C-terminal extensions are important for enzyme stability, activity and regulation. It is likely that the zinc ribbon domain is involved in higher order oligomerization or mediating interactions with other biomolecules leading to formation of larger metabolic complexes.

Study of Staphylococcus aureus N315 Pathogenic Genes by Text Mining and Enrichment Analysis of Pathways and Operons.

PubMed

Yang, Chun-Feng; Gou, Wei-Hui; Dai, Xin-Lun; Li, Yu-Mei

2018-06-01

Staphylococcus aureus (S. aureus) is a versatile pathogen found in many environments and can cause nosocomial infections in the community and hospitals. S. aureus infection is an increasingly serious threat to global public health that requires action across many government bodies, medical and health sectors, and scientific research institutions. In the present study, S. aureus N315 genes that have been shown in the literature to be pathogenic were extracted using a bibliometric method for functional enrichment analysis of pathways and operons to statistically discover novel pathogenic genes associated with S. aureus N315. A total of 383 pathogenic genes were mined from the literature using bibliometrics, and subsequently a few new pathogenic genes of S. aureus N315 were identified by functional enrichment analysis of pathways and operons. The discovery of these novel S. aureus N315 pathogenic genes is of great significance to treat S. aureus induced diseases and identify potential diagnostic markers, thus providing theoretical fundamentals for epidemiological prevention.

Compound-specific 15N analysis of amino acids in 15N tracer experiments provide an estimate of newly synthesised soil protein from inorganic and organic substrates

NASA Astrophysics Data System (ADS)

Charteris, Alice; Michaelides, Katerina; Evershed, Richard

2015-04-01

Organic N concentrations far exceed those of inorganic N in most soils and despite much investigation, the composition and cycling of this complex pool of SOM remains poorly understood. A particular problem has been separating more recalcitrant soil organic N from that actively cycling through the soil system; an important consideration in N cycling studies and for the soil's nutrient supplying capacity. The use of 15N-labelled substrates as stable isotope tracers has contributed much to our understanding of the soil system, but the complexity and heterogeneity of soil organic N prevents thorough compound-specific 15N analyses of organic N compounds and makes it difficult to examine any 15N-labelled organic products in any detail. As a result, a significant proportion of previous work has either simply assumed that since the majority of soil N is organic, all of the 15N retained in the soil is organic N (e.g. Sebilo et al., 2013) or subtracted 15N-labelled inorganic compounds from bulk values (e.g. Pilbeam et al., 1997). While the latter approach is more accurate, these methods only provide an estimate of the bulk 15N value of an extremely complex and non-uniformly labelled organic pool. A more detailed approach has been to use microbial biomass extraction (Brookes et al., 1985) and subsequent N isotopic analysis to determine the 15N value of biomass-N, representing the fraction of 15N assimilated by microbes or the 15N cycling through the 'living' or 'active' portion of soil organic N. However, this extraction method can only generate estimates and some lack of confidence in its validity and reliability remains. Here, we present an alternative technique to obtain a measure of the assimilation of an applied 15N substrate by the soil microbial biomass and an estimate of the newly synthesized soil protein, which is representative of the magnitude of the active soil microbial biomass. The technique uses a stable isotope tracer and compound-specific 15N analysis, but

Metal chelates of phosphonate-containing ligands-III Analytical applications of N,N,N',N'-ethylenediaminetetra(methylenephosphonic) acid.

PubMed

Zaki, M T; Rizkalla, E N

1980-05-01

N,N*,N',N'-Ethylenediaminetetra(methylenephosphonic) acid is used as a titrant for the direct determination of Cu, Co and Ni, with murexide as indicator. Indirect titrimetric procedures are suggested for the determination of silver, mercury, zinc and cyanide and both direct and indirect methods are applied for the analysis of binary mixtures of silver (or mercury) and copper (cobalt or nickel). The stoichiometry of the reaction, interferences of some metal ions and the pH effects on the complexation reactions are discussed. The values of the equilibrium constants of the protonated CuH(n)L (n = 1, 2, 3 and 4) as well as the unprotonated CuL chelates have been measured.

FastSim: A Fast Simulation for the SuperB Detector

NASA Astrophysics Data System (ADS)

Andreassen, R.; Arnaud, N.; Brown, D. N.; Burmistrov, L.; Carlson, J.; Cheng, C.-h.; Di Simone, A.; Gaponenko, I.; Manoni, E.; Perez, A.; Rama, M.; Roberts, D.; Rotondo, M.; Simi, G.; Sokoloff, M.; Suzuki, A.; Walsh, J.

2011-12-01

We have developed a parameterized (fast) simulation for detector optimization and physics reach studies of the proposed SuperB Flavor Factory in Italy. Detector components are modeled as thin sections of planes, cylinders, disks or cones. Particle-material interactions are modeled using simplified cross-sections and formulas. Active detectors are modeled using parameterized response functions. Geometry and response parameters are configured using xml files with a custom-designed schema. Reconstruction algorithms adapted from BaBar are used to build tracks and clusters. Multiple sources of background signals can be merged with primary signals. Pattern recognition errors are modeled statistically by randomly misassigning nearby tracking hits. Standard BaBar analysis tuples are used as an event output. Hadronic B meson pair events can be simulated at roughly 10Hz.

A method for determining customer requirement weights based on TFMF and TLR

NASA Astrophysics Data System (ADS)

Ai, Qingsong; Shu, Ting; Liu, Quan; Zhou, Zude; Xiao, Zheng

2013-11-01

'Customer requirements' (CRs) management plays an important role in enterprise systems (ESs) by processing customer-focused information. Quality function deployment (QFD) is one of the main CRs analysis methods. Because CR weights are crucial for the input of QFD, we developed a method for determining CR weights based on trapezoidal fuzzy membership function (TFMF) and 2-tuple linguistic representation (TLR). To improve the accuracy of CR weights, we propose to apply TFMF to describe CR weights so that they can be appropriately represented. Because the fuzzy logic is not capable of aggregating information without loss, TLR model is adopted as well. We first describe the basic concepts of TFMF and TLR and then introduce an approach to compute CR weights. Finally, an example is provided to explain and verify the proposed method.

Natural bond orbital analysis, electronic structure and vibrational spectral analysis of N-(4-hydroxyl phenyl) acetamide: a density functional theory.

PubMed

Govindasamy, P; Gunasekaran, S; Ramkumaar, G R

2014-09-15

The Fourier transform infrared (FT-IR) and FT-Raman spectra of N-(4-hydroxy phenyl) acetamide (N4HPA) of painkiller agent were recorded in the region 4000-450 cm(-1) and 4000-50 cm(-1) respectively. Density functional theory (DFT) has been used to calculate the optimized geometrical parameter, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations at DFT/B3LYP level with 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p) and 6-311++G(d,p) basis sets. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using Vibrational energy distribution analysis (VEDA 4) program. The oscillator's strength calculated by TD-DFT and N4HPA is approach complement with the experimental findings. The NMR chemical shifts 13C and 1H were recorded and calculated using the gauge independent atomic orbital (GIAO) method. The molecular electrostatic potential (MESP) and electron density surfaces of the molecule were constructed. The Natural charges and intermolecular contacts have been interpreted using Natural Bond orbital (NBO) analysis the HOMO-LUMO energy gap has been calculated. The thermodynamic properties like entropy, heat capacity and zero vibrational energy have been calculated. Copyright © 2014 Elsevier B.V. All rights reserved.

An Analysis of the Peculiar Type IIn Supernova 1995N

NASA Astrophysics Data System (ADS)

Baird, M. D.; Garnavich, P. M.; Schlegel, E. M.; Challis, P. M.; Kirshner, R. P.

1998-12-01

SN 1995N is a peculiar type IIn supernova. Spectroscopic and photometric data for this analysis were gathered between May 10, 1995 (two days after discovery) and July 18, 1998. A total of twenty two photometric images and eight spectra were obtained at the FLWO and MMTO. The photometric data show a broad maximum at R=17.0 occurred in late October, 1995, followed by a very slow decline at a rate of 2.39 millimag-day(-1) for R and 1.37 millimag-day(-1) for V. The R decay rate corresponds to a half life of 315 days, which is much longer than that of (56) Co. The spectra show broad hydrogen (1500 km/s FWHM) and oxygen (10000 km/s FWZI) emission features along with many unresolved emission lines. Some of the more interesting narrow lines identified correspond to high ionization states for iron such as Fe VII and Fe X which indicate temperatures as high as 10(6) degrees K. These high ionization states, the X-ray detection by Lewin et al. (1996, IAUC 6445) and the slow photometric decay suggest that SN 1995N is powered by a shock propagating through a dense circumstellar environment. From the earliest observations the energy output appears dominated by the interaction and not by radioactivity, implying that the progenitor exploded well before the discovery of SN 1995N. The situation may be similar to SN 1987A, where the rise in emission from a circumstellar interaction is only now beginning and is expected to peak some 15 years after the supernova explosion.

Effects of Increased Nitrogen Availability on C and N Cycles in Tropical Forests: A Meta-Analysis

PubMed Central

2015-01-01

Atmospheric N deposition is predicted to increase four times over its current status in tropical forests by 2030. Our ability to understand the effects of N enrichment on C and N cycles is being challenged by the large heterogeneity of the tropical forest biome. The specific response will depend on the forest’s nutrient status; however, few studies of N addition appear to incorporate the nutrient status in tropical forests, possibly due to difficulties in explaining how this status is maintained. We used a meta-analysis to explore the consequences of the N enrichment on C and N cycles in tropical montane and lowland forests. We tracked changes in aboveground and belowground plant C and N and in mineral soil in response to N addition. We found an increasing trend of plant biomass in montane forests, but not in lowland forests, as well as a greater increase in NO emission in montane forest compared with lowland forest. The N2O and NO emission increase in both forest; however, the N2O increase in lowland forest was significantly even at first time N addition. The NO emission increase showed be greater at first term compared with long term N addition. Moreover, the increase in total soil N, ammonium, microbial N, and dissolved N concentration under N enrichment indicates a rich N status of lowland forests. The available evidence of N addition experiments shows that the lowland forest is richer in N than montane forests. Finally, the greater increase in N leaching and N gas emission highlights the importance of study the N deposition effect on the global climate change. PMID:26633681

Effects of Increased Nitrogen Availability on C and N Cycles in Tropical Forests: A Meta-Analysis.

PubMed

Bejarano-Castillo, Marylin; Campo, Julio; Roa-Fuentes, Lilia L

2015-01-01

Atmospheric N deposition is predicted to increase four times over its current status in tropical forests by 2030. Our ability to understand the effects of N enrichment on C and N cycles is being challenged by the large heterogeneity of the tropical forest biome. The specific response will depend on the forest's nutrient status; however, few studies of N addition appear to incorporate the nutrient status in tropical forests, possibly due to difficulties in explaining how this status is maintained. We used a meta-analysis to explore the consequences of the N enrichment on C and N cycles in tropical montane and lowland forests. We tracked changes in aboveground and belowground plant C and N and in mineral soil in response to N addition. We found an increasing trend of plant biomass in montane forests, but not in lowland forests, as well as a greater increase in NO emission in montane forest compared with lowland forest. The N2O and NO emission increase in both forest; however, the N2O increase in lowland forest was significantly even at first time N addition. The NO emission increase showed be greater at first term compared with long term N addition. Moreover, the increase in total soil N, ammonium, microbial N, and dissolved N concentration under N enrichment indicates a rich N status of lowland forests. The available evidence of N addition experiments shows that the lowland forest is richer in N than montane forests. Finally, the greater increase in N leaching and N gas emission highlights the importance of study the N deposition effect on the global climate change.

Structural analysis of N-glycans by the glycan-labeling method using 3-aminoquinoline-based liquid matrix in negative-ion MALDI-MS.

PubMed

Nishikaze, Takashi; Kaneshiro, Kaoru; Kawabata, Shin-ichirou; Tanaka, Koichi

2012-11-06

Negative-ion fragmentation of underivatized N-glycans has been proven to be more informative than positive-ion fragmentation. Fluorescent labeling via reductive amination is often employed for glycan analysis, but little is known about the influence of the labeling group on negative-ion fragmentation. We previously demonstrated that the on-target glycan-labeling method using 3-aminoquinoline/α-cyano-4-hydroxycinnamic acid (3AQ/CHCA) liquid matrix enables highly sensitive, rapid, and quantitative N-glycan profiling analysis. The current study investigates the suitability of 3AQ-labeled N-glycans for structural analysis based on negative-ion collision-induced dissociation (CID) spectra. 3AQ-labeled N-glycans exhibited simple and informative CID spectra similar to those of underivatized N-glycans, with product ions due to cross-ring cleavages of the chitobiose core and ions specific to two antennae (D and E ions). The interpretation of diagnostic fragment ions suggested for underivatized N-glycans could be directly applied to the 3AQ-labeled N-glycans. However, fluorescently labeled N-glycans by conventional reductive amination, such as 2-aminobenzamide (2AB)- and 2-pyrydilamine (2PA)-labeled N-glycans, exhibited complicated CID spectra consisting of numerous signals formed by dehydration and multiple cleavages. The complicated spectra of 2AB- and 2PA-labeled N-glycans was found to be due to their open reducing-terminal N-acetylglucosamine (GlcNAc) ring, rather than structural differences in the labeling group in the N-glycan derivative. Finally, as an example, the on-target 3AQ labeling method followed by negative-ion CID was applied to structurally analyze neutral N-glycans released from human epidermal growth factor receptor type 2 (HER2) protein. The glycan-labeling method using 3AQ-based liquid matrix should facilitate highly sensitive quantitative and qualitative analyses of glycans.

Causal Analysis of Self-tracked Time Series Data Using a Counterfactual Framework for N-of-1 Trials.

PubMed

Daza, Eric J

2018-02-01

Many of an individual's historically recorded personal measurements vary over time, thereby forming a time series (e.g., wearable-device data, self-tracked fitness or nutrition measurements, regularly monitored clinical events or chronic conditions). Statistical analyses of such n-of-1 (i.e., single-subject) observational studies (N1OSs) can be used to discover possible cause-effect relationships to then self-test in an n-of-1 randomized trial (N1RT). However, a principled way of determining how and when to interpret an N1OS association as a causal effect (e.g., as if randomization had occurred) is needed.Our goal in this paper is to help bridge the methodological gap between risk-factor discovery and N1RT testing by introducing a basic counterfactual framework for N1OS design and personalized causal analysis.We introduce and characterize what we call the average period treatment effect (APTE), i.e., the estimand of interest in an N1RT, and build an analytical framework around it that can accommodate autocorrelation and time trends in the outcome, effect carryover from previous treatment periods, and slow onset or decay of the effect. The APTE is loosely defined as a contrast (e.g., difference, ratio) of averages of potential outcomes the individual can theoretically experience under different treatment levels during a given treatment period. To illustrate the utility of our framework for APTE discovery and estimation, two common causal inference methods are specified within the N1OS context. We then apply the framework and methods to search for estimable and interpretable APTEs using six years of the author's self-tracked weight and exercise data, and report both the preliminary findings and the challenges we faced in conducting N1OS causal discovery.Causal analysis of an individual's time series data can be facilitated by an N1RT counterfactual framework. However, for inference to be valid, the veracity of certain key assumptions must be assessed critically, and

Bulk and compound-specific isotope analysis of long-chain n-alkanes from a 85,000 year sediment core from Lake Peten Petén Itzá, Guatemala

NASA Astrophysics Data System (ADS)

Mays, J.; Brenner, M.; Curtis, J. H.; Curtis, K.; Hodell, D. A.; Correa-Metrio, A.; Escobar, J.; Dutton, A. L.; Zimmerman, A. R.; Guilderson, T. P.

2013-12-01

Sediment core PI-6 from Lake Petén Itzá, Guatemala possesses an 85-ka record of climate from lowland Central America. Variations in sediment lithology suggest large, abrupt changes in precipitation during the last glacial and deglacial periods, and into the early Holocene. Study of cores from nearby Lake Quexil demonstrated the utility of using the carbon isotopic composition of leaf wax n-alkanes to infer changes in terrestrial vegetation (Huang et al. 2001). Forty-nine samples were taken from composite Petén Itzá core PI-6 to measure carbon isotopes of bulk organic carbon and long-chain n alkanes. Changes in δ13C values indicate shifts in the relative proportion of C3 to C4 biomass. The record shows largest δ13C variations are associated with Heinrich Events. Carbon isotope values in sediments deposited during the Last Glacial Maximum (LGM) indicate moderate precipitation and little rainfall fluctuation. The deglacial was a period of pronounced climate variability, e.g. the Bölling-Allerod and Younger Dryas. Arid times of the deglacial were inferred from samples with the greatest δ13C values in organic matter, reflecting the largest proportion of C4 plants. Such inferences are supported by stable isotope measurements on ostracod shells and analysis of pollen from the same sample depths in core PI-6. Carbon stable isotope measures on bulk organic carbon and n alkane compounds show similar trends throughout the record and the C:N ratio of Petén Itzá sediments indicates a predominantly allochthonous source for bulk organic matter. Hence, isotope measures on bulk organic carbon (δ13CTOC) in sediments from this lake are sufficient to infer climate-driven shifts in vegetation, making n-alkane extraction and isotope analysis superfluous.

Weak vector boson production with many jets at the LHC √{s }=13 TeV

NASA Astrophysics Data System (ADS)

Anger, F. R.; Febres Cordero, F.; Höche, S.; Maître, D.

2018-05-01

Signatures with an electroweak vector boson and many jets play a crucial role at the Large Hadron Collider, both in the measurement of Standard-Model parameters and in searches for new physics. Precise predictions for these multiscale processes are therefore indispensable. We present next-to-leading order QCD predictions for W±/Z +jets at √{s }=13 TeV , including up to five/four jets in the final state. All production channels are included, and leptonic decays of the vector bosons are considered at the amplitude level. We assess theoretical uncertainties arising from renormalization- and factorization-scale dependence by considering fixed-order dynamical scales based on the HT variable as well as on the MiNLO procedure. We also explore uncertainties associated with different choices of parton-distribution functions. We provide event samples that can be explored through publicly available n -tuple sets, generated with BlackHat in combination with Sherpa.

Enhancement of two dimensional electron gas concentrations due to Si{sub 3}N{sub 4} passivation on Al{sub 0.3}Ga{sub 0.7}N/GaN heterostructure: strain and interface capacitance analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dinara, Syed Mukulika, E-mail: smdinara.iit@gmail.com; Jana, Sanjay Kr.; Ghosh, Saptarsi

2015-04-15

Enhancement of two dimensional electron gas (2DEG) concentrations at Al{sub 0.3}Ga{sub 0.7}N/GaN hetero interface after a-Si{sub 3}N{sub 4} (SiN) passivation has been investigated from non-destructive High Resolution X-ray Diffraction (HRXRD) analysis, depletion depth and capacitance-voltage (C-V) profile measurement. The crystalline quality and strained in-plane lattice parameters of Al{sub 0.3}Ga{sub 0.7}N and GaN were evaluated from double axis (002) symmetric (ω-2θ) diffraction scan and double axis (105) asymmetric reciprocal space mapping (DA RSM) which revealed that the tensile strain of the Al{sub 0.3}Ga{sub 0.7}N layer increased by 15.6% after SiN passivation. In accordance with the predictions from theoretical solution of Schrödinger-Poisson’smore » equations, both electrochemical capacitance voltage (ECV) depletion depth profile and C-V characteristics analyses were performed which implied effective 9.5% increase in 2DEG carrier density after passivation. The enhancement of polarization charges results from increased tensile strain in the Al{sub 0.3}Ga{sub 0.7}N layer and also due to the decreased surface states at the interface of SiN/Al{sub 0.3}Ga{sub 0.7}N layer, effectively improving the carrier confinement at the interface.« less

Quantitative Glycoproteomics Analysis Reveals Changes in N-Glycosylation Level Associated with Pancreatic Ductal Adenocarcinoma

PubMed Central

2015-01-01

Glycosylation plays an important role in epithelial cancers, including pancreatic ductal adenocarcinoma. However, little is known about the glycoproteome of the human pancreas or its alterations associated with pancreatic tumorigenesis. Using quantitative glycoproteomics approach, we investigated protein N-glycosylation in pancreatic tumor tissue in comparison with normal pancreas and chronic pancreatitis tissue. The study lead to the discovery of a roster of glycoproteins with aberrant N-glycosylation level associated with pancreatic cancer, including mucin-5AC (MUC5AC), carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), insulin-like growth factor binding protein (IGFBP3), and galectin-3-binding protein (LGALS3BP). Pathway analysis of cancer-associated aberrant glycoproteins revealed an emerging phenomenon that increased activity of N-glycosylation was implicated in several pancreatic cancer pathways, including TGF-β, TNF, NF-kappa-B, and TFEB-related lysosomal changes. In addition, the study provided evidence that specific N-glycosylation sites within certain individual proteins can have significantly altered glycosylation occupancy in pancreatic cancer, reflecting the complexity of the molecular mechanisms underlying cancer-associated glycosylation events. PMID:24471499

Quantitative glycoproteomics analysis reveals changes in N-glycosylation level associated with pancreatic ductal adenocarcinoma.

PubMed

Pan, Sheng; Chen, Ru; Tamura, Yasuko; Crispin, David A; Lai, Lisa A; May, Damon H; McIntosh, Martin W; Goodlett, David R; Brentnall, Teresa A

2014-03-07

Glycosylation plays an important role in epithelial cancers, including pancreatic ductal adenocarcinoma. However, little is known about the glycoproteome of the human pancreas or its alterations associated with pancreatic tumorigenesis. Using quantitative glycoproteomics approach, we investigated protein N-glycosylation in pancreatic tumor tissue in comparison with normal pancreas and chronic pancreatitis tissue. The study lead to the discovery of a roster of glycoproteins with aberrant N-glycosylation level associated with pancreatic cancer, including mucin-5AC (MUC5AC), carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), insulin-like growth factor binding protein (IGFBP3), and galectin-3-binding protein (LGALS3BP). Pathway analysis of cancer-associated aberrant glycoproteins revealed an emerging phenomenon that increased activity of N-glycosylation was implicated in several pancreatic cancer pathways, including TGF-β, TNF, NF-kappa-B, and TFEB-related lysosomal changes. In addition, the study provided evidence that specific N-glycosylation sites within certain individual proteins can have significantly altered glycosylation occupancy in pancreatic cancer, reflecting the complexity of the molecular mechanisms underlying cancer-associated glycosylation events.

Activation Strain Analysis of SN2 Reactions at C, N, O, and F Centers.

PubMed

Kubelka, Jan; Bickelhaupt, F Matthias

2017-02-02

Fundamental principles that determine chemical reactivity and reaction mechanisms are the very foundation of chemistry and many related fields of science. Bimolecular nucleophilic substitutions (S N 2) are among the most common and therefore most important reaction types. In this report, we examine the trends in the S N 2 reactions with respect to increasing electronegativity of the reaction center by comparing the well-studied backside S N 2 Cl - + CH 3 Cl with similar Cl - substitutions on the isoelectronic series with the second period elements N, O, and F in place of C. Relativistic (ZORA) DFT calculations are used to construct the gas phase reaction potential energy surfaces (PES), and activation strain analysis, which allows decomposition of the PES into the geometrical strain and interaction energy, is employed to analyze the observed trends. We find that S N 2@N and S N 2@O have similar PES to the prototypical S N 2@C, with the well-defined reaction complex (RC) local minima and a central barrier, but all stationary points are, respectively, increasingly stable in energy. The S N 2@F, by contrast, exhibits only a single-well PES with no barrier. Using the activation strain model, we show that the trends are due to the interaction energy and originate mainly from the decreasing energy of the empty acceptor orbital (σ* A-Cl ) on the reaction center A in the order of C, N, O, and F. The decreasing steric congestion around the central atom is also a likely contributor to this trend. Additional decomposition of the interaction energy using Kohn-Sham molecular orbital (KS-MO) theory provides further support for this explanation, as well as suggesting electrostatic energy as the primary reason for the distinct single-well PES profile for the FCl reaction.

Performance analysis of junction-less double Gate n-p-n impact ionization MOS transistor (JLDG n-IMOS)

NASA Astrophysics Data System (ADS)

Chauhan, Manvendra Singh; Chauhan, R. K.

2018-04-01

This paper demonstrates a Junction-less Double Gate n-p-n Impact ionization MOS transistor (JLDG n-IMOS) on a very light doped p-type silicon body. Device structure proposed in the paper is based on charge plasma concept. There is no metallurgical junctions in the proposed device and does not need any impurity doping to create the drain and source regions. Due to doping-less nature, the fabrication process is simple for JLDG n-IMOS. The double gate engineering in proposed device leads to reduction in avalanche breakdown via impact ionization, generating large number of carriers in drain-body junction, resulting high ION current, small IOFF current and great improvement in ION/IOFF ratio. The simulation and examination of the proposed device have been performed on ATLAS device simulatorsoftware.

Extending Phrase-Based Decoding with a Dependency-Based Reordering Model

DTIC Science & Technology

2009-11-01

strictly within the confines of phrase-based translation. The hope was to introduce an approach that could take advantage of monolingual syntactic...tuple represents one element of the XML markup, where element is the name of this element, attributes is a dictionary (mapping strings to strings...representing the range of possible compressions, in the form of a dictionary mapping the latter to the former. To represent multiple dependency

Analysis of nonhuman N-glycans as the minor constituents in recombinant monoclonal antibody pharmaceuticals.

PubMed

Maeda, Eiki; Kita, Soichiro; Kinoshita, Mitsuhiro; Urakami, Koji; Hayakawa, Takao; Kakehi, Kazuaki

2012-03-06

Minor N-linked glycans containing N-glycolylneuraminic acid residues and/or α-Gal epitopes (i.e., galactose-α1,3-galactose residues) have been reported to be present in recombinant monoclonal antibody (mAb) therapeutics. These contaminations are due to their production processes using nonhuman mammalian cell lines in culture media containing animal-derived materials. In case of the treatment of tumors, we inevitably use such mAbs by careful risk-benefit considerations to prolong patients' lives. However, expanding their clinical applications such as for rheumatism, asthma, and analgesia demands more careful evaluation of the product characteristics. The present work for detailed evaluations of N-glycans demonstrates the methods using capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) and a combination of high-performance liquid chromatography and electrospray ionization time-of-flight mass spectrometry. The CE-LIF method provides excellent separation of both major and minor N-glycans from six commercial mAb pharmaceuticals within 30 min and clearly indicates that a possible trigger of immunogenicity in humans due to the presence of nonhuman N-glycans is present. We strongly believe that the proposed method will be a powerful tool for the analysis of N-glycans of recombinant mAb products in various development stages, such as clone selection, process control, and routine release testing to ensure safety and efficacy of the products.

Zipf's Law in Short-Time Timbral Codings of Speech, Music, and Environmental Sound Signals

PubMed Central

Haro, Martín; Serrà, Joan; Herrera, Perfecto; Corral, Álvaro

2012-01-01

Timbre is a key perceptual feature that allows discrimination between different sounds. Timbral sensations are highly dependent on the temporal evolution of the power spectrum of an audio signal. In order to quantitatively characterize such sensations, the shape of the power spectrum has to be encoded in a way that preserves certain physical and perceptual properties. Therefore, it is common practice to encode short-time power spectra using psychoacoustical frequency scales. In this paper, we study and characterize the statistical properties of such encodings, here called timbral code-words. In particular, we report on rank-frequency distributions of timbral code-words extracted from 740 hours of audio coming from disparate sources such as speech, music, and environmental sounds. Analogously to text corpora, we find a heavy-tailed Zipfian distribution with exponent close to one. Importantly, this distribution is found independently of different encoding decisions and regardless of the audio source. Further analysis on the intrinsic characteristics of most and least frequent code-words reveals that the most frequent code-words tend to have a more homogeneous structure. We also find that speech and music databases have specific, distinctive code-words while, in the case of the environmental sounds, this database-specific code-words are not present. Finally, we find that a Yule-Simon process with memory provides a reasonable quantitative approximation for our data, suggesting the existence of a common simple generative mechanism for all considered sound sources. PMID:22479497

Sinks for nitrogen inputs in terrestrial ecosystems: a meta-analysis of 15N tracer field studies.

PubMed

Templer, P H; Mack, M C; Chapin, F S; Christenson, L M; Compton, J E; Crook, H D; Currie, W S; Curtis, C J; Dail, D B; D'Antonio, C M; Emmett, B A; Epstein, H E; Goodale, C L; Gundersen, P; Hobbie, S E; Holland, K; Hooper, D U; Hungate, B A; Lamontagne, S; Nadelhoffer, K J; Osenberg, C W; Perakis, S S; Schleppi, P; Schimel, J; Schmidt, I K; Sommerkorn, M; Spoelstra, J; Tietema, A; Wessel, W W; Zak, D R

2012-08-01

Effects of anthropogenic nitrogen (N) deposition and the ability of terrestrial ecosystems to store carbon (C) depend in part on the amount of N retained in the system and its partitioning among plant and soil pools. We conducted a meta-analysis of studies at 48 sites across four continents that used enriched 15N isotope tracers in order to synthesize information about total ecosystem N retention (i.e., total ecosystem 15N recovery in plant and soil pools) across natural systems and N partitioning among ecosystem pools. The greatest recoveries of ecosystem 15N tracer occurred in shrublands (mean, 89.5%) and wetlands (84.8%) followed by forests (74.9%) and grasslands (51.8%). In the short term (< 1 week after 15N tracer application), total ecosystem 15N recovery was negatively correlated with fine-root and soil 15N natural abundance, and organic soil C and N concentration but was positively correlated with mean annual temperature and mineral soil C:N. In the longer term (3-18 months after 15N tracer application), total ecosystem 15N retention was negatively correlated with foliar natural-abundance 15N but was positively correlated with mineral soil C and N concentration and C:N, showing that plant and soil natural-abundance 15N and soil C:N are good indicators of total ecosystem N retention. Foliar N concentration was not significantly related to ecosystem 15N tracer recovery, suggesting that plant N status is not a good predictor of total ecosystem N retention. Because the largest ecosystem sinks for 15N tracer were below ground in forests, shrublands, and grasslands, we conclude that growth enhancement and potential for increased C storage in aboveground biomass from atmospheric N deposition is likely to be modest in these ecosystems. Total ecosystem 15N recovery decreased with N fertilization, with an apparent threshold fertilization rate of 46 kg N x ha(-1) x yr(-1) above which most ecosystems showed net losses of applied 15N tracer in response to N fertilizer

Sinks for nitrogen inputs in terrestrial ecosystems: a meta-analysis of 15N tracer field studies

USGS Publications Warehouse

Templer, P.H.; Mack, M.C.; Chapin, F. S.; Christenson, L.M.; Compton, J.E.; Crook, H.D.; Currie, W.S.; Curtis, C.J.; Dail, D.B.; D'Antonio, C. M.; Emmett, B.A.; Epstein, H.E.; Goodale, C.L.; Gundersen, P.; Hobbie, S.E.; Holland, K.; Hooper, D.U.; Hungate, B.A.; Lamontagne, S.; Nadelhoffer, K.J.; Osenberg, C.W.; Perakis, S.S.; Schleppi, P.; Schimel, J.; Schmidt, I.K.; Sommerkorn, M.; Spoelstra, J.; Tietema, A.; Wessel, W.W.; Zak, D.R.

2012-01-01

Effects of anthropogenic nitrogen (N) deposition and the ability of terrestrial ecosystems to store carbon (C) depend in part on the amount of N retained in the system and its partitioning among plant and soil pools. We conducted a meta-analysis of studies at 48 sites across four continents that used enriched 15N isotope tracers in order to synthesize information about total ecosystem N retention (i.e., total ecosystem 15N recovery in plant and soil pools) across natural systems and N partitioning among ecosystem pools. The greatest recoveries of ecosystem 15N tracer occurred in shrublands (mean, 89.5%) and wetlands (84.8%) followed by forests (74.9%) and grasslands (51.8%). In the short term (15N tracer application), total ecosystem 15N recovery was negatively correlated with fine-root and soil 15N natural abundance, and organic soil C and N concentration but was positively correlated with mean annual temperature and mineral soil C:N. In the longer term (3–18 months after 15N tracer application), total ecosystem 15N retention was negatively correlated with foliar natural-abundance 15N but was positively correlated with mineral soil C and N concentration and C: N, showing that plant and soil natural-abundance 15N and soil C:N are good indicators of total ecosystem N retention. Foliar N concentration was not significantly related to ecosystem 15N tracer recovery, suggesting that plant N status is not a good predictor of total ecosystem N retention. Because the largest ecosystem sinks for 15N tracer were below ground in forests, shrublands, and grasslands, we conclude that growth enhancement and potential for increased C storage in aboveground biomass from atmospheric N deposition is likely to be modest in these ecosystems. Total ecosystem 15N recovery decreased with N fertilization, with an apparent threshold fertilization rate of 46 kg N·ha-1·yr-1 above which most ecosystems showed net losses of applied 15N tracer in response to N fertilizer addition.

Architecture of the hydrophobic and hydrophilic layers as found from crystal structure analysis of N-benzyl-N,N-dimethylalkylammonium bromides.

PubMed

Hodorowicz, Maciej; Stadnicka, Katarzyna; Czapkiewicz, Jan

2005-10-01

The molecular and crystal structures of N-benzyl-N,N-dimethylalkylammonium bromides monohydrates with chain length n=8-10 have been determined. The crystals are isostructural with the N-benzyl-N,N-dimethyldodecylammonium bromide monohydrate. The structures consist of alternated hydrophobic and hydrophilic layers perpendicular to [001]. The attraction between N+ of the cation head-groups and Br- anions is achieved through weak C_H...Br interactions. The water molecules incorporated into ionic layers are donors for two O_H...Br hydrogen bonds and serve as the acceptors in two weak interactions of C_H...O type. The methylene chains, with the slightly curved general shape, have the extended all-trans conformation. The mutual packing of the chains in the hydrophobic layers is governed by weak C_H...pi interactions.

N-propyl nitrate vibrational spectrum analysis using DFT B3LYP quantum-chemical method

NASA Astrophysics Data System (ADS)

Shaikhullina, R. M.; Hrapkovsky, G. M.; Shaikhullina, M. M.

2018-05-01

Calculation of a molecular structure, conformation and related vibrational spectra of the n- propyl nitrate C3H7NO3 was carried out by means of density functional theory (DFT) by employing the Gaussian 03 package. The molecular geometries were fully optimized by using the Becker's three-parameter hybrid exchange functional combined with the Lee–Yang–Parr correlation functional (B3LYP) and using the 6-31G(d) basis set. By scanning the dihedral angles around C-O and C-C bonds, five energetically most favorable conformers of n-propyl nitrate - TG, TT, GT, GG and G´G forms were found. Vibrational spectra of the most energetically favorable conformers were calculated. The comparative analysis of calculated and experimental spectra is carried out, the spectral features of the conformational state of n-propyl nitrate and the spectral effects of formation of intramolecular hydrogen bonds are established.

Mechanical Properties and Thermal Shock Resistance Analysis of BNNT/Si3N4 Composites

NASA Astrophysics Data System (ADS)

Wang, Shouren; Wang, Gaoqi; Wen, Daosheng; Yang, Xuefeng; Yang, Liying; Guo, Peiquan

2018-04-01

BNNT/Si3N4 ceramic composites with different weight amount of BNNT fabricated by hot isostatic pressing were introduced. The mechanical properties and thermal shock resistance of the composites were investigated. The results showed that BNNT-added ceramic composites have a finer and more uniform microstructure than that of BNNT-free Si3N4 ceramic because of the retarding effect of BNNT on Si3N4 grain growth. The addition of 1.5 wt.% BNNT results in simultaneous increase in flexural strength, fracture toughness, and thermal shock resistance. The analysis of the results indicates that BNNT brings many thermal transport channels in the microstructure, increasing the efficiency of thermal transport, therefore results in increase of thermal shock resistance. In addition, BNNT improves the residual flexural strength of composites by crack deflection, bridging, branching and pinning, which increase the crack propagation resistance.

Numerical analysis of the reverse blocking enhancement in High-K passivation AlGaN/GaN Schottky barrier diodes with gated edge termination

NASA Astrophysics Data System (ADS)

Bai, Zhiyuan; Du, Jiangfeng; Xin, Qi; Li, Ruonan; Yu, Qi

2018-02-01

We conducted a numerical analysis on high-K dielectric passivated AlGaN/GaN Schottky barrier diodes (HPG-SBDs) with a gated edge termination (GET). The reverse blocking characteristics were significantly enhanced without the stimulation of any parasitic effect by varying the dielectric thickness dge under the GET, thickness TP, and dielectric constant εr of the high-K passivation layer. The leakage current was reduced by increasing εr and decreasing dge. The breakdown voltage of the device was enhanced by increasing εr and TP. The highest breakdown voltage of 970 V and the lowest leakage current of 0.5 nA/mm were achieved under the conditions of εr = 80, TP = 800 nm, and dge = 10 nm. C-V simulation revealed that the HPG-SBDs induced no parasitic capacitance by comparing the integrated charges of the devices with different high-K dielectrics and different dge.

Influence of N2 partial pressure on structural and microhardness properties of TiN/ZrN multilayers deposited by Ar/N2 vacuum arc discharge

NASA Astrophysics Data System (ADS)

Naddaf, M.; Abdallah, B.; Ahmad, M.; A-Kharroub, M.

2016-08-01

The influence of N2 partial pressure on structural, mechanical and wetting properties of multilayered TiN/ZrN thin films deposited on silicon substrates by vacuum arc discharge of (N2 + Ar) gas mixtures is investigated. X-ray diffraction (XRD) results show that the average texturing coefficient of (1 1 1) orientation and the grain size of both TiN and ZrN individual layers increase with increasing the N2 partial pressure. The Rutherford back scattering (RBS) measurements and analysis reveal that incorporation of the nitrogen in the film increases with increasing the N2 partial pressure and both TiN and ZrN individual layers have a nitrogen over-stoichiometry for N2 partial pressure ⩾50%. The change in the film micro-hardness is correlated to the changes in crystallographic texture, grain size, stoichiometry and the residual stress in the film as a function of the N2 partial pressure. In particular, stoichiometry of ZrN and TiN individual is found to play the vital role in determining the multilayer hardness. The multilayer film deposited at N2 partial pressure of 25% has the best stoichiometric ratio of both TiN and ZrN layers and the highest micro-hardness of about 32 GPa. In addition, water contact angle (WCA) measurements and analysis show a decrease in the work of adhesion on increasing the N2 partial pressure.

Improvement in crystal quality and optical properties of n-type GaN employing nano-scale SiO2 patterned n-type GaN substrate.

PubMed

Jo, Min Sung; Sadasivam, Karthikeyan Giri; Tawfik, Wael Z; Yang, Seung Bea; Lee, Jung Ju; Ha, Jun Seok; Moon, Young Boo; Ryu, Sang Wan; Lee, June Key

2013-01-01

n-type GaN epitaxial layers were regrown on the patterned n-type GaN substrate (PNS) with different size of silicon dioxide (SiO2) nano dots to improve the crystal quality and optical properties. PNS with SiO2 nano dots promotes epitaxial lateral overgrowth (ELOG) for defect reduction and also acts as a light scattering point. Transmission electron microscopy (TEM) analysis suggested that PNS with SiO2 nano dots have superior crystalline properties. Hall measurements indicated that incrementing values in electron mobility were clear indication of reduction in threading dislocation and it was confirmed by TEM analysis. Photoluminescence (PL) intensity was enhanced by 2.0 times and 3.1 times for 1-step and 2-step PNS, respectively.

Structural analysis of N-linked carbohydrate chains of funnel web spider (Agelenopsis aperta) venom peptide isomerase.

PubMed

Shikata, Y; Ohe, H; Mano, N; Kuwada, M; Asakawa, N

1998-06-01

The structure of the N-linked carbohydrate chains of peptide isomerase from the venom of the funnel web spider (Agelenopsis aperta) has been analyzed. Carbohydrates were released from peptide isomerase by hydrazinolysis and reductively aminated with 2-aminopyridine. The fluorescent derivatives were purified by phenol/chloroform extraction, followed by size-exclusion HPLC. The structure of the purified pyridylamino (PA-) carbohydrate chains were analyzed by a combination of two-dimensional HPLC mapping, sugar composition analysis, sequential exoglycosidase digestions, and mass spectrometry. The peptide isomerase contains six kinds of N-linked carbohydrate chains of truncated high-mannose type, with a fucose alpha 1-6 linked to the reducing N-acetylglucosamine in approximately 80% of them.

19F DOSY NMR analysis for spin systems with nJFF couplings.

PubMed

Dal Poggetto, Guilherme; Favaro, Denize C; Nilsson, Mathias; Morris, Gareth A; Tormena, Cláudio F

2014-04-01

NMR is a powerful method for identification and quantification of drug components and contaminations. These problems present themselves as mixtures, and here, one of the most powerful tools is DOSY. DOSY works best when there is no spectral overlap between components, so drugs containing fluorine substituents are well-suited for DOSY analysis as (19)F spectra are typically very sparse. Here, we demonstrate the use of a modified (19)F DOSY experiment (on the basis of the Oneshot sequences) for various fluorinated benzenes. For compounds with significant (n) JFF coupling constants, as is common, the undesirable J-modulation can be efficiently suppressed using the Oneshot45 pulse sequence. This investigation highlights (19)F DOSY as a valuable and robust method for analysis of molecular systems containing fluorine atoms even where there are large fluorine-fluorine couplings. Copyright © 2014 John Wiley & Sons, Ltd.

Communicating uncertainty--how Australian television reported H1N1 risk in 2009: a content analysis.

PubMed

Fogarty, Andrea S; Holland, Kate; Imison, Michelle; Blood, R Warwick; Chapman, Simon; Holding, Simon

2011-03-24

Health officials face particular challenges in communicating with the public about emerging infectious diseases of unknown severity such as the 2009 H1N1(swine 'flu) pandemic (pH1N1). Statements intended to create awareness and convey the seriousness of infectious disease threats can draw accusations of scare-mongering, while officials can be accused of complacency if such statements are not made. In these communication contexts, news journalists, often reliant on official sources to understand issues are pivotal in selecting and emphasising aspects of official discourse deemed sufficiently newsworthy to present to the public. This paper presents a case-study of news communication regarding the emergence of pH1N1. We conducted a content analysis of all television news items about pH1N1. We examined news and current affairs items broadcast on 5 free-to-air Sydney television channels between April 25 2009 (the first report) and October 9 (prior to the vaccine release) for statements about [1] the seriousness of the disease [2] how the public could minimise contagion [3] government responses to emerging information. pH1N1 was the leading health story for eight of 24 weeks and was in the top 5 for 20 weeks. 353 news items were identified, yielding 3086 statements for analysis, with 63.4% related to the seriousness of the situation, 12.9% providing advice for viewers and 23.6% involving assurances from government. Coverage focused on infection/mortality rates, the spread of the virus, the need for public calm, the vulnerability of particular groups, direct and indirect advice for viewers, and government reassurances about effective management. Overall, the reporting of 2009 pH1N1 in Sydney, Australia was generally non-alarmist, while conveying that pH1N1 was potentially serious. Daily infection rate tallies and commentary on changes in the pandemic alert level were seldom contextualised to assist viewers in understanding personal relevance. Suggestions are made about

A meta-analysis of fertilizer-induced soil NO and combined NO+N2 O emissions.

PubMed

Liu, Shuwei; Lin, Feng; Wu, Shuang; Ji, Cheng; Sun, Yi; Jin, Yaguo; Li, Shuqing; Li, Zhaofu; Zou, Jianwen

2017-06-01

Soils are among the important sources of atmospheric nitric oxide (NO) and nitrous oxide (N 2 O), acting as a critical role in atmospheric chemistry. Updated data derived from 114 peer-reviewed publications with 520 field measurements were synthesized using meta-analysis procedure to examine the N fertilizer-induced soil NO and the combined NO+N 2 O emissions across global soils. Besides factors identified in earlier reviews, additional factors responsible for NO fluxes were fertilizer type, soil C/N ratio, crop residue incorporation, tillage, atmospheric carbon dioxide concentration, drought and biomass burning. When averaged across all measurements, soil NO-N fluxes were estimated to be 4.06 kg ha -1  yr -1 , with the greatest (9.75 kg ha -1  yr -1 ) in vegetable croplands and the lowest (0.11 kg ha -1  yr -1 ) in rice paddies. Soil NO emissions were more enhanced by synthetic N fertilizer (+38%), relative to organic (+20%) or mixed N (+18%) sources. Compared with synthetic N fertilizer alone, synthetic N fertilizer combined with nitrification inhibitors substantially reduced soil NO emissions by 81%. The global mean direct emission factors of N fertilizer for NO (EF NO ) and combined NO+N 2 O (EF c ) were estimated to be 1.16% and 2.58%, with 95% confidence intervals of 0.71-1.61% and 1.81-3.35%, respectively. Forests had the greatest EF NO (2.39%). Within the croplands, the EF NO (1.71%) and EF c (4.13%) were the greatest in vegetable cropping fields. Among different chemical N fertilizer varieties, ammonium nitrate had the greatest EF NO (2.93%) and EF c (5.97%). Some options such as organic instead of synthetic N fertilizer, decreasing N fertilizer input rate, nitrification inhibitor and low irrigation frequency could be adopted to mitigate soil NO emissions. More field measurements over multiyears are highly needed to minimize the estimate uncertainties and mitigate soil NO emissions, particularly in forests and vegetable croplands. © 2016 John Wiley

Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes

PubMed Central

Xie, Jian-Bo; Du, Zhenglin; Bai, Lanqing; Tian, Changfu; Zhang, Yunzhi; Xie, Jiu-Yan; Wang, Tianshu; Liu, Xiaomeng; Chen, Xi; Cheng, Qi; Chen, Sanfeng; Li, Jilun

2014-01-01

We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ70-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation. PMID:24651173

Parallelizing Data-Centric Programs

DTIC Science & Technology

2013-09-25

results than current techniques, such as ImageWebs [HGO+10], given the same budget of matches performed. 4.2 Scalable Parallel Similarity Search The work...algorithms. 5 Data-Driven Applications in the Cloud In this project, we investigated what happens when data-centric software is moved from expensive custom ...returns appropriate answer tuples. Figure 9 (b) shows the mutual constraint satisfaction that takes place in answering for 122. The intent is that

Optimization of Extended Relational Database Systems

DTIC Science & Technology

1986-07-23

control functions are integrated into a single system in a homogeneoua way. As a first exam - ple, consider previous work in supporting various semantic...sizes are reduced and, wnk? quently, the number of materializations that will be needed is aba lower. For exam - pie, in the above query tuple...retrieve (EMP.name) where EMP hobbies instrument = ’ violin ’ When the various entries in the hobbies field are materialized, only those queries that

Galerkin analysis of kinematic dynamos in the von Kármán geometry

NASA Astrophysics Data System (ADS)

Marié, L.; Normand, C.; Daviaud, F.

2006-01-01

We investigate dynamo action by solving the kinematic dynamo problem for velocity fields of the von Kármán type between two coaxial counter-rotating propellers in a cylinder. A Galerkin method is implemented that takes advantage of the symmetries of the flow and their subsequent influence on the nature of the magnetic field at the dynamo threshold. Distinct modes of instability have been identified that differ by their spatial and temporal behaviors. Our calculations give the result that a stationary and antisymmetric mode prevails at the dynamo threshold. We then present a quantitative analysis of the results based on the parametric study of four interaction coefficients obtained by reduction of our initially large eigenvalue problem. We propose these coefficients to measure the relative importance of the different mechanisms at play in the von Kármán kinematic dynamo.

Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses

PubMed Central

Winkler, James; Kao, Katy C.

2011-01-01

Background The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates pose significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Currently, these inhibitory compounds must be removed through additional downstream processing or sufficiently diluted to create environments suitable for most industrially important microbial strains. Simultaneously, product toxicity must also be overcome to allow for efficient production of next generation biofuels such as n-butanol, isopropanol, and others from these low cost feedstocks. Methodology and Principal Findings This study explores the high ferulic acid and n-butanol tolerance in Lactobacillus brevis, a lactic acid bacterium often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis reveals that the presence of ferulic acid triggers the expression of currently uncharacterized membrane proteins, possibly in an effort to counteract ferulic acid induced changes in membrane fluidity and ion leakage. In contrast to the ferulic acid stress response, n-butanol challenges to growing cultures primarily induce genes within the fatty acid synthesis pathway and reduced the proportion of 19∶1 cyclopropane fatty acid within the L. brevis membrane. Both inhibitors also triggered generalized stress responses. Separate attempts to alter flux through the Escherichia coli fatty acid synthesis by overexpressing acetyl-CoA carboxylase subunits and deleting cyclopropane fatty acid synthase (cfa) both failed to improve n-butanol tolerance in E. coli, indicating that additional components of the stress response are required to confer n-butanol resistance. Conclusions Several promising routes for understanding both ferulic acid and n-butanol tolerance have been identified from L. brevis gene expression data. These insights may be used to guide further engineering of

Complexity multiscale asynchrony measure and behavior for interacting financial dynamics

NASA Astrophysics Data System (ADS)

Yang, Ge; Wang, Jun; Niu, Hongli

2016-08-01

A stochastic financial price process is proposed and investigated by the finite-range multitype contact dynamical system, in an attempt to study the nonlinear behaviors of real asset markets. The viruses spreading process in a finite-range multitype system is used to imitate the interacting behaviors of diverse investment attitudes in a financial market, and the empirical research on descriptive statistics and autocorrelation behaviors of return time series is performed for different values of propagation rates. Then the multiscale entropy analysis is adopted to study several different shuffled return series, including the original return series, the corresponding reversal series, the random shuffled series, the volatility shuffled series and the Zipf-type shuffled series. Furthermore, we propose and compare the multiscale cross-sample entropy and its modification algorithm called composite multiscale cross-sample entropy. We apply them to study the asynchrony of pairs of time series under different time scales.

Dependence of exponents on text length versus finite-size scaling for word-frequency distributions

NASA Astrophysics Data System (ADS)

Corral, Álvaro; Font-Clos, Francesc

2017-08-01

Some authors have recently argued that a finite-size scaling law for the text-length dependence of word-frequency distributions cannot be conceptually valid. Here we give solid quantitative evidence for the validity of this scaling law, using both careful statistical tests and analytical arguments based on the generalized central-limit theorem applied to the moments of the distribution (and obtaining a novel derivation of Heaps' law as a by-product). We also find that the picture of word-frequency distributions with power-law exponents that decrease with text length [X. Yan and P. Minnhagen, Physica A 444, 828 (2016), 10.1016/j.physa.2015.10.082] does not stand with rigorous statistical analysis. Instead, we show that the distributions are perfectly described by power-law tails with stable exponents, whose values are close to 2, in agreement with the classical Zipf's law. Some misconceptions about scaling are also clarified.

National Practice Patterns for Clinical T1N0 Nasopharyngeal Cancer in the Elderly: A National Cancer Data Base Analysis.

PubMed

Post, Carl M; Lin, Chi; Adeberg, Sebastian; Gupta, Mrigank; Zhen, Weining; Verma, Vivek

2018-03-01

The standard of care for T1N0 nasopharyngeal cancer (NPC) is definitive radiation therapy (RT). However, practice patterns in the elderly may not necessarily follow national guidelines. Herein, we investigated national practice patterns for T1N0 NPC. The National Cancer Data Base (NCDB) was queried for clinical T1N0 primary NPC cases (2004-2013) in patients ≥70 years old. Patient, tumor, and treatment parameters were extracted. Kaplan-Meier analysis was used to compare overall survival (OS) between patients receiving RT versus those under observation. Logistic regression was used to examine variables associated with receipt of RT. Cox proportional hazards modeling determined variables associated with OS. Landmark analysis of patients surviving 1 year or more was performed to assess survival differences between groups. In total, data of 147 patients were analyzed. RT was delivered to 89 patients (61%), whereas 58 (39%) patients underwent observation. On multivariable analysis, older patients were less likely to receive RT (p=0.003), but there were no differences between groups in terms of Charlson-Deyo comorbidity index. Median and 5-year OS in patients receiving RT versus those under observation were 71 and 33 months, and 59% and 48% (p=0.011), respectively. For patients surviving 1 year or more (n=96), there was a strong trend showing that receipt of RT was associated with better median and 5-year OS. This National Data Base analysis shows that observation is relatively common for T1N0 NPC in the elderly, but is associated with poorer survival. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Quantitative analysis of hydrogen in SiO{sub 2}/SiN/SiO{sub 2} stacks using atom probe tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kunimune, Yorinobu, E-mail: yorinobu.kunimune.vz@renesas.com; Shimada, Yasuhiro; Sakurai, Yusuke

2016-04-15

We have demonstrated that it is possible to reproducibly quantify hydrogen concentration in the SiN layer of a SiO{sub 2}/SiN/SiO{sub 2} (ONO) stack structure using ultraviolet laser-assisted atom probe tomography (APT). The concentration of hydrogen atoms detected using APT increased gradually during the analysis, which could be explained by the effect of hydrogen adsorption from residual gas in the vacuum chamber onto the specimen surface. The amount of adsorbed hydrogen in the SiN layer was estimated by analyzing another SiN layer with an extremely low hydrogen concentration (<0.2 at. %). Thus, by subtracting the concentration of adsorbed hydrogen, the actualmore » hydrogen concentration in the SiN layer was quantified as approximately 1.0 at. %. This result was consistent with that obtained by elastic recoil detection analysis (ERDA), which confirmed the accuracy of the APT quantification. The present results indicate that APT enables the imaging of the three-dimensional distribution of hydrogen atoms in actual devices at a sub-nanometer scale.« less

Interfacial coherency stress distribution in TiN/AlN bilayer and multilayer films studied by FEM analysis

PubMed Central

Chawla, Vipin; Holec, David; Mayrhofer, Paul H.

2012-01-01

The development of interfacial coherency stresses in TiN/AlN bilayer and multilayer films was investigated by finite element method (ABAQUS) using the four-node bilinear quadrilateral axisymmetric element CAX4R. The TiN and AlN layers are always in compression and tension at the interface, respectively, as may be expected from the fact TiN has larger lattice parameter than AlN. Both, the bi-layer and the multilayer stacks bend due to the coherency stresses. For the TiN/AlN bilayer system, the curvature of the bending is largest for the TiN/AlN thickness ratios ∼0.5 and ∼2 (at which one of the two layers is fully in compression or tension), while it is smaller for the layers with the same thickness (at which both layers posses regions with compressive as well as tensile stresses). This stress distribution over the bi-layer thickness is shown to be strongly influenced by the presence and the properties of a substrate. Furthermore, the coherency stress profile and specimen curvature of a TiN/AlN multilayer system was studied as a function of the top-most layer thickness. The curvature is maximum for equal number of TiN and AlN layers, and decreases with increasing the number of TiN/AlN periods. Within the growth of an additional TiN/AlN bilayer, the curvature first decreases to zero for a vertically symmetrical geometry over the layers when the TiN layer growth is finished (e.g. for (n + 1) layers of TiN and n layers of AlN). At this stage, the coherency stresses in TiN and AlN are same in each layer type (independent on the layer position). The growth of the second half of the TiN/AlN bi-layer (i.e. the AlN) to finish the period, again bends the specimen, and generates a non-uniform stress distribution. This suggests that the top layer as well as the overall specimen geometry plays a critical role on the actual coherency stress profile. PMID:27570370

Morphometric analysis of cisplatin-induced neurite outgrowth in N1E-115 neuroblastoma cells.

PubMed

Konings, P N; Philipsen, R L; van den Broek, J H; Ruigt, G S

1994-08-29

Cisplatin, a widely used cytostatic drug for the control of a variety of neoplastic tumors, unexpectedly induced neurite outgrowth in N1E-115 neuroblastoma cells and this phenomenon was studied further in detail with morphometric analysis. As expected, cisplatin dose-dependently reduced cell number. At the same time, however, cisplatin affected the morphology of the neuroblastoma cells that changed from small rounded cell bodies into large flat cell bodies with neurites. The neurite length/cell as a function of cisplatin concentration showed a bell-shaped curve. The maximal effect (1200% of control) on neurite length/cell was observed at 1 microgram/ml cisplatin. In conclusion, cisplatin induced cellular differentiation in N1E-115 neuroblastoma cells at and just above threshold doses for cytostatic activity.

Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics.

PubMed

Prudova, Anna; auf dem Keller, Ulrich; Butler, Georgina S; Overall, Christopher M

2010-05-01

Proteolysis is a major protein posttranslational modification that, by altering protein structure, affects protein function and, by truncating the protein sequence, alters peptide signatures of proteins analyzed by proteomics. To identify such modified and shortened protease-generated neo-N-termini on a proteome-wide basis, we developed a whole protein isobaric tag for relative and absolute quantitation (iTRAQ) labeling method that simultaneously labels and blocks all primary amines including protein N- termini and lysine side chains. Blocking lysines limits trypsin cleavage to arginine, which effectively elongates the proteolytically truncated peptides for improved MS/MS analysis and peptide identification. Incorporating iTRAQ whole protein labeling with terminal amine isotopic labeling of substrates (iTRAQ-TAILS) to enrich the N-terminome by negative selection of the blocked mature original N-termini and neo-N-termini has many advantages. It enables simultaneous characterization of the natural N-termini of proteins, their N-terminal modifications, and proteolysis product and cleavage site identification. Furthermore, iTRAQ-TAILS also enables multiplex N-terminomics analysis of up to eight samples and allows for quantification in MS2 mode, thus preventing an increase in spectral complexity and extending proteome coverage by signal amplification of low abundance proteins. We compared the substrate degradomes of two closely related matrix metalloproteinases, MMP-2 (gelatinase A) and MMP-9 (gelatinase B), in fibroblast secreted proteins. Among 3,152 unique N-terminal peptides identified corresponding to 1,054 proteins, we detected 201 cleavage products for MMP-2 and unexpectedly only 19 for the homologous MMP-9 under identical conditions. Novel substrates identified and biochemically validated include insulin-like growth factor binding protein-4, complement C1r component A, galectin-1, dickkopf-related protein-3, and thrombospondin-2. Hence, N-terminomics analyses

Multiplex N-terminome Analysis of MMP-2 and MMP-9 Substrate Degradomes by iTRAQ-TAILS Quantitative Proteomics*

PubMed Central

Prudova, Anna; auf dem Keller, Ulrich; Butler, Georgina S.; Overall, Christopher M.

2010-01-01

Proteolysis is a major protein posttranslational modification that, by altering protein structure, affects protein function and, by truncating the protein sequence, alters peptide signatures of proteins analyzed by proteomics. To identify such modified and shortened protease-generated neo-N-termini on a proteome-wide basis, we developed a whole protein isobaric tag for relative and absolute quantitation (iTRAQ) labeling method that simultaneously labels and blocks all primary amines including protein N- termini and lysine side chains. Blocking lysines limits trypsin cleavage to arginine, which effectively elongates the proteolytically truncated peptides for improved MS/MS analysis and peptide identification. Incorporating iTRAQ whole protein labeling with terminal amine isotopic labeling of substrates (iTRAQ-TAILS) to enrich the N-terminome by negative selection of the blocked mature original N-termini and neo-N-termini has many advantages. It enables simultaneous characterization of the natural N-termini of proteins, their N-terminal modifications, and proteolysis product and cleavage site identification. Furthermore, iTRAQ-TAILS also enables multiplex N-terminomics analysis of up to eight samples and allows for quantification in MS2 mode, thus preventing an increase in spectral complexity and extending proteome coverage by signal amplification of low abundance proteins. We compared the substrate degradomes of two closely related matrix metalloproteinases, MMP-2 (gelatinase A) and MMP-9 (gelatinase B), in fibroblast secreted proteins. Among 3,152 unique N-terminal peptides identified corresponding to 1,054 proteins, we detected 201 cleavage products for MMP-2 and unexpectedly only 19 for the homologous MMP-9 under identical conditions. Novel substrates identified and biochemically validated include insulin-like growth factor binding protein-4, complement C1r component A, galectin-1, dickkopf-related protein-3, and thrombospondin-2. Hence, N-terminomics analyses

Statistical properties of DNA sequences

NASA Technical Reports Server (NTRS)

Peng, C. K.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Simons, M.; Stanley, H. E.

1995-01-01

We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33301 coding and 29453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.

Analysis of N-Nitrosodimethylamine and N-Nitrodimethylamine in Groundwater

NASA Technical Reports Server (NTRS)

Greene, Ben; Mast, Dion; Baker, David L.

2006-01-01

A method for the analytical determination of N-nitrosodimethylamine (NDMA) and N-nitrodimethylamine (DMN) at parts-per-trillion (ppt) concentrations in groundwater is reported. The method uses a solid phase extraction (SPE) cartridge containing 2 g of activated coconut charcoal to extract a 500-mL water sample. NDMA and DMN are eluted from the SPE cartridge using acetone. The acetone is concentrated and brought to a final volume of 1.0 mL, which results in a theoretical 500-fold concentration of the analytes. The extracts are analyzed by gas chromatography (GC) with a nitrogenphosphorous detector (NPD), which is a highly sensitive and relatively inexpensive technique. The measured extraction efficiencies averaged 61 percent for NDMA and 74 percent for DMN. Extraction efficiencies were independent of NDMA and DMN concentrations from 40 to 2000 ppt. Several samples could be extracted then analyzed in a single day with the use of an extraction manifold and GC autosampler. A reporting limit of 10 ppt for NDMA and DMN was achieved. The MDLs for NDMA and DMN were 6.4 and 5.8 ppt, respectively. A typical turn-around time from beginning of extraction to reporting was 4 h. The method avoids the use of halogenated solvents, such as dichloromethane, and subsequent solvent exchange procedures necessary for use of the NPD detector.

Experimental charge density analysis of a gallium(I) N-heterocyclic carbene analogue.

PubMed

Overgaard, Jacob; Jones, Cameron; Dange, Deepak; Platts, James A

2011-09-05

The experimental electron density of the only known example of a four-membered Ga(I) N-heterocyclic carbene analogue has been determined by multipole modeling of 90 K X-ray diffraction data and compared to theoretical data. In order to obtain a satisfactory model, it is necessary to modify the radial dependency of the core electrons of Ga using two separate scaling parameters for s,p- and d-electrons. Evidence for significant lone-pair density on Ga is found in the electron density and derived properties despite the partial positive charge of this atom. Static deformation density and molecular electrostatic potential clearly show a directional lone pair on Ga, whereas the Laplacian of the total electron density does not; this feature is, however, present in the Laplacian of the valence-only density. The Ga center also acts as an acceptor in four intramolecular C-H···Ga contacts, whose nature is probed by density properties. Substantial covalent character is apparent in the Ga-N bonds, but no sign of donation from filled N p-orbitals to empty Ga p-orbitals is found, whereas π-delocalization over the organic ligand is evident. This study highlights the utility of experimental charge density analysis as a technique to investigate the unusual bonding and electronic characteristics of low oxidation state/low coordinate p-block complexes.

A cost-benefit analysis of varicella vaccination in Aragón.

PubMed

Peña Blasco, Guillermo; Blasco Pérez-Aramendía, M Jesús

2017-10-01

Varicella, a contagious and infectious disease that is usually benign in children, may become complicated among adults and vulnerable children and may even be life-threatening. There are effective vaccines. A retrospective study was conducted about costs and resulting hospitalizations related to this disease in the population of Aragón in the 2004-2014 period. Costs were compared to the expenses that would have been incurred if those people had received the vaccine and also to the expenses of vaccinating the 1-year-old population over the entire period. A cost-benefit analysis was done to assess the economic impact of varicella vaccination. Data for the 11-year period were provided by the Autonomous Community of Aragón (Spain) and included annual varicella incidence, hospital discharges of varicella cases, costs of primary health care visits and hospitalizations for each year, costs of each workday as per the minimum annual salary and of drugs used). Capitalized costs were estimated and compared to capitalized expenses of vaccination, and a sensitivity analysis was performed. A benefit-cost ratio of 1.6 was obtained considering that all children who had varicella had been vaccinated and had received a booster dose. A benefit-cost ratio of 1.24 was obtained considering that the vaccine had been administered to every 1-year-old individual at a price of EUR 28.59 per vaccine. Over the 11-year period, 53% of hospitalizations corresponded to children younger than 5 years old. Public campaigns for the immunization of children younger than 4 years old with 2 doses lead to cost savings and are cost-effective because the vaccine price results in a benefit-cost ratio greater than 1. A major reduction is expected in the number of hospitalizations among children aged 3-4 years. Sociedad Argentina de Pediatría

ALE Meta-Analysis of Schizophrenics Performing the N-Back Task

NASA Astrophysics Data System (ADS)

Harrell, Zachary

2010-10-01

MRI/fMRI has already proven itself as a valuable tool in the diagnosis and treatment of many illnesses of the brain, including cognitive problems. By exploiting the differences in magnetic susceptibility between oxygenated and deoxygenated hemoglobin, fMRI can measure blood flow in various regions of interest within the brain. This can determine the level of brain activity in relation to motor or cognitive functions and provide a metric for tissue damage or illness symptoms. Structural imaging techniques have shown lesions or deficiencies in tissue volumes in schizophrenics corresponding to areas primarily in the frontal and temporal lobes. These areas are currently known to be involved in working memory and attention, which many schizophrenics have trouble with. The ALE (Activation Likelihood Estimation) Meta-Analysis is able to statistically determine the significance of brain area activations based on the post-hoc combination of multiple studies. This process is useful for giving a general model of brain function in relation to a particular task designed to engage the affected areas (such as working memory for the n-back task). The advantages of the ALE Meta-Analysis include elimination of single subject anomalies, elimination of false/extremely weak activations, and verification of function/location hypotheses.

General methods for analysis of sequential "n-step" kinetic mechanisms: application to single turnover kinetics of helicase-catalyzed DNA unwinding.

PubMed

Lucius, Aaron L; Maluf, Nasib K; Fischer, Christopher J; Lohman, Timothy M

2003-10-01

Helicase-catalyzed DNA unwinding is often studied using "all or none" assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using "n-step" sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the "kinetic step size", m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using "n-step" sequential mechanisms has previously been limited by an inability to float the number of "unwinding steps", n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, f(ss)(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain f(ss)(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation.

Optical implementation of inner product neural associative memory

NASA Technical Reports Server (NTRS)

Liu, Hua-Kuang (Inventor)

1995-01-01

An optical implementation of an inner-product neural associative memory is realized with a first spatial light modulator for entering an initial two-dimensional N-tuple vector and for entering a thresholded output vector image after each iteration until convergence is reached, and a second spatial light modulator for entering M weighted vectors of inner-product scalars multiplied with each of the M stored vectors, where the inner-product scalars are produced by multiplication of the initial input vector in the first iterative cycle (and thresholded vectors in subsequent iterative cycles) with each of the M stored vectors, and the weighted vectors are produced by multiplication of the scalars with corresponding ones of the stored vectors. A Hughes liquid crystal light valve is used for the dual function of summing the weighted vectors and thresholding the sum vector. The thresholded vector is then entered through the first spatial light modulator for reiteration of the process cycle until convergence is reached.

Mass Isotopomer Analysis of Metabolically Labeled Nucleotide Sugars and N- and O-Glycans for Tracing Nucleotide Sugar Metabolisms*

PubMed Central

Nakajima, Kazuki; Ito, Emi; Ohtsubo, Kazuaki; Shirato, Ken; Takamiya, Rina; Kitazume, Shinobu; Angata, Takashi; Taniguchi, Naoyuki

2013-01-01

Nucleotide sugars are the donor substrates of various glycosyltransferases, and an important building block in N- and O-glycan biosynthesis. Their intercellular concentrations are regulated by cellular metabolic states including diseases such as cancer and diabetes. To investigate the fate of UDP-GlcNAc, we developed a tracing method for UDP-GlcNAc synthesis and use, and GlcNAc utilization using 13C6-glucose and 13C2-glucosamine, respectively, followed by the analysis of mass isotopomers using LC-MS. Metabolic labeling of cultured cells with 13C6-glucose and the analysis of isotopomers of UDP-HexNAc (UDP-GlcNAc plus UDP-GalNAc) and CMP-NeuAc revealed the relative contributions of metabolic pathways leading to UDP-GlcNAc synthesis and use. In pancreatic insulinoma cells, the labeling efficiency of a 13C6-glucose motif in CMP-NeuAc was lower compared with that in hepatoma cells. Using 13C2-glucosamine, the diversity of the labeling efficiency was observed in each sugar residue of N- and O-glycans on the basis of isotopomer analysis. In the insulinoma cells, the low labeling efficiencies were found for sialic acids as well as tri- and tetra-sialo N-glycans, whereas asialo N-glycans were found to be abundant. Essentially no significant difference in secreted hyaluronic acids was found among hepatoma and insulinoma cell lines. This indicates that metabolic flows are responsible for the low sialylation in the insulinoma cells. Our strategy should be useful for systematically tracing each stage of cellular GlcNAc metabolism. PMID:23720760

Enhanced detectability of fluorinated derivatives of N,N-dialkylamino alcohols and precursors of nitrogen mustards by gas chromatography coupled to Fourier transform infrared spectroscopy analysis for verification of chemical weapons convention.

PubMed

Garg, Prabhat; Purohit, Ajay; Tak, Vijay K; Dubey, D K

2009-11-06

N,N-Dialkylamino alcohols, N-methyldiethanolamine, N-ethyldiethanolamine and triethanolamine are the precursors of VX type nerve agents and three different nitrogen mustards respectively. Their detection and identification is of paramount importance for verification analysis of chemical weapons convention. GC-FTIR is used as complimentary technique to GC-MS analysis for identification of these analytes. One constraint of GC-FTIR, its low sensitivity, was overcome by converting the analytes to their fluorinated derivatives. Owing to high absorptivity in IR region, these derivatives facilitated their detection by GC-FTIR analysis. Derivatizing reagents having trimethylsilyl, trifluoroacyl and heptafluorobutyryl groups on imidazole moiety were screened. Derivatives formed there were analyzed by GC-FTIR quantitatively. Of these reagents studied, heptafluorobutyrylimidazole (HFBI) produced the greatest increase in sensitivity by GC-FTIR detection. 60-125 folds of sensitivity enhancement were observed for the analytes by HFBI derivatization. Absorbance due to various functional groups responsible for enhanced sensitivity were compared by determining their corresponding relative molar extinction coefficients ( [Formula: see text] ) considering uniform optical path length. The RSDs for intraday repeatability and interday reproducibility for various derivatives were 0.2-1.1% and 0.3-1.8%. Limit of detection (LOD) was achieved up to 10-15ng and applicability of the method was tested with unknown samples obtained in international proficiency tests.

Global dynamic analysis of a H7N9 avian-human influenza model in an outbreak region.

PubMed

Chen, Yongxue; Wen, Yongxian

2015-02-21

In 2013 in China a new type of avian influenza virus, H7N9, began to infect humans and had aroused severe fatality in the infected humans. We know that the spread is from poultry to humans, and the H7N9 avian influenza is low pathogenic in the poultry world but highly pathogenic in the human world, but the transmission mechanism is unclear. Since it has no signs of human-to-human transmission and outbreaks are isolated in some cities in China, in order to investigate the transmission mechanism of human infection with H7N9 avian influenza, an eco-epidemiological model in an outbreak region is proposed and analyzed dynamically. Researches and reports show that gene mutation makes the new virus be capable of infecting humans, therefore the mutation factor is taken into account in the model. The global dynamic analysis is conducted, different thresholds are identified, persistence and global qualitative behaviors are obtained. The impact of H7N9 avian influenza on the people population is concerned. Finally, the numerical simulations are carried out to support the theoretical analysis and to investigate the disease control measures. It seems that we may take people׳s hygiene and prevention awareness factor as a significant policy to achieve the aim of both the disease control and the economic returns. Copyright © 2014 Elsevier Ltd. All rights reserved.

Automorphic Forms and Mock Modular Forms in String Theory

NASA Astrophysics Data System (ADS)

Nazaroglu, Caner

We study a variety of modular invariant objects in relation to string theory. First, we focus on Jacobi forms over generic rank lattices and Siegel forms that appear in N = 2, D = 4 compactifications of heterotic string with Wilson lines. Constraints from low energy spectrum and modularity are employed to deduce the relevant supersymmetric partition functions entirely. This procedure is applied on models that lead to Jacobi forms of index 3, 4, 5 as well as Jacobi forms over root lattices A2 and A3. These computations are then checked against an explicit orbifold model which can be Higgsed to the models under question. Models with a single Wilson line are then studied in detail with their relation to paramodular group Gammam as T-duality group made explicit. These results on the heterotic string side are then turned into predictions for geometric invariants using TypeII - Heterotic duality. Secondly, we study theta functions for indenite signature lattices of generic signature. Building on results in literature for signature (n-1,1) and (n-2,2) lattices, we work out the properties of generalized error functions which we call r-tuple error functions. We then use these functions to build such indenite theta functions and describe their modular completions.

METHOD DEVELOPMENT FOR THE ANALYSIS OF N-NITROSODIMETHYLAMINE AND OTHER N-NITROSAMINES IN DRINKING WATER AT LOW NANOGRAM/LITER CONCENTRATIONS USING SOLID PHASE EXTRACTION AND GAS CHROMATOGRAPHY WITH CHEMICAL IONIZATION TANDEM MASS SPECTROMETRY

EPA Science Inventory

N-Nitrosodimethylamine (NDMA) is a probable human carcinogen that has been identified as a drinking water contaminant of concern. United States Environmental Protection Agency (USEPA) Method 521 has been developed for the analysis of NDMA and six additional N-nitrosamines in dri...

Quantitative secondary ion mass spectrometric analysis of secondary ion polarity in GaN films implanted with oxygen

NASA Astrophysics Data System (ADS)

Hashiguchi, Minako; Sakaguchi, Isao; Adachi, Yutaka; Ohashi, Naoki

2016-10-01

Quantitative analyses of N and O ions in GaN thin films implanted with oxygen ions (16O+) were conducted by secondary ion mass spectrometry (SIMS). Positive (CsM+) and negative secondary ions extracted by Cs+ primary ion bombardment were analyzed for oxygen quantitative analysis. The oxygen depth profiles were obtained using two types of primary ion beams: a Gaussian-type beam and a broad spot beam. The oxygen peak concentrations in GaN samples were from 3.2 × 1019 to 7.0 × 1021 atoms/cm3. The depth profiles show equivalent depth resolutions in the two analyses. The intensity of negative oxygen ions was approximately two orders of magnitude higher than that of positive ions. In contrast, the O/N intensity ratio measured using CsM+ molecular ions was close to the calculated atomic density ratio, indicating that the SIMS depth profiling using CsM+ ions is much more effective for the measurements of O and N ions in heavy O-implanted GaN than that using negative ions.

Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi

PubMed Central

Swem, Lee R.; Swem, Danielle L.; Wingreen, Ned S.; Bassler, Bonnie L.

2008-01-01

Summary Quorum sensing, a process of bacterial cell-cell communication, relies on production, detection, and response to autoinducer signaling molecules. Here we focus on LuxN, a nine transmembrane domain protein from Vibrio harveyi, and the founding example of membrane-bound receptors for acyl-homoserine lactone (AHL) autoinducers. Previously, nothing was known about signal recognition by membrane-bound AHL receptors. We used mutagenesis and suppressor analyses to identify the AHL-binding domain of LuxN, and discovered LuxN mutants that confer decreased and increased AHL sensitivity. Our analysis of dose-response curves of multiple LuxN mutants pins these inverse phenotypes on quantifiable opposing shifts in the free-energy bias of LuxN for its kinase and phosphatase states. To extract signaling parameters, we exploited a strong LuxN antagonist, one of fifteen small-molecule antagonists we identified. We find that quorum-sensing-mediated communication can be manipulated positively and negatively to control bacterial behavior, and that signaling parameters can be deduced from in vivo data. PMID:18692469

Effects of derivatization reagents consisting of n-alkyl chloroformate/n-alcohol combinations in LC-ESI-MS/MS analysis of zwitterionic antiepileptic drugs.

PubMed

Kostić, Nađa; Dotsikas, Yannis; Malenović, Anđelija; Medenica, Mirjana

2013-11-15

In the current study, three antiepileptic drugs with zwitterionic properties, namely vigabatrin, pregabalin and gabapentin, were chosen as model analytes to undergo derivatization by applying various n-alkyl chloroformate/n-alcohol combinations, followed by LC-ESI-MS/MS analysis. The employment of 16 combinations per drug using methyl, ethyl, propyl or butyl chloroformate coupled with methanol, ethanol, propanol or butanol, greatly affected a series of parameters of the derivatives, such as retention time on C8 column, signal expressed via areas, limit of detection values, as well as the yields of the main and side reactions. Practically, even slight modification of n-alkyl group of either chloroformate or alcohol resulted in significant changes in the chromatographic and mass spectrometric behavior of the novel derivative. It was clearly demonstrated that all the estimated parameters were highly correlated with the length of n-alkyl groups of the involved chloroformate and alcohol. The most significant influence was monitored in peak area values, indicating that the length of the n-alkyl chain plays an important role in electrospray ionization efficiency. For this parameter, increasing the n-alkyl chain from methyl to butyl led to increment up to 2089%, 508.7% and 1075% for area values of derivatized vigabatrin, pregabalin and gabapentin, respectively. These changes affected also the corresponding values of limits of detection, with the estimated improvements up to 1553%, 397.7% and 875.0% for the aforementioned derivatized drugs, respectively. Besides the obvious utilization of these conclusions in the development of bioanalytical methods for these analytes with the current protocol, this study offers valuable data which can be useful in more general approaches, giving insights into the effects of this derivatization reaction and its performances. Copyright © 2013 Elsevier B.V. All rights reserved.

Full-Genome Analysis of Avian Influenza A(H5N1) Virus from a Human, North America, 2013

PubMed Central

Pabbaraju, Kanti; Tellier, Raymond; Wong, Sallene; Li, Yan; Bastien, Nathalie; Tang, Julian W.; Drews, Steven J.; Jang, Yunho; Davis, C. Todd; Tipples, Graham A.

2014-01-01

Full-genome analysis was conducted on the first isolate of a highly pathogenic avian influenza A(H5N1) virus from a human in North America. The virus has a hemagglutinin gene of clade 2.3.2.1c and is a reassortant with an H9N2 subtype lineage polymerase basic 2 gene. No mutations conferring resistance to adamantanes or neuraminidase inhibitors were found. PMID:24755439

Bis(N'-{(E)-[(2E)-1,3-di-phenyl-prop-2-en-1-yl-idene]amino}-N-ethyl-carbamimido-thio-ato-κ2N',S)zinc(II): crystal structure and Hirshfeld surface analysis.

PubMed

Tan, Ming Yueh; Crouse, Karen A; Ravoof, Thahira B S A; Jotani, Mukesh M; Tiekink, Edward R T

2017-07-01

The title Zn II complex, [Zn(C 18 H 18 N 3 S) 2 ], (I), features two independent but chemically equivalent mol-ecules in the asymmetric unit. In each, the thio-semicarbazonate monoanion coordinates the Zn II atom via the thiol-ate-S and imine-N atoms, with the resulting N 2 S 2 donor set defining a distorted tetra-hedral geometry. The five-membered ZnSCN 2 chelate rings adopt distinct conformations in each independent mol-ecule, i.e. one ring is almost planar while the other is twisted about the Zn-S bond. In the crystal, the two mol-ecules comprising the asymmetric unit are linked by amine-N-H⋯N(imine) and amine-N-H⋯S(thiol-ate) hydrogen bonds via an eight-membered heterosynthon, {⋯HNCN⋯HNCS}. The dimeric aggregates are further consolidated by benzene-C-H⋯S(thiol-ate) inter-actions and are linked into a zigzag supra-molecular chain along the c axis via amine-N-H⋯S(thiol-ate) hydrogen bonds. The chains are connected into a three-dimensional architecture via phenyl-C-H⋯π(phen-yl) and π-π inter-actions, the latter occurring between chelate and phenyl rings [inter-centroid separation = 3.6873 (11) Å]. The analysis of the Hirshfeld surfaces calculated for (I) emphasizes the different inter-actions formed by the independent mol-ecules in the crystal and the impact of the π-π inter-actions between chelate and phenyl rings.

The histone H3 N-terminal tail: a computational analysis of the free energy landscape and kinetics.

PubMed

Zheng, Yuqing; Cui, Qiang

2015-05-28

Histone tails are the short peptide protrusions outside of the nucleosome core particle and they play a critical role in regulating chromatin dynamics and gene activity. A histone H3 N-terminal tail, like other histone tails, can be covalently modified on different residues to activate or repress gene expression. Previous studies have indicated that, despite its intrinsically disordered nature, the histone H3 N-terminal tail has regions of notable secondary structural propensities. To further understand the structure-dynamics-function relationship in this system, we have carried out 75.6 μs long implicit solvent simulations and 29.3 μs long explicit solvent simulations. The extensive samplings allow us to better characterize not only the underlying free energy landscape but also kinetic properties through Markov state models (MSM). Dihedral principal component analysis (dPCA) and locally scaled diffusion map (LSDMap) analysis yield consistent results that indicate an overall flat free energy surface with several shallow basins that correspond to conformations with a high α-helical propensity in two regions of the peptide. Kinetic information extracted from Markov state models reveals rapid transitions between different metastable states with mean first passage times spanning from several hundreds of nanoseconds to hundreds of microseconds. These findings shed light on how the dynamical nature of the histone H3 N-terminal tail is related to its function. The complementary nature of dPCA, LSDMap and MSM for the analysis of biomolecules is also discussed.

Characterization and functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in tilapia.

PubMed

Li, Hong Lian; Gu, Xiao Hui; Li, Bi Jun; Chen, Xiao; Lin, Hao Ran; Xia, Jun Hong

2017-01-01

Hypoxia is a major cause of fish morbidity and mortality in the aquatic environment. Hypoxia-inducible factors are very important modulators in the transcriptional response to hypoxic stress. In this study, we characterized and conducted functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in Nile tilapia (Oreochromis niloticus). By cloning and Sanger sequencing, we obtained the full length cDNA sequences for HIF1α (2686bp) and HIF1αn (1308bp), respectively. The CDS of HIF1α includes 15 exons encoding 768 amino acid residues and the CDS of HIF1αn contains 8 exons encoding 354 amino acid residues. The complete CDS sequences of HIF1α and HIF1αn cloned from tilapia shared very high homology with known genes from other fishes. HIF1α show differentiated expression in different tissues (brain, heart, gill, spleen, liver) and at different hypoxia exposure times (6h, 12h, 24h). HIF1αn expression level under hypoxia is generally increased (6h, 12h, 24h) and shows extremely highly upregulation in brain tissue under hypoxia. A functional determination site analysis in the protein sequences between fish and land animals identified 21 amino acid sites in HIF1α and 2 sites in HIF1αn as significantly associated sites (α = 0.05). Phylogenetic tree-based positive selection analysis suggested 22 sites in HIF1α as positively selected sites with a p-value of at least 95% for fish lineages compared to the land animals. Our study could be important for clarifying the mechanism of fish adaptation to aquatic hypoxia environment.

Thermal-hydraulic analysis of N Reactor graphite and shield cooling system performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Low, J.O.; Schmitt, B.E.

1988-02-01

A series of bounding (worst-case) calculations were performed using a detailed hydrodynamic RELAP5 model of the N Reactor graphite and shield cooling system (GSCS). These calculations were specifically aimed to answer issues raised by the Westinghouse Independent Safety Review (WISR) committee. These questions address the operability of the GSCS during a worst-case degraded-core accident that requires the GDCS to mitigate the consequences of the accident. An accident scenario previously developed was designed as the hydrogen-mitigation design-basis accident (HMDBA). Previous HMDBA heat transfer analysis,, using the TRUMP-BD code, was used to define the thermal boundary conditions that the GSDS may bemore » exposed to. These TRUMP/HMDBA analysis results were used to define the bounding operating conditions of the GSCS during the course of an HMDBA transient. Nominal and degraded GSCS scenarios were investigated using RELAP5 within or at the bounds of the HMDBA transient. 10 refs., 42 figs., 10 tabs.« less

[The elaboration of gas chromatographic method of the determination of N-nitrosamines (N-nitrosodimethylamine, N-nitrosodiethylamine) in biological samples (urine)].

PubMed

Zaytseva, N V; Ulanova, T S; Nurislamova, T V; Popova, N A

2014-01-01

The issues of the elaboration of a method for the determination of N-nitrosamines (N-nitrosodimethylamine, N-nitrosodiethylamine) in urine by means of the method of capillary gas chromatography with the use of a thermionic detector are considered. There were performed investigations on the study of the efficacy of the extraction of N-nitrosamines from the urine by steam distillation and gas chromatographic detection of headspace. With the aim of the maximal recovery of N-nitrosamines from the urine and setting parameters of the extraction two method were used to prepare the bioassay for the analysis the alkalization with potassium hydroxide and the addition of salting out reagent--neutral salts of alkali and alkaline earth metals. During the process of performed studies there was found that the greatest degree of extraction of N-nitrosamines from the urine by the method of headspace analysis is achieved if using the salting-out agent in an amount of 16 g of sodium sulfate and for N-nitrosodimethylamine is 99%, for N-nitrosodiethylamine--100%.

Communicating uncertainty - how Australian television reported H1N1 risk in 2009: a content analysis

PubMed Central

2011-01-01

Background Health officials face particular challenges in communicating with the public about emerging infectious diseases of unknown severity such as the 2009 H1N1(swine 'flu) pandemic (pH1N1). Statements intended to create awareness and convey the seriousness of infectious disease threats can draw accusations of scare-mongering, while officials can be accused of complacency if such statements are not made. In these communication contexts, news journalists, often reliant on official sources to understand issues are pivotal in selecting and emphasising aspects of official discourse deemed sufficiently newsworthy to present to the public. This paper presents a case-study of news communication regarding the emergence of pH1N1. Methods We conducted a content analysis of all television news items about pH1N1. We examined news and current affairs items broadcast on 5 free-to-air Sydney television channels between April 25 2009 (the first report) and October 9 (prior to the vaccine release) for statements about [1] the seriousness of the disease [2] how the public could minimise contagion [3] government responses to emerging information. Results pH1N1 was the leading health story for eight of 24 weeks and was in the top 5 for 20 weeks. 353 news items were identified, yielding 3086 statements for analysis, with 63.4% related to the seriousness of the situation, 12.9% providing advice for viewers and 23.6% involving assurances from government. Coverage focused on infection/mortality rates, the spread of the virus, the need for public calm, the vulnerability of particular groups, direct and indirect advice for viewers, and government reassurances about effective management. Conclusions Overall, the reporting of 2009 pH1N1 in Sydney, Australia was generally non-alarmist, while conveying that pH1N1 was potentially serious. Daily infection rate tallies and commentary on changes in the pandemic alert level were seldom contextualised to assist viewers in understanding personal

Rank-frequency distributions of Romanian words

NASA Astrophysics Data System (ADS)

Cocioceanu, Adrian; Raportaru, Carina Mihaela; Nicolin, Alexandru I.; Jakimovski, Dragan

2017-12-01

The calibration of voice biometrics solutions requires detailed analyses of spoken texts and in this context we investigate by computational means the rank-frequency distributions of Romanian words and word series to determine the most common words and word series of the language. To this end, we have constructed a corpus of approximately 2.5 million words and then determined that the rank-frequency distributions of the Romanian words, as well as series of two, and three subsequent words, obey the celebrated Zipf law.

Design, fabrication, and performance analysis of GaN vertical electron transistors with a buried p/n junction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yeluri, Ramya, E-mail: ramyay@ece.ucsb.edu; Lu, Jing; Keller, Stacia

2015-05-04

The Current Aperture Vertical Electron Transistor (CAVET) combines the high conductivity of the two dimensional electron gas channel at the AlGaN/GaN heterojunction with better field distribution offered by a vertical design. In this work, CAVETs with buried, conductive p-GaN layers as the current blocking layer are reported. The p-GaN layer was regrown by metalorganic chemical vapor deposition and the subsequent channel regrowth was done by ammonia molecular beam epitaxy to maintain the p-GaN conductivity. Transistors with high ON current (10.9 kA/cm{sup 2}) and low ON-resistance (0.4 mΩ cm{sup 2}) are demonstrated. Non-planar selective area regrowth is identified as the limiting factormore » to transistor breakdown, using planar and non-planar n/p/n structures. Planar n/p/n structures recorded an estimated electric field of 3.1 MV/cm, while non-planar structures showed a much lower breakdown voltage. Lowering the p-GaN regrowth temperature improved breakdown in the non-planar n/p/n structure. Combining high breakdown voltage with high current will enable GaN vertical transistors with high power densities.« less

Quantum chemical characterization of N-(2-hydroxybenzylidene)acetohydrazide (HBAH): a detailed vibrational and NLO analysis.

PubMed

Tamer, Ömer; Avcı, Davut; Atalay, Yusuf

2014-01-03

The molecular modeling of N-(2-hydroxybenzylidene)acetohydrazide (HBAH) was carried out using B3LYP, CAMB3LYP and PBE1PBE levels of density functional theory (DFT). The molecular structure of HBAH was solved by means of IR, NMR and UV-vis spectroscopies. In order to find the stable conformers, conformational analysis was performed based on B3LYP level. A detailed vibrational analysis was made on the basis of potential energy distribution (PED). HOMO and LUMO energies were calculated, and the obtained energies displayed that charge transfer occurs in HBAH. NLO analysis indicated that HBAH can be used as an effective NLO material. NBO analysis also proved that charge transfer, conjugative interactions and intramolecular hydrogen bonding interactions occur through HBAH. Additionally, major contributions from molecular orbitals to the electronic transitions were investigated theoretically. Copyright © 2013 Elsevier B.V. All rights reserved.

Breaking the GaN material limits with nanoscale vertical polarisation super junction structures: A simulation analysis

NASA Astrophysics Data System (ADS)

Unni, Vineet; Sankara Narayanan, E. M.

2017-04-01

This is the first report on the numerical analysis of the performance of nanoscale vertical superjunction structures based on impurity doping and an innovative approach that utilizes the polarisation properties inherent in III-V nitride semiconductors. Such nanoscale vertical polarisation super junction structures can be realized by employing a combination of epitaxial growth along the non-polar crystallographic axes of Wurtzite GaN and nanolithography-based processing techniques. Detailed numerical simulations clearly highlight the limitations of a doping based approach and the advantages of the proposed solution for breaking the unipolar one-dimensional material limits of GaN by orders of magnitude.

Suppression of gate leakage current in in-situ grown AlN/InAlN/AlN/GaN heterostructures based on the control of internal polarization fields

NASA Astrophysics Data System (ADS)

Kotani, Junji; Yamada, Atsushi; Ishiguro, Tetsuro; Yamaguchi, Hideshi; Nakamura, Norikazu

2017-03-01

This paper investigates the gate leakage characteristics of in-situ AlN capped InAlN/AlN/GaN heterostructures grown by metal-organic vapor phase epitaxy. It was revealed that the leakage characteristics of AlN capped InAlN/AlN/GaN heterostructures are strongly dependent on the growth temperature of the AlN cap. For an AlN capped structure with an AlN growth temperature of 740 °C, the leakage current even increased although there exists a large bandgap material on InAlN/AlN/GaN heterostructures. On the other hand, a large reduction of the gate leakage current by 4-5 orders of magnitudes was achieved with a very low AlN growth temperature of 430 °C. X-ray diffraction analysis of the AlN cap grown at 740 °C indicated that the AlN layer is tensile-strained. In contrast to this result, the amorphous structure was confirmed for the AlN cap grown at 430 °C by transmission electron microscopy. Furthermore, theoretical analysis based on one-dimensional band simulation was carried out, and the large increase in two-dimensional electron gas (2DEG) observed in Hall measurements was well reproduced by taking into account the spontaneous and piezo-electric polarization in the AlN layer grown at 740 °C. For the AlN capped structure grown at 430 °C, it is believed that the reduced polarization field in the AlN cap suppressed the penetration of 2DEG into the InAlN barrier layer, resulting in a small impact on 2DEG mobility and density. We believe that an in-situ grown AlN cap with a very low growth temperature of 430 °C is a promising candidate for high-frequency/high-power GaN-based devices with low gate leakage current.

Synthesis, characterization, and the antioxidant activity of N,N,N-trimethyl chitosan salts.

PubMed

Zhang, Jingjing; Tan, Wenqiang; Wang, Gang; Yin, Xiuli; Li, Qing; Dong, Fang; Guo, Zhanyong

2018-06-05

Chitosan, possessing excellent properties, has been drawing broad attention. For the further utilization of chitosan, chemical modification is performed in improving its water solubility and the bioactivities. In the current study, four N,N,N-trimethyl chitosan salts, including N,N,N-trimethyl chitosan citrate (TMCSCi), N,N,N-trimethyl chitosan acetylsalicylate (TMCSAc), N,N,N-trimethyl chitosan ascorbate (TMCSAs), and N,N,N-trimethyl chitosan gallate (TMCSGa), were prepared via N,N,N-trimethyl chitosan iodide (TMCSI). The as-prepared products were characterized by FT-IR and 1 H NMR. Meanwhile, the degrees of substitution were calculated by elemental analysis results. Furthermore, scavenging activities (against DPPH radicals and superoxide radicals) test and reducing power test were selected to evaluate the antioxidant property of N,N,N-trimethyl chitosan salts in vitro. The results indicated that TMCSAs and TMCSGa displayed excellent activity, probably due to the enhancement of ascorbate and gallate in antioxidant activity. However, because of the weak antioxidant property of citrate and acetylsalicylate, the activity was lower for TMCSCi and TMCSAc. For example, in the DPPH radicals scavenging assay, the scavenging rates of chitosan, TMCSI, TMCSCi, TMCSAc, TMCSAs, and TMCSGa were 25.22, 84.11, 6.90, 2.70, 94.92, and 96.75% at 0.4 mg/mL, respectively. Generally, TMCSAs and TMCSGa could be regarded as a potential source of antioxidants. Copyright © 2017. Published by Elsevier B.V.

HPLC Analysis and Cytotoxicity of n-Butanol Extract from Glyphaea brevis Roots Against C6 Glioma Cells.

PubMed

Konan, Koffi Marcel; Mamyrbekova-Bekro, Janat Akhanovna; Bakalara, Norbert; Virieux, David; Pirat, Jean-Luc; Bekro, Yves-Alain

2014-01-01

The n-butanol extract of the roots of Glyphaea brevis was analysed. HPLC analysis suggested the presence of phenolic compounds like protocatechuic acid (PCA). The extract showed moderate cytotoxic activity against C6 glioma cells (EC50 > 1 mg/ml).

Storage and Database Management for Big Data

DTIC Science & Technology

2015-07-27

and value ), each cell is actually a seven tuple where the column is broken into three parts, and there is an additional field for a timestamp as seen...questions require a careful understanding of the technology field in addition to the types of problems that are being solved. This chapter aims to address...formats such as comma separated values (CSV), JavaScript Object Notation (JSON) [21], or other proprietary sensor formats. Most often, this raw data

Trust-Based Service Composition and Binding for Tactical Networks with Multiple Objectives

DTIC Science & Technology

2013-12-01

services, then it will have a set of four-tuple records for each abstract service that it can provide. We assume that the service quality of a SP in...user (i.e., a SR) does not have knowledge of the “best” service quality , so its satisfaction level with services received is based on what has been...hand, when USRm is less than USTm, identifies the culprits with low performance (by comparing the advertised service quality profile with the

On the orthogonal dissipative lax-phillips scattering theory

NASA Astrophysics Data System (ADS)

Neidhardt, Hagen

1988-08-01

The paper is devoted to the so-called orthogonal dissipative Lax-Phillips scattering theory. A parametrization of all possible orthogonal dissipative Lax-Phillips scattering theories is obtained in terms of ordered 6-tuples consisting of unilateral shifts and contractions which can be, roughly speaking, freely chosen. In this parametrization the wave and scattering operators as well as the scattering matrix are explicitly calculated. Moreover, a description of all analytical contraction-valued functions admitting a Darlington synthesis is found.

System Engineering and Evolution Decision Support

DTIC Science & Technology

2001-09-30

collection of Tuple Space model was first conceived in the mid- 1980 at objects that isolates the requestor of services from the Yale University by...Academic Press, NY, 1980 , pp. 325-347. [2] V. Berzins, M. Shing, Luqi, M. Saluto and J. Williams, Re-engineering the Janus(A) Combat Simulation System...Naval Postgraduate School Monterey, CA 93943-5100 3. Research Office, Code 09 Naval Postgraduate School Monterey, CA 93943-5000 4. Dr. David Hislop U.S

National Computer Security Conference (16th) held at Baltimore Convention Center, Baltimore, Maryland on September 20-23, 1993. Proceedings

DTIC Science & Technology

1993-09-23

answer to the question: Is subject s allowed access type a on object o? An authorization was thus seen as a 3-tuple (s,o,a). This view of access...called trusted in a Bell-LaPadula architecture. Work at Carnegie Mellon University on type enforcement contemporaneous with Denning’s was not addressed in...34Implementation Considerations for the Typed Access Matrix Model in a Distributed Environment," Proceedings of the 15th National Computer Security

Preparation and Analysis of N-Terminal Chemokine Receptor Sulfopeptides Using Tyrosylprotein Sulfotransferase Enzymes.

PubMed

Seibert, Christoph; Sanfiz, Anthony; Sakmar, Thomas P; Veldkamp, Christopher T

2016-01-01

In most chemokine receptors, one or multiple tyrosine residues have been identified within the receptor N-terminal domain that are, at least partially, modified by posttranslational tyrosine sulfation. For example, tyrosine sulfation has been demonstrated for Tyr-3, -10, -14, and -15 of CCR5, for Tyr-3, -14, and -15 of CCR8, and for Tyr-7, -12, and -21 of CXCR4. While there is evidence for several chemokine receptors that tyrosine sulfation is required for optimal interaction with the chemokine ligands, the precise role of tyrosine sulfation for chemokine receptor function remains unclear. Furthermore, the function of the chemokine receptor N-terminal domain in chemokine binding and receptor activation is also not well understood. Sulfotyrosine peptides corresponding to the chemokine receptor N-termini are valuable tools to address these important questions both in structural and functional studies. However, due to the lability of the sulfotyrosine modification, these peptides are difficult to obtain using standard peptide chemistry methods. In this chapter, we provide methods to prepare sulfotyrosine peptides by enzymatic in vitro sulfation of peptides using purified recombinant tyrosylprotein sulfotransferase (TPST) enzymes. In addition, we also discuss alternative approaches for the generation of sulfotyrosine peptides and methods for sulfopeptide analysis. © 2016 Elsevier Inc. All rights reserved.

Preparation and analysis of N-terminal chemokine receptor sulfopeptides using tyrosylprotein sulfotransferase enzymes

PubMed Central

Seibert, Christoph; Sanfiz, Anthony; Sakmar, Thomas P.; Veldkamp, Christopher T.

2016-01-01

In most chemokine receptors, one or multiple tyrosine residues have been identified within the receptor N-terminal domain that are, at least partially, modified by post-translational tyrosine sulfation. For example, tyrosine sulfation has been demonstrated for Tyr-3, -10, -14, and -15 of CCR5, for Tyr-3, -14, and -15 of CCR8 and for Tyr-7, -12, and -21 of CXCR4. While there is evidence for several chemokine receptors that tyrosine sulfation is required for optimal interaction with the chemokine ligands, the precise role of tyrosine sulfation for chemokine receptor function remains unclear. Furthermore, the function of the chemokine receptor N-terminal domain in chemokine binding and receptor activation is also not well understood. Sulfotyrosine peptides corresponding to the chemokine receptor N-termini are valuable tools to address these important questions both in structural and functional studies. However, due to the liability of the sulfotyrosine modification, these peptides are difficult to obtain using standard peptide chemistry methods. In this chapter, we provide methods to prepare sulfotyrosine peptides by enzymatic in vitro sulfation of peptides using purified recombinant tyrosylprotein sulfotransferase (TPST) enzymes. In addition, we also discuss alternative approaches for the generation of sulfotyrosine peptides and methods from sulfopeptide analysis. PMID:26921955

Comparative analysis of monoclonal antibody N-glycosylation using stable isotope labelling and UPLC-fluorescence-MS.

PubMed

Millán Martín, Silvia; Delporte, Cédric; Farrell, Amy; Navas Iglesias, Natalia; McLoughlin, Niaobh; Bones, Jonathan

2015-03-07

A twoplex method using (12)C6 and (13)C6 stable isotope analogues (Δmass = 6 Da) of 2-aminobenzoic acid (2-AA) is described for quantitative analysis of N-glycans present on monoclonal antibodies and other glycoproteins using ultra performance liquid chromatography with sequential fluorescence and accurate mass tandem quadrupole time of flight (QToF) mass spectrometric detection.

Selectivity of N170 for visual words in the right hemisphere: Evidence from single-trial analysis.

PubMed

Yang, Hang; Zhao, Jing; Gaspar, Carl M; Chen, Wei; Tan, Yufei; Weng, Xuchu

2017-08-01

Neuroimaging and neuropsychological studies have identified the involvement of the right posterior region in the processing of visual words. Interestingly, in contrast, ERP studies of the N170 typically demonstrate selectivity for words more strikingly over the left hemisphere. Why is right hemisphere selectivity for words during the N170 epoch typically not observed, despite the clear involvement of this region in word processing? One possibility is that amplitude differences measured on averaged ERPs in previous studies may have been obscured by variation in peak latency across trials. This study examined this possibility by using single-trial analysis. Results show that words evoked greater single-trial N170s than control stimuli in the right hemisphere. Additionally, we observed larger trial-to-trial variability on N170 peak latency for words as compared to control stimuli over the right hemisphere. Results demonstrate that, in contrast to much of the prior literature, the N170 can be selective to words over the right hemisphere. This discrepancy is explained in terms of variability in trial-to-trial peak latency for responses to words over the right hemisphere. © 2017 Society for Psychophysiological Research.

Nitrogen removal in Myriophyllum aquaticum wetland microcosms for swine wastewater treatment: 15 N-labelled nitrogen mass balance analysis.

PubMed

Zhang, Shunan; Liu, Feng; Xiao, Runlin; He, Yang; Wu, Jinshui

2017-01-01

Ecological treatments are effective for treating agricultural wastewater. In this study, wetland microcosms vegetated with Myriophyllum aquaticum were designed for nitrogen (N) removal from two strengths of swine wastewater, and 15 N-labelled ammonium (NH 4 + -N) was added to evaluate the dominant NH 4 + -N removal pathway. The results showed that 98.8% of NH 4 + -N and 88.3% of TN (TN: 248.6 mg L -1 ) were removed from low-strength swine wastewater (SW1) after an incubation of 21 days, with corresponding values for high-strength swine wastewater (SW2) being 99.2% of NH 4 + -N and 87.8% of TN (TN: 494.9 mg L -1 ). Plant uptake and soil adsorption respectively accounted for 24.0% and 15.6% of the added 15 N. Meanwhile, above-ground tissues of M. aquaticum had significantly higher biomass and TN content than below-ground (P < 0.05). 15 N mass balance analysis indicated that gas losses contributed 52.0% to the added 15 N, but the N 2 O flux constituted only 7.5% of total gas losses. The dynamics of NO 3 - -N and N 2 O flux revealed that strong nitrification and denitrification occurred in M. aquaticum microcosms, which was a dominant N removal pathway. These findings demonstrated that M. aquaticum could feasibly be used to construct wetlands for high N-loaded animal wastewater treatment. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

1H, 13C, 15N NMR analysis of sildenafil base and citrate (Viagra) in solution, solid state and pharmaceutical dosage forms.

PubMed

Wawer, Iwona; Pisklak, Maciej; Chilmonczyk, Zdzisław

2005-08-10

Sildenafil citrate (SC) (Viagra) and sildenafil base in pure form are easily and unequivocally characterized by multinuclear NMR spectroscopy. Analysis of chemical shifts indicates that: (i) N6-H forms intramolecular hydrogen bonds, (ii) N25 is protonated in the salt and (iii) intermolecular OH...N hydrogen bonds involving N2 and N4 are present in the solid sildenafil citrate. 13C CPMAS NMR method has been proposed for the identification and quantitation of Viagra in its pharmaceutical formulations.

Phylogenetic Analysis and Pathogenicity Assessment of Two Strains of Avian Influenza Virus Subtype H9N2 Isolated from Migratory Birds: High Homology of Internal Genes with Human H10N8 Virus.

PubMed

Ye, Ge; Liang, Chai Hong; Hua, Deng Guo; Song, Lei Yong; Xiang, Yang Guo; Guang, Chen; Lan, Chen Hua; Ping, Hua Yu

2016-01-01

Two human-infecting avian influenza viruses (AIVs), H7N9 and H10N8, have emerged in China, which further indicate that the H9N2 subtype of AIVs, as an internal gene donor, may have an important role in the generation of new viruses with cross-species transmissibility and pathogenicity. H9N2 viruses that contain such internal genes widely exist in poultry but are rarely reported in migratory birds. In this study, two strains of the H9N2 virus were isolated from fecal samples of migratory birds in 2014: one strain from Caizi Lake in Anhui Province and one from Chen Lake in Hubei Province of China. Nucleotide sequence analysis revealed high homology of all six internal genes of these two strains with the internal genes of the human H10N8 virus in Jiangxi Province, as well as with the human H7N9 virus. Phylogenetic analysis indicated a possible origin of these two strains from poultry in South China. Both of the two viruses tested could replicated in respiratory organs of infective mice without adaption, by both strains of the H9N2 AIVs from wild birds, suggesting their potential capacity for directly infecting mammals. Our findings indicate the existence of H9N2 viruses that contain internal genes highly homologous with human H10N8 or H7N9 viruses. Wild birds can contribute to the spread of the H9N2 virus that contains the "harmful" internal gene complex, leading to gene rearrangement with other influenza viruses and to the generation of new pathogenic viruses. Therefore, strengthening AIV surveillance in wild birds can promote an understanding of the presence and prevalence of viruses and provide scientific evidence for the prevention and control of AIVs and human-infecting AIVs.

HPLC Analysis and Cytotoxicity of n-Butanol Extract from Glyphaea brevis Roots Against C6 Glioma Cells

PubMed Central

Konan, Koffi Marcel; Mamyrbekova-Bekro, Janat Akhanovna; Bakalara, Norbert; Virieux, David; Pirat, Jean-Luc; Bekro, Yves-Alain

2014-01-01

The n-butanol extract of the roots of Glyphaea brevis was analysed. HPLC analysis suggested the presence of phenolic compounds like protocatechuic acid (PCA). The extract showed moderate cytotoxic activity against C6 glioma cells (EC50 > 1 mg/ml). PMID:24634849

Characterization and functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in tilapia

PubMed Central

Li, Hong Lian; Gu, Xiao Hui; Li, Bi Jun; Chen, Xiao; Lin, Hao Ran; Xia, Jun Hong

2017-01-01

Hypoxia is a major cause of fish morbidity and mortality in the aquatic environment. Hypoxia-inducible factors are very important modulators in the transcriptional response to hypoxic stress. In this study, we characterized and conducted functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in Nile tilapia (Oreochromis niloticus). By cloning and Sanger sequencing, we obtained the full length cDNA sequences for HIF1α (2686bp) and HIF1αn (1308bp), respectively. The CDS of HIF1α includes 15 exons encoding 768 amino acid residues and the CDS of HIF1αn contains 8 exons encoding 354 amino acid residues. The complete CDS sequences of HIF1α and HIF1αn cloned from tilapia shared very high homology with known genes from other fishes. HIF1α show differentiated expression in different tissues (brain, heart, gill, spleen, liver) and at different hypoxia exposure times (6h, 12h, 24h). HIF1αn expression level under hypoxia is generally increased (6h, 12h, 24h) and shows extremely highly upregulation in brain tissue under hypoxia. A functional determination site analysis in the protein sequences between fish and land animals identified 21 amino acid sites in HIF1α and 2 sites in HIF1αn as significantly associated sites (α = 0.05). Phylogenetic tree-based positive selection analysis suggested 22 sites in HIF1α as positively selected sites with a p-value of at least 95% for fish lineages compared to the land animals. Our study could be important for clarifying the mechanism of fish adaptation to aquatic hypoxia environment. PMID:28278251

Biomarker of Long-Chain n-3 Fatty Acid Intake and Breast Cancer: Accumulative Evidence from an Updated Meta-Analysis of Epidemiological Studies.

PubMed

Yang, Bo; Ren, Xiao L; Wang, Zhi Y; Wang, Liang; Zhao, Feng; Guo, Xiao J; Li, Duo

2018-06-14

We aimed to summarize the up-to-date epidemiology evidence on biomarkers of long-chain (LC) n-3 fatty acid (FA) intake in relation to breast cancer (BC). Epidemiology studies determining FA levels in biospecimen (circulating blood or adipose tissue (AT)) were identified from PubMed, EMBASE, and Cochrane Library databases until March 2018. Multivariate-adjusted risk ratios (RRs) with 95% confidence intervals (CIs) were pooled using a random-effect model. Difference in biospecimen proportions of LC n-3 FA between BC cases and non-cases were analyzed as a standardized mean difference (SMD). Thirteen cohort and eleven case-control studies were eligible for the present meta-analysis. The estimated SMD was -0.14 (95% CI: -0.27, -0.11) for LC n-3 FA and -0.27 (95% CI: -0.42, -0.11) for LC n-3/n-6 FA ratio. When comparing the top tertiles with the bottom baseline levels, circulating LC n-3 FA was significantly associated with a lower risk of BC (RR: 0.84, 95% CI: 0.74, 0.96), but not AT (RR: 1.02, 95% CI: 0.70, 1.48). Significant inverse dose-response associations were observed for each 1% increment of circulating 20:5n-3 and 22:6n-3. This meta-analysis highlights that circulating LC n-3 FA as a biomarker of intake may be an independent predictive factor for BC, especially 20:5n-3 and 22:6n-3.

Statistical Model Analysis of (n,p) Cross Sections and Average Energy For Fission Neutron Spectrum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Odsuren, M.; Khuukhenkhuu, G.

2011-06-28

Investigation of charged particle emission reaction cross sections for fast neutrons is important to both nuclear reactor technology and the understanding of nuclear reaction mechanisms. In particular, the study of (n,p) cross sections is necessary to estimate radiation damage due to hydrogen production, nuclear heating and transmutations in the structural materials of fission and fusion reactors. On the other hand, it is often necessary in practice to evaluate the neutron cross sections of the nuclides for which no experimental data are available.Because of this, we carried out the systematical analysis of known experimental (n,p) and (n,a) cross sections for fastmore » neutrons and observed a systematical regularity in the wide energy interval of 6-20 MeV and for broad mass range of target nuclei. To explain this effect using the compound, pre-equilibrium and direct reaction mechanisms some formulae were deduced. In this paper, in the framework of the statistical model known experimental (n,p) cross sections averaged over the thermal fission neutron spectrum of U-235 are analyzed. It was shown that the experimental data are satisfactorily described by the statistical model. Also, in the case of (n,p) cross sections the effective average neutron energy for fission spectrum of U-235 was found to be around 3 MeV.« less

Electrostatic analysis of n-doped SrTiO{sub 3} metal-insulator-semiconductor systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamerbeek, A. M., E-mail: a.m.kamerbeek@rug.nl; Banerjee, T.; Hueting, R. J. E.

2015-12-14

Electron doped SrTiO{sub 3}, a complex-oxide semiconductor, possesses novel electronic properties due to its strong temperature and electric-field dependent permittivity. Due to the high permittivity, metal/n-SrTiO{sub 3} systems show reasonably strong rectification even when SrTiO{sub 3} is degenerately doped. Our experiments show that the insertion of a sub nanometer layer of AlO{sub x} in between the metal and n-SrTiO{sub 3} interface leads to a dramatic reduction of the Schottky barrier height (from around 0.90 V to 0.25 V). This reduces the interface resistivity by 4 orders of magnitude. The derived electrostatic analysis of the metal-insulator-semiconductor (n-SrTiO{sub 3}) system is consistent with thismore » trend. When compared with a Si based MIS system, the change is much larger and mainly governed by the high permittivity of SrTiO{sub 3}. The non-linear permittivity of n-SrTiO{sub 3} leads to unconventional properties such as a temperature dependent surface potential non-existent for semiconductors with linear permittivity such as Si. This allows tuning of the interfacial band alignment, and consequently the Schottky barrier height, in a much more drastic way than in conventional semiconductors.« less

Scientific Production about the Adherence to Antiretroviral Therapy

PubMed Central

de Oliveira, Regina Célia; de Andrade Moraes, Danielle Chianca; Santos, Cleytiane Stephany Silva; da Silva Monteiro, Gicely Regina Sobral; da Rocha Cabral, Juliana; Beltrão, Roberta Andrade; da Silva, Calos Roberto Lyra

2017-01-01

Objective To identify the elite of authors about the subject adherence to antiretroviral therapy; to identify the journals turned to publishing articles about adherence to antiretroviral therapy; and to identify and analyze the most commonly used words in abstracts of articles about adherence to antiretroviral therapy. Method A bibliometric study conducted through the Scopus base. We used articles published between 1996 and 2014, after application of the eligibility criteria, there were composed the sample with 24 articles. The data were analyzed descriptively. Were used the laws of bibliometric (Lotka, Bradford and Zipf) and the conceptual cloud map of words, through the program Cmap tools. Results Lotka’s Law identified the 5 authors more productive (46% of the total published). Bradford is impaired in this study. Concerning Zipf, 3 zones were determined, 31.47% of the words with in the first zone, 26.46% in the second and 42.06% in the third. In the conceptual map, the words/factors that positively and negatively influence adherence were emphasized, among them the need for more research in the health services. Conclusion There are few publications about the accession to antiretroviral therapy, and the scientific production is in the process of maturation. One can infer that the theme researched is not yet an obsolete topic. It should be noted that the Bibliometric was a relevant statistic tool to generate information about the publications about the antiretroviral therapy. PMID:28979571

Inferring cultural regions from correlation networks of given baby names

NASA Astrophysics Data System (ADS)

Pomorski, Mateusz; Krawczyk, Małgorzata J.; Kułakowski, Krzysztof; Kwapień, Jarosław; Ausloos, Marcel

2016-03-01

We report investigations on the statistical characteristics of the baby names given between 1910 and 2010 in the United States of America. For each year, the 100 most frequent names in the USA are sorted out. For these names, the correlations between the names profiles are calculated for all pairs of states (minus Hawaii and Alaska). The correlations are used to form a weighted network which is found to vary mildly in time. In fact, the structure of communities in the network remains quite stable till about 1980. The goal is that the calculated structure approximately reproduces the usually accepted geopolitical regions: the Northeast, the South, and the "Midwest + West" as the third one. Furthermore, the dataset reveals that the name distribution satisfies the Zipf law, separately for each state and each year, i.e. the name frequency f ∝r-α, where r is the name rank. Between 1920 and 1980, the exponent α is the largest one for the set of states classified as 'the South', but the smallest one for the set of states classified as "Midwest + West". Our interpretation is that the pool of selected names was quite narrow in the Southern states. The data is compared with some related statistics of names in Belgium, a country also with different regions, but having quite a different scale than the USA. There, the Zipf exponent is low for young people and for the Brussels citizens.

Raman analysis of phonon modes in a short period AlN/GaN superlattice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarkar, Ketaki; Datta, Debopam; Gosztola, David J.

AlN/GaN-based optoelectronic devices have been the subject of intense research underlying the commercialization of efficient devices. Areas of considerable interest are the study of their lattice dynamics, phonon transport, and electron-phonon interactions specific to the interface of these heterostructures which results in additional optical phonon modes known as interface phonon modes. In this study, the framework of the dielectric continuum model (DCM) has been used to compare and analyze the optical phonon modes obtained from experimental Raman scattering measurements on AlN/GaN short-period superlattices. We have observed the localized E2(high), A1(LO) and the E1(TO) modes in superlattice measurements at frequencies shiftedmore » from their bulk values. To the best of our knowledge, the nanostructures used in these studies are among the smallest yielding useful Raman signatures for the interface modes. In addition, we have also identified an additional spread of interface phonon modes in the TO range resulting from the superlattice periodicity. The Raman signature contribution from the underlying AlxGa1-xN ternary has also been observed and analyzed. A temperature calibrationwas done based on Stokes/anti-Stokes ratio of A1(LO) using Raman spectroscopy in a broad operating temperature range. Good agreement between the experimental results and theoretically calculated calibration plot predicted using Bose-Einstein statistics was obtained.« less

Raman analysis of phonon modes in a short period AlN/GaN superlattice

NASA Astrophysics Data System (ADS)

Sarkar, Ketaki; Datta, Debopam; Gosztola, David J.; Shi, Fengyuan; Nicholls, Alan; Stroscio, Michael A.; Dutta, Mitra

2018-03-01

AlN/GaN-based optoelectronic devices have been the subject of intense research underlying the commercialization of efficient devices. Areas of considerable interest are the study of their lattice dynamics, phonon transport, and electron-phonon interactions specific to the interface of these heterostructures which results in additional optical phonon modes known as interface phonon modes. In this study, the framework of the dielectric continuum model (DCM) has been used to compare and analyze the optical phonon modes obtained from experimental Raman scattering measurements on AlN/GaN short-period superlattices. We have observed the localized E2(high), A1(LO) and the E1(TO) modes in superlattice measurements at frequencies shifted from their bulk values. To the best of our knowledge, the nanostructures used in these studies are among the smallest yielding useful Raman signatures for the interface modes. In addition, we have also identified an additional spread of interface phonon modes in the TO range resulting from the superlattice periodicity. The Raman signature contribution from the underlying AlxGa1-xN ternary has also been observed and analyzed. A temperature calibration was done based on Stokes/anti-Stokes ratio of A1(LO) using Raman spectroscopy in a broad operating temperature range. Good agreement between the experimental results and theoretically calculated calibration plot predicted using Bose-Einstein statistics was obtained.

Microarray-based gene expression analysis of strong seed dormancy in rice cv. N22 and less dormant mutant derivatives.

PubMed

Wu, Tao; Yang, Chunyan; Ding, Baoxu; Feng, Zhiming; Wang, Qian; He, Jun; Tong, Jianhua; Xiao, Langtao; Jiang, Ling; Wan, Jianmin

2016-02-01

Seed dormancy in rice is an important trait related to the pre-harvest sprouting resistance. In order to understand the molecular mechanisms of seed dormancy, gene expression was investigated by transcriptome analysis using seeds of the strongly dormant cultivar N22 and its less dormant mutants Q4359 and Q4646 at 24 days after heading (DAH). Microarray data revealed more differentially expressed genes in Q4359 than in Q4646 compared to N22. Most genes differing between Q4646 and N22 also differed between Q4359 and N22. GO analysis of genes differentially expressed in both Q4359 and Q4646 revealed that some genes such as those for starch biosynthesis were repressed, whereas metabolic genes such as those for carbohydrate metabolism were enhanced in Q4359 and Q4646 seeds relative to N22. Expression of some genes involved in cell redox homeostasis and chromatin remodeling differed significantly only between Q4359 and N22. The results suggested a close correlation between cell redox homeostasis, chromatin remodeling and seed dormancy. In addition, some genes involved in ABA signaling were down-regulated, and several genes involved in GA biosynthesis and signaling were up-regulated. These observations suggest that reduced seed dormancy in Q4359 was regulated by ABA-GA antagonism. A few differentially expressed genes were located in the regions containing qSdn-1 and qSdn-5 suggesting that they could be candidate genes underlying seed dormancy. Our work provides useful leads to further determine the underling mechanisms of seed dormancy and for cloning seed dormancy genes from N22. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Influenza A H5N1 and H7N9 in China: A spatial risk analysis

PubMed Central

Gardner, Lauren; MacIntyre, Raina; Sarkar, Sahotra

2017-01-01

Background Zoonotic avian influenza poses a major risk to China, and other parts of the world. H5N1 has remained endemic in China and globally for nearly two decades, and in 2013, a novel zoonotic influenza A subtype H7N9 emerged in China. This study aimed to improve upon our current understanding of the spreading mechanisms of H7N9 and H5N1 by generating spatial risk profiles for each of the two virus subtypes across mainland China. Methods and findings In this study, we (i) developed a refined data set of H5N1 and H7N9 locations with consideration of animal/animal environment case data, as well as spatial accuracy and precision; (ii) used this data set along with environmental variables to build species distribution models (SDMs) for each virus subtype in high resolution spatial units of 1km2 cells using Maxent; (iii) developed a risk modelling framework which integrated the results from the SDMs with human and chicken population variables, which was done to quantify the risk of zoonotic transmission; and (iv) identified areas at high risk of H5N1 and H7N9 transmission. We produced high performing SDMs (6 of 8 models with AUC > 0.9) for both H5N1 and H7N9. In all our SDMs, H7N9 consistently showed higher AUC results compared to H5N1, suggesting H7N9 suitability could be better explained by environmental variables. For both subtypes, high risk areas were primarily located in south-eastern China, with H5N1 distributions found to be more diffuse and extending more inland compared to H7N9. Conclusions We provide projections of our risk models to public health policy makers so that specific high risk areas can be targeted for control measures. We recommend comparing H5N1 and H7N9 prevalence rates and survivability in the natural environment to better understand the role of animal and environmental transmission in human infections. PMID:28376125

Elimination of columnar microstructure in N-face InAlN, lattice-matched to GaN, grown by plasma-assisted molecular beam epitaxy in the N-rich regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmadi, Elaheh; Wienecke, Steven; Keller, Stacia

2014-02-17

The microstructure of N-face InAlN layers, lattice-matched to GaN, was investigated by scanning transmission electron microscopy and atom probe tomography. These layers were grown by plasma-assisted molecular beam epitaxy (PAMBE) in the N-rich regime. Microstructural analysis shows an absence of the lateral composition modulation that was previously observed in InAlN films grown by PAMBE. A room temperature two-dimensional electron gas (2DEG) mobility of 1100 cm{sup 2}/V s and 2DEG sheet charge density of 1.9 × 10{sup 13} cm{sup −2} was measured for N-face GaN/AlN/GaN/InAlN high-electron-mobility transistors with lattice-matched InAlN back barriers.

Measurement of 235U(n,n'γ) and 235U(n,2nγ) reaction cross sections

NASA Astrophysics Data System (ADS)

Kerveno, M.; Thiry, J. C.; Bacquias, A.; Borcea, C.; Dessagne, P.; Drohé, J. C.; Goriely, S.; Hilaire, S.; Jericha, E.; Karam, H.; Negret, A.; Pavlik, A.; Plompen, A. J. M.; Romain, P.; Rouki, C.; Rudolf, G.; Stanoiu, M.

2013-02-01

The design of generation IV nuclear reactors and the studies of new fuel cycles require knowledge of the cross sections of various nuclear reactions. Our research is focused on (n,xnγ) reactions occurring in these new reactors. The aim is to measure unknown cross sections and to reduce the uncertainty on present data for reactions and isotopes of interest for transmutation or advanced reactors. The present work studies the 235U(n,n'γ) and 235U(n,2nγ) reactions in the fast neutron energy domain (up to 20 MeV). The experiments were performed with the Geel electron linear accelerator GELINA, which delivers a pulsed white neutron beam. The time characteristics enable measuring neutron energies with the time-of-flight (TOF) technique. The neutron induced reactions [in this case inelastic scattering and (n,2n) reactions] are identified by on-line prompt γ spectroscopy with an experimental setup including four high-purity germanium (HPGe) detectors. A fission ionization chamber is used to monitor the incident neutron flux. The experimental setup and analysis methods are presented and the model calculations performed with the TALYS-1.2 code are discussed.

Cross-language Babel structs—making scientific interfaces more efficient

NASA Astrophysics Data System (ADS)

Prantl, Adrian; Ebner, Dietmar; Epperly, Thomas G. W.

2013-01-01

Babel is an open-source language interoperability framework tailored to the needs of high-performance scientific computing. As an integral element of the Common Component Architecture, it is employed in a wide range of scientific applications where it is used to connect components written in different programming languages. In this paper we describe how we extended Babel to support interoperable tuple data types (structs). Structs are a common idiom in (mono-lingual) scientific application programming interfaces (APIs); they are an efficient way to pass tuples of nonuniform data between functions, and are supported natively by most programming languages. Using our extended version of Babel, developers of scientific codes can now pass structs as arguments between functions implemented in any of the supported languages. In C, C++, Fortran 2003/2008 and Chapel, structs can be passed without the overhead of data marshaling or copying, providing language interoperability at minimal cost. Other supported languages are Fortran 77, Fortran 90/95, Java and Python. We will show how we designed a struct implementation that is interoperable with all of the supported languages and present benchmark data to compare the performance of all language bindings, highlighting the differences between languages that offer native struct support and an object-oriented interface with getter/setter methods. A case study shows how structs can help simplify the interfaces of scientific codes significantly.

Multiple alignment-free sequence comparison

PubMed Central

Ren, Jie; Song, Kai; Sun, Fengzhu; Deng, Minghua; Reinert, Gesine

2013-01-01

Motivation: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, and , extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequences, and second, , and , averages of sums of pairwise comparison statistics. The two tasks we consider are, first, to identify sequences that are similar to a set of target sequences, and, second, to measure the similarity within a set of sequences. Results: Our investigation uses both simulated data as well as cis-regulatory module data where the task is to identify cis-regulatory modules with similar transcription factor binding sites. We find that although for real data, all of our statistics show a similar performance, on simulated data the Shepp-type statistics are in some instances outperformed by star-type statistics. The multiple alignment-free statistics are more sensitive to contamination in the data than the pairwise average statistics. Availability: Our implementation of the five statistics is available as R package named ‘multiAlignFree’ at be http://www-rcf.usc.edu/∼fsun/Programs/multiAlignFree/multiAlignFreemain.html. Contact: reinert@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23990418

Identical acyl transfer reactions between pyridine N-oxides and their N-acylonium salts

NASA Astrophysics Data System (ADS)

Rybachenko, V. I.; Shroeder, G.; Chotii, K. Yu.; Kovalenko, V. V.; Red'Ko, A. N.; Gierzyk, B.

2007-10-01

28 identical acyl exchange reactions R-CO-Nu+, X- + Nu between pyridine N-oxides in acetonitrile were studied. Here, X- = BPh{4/-} and R = methyl, N,N-dimethylamino, N,N-diethylamino, 4-morpholino, 1-piperidino, N-methyl, N-phenylamino, or N,N-diphenylamino group. The IR and NMR spectroscopic characteristics of acyloxypyridinium salts were determined, and the quantum-chemical parameters of all reagents calculated. The results were subjected to correlation analysis. It was found that the rate of identical acyl transfer reactions was controlled by the interaction of frontier orbitals in the transition state.

Gauss Modular-Arithmetic Congruence = Signal X Noise PRODUCT: Clock-model Archimedes HYPERBOLICITY Centrality INEVITABILITY: Definition: Complexity= UTTER-SIMPLICITY: Natural-Philosophy UNITY SIMPLICITY Redux!!!

NASA Astrophysics Data System (ADS)

Kummer, E. E.; Siegel, Edward Carl-Ludwig

2011-03-01

Clock-model Archimedes [http://linkage.rockeller.edu/ wli/moved.8.04/ 1fnoise/ index. ru.html] HYPERBOLICITY inevitability throughout physics/pure-maths: Newton-law F=ma, Heisenberg and classical uncertainty-principle=Parseval/Plancherel-theorems causes FUZZYICS definition: (so miscalled) "complexity" = UTTER-SIMPLICITY!!! Watkins[www.secamlocal.ex.ac.uk/people/staff/mrwatkin/]-Hubbard[World According to Wavelets (96)-p.14!]-Franklin[1795]-Fourier[1795;1822]-Brillouin[1922] dual/inverse-space(k,w) analysis key to Fourier-unification in Archimedes hyperbolicity inevitability progress up Siegel cognition hierarchy-of-thinking (HoT): data-info.-know.-understand.-meaning-...-unity-simplicity = FUZZYICS!!! Frohlich-Mossbauer-Goldanskii-del Guidice [Nucl.Phys.B:251,375(85);275,185 (86)]-Young [arXiv-0705.4678y2, (5/31/07] theory of health/life=aqueous-electret/ ferroelectric protoplasm BEC = Archimedes-Siegel [Schrodinger Cent.Symp.(87); Symp.Fractals, MRS Fall Mtg.(89)-5-pprs] 1/w-"noise" Zipf-law power-spectrum hyperbolicity INEVITABILITY= Chi; Dirac delta-function limit w=0 concentration= BEC = Chi-Quong.

The fatigue of high office

NASA Astrophysics Data System (ADS)

Ramsden, Jeremy J.; Naran, Deven

2007-03-01

The word frequencies of the speeches of some contemporary politicians have been determined over a decade of office. By fitting Mandelbrot's simple canonical law (a development of Zipf 's law) to the data, the average cybernetic temperature θ was determined for each year of office. Two contrasting cases were examined. The first, that of the British Prime Minister Tony Blair, showed a steady decline of θ punctuated by partial recovery following certain key events such as re-election. The second, that of the Australian Prime Minister John Howard, showed a more uniform temperature. It is suggested that the first case is an example of the phenomenon of fatigue or habituation, inevitable in any complex system rich in equilibrium states, and the partial de-habituation observed is a consequence of a sharp disturbance to the system. Given the relative ease of carrying out the analysis, it could become a routine tool regularly applied to holders of high office to determine their continuing fitness to occupy the office.

Comparison of trap characteristics between AlGaN/GaN and AlGaN/InGaN/GaN heterostructure by frequency dependent conductance measurement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakraborty, Apurba, E-mail: apurba.chakraborty86@gmail.com; Biswas, Dhrubes; Advanced Technology Development Centre, IIT Kharagpur, Kharagpur 721302

2015-02-23

Frequency dependent conductance measurement is carried out to observe the trapping effect in AlGaN/InGaN/GaN double heterostructure and compared that with conventional AlGaN/GaN single heterostructure. It is found that the AlGaN/InGaN/GaN diode structure does not show any trapping effect, whereas single heterostructure AlGaN/GaN diode suffers from two kinds of trap energy states in near depletion to higher negative voltage bias region. This conductance behaviour of AlGaN/InGaN/GaN heterostructure is owing to more Fermi energy level shift from trap energy states at AlGaN/InGaN junction compare to single AlGaN/GaN heterostructure and eliminates the trapping effects. Analysis yielded interface trap energy state in AlGaN/GaN ismore » to be with time constant of (33.8–76.5) μs and trap density of (2.38–0.656) × 10{sup 12 }eV{sup −1} cm{sup −2} in −3.2 to −4.8 V bias region, whereas for AlGaN/InGaN/GaN structure no interface energy states are found and the extracted surface trap energy concentrations and time constants are (5.87–4.39) ×10{sup 10} eV{sup −1} cm{sup −2} and (17.8–11.3) μs, respectively, in bias range of −0.8–0.0 V.« less

Immunogenicity and safety of pandemic influenza A (H1N1) 2009 vaccine: systematic review and meta-analysis.

PubMed

Yin, J Kevin; Khandaker, Gulam; Rashid, Harunor; Heron, Leon; Ridda, Iman; Booy, Robert

2011-09-01

The emergence of the 2009 H1N1 pandemic has highlighted the need to have immunogenicity and safety data on the new pandemic vaccines. There is already considerable heterogeneity in the types of vaccine available and of study performed around the world. A systematic review and meta-analysis is needed to assess the immunogenicity and safety of pandemic influenza A (H1N1) 2009 vaccines. We searched Medline, EMBASE, the Cochrane Library and other online databases up to 1st October 2010 for studies in any language comparing different pandemic H1N1 vaccines, with or without placebo, in healthy populations aged at least 6 months. The primary outcome was seroprotection according to haemagglutination inhibition (HI). Safety outcomes were adverse events. Meta-analysis was performed for the primary outcome. We identified 18 articles, 1 only on safety and 17 on immunogenicity, although 1 was a duplicate. We included 16 articles in the meta-analysis, covering 17,921 subjects. Adequate seroprotection (≥70%) was almost invariably achieved in all age groups, and even after one dose and at low antigen content (except in children under 3 years receiving one dose of non-adjuvanted vaccine). Non-adjuvanted vaccine from international companies and adjuvanted vaccines containing oil in water emulsion (e.g. AS03, MF59), rather than aluminium, performed better. Two serious vaccination-associated adverse events were reported, both of which resolved fully. No death or case of Guillain-Barré syndrome was reported. The pandemic influenza (H1N1) 2009 vaccine, with or without adjuvant, appears generally to be seroprotective after just one dose and safe among healthy populations aged ≥36 months; very young children (6-35 months) may need to receive two doses of non-adjuvanted vaccine or one dose of AS03(A/B)-adjuvanted product to achieve seroprotection. © 2011 Blackwell Publishing Ltd.

Analysis of PNGase F-resistant N-glycopeptides using SugarQb for Proteome Discoverer 2.1 reveals cryptic substrate specificities.

PubMed

Stadlmann, Johannes; Hoi, David M; Taubenschmid, Jasmin; Mechtler, Karl; Penninger, Josef M

2018-05-18

SugarQb (www.imba.oeaw.ac.at/sugarqb) is a freely available collection of computational tools for the automated identification of intact glycopeptides from high-resolution HCD MS/MS data-sets in the Proteome Discoverer environment. We report the migration of SugarQb to the latest and free version of Proteome Discoverer 2.1, and apply it to the analysis of PNGase F-resistant N-glycopeptides from mouse embryonic stem cells. The analysis of intact glycopeptides highlights unexpected technical limitations to PNGase F-dependent glycoproteomic workflows at the proteome level, and warrants a critical re-interpretation of seminal data-sets in the context of N-glycosylation-site prediction. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Association of N-acetyltransferase 1 polymorphism and bladder cancer risk: an updated meta-analysis and trial sequential analysis.

PubMed

Xu, Zicheng; Li, Xiao; Qin, Zhiqiang; Xue, Jianxin; Wang, Jingyuan; Liu, Zhentao; Cai, Hongzhou; Yu, Bin; Xu, Ting; Zou, Qin

2017-07-24

Individual studies of the association between N-acetyltransferase 1 (NAT1)*10 allele and bladder cancer susceptibility have shown inconclusive results. To derive a more precise estimation of any such relationship, we performed this systemic review and updated meta-analysis based on 17 publications. A total of 17 studies were investigated with 4,322 bladder cancer cases and 4,944 controls. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of the association. Subgroup analyses were conducted based on ethnicity, sex, source of controls and detecting methods. Then trial sequential analysis was performed to evaluate whether the evidence of the results was sufficient and reduce the risk of type I error. There was no association between NAT1*10 allele and bladder cancer risk in a random-effects model (OR = 0.96, 95% CI, 0.84-1.10) or in a fixed-effects model (OR = 0.95, 95% CI, 0.87-1.03). In addition, no significantly increased risk of bladder cancer was found in any other subgroup analysis. Then, trial sequential analyses demonstrated that the results of our study need to be further verified. Despite its limitations, the results of the present meta-analysis suggested that there was no association between NAT1*10 allele and bladder cancer risk. More importantly, our findings need to be further validated regarding whether being without the NAT1*10 allele could in the future be shown to be a potential marker for the risk of bladder cancer.

Site-specific 15N isotopic signatures of abiotically produced N2O

NASA Astrophysics Data System (ADS)

Heil, Jannis; Wolf, Benjamin; Brüggemann, Nicolas; Emmenegger, Lukas; Tuzson, Béla; Vereecken, Harry; Mohn, Joachim

2014-08-01

Efficient nitrous oxide (N2O) mitigation strategies require the identification of the main source and sink processes and their contribution to total soil N2O production. Several abiotic reactions of nitrification intermediates leading to N2O production are known, but their contribution to total N2O production in soils is uncertain. As the site preference (SP) of 15N in N2O is a promising tool to give more insight into N2O production processes, we investigated the SP of N2O produced by different abiotic reactions in a laboratory study. All reactions involved the nitrification intermediate hydroxylamine (NH2OH) in combination with nitrite (NO2-), Fe3+, Fe2+ and Cu2+, reactants commonly or potentially found in soils, at different concentrations and pH values. N2O production and its four main isotopic species (14N14N16O, 15N14N16O, 14N15N16O, and 14N14N18O) were quantified simultaneously and online at high temporal resolution using quantum cascade laser absorption spectroscopy. Thereby, our study presents the first continuous analysis of δ18O in N2O. The experiments revealed the possibility of purely abiotic reactions over a wide range of acidity (pH 3-8) by different mechanisms. All studied abiotic pathways produced N2O with a characteristic SP in the range of 34-35‰, unaffected by process conditions and remaining constant over the course of the experiments. These findings reflect the benefit of continuous N2O isotopic analysis by laser spectroscopy, contribute new information to the challenging source partitioning of N2O emissions from soils, and emphasize the potentially significant role of coupled biotic-abiotic reactions in soils.

Hippophae rhamnoides N-glycoproteome analysis: a small step towards sea buckthorn proteome mining.

PubMed

Sougrakpam, Yaiphabi; Deswal, Renu

2016-10-01

Hippophae rhamnoides is a hardy shrub capable of growing under extreme environmental conditions namely, high salt, drought and cold. Its ability to grow under extreme conditions and its wide application in pharmaceutical and nutraceutical industry calls for its in-depth analysis. N-glycoproteome mining by con A affinity chromatography from seedling was attempted. The glycoproteome was resolved on first and second dimension gel electrophoresis. A total of 48 spots were detected and 10 non-redundant proteins were identified by MALDI-TOF/TOF. Arabidopsis thaliana protein disulfide isomerase-like 1-4 (ATPDIL1-4) electron transporter, protein disulphide isomerase, calreticulin 1 (CRT1), glycosyl hydrolase family 38 (GH 38) protein, phantastica, maturase k, Arabidopsis trithorax related protein 6 (ATXR 6), cysteine protease inhibitor were identified out of which ATXR 6, phantastica and putative ATPDIL1-4 electron transporter are novel glycoproteins. Calcium binding protein CRT1 was validated for its calcium binding by stains all staining. GO analysis showed involvement of GH 38 and ATXR 6 in glycan and lysine degradation pathways. This is to our knowledge the first report of glycoproteome analysis for any Elaeagnaceae member.

Chemometric analysis of soil pollution data using the Tucker N-way method.

PubMed

Stanimirova, I; Zehl, K; Massart, D L; Vander Heyden, Y; Einax, J W

2006-06-01

N-way methods, particularly the Tucker method, are often the methods of choice when analyzing data sets arranged in three- (or higher) way arrays, which is the case for most environmental data sets. In the future, applying N-way methods will become an increasingly popular way to uncover hidden information in complex data sets. The reason for this is that classical two-way approaches such as principal component analysis are not as good at revealing the complex relationships present in data sets. This study describes in detail the application of a chemometric N-way approach, namely the Tucker method, in order to evaluate the level of pollution in soil from a contaminated site. The analyzed soil data set was five-way in nature. The samples were collected at different depths (way 1) from two locations (way 2) and the levels of thirteen metals (way 3) were analyzed using a four-step-sequential extraction procedure (way 4), allowing detailed information to be obtained about the bioavailability and activity of the different binding forms of the metals. Furthermore, the measurements were performed under two conditions (way 5), inert and non-inert. The preferred Tucker model of definite complexity showed that there was no significant difference in measurements analyzed under inert or non-inert conditions. It also allowed two depth horizons, characterized by different accumulation pathways, to be distinguished, and it allowed the relationships between chemical elements and their biological activities and mobilities in the soil to be described in detail.

A novel method for collection of soil-emitted nitric oxide (NO) for natural abundance stable N isotope analysis

NASA Astrophysics Data System (ADS)

Yu, Z.; Elliott, E. M.

2016-12-01

The global inventory of NO emissions is poorly constrained with a large portion of the uncertainty attributed to soil NO emissions that result from soil abiotic and microbial processes. While natural abundance stable N isotopes (δ15N) in various soil N-containing compounds have proven to be a robust tracer of soil N cycling, soil δ15N-NO is rarely quantified mainly due to the diffuse nature, low concentrations, and high reactivity of soil-emitted NO. Here, we present the development and application of a dynamic flux chamber system capable of simultaneously measuring soil NO fluxes and collecting NO for δ15N-NO measurements. The system couples a widely used flow-through soil chamber with a NO collection train, in which NO can be converted to NO2 through O3 titration in a Teflon reaction coil, followed by NO2 collection in a 20% triethanolamine (TEA) solution as nitrite and nitrate for δ15N analysis using the denitrifier method. The efficiency of NO-NO2 conversion in the reaction coil and the recovery of NO in the TEA solution were determined experimentally and found to be quantitative (>99%) over a 10 to 749 ppbv NO mixing ratio range. An analytical NO tank (δ15N-NO=71.0±0.4‰) was used to calibrate the method for δ15N-NO analysis. The resulting accuracy and precision (1σ) of the method across various environmental conditions were 1.6‰ and 1.2‰, respectively. Using this new method, controlled laboratory incubations have been conducted to characterize NO emissions induced by rewetting of air-dried surface soil sampled from an urban forest. Pulsed NO emissions, up to 30 times higher than maximum soil NO emissions under steady state, were triggered upon the rewetting and lasted for next 36 hours. While the measured δ15N-NO over the course of the NO pulsing ranged from -52.0‰ and -34.6‰, reinforcing the notion that soil δ15N-NO is lower than those of fossil-fuel combustion sources, a transient δ15N-NO shift was captured immediately after the

Distributed Computing for Signal Processing: Modeling of Asynchronous Parallel Computation. Appendix G. On the Design and Modeling of Special Purpose Parallel Processing Systems.

DTIC Science & Technology

1985-05-01

unit in the data base, with knowing one generic assembly language. °-’--a 139 The 5-tuple describing single operation execution time of the operations...TSi-- generate , random eventi ( ,.0-15 tieit tmls - ((floa egus ()16 274 r Ispt imet imel I at :EVE’JS- II ktime=0.0; /0 present time 0/ rrs ptime=0.0...computing machinery capable of performing these tasks within a given time constraint. Because the majority of the available computing machinery is general

Flexible Decision Support in Device-Saturated Environments

DTIC Science & Technology

2003-10-01

also output tuples to a remote MySQL or Postgres database. 3.3 GUI The GUI allows the user to pose queries using SQL and to display query...DatabaseConnection.java – handles connections to an external database (such as MySQL or Postgres ). • Debug.java – contains the code for printing out Debug messages...also provided. It is possible to output the results of queries to a MySQL or Postgres database for archival and the GUI can query those results

Data Triage

DTIC Science & Technology

2007-06-01

particle accelerators cannot run unless enough network band- width is available to absorb their data streams. DOE scientists running simulations routinely...send tuples to TelegraphCQ. To simulate a less-powerful machine, I increased the playback rate of the trace by a factor of 10 and reduced the query...III CPUs and 1.5 GB of main memory. To simulate using a less powerful embedded CPU, I wrote a program that would “play back” the trace at a multiple

Identification, sequence analysis, and infectivity of H9N2 avian influenza viruses isolated from geese.

PubMed

Zhu, Rui; Yang, Xueqin; Zhang, Jianjun; Xu, Danwen; Fan, Jiawen; Shi, Huoying; Wang, Shifeng; Liu, Xiufan

2018-05-31

The subtype H9N2 avian influenza virus greatly threatens the Chinese poultry industry, even with annual vaccination. Waterfowl can be asymptomatically infected with the H9N2 virus. In this study, three H9N2 virus strains, designated A/Goose/Jiangsu/YZ527/2011 (H9N2, Gs/JS/YZ527/11), A/Goose/Jiangsu/SQ119/2012 (H9N2, Gs/JS/SQ119/12), and A/Goose/Jiangsu/JD564/2012 (H9N2, Gs/JS/JD564/12), were isolated from domestic geese. Molecular characterization of the three isolates showed that the Gs/JS/YZ527/11 virus is a double-reassortant virus, combining genes of A/Quail/Hong Kong/G1/97 (H9N2, G1/97)-like and A/Chicken/Shanghai/F/98 (H9N2, F/98)-like; the Gs/JS/SQ119/12 virus is a triple-reassortant virus combining genes of G1/97-like, F/98-like, and A/Duck/Shantou/163/2004 (H9N2, ST/163/04)-like. The sequences of Gs/JS/JD564/12 share high homology with those of the F/98 virus, except for the neuraminidase gene, whereas the internal genes of Gs/JS/YZ527/11 and Gs/JS/SQ119/12 are closely related to those of the H7N9 viruses. An infectivity analysis of the three isolates showed that Gs/JS/SQ119/12 and Gs/JS/YZ527/11 replicated well, with seroconversion, in geese and chickens, the Gs/JS/JD564/12 did not infect well in geese or chickens, and the F/98 virus only infected chickens, with seroconversion. Emergence of these new reassortant H9N2 avian influenza viruses indicates that these viruses can infect both chicken and goose and can produce different types of lesions in each species.

Identification, sequence analysis, and infectivity of H9N2 avian influenza viruses isolated from geese

PubMed Central

Zhu, Rui; Yang, Xueqin; Zhang, Jianjun; Xu, Danwen; Fan, Jiawen; Wang, Shifeng; Liu, Xiufan

2018-01-01

The subtype H9N2 avian influenza virus greatly threatens the Chinese poultry industry, even with annual vaccination. Waterfowl can be asymptomatically infected with the H9N2 virus. In this study, three H9N2 virus strains, designated A/Goose/Jiangsu/YZ527/2011 (H9N2, Gs/JS/YZ527/11), A/Goose/Jiangsu/SQ119/2012 (H9N2, Gs/JS/SQ119/12), and A/Goose/Jiangsu/JD564/2012 (H9N2, Gs/JS/JD564/12), were isolated from domestic geese. Molecular characterization of the three isolates showed that the Gs/JS/YZ527/11 virus is a double-reassortant virus, combining genes of A/Quail/Hong Kong/G1/97 (H9N2, G1/97)-like and A/Chicken/Shanghai/F/98 (H9N2, F/98)-like; the Gs/JS/SQ119/12 virus is a triple-reassortant virus combining genes of G1/97-like, F/98-like, and A/Duck/Shantou/163/2004 (H9N2, ST/163/04)-like. The sequences of Gs/JS/JD564/12 share high homology with those of the F/98 virus, except for the neuraminidase gene, whereas the internal genes of Gs/JS/YZ527/11 and Gs/JS/SQ119/12 are closely related to those of the H7N9 viruses. An infectivity analysis of the three isolates showed that Gs/JS/SQ119/12 and Gs/JS/YZ527/11 replicated well, with seroconversion, in geese and chickens, the Gs/JS/JD564/12 did not infect well in geese or chickens, and the F/98 virus only infected chickens, with seroconversion. Emergence of these new reassortant H9N2 avian influenza viruses indicates that these viruses can infect both chicken and goose and can produce different types of lesions in each species. PMID:29366299

Retrieval analysis of titanium nitride (TiN) coated prosthetic femoral heads articulating with polyethylene.

PubMed

Łapaj, Łukasz; Wendland, Justyna; Markuszewski, Jacek; Mróz, Adrian; Wiśniewski, Tomasz

2015-03-01

Data regarding in vivo performance of titanium nitride (TiN) coated prosthetic femoral heads is scarce, and available studies of older generations of implants demonstrated coating wear in vivo. That is why we conducted a retrieval analysis of 11 femoral heads (articulating in vivo for 1-56 months) with TiN film formed using physical vapor deposition (PVD), to verify if coating failure is a problem in contemporary implants. Retrieved implants were examined using scanning electron microscope, coating roughness was evaluated with a contact profilometer and adhesion was tested using a Rockwell HRC test according to VDI 3824 guideline. Although no gross failure of the TiN coating was observed in our retrievals, all implants had defects typical for PVD coatings, such as pinholes, small titanium droplets and blisters with delaminated coating. In some heads the coating was contaminated with small niobium (Nb) droplets uniformly scattered on the entire surface of the film. Presence of Nb contamination was associated with an increased number and area of other types of defects and poorer coating adhesion. In one component, subjected to multiple dislocations we found severe delamination and cracking of the coating, increased roughness and the presence of third bodies. Our results indicate, that although wear of the coating is lower than seen in older generations of implants, inconsistent quality of the TiN film among different implants indicates the need for strict monitoring of the manufacturing process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Tribology of monolayer films: comparison between n-alkanethiols on gold and n-alkyl trichlorosilanes on silicon.

PubMed

Booth, Brandon D; Vilt, Steven G; McCabe, Clare; Jennings, G Kane

2009-09-01

This Article presents a quantitative comparison of the frictional performance for monolayers derived from n-alkanethiolates on gold and n-alkyl trichlorosilanes on silicon. Monolayers were characterized by pin-on-disk tribometry, contact angle analysis, ellipsometry, and electrochemical impedance spectroscopy (EIS). Pin-on-disk microtribometry provided frictional analysis at applied normal loads from 10 to 1000 mN at a speed of 0.1 mm/s. At low loads (10 mN), methyl-terminated n-alkanethiolate self-assembled monolayers (SAMs) exhibited a 3-fold improvement in coefficient of friction over SAMs with hydroxyl- or carboxylic-acid-terminated surfaces. For monolayers prepared from both n-alkanethiols on gold and n-alkyl trichlorosilanes on silicon, a critical chain length of at least eight carbons is required for beneficial tribological performance at an applied load of 9.8 mN. Evidence for disruption of chemisorbed alkanethiolate SAMs with chain lengths n analysis of tribology wear tracks. The direct comparison between the tribological stability of alkanethiolate and silane monolayers shows that monolayers prepared from n-octadecyl dimethylchlorosilane and n-octadecyl trichlorosilane withstood normal loads at least 30 times larger than those that damaged octadecanethiolate SAMs. Collectively, our results show that the tribological properties of monolayer films are dependent on their internal stabilities, which are influenced by cohesive chain interactions (van der Waals) and the adsorbate-substrate bond.

Variation of acharan sulfate and monosaccharide composition and analysis of neutral N-glycans in African giant snail (Achatina fulica).

PubMed

Park, Youmie; Zhang, Zhenqing; Laremore, Tatiana N; Li, Boyangzi; Sim, Joon-Soo; Im, A-Rang; Ahn, Mi Young; Kim, Yeong Shik; Linhardt, Robert J

2008-12-01

Acharan sulfate content from African giant snail (Achatina fulica) was compared in eggs and snails of different ages. Acharan sulfate was not found in egg. Acharan sulfate disaccharide -->4)-alpha-D-GlcNpAc (1-->4)-alpha-L-IdoAp2S(1-->, analyzed by SAX (strong-anion exchange)-HPLC was observed soon after hatching and increases as the snails grow. Monosaccharide compositional analysis showed that mole % of glucosamine, a major monosaccharide of acharan sulfate, increased with age while mole % of galactose decreased with age. These results suggest that galactans represent a major energy source during development, while acharan sulfate appearing immediately after hatching, is essential for the snail growth. The structures of neutral N-glycans released from eggs by peptide N-glycosidase F (PNGase F), were next elucidated using ESI-MS/MS, MALDI-MS/MS, enzyme digestion, and monosaccharide composition analysis. Three types of neutral N-glycan structures were observed, truncated (Hex(2-4)-HexNAc(2)), high mannose (Hex(5-9)-HexNAc(2)), and complex (Hex(3)-HexNAc(2-10)) types. None showed core fucosylation.

Structural, molecular orbital and optical characterizations of binuclear mixed ligand copper (II) complex of phthalate with N,N,N',N'-tetramethylethylenediamine and its applications.

PubMed

Taha, A; Farag, A A M; Ammar, A H; Ahmed, H M

2014-09-15

A new binuclear mixed ligand complex, [Cu2(Phth)(Me4en)2(H2O)2(NO3)2]·H2O (where, Phth=phthalate, and (Me4en)=N,N,N',N'tetramethylethylenediamine) was synthesized and characterized using analytical, spectral, magnetic, molar conductance, thermal gravimetric analysis (TGA), X-ray diffraction (XRD) and transmission electron microscope (TEM) measurements. The XRD data of Cu(II)-complex was analyzed on the basis of Williamson-Hall (W-H) and compared with TEM results. The results indicate that the complex is well crystalline and correspond to hexagonal crystal structure. Analysis of the absorption coefficient near the absorption edge reveals that the optical band gaps are indirect allowed transition with values of 1.17 and 1.78 eV. The d-d absorption bands of the complex (dissolved in various solvents) exhibit a color changes (solvatochromic). Specific and non-specific interactions of solvent molecules with the complex were investigated using Multiple Linear Regression Analysis (MLRA). Transient photocurrent characteristics of Cu(II)-complex/n-Si heterojunctions indicate that photocurrent under illumination increase with increasing of light intensity and explained by continuous distribution of traps. Structural parameters of the free ligands and their Cu(II)-complex were calculated on the basis of semi-empirical PM3 level and compared with the experimental data. The present copper (II) complex was screened for its antimicrobial activity against some Gram-positive and Gram-negative bacteria and fungus strain. Copyright © 2014 Elsevier B.V. All rights reserved.

Cost-effectiveness analysis of N95 respirators and medical masks to protect healthcare workers in China from respiratory infections.

PubMed

Mukerji, Shohini; MacIntyre, C Raina; Seale, Holly; Wang, Quanyi; Yang, Peng; Wang, Xiaoli; Newall, Anthony T

2017-07-03

There are substantial differences between the costs of medical masks and N95 respirators. Cost-effectiveness analysis is required to assist decision-makers evaluating alternative healthcare worker (HCW) mask/respirator strategies. This study aims to compare the cost-effectiveness of N95 respirators and medical masks for protecting HCWs in Beijing, China. We developed a cost-effectiveness analysis model utilising efficacy and resource use data from two cluster randomised clinical trials assessing various mask/respirator strategies conducted in HCWs in Level 2 and 3 Beijing hospitals for the 2008-09 and 2009-10 influenza seasons. The main outcome measure was the incremental cost-effectiveness ratio (ICER) per clinical respiratory illness (CRI) case prevented. We used a societal perspective which included intervention costs, the healthcare costs of CRI in HCWs and absenteeism costs. The incremental cost to prevent a CRI case with continuous use of N95 respirators when compared to medical masks ranged from US $490-$1230 (approx. 3000-7600 RMB). One-way sensitivity analysis indicated that the CRI attack rate and intervention effectiveness had the greatest impact on cost-effectiveness. The determination of cost-effectiveness for mask/respirator strategies will depend on the willingness to pay to prevent a CRI case in a HCW, which will vary between countries. In the case of a highly pathogenic pandemic, respirator use in HCWs would likely be a cost-effective intervention.

General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding

PubMed Central

Lucius, Aaron L.; Maluf, Nasib K.; Fischer, Christopher J.; Lohman, Timothy M.

2003-01-01

Helicase-catalyzed DNA unwinding is often studied using “all or none” assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using “n-step” sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the “kinetic step size”, m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using “n-step” sequential mechanisms has previously been limited by an inability to float the number of “unwinding steps”, n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, fss(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain fss(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation. PMID:14507688

Electrical and Structural Analysis on the Formation of n-type Junction in Germanium

NASA Astrophysics Data System (ADS)

Aziz, Umar Abdul; Nadhirah Mohamad Rashid, Nur; Rahmah Aid, Siti; Centeno, Anthony; Ikenoue, Hiroshi; Xie, Fang

2017-05-01

Germanium (Ge) has re-emerged as a potential candidate to replace silicon (Si) as a substrate, due to its higher carrier mobility properties that are the key point for the realization of devices high drive current. However, the fabrication process of Ge is confronted with many problems such as low dopant electrical activation and the utilization of heavy n-type dopant atoms during ion implantation. These problems result in more damage and defects that can affect dopant activation. This paper reports the electrical and structural analysis on the formation of n-type junction in Ge substrate by ion implantation, followed by excimer laser annealing (ELA) using KrF laser. ELA parameters such as laser fluences were varied from 100 - 2000 mJ/cm2 and shot number between 1 - 1000 to obtain the optimized parameter of ELA with a high degree of damage and defect removal. Low resistance with a high degree of crystallinity is obtained for the samples annealed with less than five shot number. Higher shot number with high laser fluence, shows a high degree of ablation damage.

Quaternary ammonium salt N-(dodecyloxycarboxymethyl)-N,N,N-trimethyl ammonium chloride induced alterations in Saccharomyces cerevisiae physiology.

PubMed

Oblak, Ewa; Piecuch, Agata; Maciaszczyk-Dziubinska, Ewa; Wawrzycka, Donata

2016-12-01

We investigated the influence of the quaternary ammonium salt (QAS) called IM (N-(dodecyloxycarboxymethyl)- N,N,N-trimethyl ammonium chloride) on yeast cells of the parental strain and the IM-resistant mutant (EO25 IMR) growth. The phenotype of this mutant was pleiotropic. The IMR mutant exhibited resistance to ethanol, osmotic shock and oxidative stress, as well as increased sensitivity to UV. Moreover, it was noted that mutant EO25 appears to have an increased resistance to clotrimazole, ketoconazole, fluconazole, nystatin and cycloheximide. It also tolerated growth in the presence of crystal violet, DTT and metals (selenium, tin, arsenic). It was shown that the presence of IM decreased ergosterol level in mutant plasma membrane and increased its unsaturation. These results indicate changes in the cell lipid composition. Western blot analysis showed the induction of Pma1 level by IM. RT-PCR revealed an increased PMA1 expression after IM treatment.

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.

PubMed

Zhou, Xinrui; Zheng, Jie; Ivan, Fransiskus Xaverius; Yin, Rui; Ranganathan, Shoba; Chow, Vincent T K; Kwoh, Chee-Keong

2018-05-09

Influenza viruses are undergoing continuous and rapid evolution. The fatal influenza A/H7N9 has drawn attention since the first wave of infections in March 2013, and raised more grave concerns with its increased potential to spread among humans. Experimental studies have revealed several host and virulence markers, indicating differential host binding preferences which can help estimate the potential of causing a pandemic. Here we systematically investigate the sequence pattern and structural characteristics of novel influenza A/H7N9 using computational approaches. The sequence analysis highlighted mutations in protein functional domains of influenza viruses. Molecular docking and molecular dynamics simulation revealed that the hemagglutinin (HA) of A/Taiwan/1/2017(H7N9) strain enhanced the binding with both avian and human receptor analogs, compared with the previous A/Shanghai/02/2013(H7N9) strain. The Molecular Mechanics - Poisson Boltzmann Surface Area (MM-PBSA) calculation revealed the change of residue-ligand interaction energy and detected the residues with conspicuous binding preference. The results are novel and specific to the emerging influenza A/Taiwan/1/2017(H7N9) strain compared with A/Shanghai/02/2013(H7N9). Its enhanced ability to bind human receptor analogs, which are abundant in the human upper respiratory tract, may be responsible for the recent outbreak. Residues showing binding preference were detected, which could facilitate monitoring the circulating influenza viruses.

Content analysis of press coverage during the H1N1 influenza pandemic in Germany 2009-2010.

PubMed

Husemann, Sabine; Fischer, Florian

2015-04-15

The H1N1 influenza pandemic occurred in Germany between April 2009 and August 2010. Pandemics often lead to uncertainty amongst the public and so risk communication on health-related issues is one of the key areas of action for health authorities and other healthcare institutions. The mass media may contribute to risk communication, so this study analysed press coverage during the H1N1 pandemic in Germany. A comprehensive analysis of the press coverage during the H1N1 pandemic was conducted in two steps. First, a temporal analysis was carried out of newspaper articles over the entire course of the pandemic, a total of 15,353 articles. The newspaper articles were obtained from the database Nexis. The total number of articles about the influenza pandemic during each individual week was plotted against the number of incident influenza cases during that week. Second, a quantitative content analysis of 140 newspaper articles from selected dates was conducted. This study indicates that media awareness seems to be strongly related to the actual situation in the pandemic, because changes in the number of infected people were associated with nearly identical changes in the number of newspaper articles. Few articles contained information on the agent of the influenza or support measures. Information on vaccination was included in 32.9% of all articles. Almost half of the articles (48.6%) used case reports. Fear appeals were used in only 10.7% of the newspaper articles; 32.9% of the articles contained the message characteristic "self-efficacy". The newspaper articles that were analysed in the content analysis included different information and message characteristics. The extent of information provided differed during the pandemic. As current research indicates, the use of message characteristics such as fear appeals and self-efficacy, which were also included in the analysed newspaper articles, can help to make health messages effective.

Controlled synthesis of AlN/GaN multiple quantum well nanowire structures and their optical properties.

PubMed

Qian, Fang; Brewster, Megan; Lim, Sung K; Ling, Yichuan; Greene, Christopher; Laboutin, Oleg; Johnson, Jerry W; Gradečak, Silvija; Cao, Yu; Li, Yat

2012-06-13

We report the controlled synthesis of AlN/GaN multi-quantum well (MQW) radial nanowire heterostructures by metal-organic chemical vapor deposition. The structure consists of a single-crystal GaN nanowire core and an epitaxially grown (AlN/GaN)(m) (m = 3, 13) MQW shell. Optical excitation of individual MQW nanowires yielded strong, blue-shifted photoluminescence in the range 340-360 nm, with respect to the GaN near band-edge emission at 368.8 nm. Cathodoluminescence analysis on the cross-sectional MQW nanowire samples showed that the blue-shifted ultraviolet luminescence originated from the GaN quantum wells, while the defect-associated yellow luminescence was emitted from the GaN core. Computational simulation provided a quantitative analysis of the mini-band energies in the AlN/GaN superlattices and suggested the observed blue-shifted emission corresponds to the interband transitions between the second subbands of GaN, as a result of quantum confinement and strain effect in these AlN/GaN MQW nanowire structures.

Stimulation of N2 O emission by manure application to agricultural soils may largely offset carbon benefits: a global meta-analysis.

PubMed

Zhou, Minghua; Zhu, Bo; Wang, Shijie; Zhu, Xinyu; Vereecken, Harry; Brüggemann, Nicolas

2017-10-01

Animal manure application as organic fertilizer does not only sustain agricultural productivity and increase soil organic carbon (SOC) stocks, but also affects soil nitrogen cycling and nitrous oxide (N 2 O) emissions. However, given that the sign and magnitude of manure effects on soil N 2 O emissions is uncertain, the net climatic impact of manure application in arable land is unknown. Here, we performed a global meta-analysis using field experimental data published in peer-reviewed journals prior to December 2015. In this meta-analysis, we quantified the responses of N 2 O emissions to manure application relative to synthetic N fertilizer application from individual studies and analyzed manure characteristics, experimental duration, climate, and soil properties as explanatory factors. Manure application significantly increased N 2 O emissions by an average 32.7% (95% confidence interval: 5.1-58.2%) compared to application of synthetic N fertilizer alone. The significant stimulation of N 2 O emissions occurred following cattle and poultry manure applications, subsurface manure application, and raw manure application. Furthermore, the significant stimulatory effects on N 2 O emissions were also observed for warm temperate climate, acid soils (pH < 6.5), and soil texture classes of sandy loam and clay loam. Average direct N 2 O emission factors (EFs) of 1.87% and 0.24% were estimated for upland soils and rice paddy soils receiving manure application, respectively. Although manure application increased SOC stocks, our study suggested that the benefit of increasing SOC stocks as GHG sinks could be largely offset by stimulation of soil N 2 O emissions and aggravated by CH 4 emissions if, particularly for rice paddy soils, the stimulation of CH 4 emissions by manure application was taken into account. © 2017 John Wiley & Sons Ltd.

Genetic and phylogenetic analysis of multi-continent human influenza A(H1N2) reassortant viruses isolated in 2001 through 2003.

PubMed

Chen, M-J; La, T; Zhao, P; Tam, J S; Rappaport, R; Cheng, S-M

2006-12-01

Genetic analyses were performed on 228 influenza A(H1) viruses derived from clinical subjects participating in an experimental vaccine trial conducted in 20 countries on four continents between 2001 and 2003. HA1 phylogenetic analysis of these viruses showed multiple clades circulated around the world with regional prevalence patterns. Sixty-five of the A(H1) viruses were identified as A(H1N2), 40 of which were isolated from South Africa. The A(H1) sequences of these viruses cluster with published H1N2 viruses phylogenetically and share with them diagnostic signature V169A and A193T changes. The results also showed for the first time that H1N2 viruses were prominent in South Africa during the 2001-2002 influenza season, accounting for over 90% of the A(H1) cases in our study, and infecting both children (29/31) and the elderly (11/13). Phylogenetic analysis of the 65 H1N2 viruses we identified, in conjunction with the 56 recent H1N2 viruses currently available in the database, provided a comprehensive view of the circulation and evolution of distinct clades of H1N2 viruses in a temporal manner between early 2001 and mid-2003, shortly after the appearance of these recent reassortant viruses in or near year 2000.

Top-Down Chemoenzymatic Approach to Synthesizing Diverse High-Mannose N-Glycans and Related Neoglycoproteins for Carbohydrate Microarray Analysis.

PubMed

Toonstra, Christian; Wu, Lisa; Li, Chao; Wang, Denong; Wang, Lai-Xi

2018-05-22

High-mannose-type N-glycans are an important component of neutralizing epitopes on HIV-1 envelope glycoprotein gp120. They also serve as signals for protein folding, trafficking, and degradation in protein quality control. A number of lectins and antibodies recognize high-mannose-type N-glycans, and glycan array technology has provided an avenue to probe these oligomannose-specific proteins. We describe in this paper a top-down chemoenzymatic approach to synthesize a library of high-mannose N-glycans and related neoglycoproteins for glycan microarray analysis. The method involves the sequential enzymatic trimming of two readily available natural N-glycans, the Man 9 GlcNAc 2 Asn prepared from soybean flour and the sialoglycopeptide (SGP) isolated from chicken egg yolks, coupled with chromatographic separation to obtain a collection of a full range of natural high-mannose N-glycans. The Asn-linked N-glycans were conjugated to bovine serum albumin (BSA) to provide neoglycoproteins containing the oligomannose moieties. The glycoepitopes displayed were characterized using an array of glycan-binding proteins, including the broadly virus-neutralizing agents, glycan-specific antibody 2G12, Galanthus nivalis lectin (GNA), and Narcissus pseudonarcissus lectin (NPA).

AzTEC Survey of the Central Molecular Zone: Modeling Dust SEDs and N-PDF with Hierarchical Bayesian Analysis

NASA Astrophysics Data System (ADS)

Tang, Yuping; Wang, Daniel; Wilson, Grant; Gutermuth, Robert; Heyer, Mark

2018-01-01

We present the AzTEC/LMT survey of dust continuum at 1.1mm on the central ˜ 200pc (CMZ) of our Galaxy. A joint SED analysis of all existing dust continuum surveys on the CMZ is performed, from 160µm to 1.1mm. Our analysis follows a MCMC sampling strategy incorporating the knowledge of PSFs in different maps, which provides unprecedented spacial resolution on distributions of dust temperature, column density and emissivity index. The dense clumps in the CMZ typically show low dust temperature ( 20K), with no significant sign of buried star formation, and a weak evolution of higher emissivity index toward dense peak. A new model is proposed, allowing for varying dust temperature inside a cloud and self-shielding of dust emission, which leads to similar conclusions on dust temperature and grain properties. We further apply a hierarchical Bayesian analysis to infer the column density probability distribution function (N-PDF), while simultaneously removing the Galactic foreground and background emission. The N-PDF shows a steep power-law profile with α > 3, indicating that formation of dense structures are suppressed.

Did advances in global surveillance and notification systems make a difference in the 2009 H1N1 pandemic?--a retrospective analysis.

PubMed

Zhang, Ying; Lopez-Gatell, Hugo; Alpuche-Aranda, Celia M; Stoto, Michael A

2013-01-01

The 2009 H1N1 outbreak provides an opportunity to identify strengths and weaknesses of disease surveillance and notification systems that have been implemented in the past decade. Drawing on a systematic review of the scientific literature, official documents, websites, and news reports, we constructed a timeline differentiating three kinds of events: (1) the emergence and spread of the pH1N1 virus, (2) local health officials' awareness and understanding of the outbreak, and (3) notifications about the events and their implications. We then conducted a "critical event" analysis of the surveillance process to ascertain when health officials became aware of the epidemiologic facts of the unfolding pandemic and whether advances in surveillance notification systems hastened detection. This analysis revealed three critical events. First, medical personnel identified pH1N1in California children because of an experimental surveillance program, leading to a novel viral strain being identified by CDC. Second, Mexican officials recognized that unconnected outbreaks represented a single phenomenon. Finally, the identification of a pH1N1 outbreak in a New York City high school was hastened by awareness of the emerging pandemic. Analysis of the timeline suggests that at best the global response could have been about one week earlier (which would not have stopped spread to other countries), and could have been much later. This analysis shows that investments in global surveillance and notification systems made an important difference in the 2009 H1N1 pandemic. In particular, enhanced laboratory capacity in the U.S. and Canada led to earlier detection and characterization of the 2009 H1N1. This includes enhanced capacity at the federal, state, and local levels in the U.S., as well as a trilateral agreement enabling collaboration among U.S., Canada, and Mexico. In addition, improved global notification systems contributed by helping health officials understand the relevance and

Stable isotope tracking of endangered sea turtles: validation with satellite telemetry and δ15N analysis of amino acids.

PubMed

Seminoff, Jeffrey A; Benson, Scott R; Arthur, Karen E; Eguchi, Tomoharu; Dutton, Peter H; Tapilatu, Ricardo F; Popp, Brian N

2012-01-01

Effective conservation strategies for highly migratory species must incorporate information about long-distance movements and locations of high-use foraging areas. However, the inherent challenges of directly monitoring these factors call for creative research approaches and innovative application of existing tools. Highly migratory marine species, such as marine turtles, regularly travel hundreds or thousands of kilometers between breeding and feeding areas, but identification of migratory routes and habitat use patterns remains elusive. Here we use satellite telemetry in combination with compound-specific isotope analysis of amino acids to confirm that insights from bulk tissue stable isotope analysis can reveal divergent migratory strategies and within-population segregation of foraging groups of critically endangered leatherback sea turtles (Dermochelys coriacea) across the Pacific Ocean. Among the 78 turtles studied, we found a distinct dichotomy in δ(15)N values of bulk skin, with distinct "low δ(15)N" and "high δ(15)N" groups. δ(15)N analysis of amino acids confirmed that this disparity resulted from isotopic differences at the base of the food chain and not from differences in trophic position between the two groups. Satellite tracking of 13 individuals indicated that their bulk skin δ(15)N value was linked to the particular foraging region of each turtle. These findings confirm that prevailing marine isoscapes of foraging areas can be reflected in the isotopic compositions of marine turtle body tissues sampled at nesting beaches. We use a Bayesian mixture model to show that between 82 and 100% of the 78 skin-sampled turtles could be assigned with confidence to either the eastern Pacific or western Pacific, with 33 to 66% of all turtles foraging in the eastern Pacific. Our forensic approach validates the use of stable isotopes to depict leatherback turtle movements over broad spatial ranges and is timely for establishing wise conservation efforts in

Latent morpho-semantic analysis : multilingual information retrieval with character n-grams and mutual information.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bader, Brett William; Chew, Peter A.; Abdelali, Ahmed

We describe an entirely statistics-based, unsupervised, and language-independent approach to multilingual information retrieval, which we call Latent Morpho-Semantic Analysis (LMSA). LMSA overcomes some of the shortcomings of related previous approaches such as Latent Semantic Analysis (LSA). LMSA has an important theoretical advantage over LSA: it combines well-known techniques in a novel way to break the terms of LSA down into units which correspond more closely to morphemes. Thus, it has a particular appeal for use with morphologically complex languages such as Arabic. We show through empirical results that the theoretical advantages of LMSA can translate into significant gains in precisionmore » in multilingual information retrieval tests. These gains are not matched either when a standard stemmer is used with LSA, or when terms are indiscriminately broken down into n-grams.« less

N-acetylcysteine for major mental disorders: a systematic review and meta-analysis of randomized controlled trials.

PubMed

Zheng, W; Zhang, Q-E; Cai, D-B; Yang, X-H; Qiu, Y; Ungvari, G S; Ng, C H; Berk, M; Ning, Y-P; Xiang, Y-T

2018-05-01

This systematic review and meta-analysis of randomized controlled trials (RCTs) examined the efficacy and safety of adjunctive N-acetylcysteine (NAC), an antioxidant drug, in treating major depressive disorder (MDD), bipolar disorder, and schizophrenia. The PubMed, Cochrane Library, PsycINFO, CNKI, CBM, and WanFang databases were independently searched and screened by two researchers. Standardized mean differences (SMDs), risk ratios, and their 95% confidence intervals (CIs) were computed. Six RCTs (n = 701) of NAC for schizophrenia (three RCTs, n = 307), bipolar disorder (two RCTs, n = 125), and MDD (one RCT, n = 269) were identified and analyzed as separate groups. Adjunctive NAC significantly improved total psychopathology (SMD = -0.74, 95% CI: -1.43, -0.06; I 2 = 84%, P = 0.03) in schizophrenia, but it had no significant effect on depressive and manic symptoms as assessed by the Young Mania Rating Scale in bipolar disorder and only a small effect on major depressive symptoms. Adverse drug reactions to NAC and discontinuation rates between the NAC and control groups were similar across the three disorders. Adjunctive NAC appears to be a safe treatment that has efficacy for schizophrenia, but not for bipolar disorder or MDD. Further higher quality RCTs are warranted to determine the role of adjunctive NAC in the treatment of major psychiatric disorders. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Functional analysis of AtlA, the major N-acetylglucosaminidase of Enterococcus faecalis.

PubMed

Eckert, Catherine; Lecerf, Maxime; Dubost, Lionel; Arthur, Michel; Mesnage, Stéphane

2006-12-01

The major peptidoglycan hydrolase of Enterococcus faecalis, AtlA, has been identified, but its enzyme activity remains unknown. We have used tandem mass spectrometry analysis of peptidoglycan hydrolysis products obtained using the purified protein to show that AtlA is an N-acetylglucosaminidase. To gain insight into the regulation of its enzyme activity, the three domains of AtlA were purified alone or in combination following expression of truncated forms of the atlA gene in Escherichia coli or partial digestion of AtlA by proteinase K. The central domain of AtlA was catalytically active, but its activity was more than two orders of magnitude lower than that of the complete protein. Partial proteolysis of AtlA was detected in vivo: zymograms of E. faecalis extracts revealed two catalytically active protein bands of 62 and 72 kDa that were both absent in extracts from an atlA null mutant. Limited digestion of AtlA by proteinase K in vitro suggested that the proteolytic cleavage of AtlA in E. faecalis extracts corresponds to the truncation of the N-terminal domain, which is rich in threonine and glutamic acid residues. We show that the truncation of the N-terminal domain from recombinant AtlA has no impact on enzyme activity. The C-terminal domain of the protein, which contains six LysM modules bound to highly purified peptidoglycan, was required for optimal enzyme activity. These data indicate that AtlA is not produced as a proenzyme and that control of the AtlA glucosaminidase activity is likely to occur at the level of LysM-mediated binding to peptidoglycan.

Functional Analysis of AtlA, the Major N-Acetylglucosaminidase of Enterococcus faecalis▿

PubMed Central

Eckert, Catherine; Lecerf, Maxime; Dubost, Lionel; Arthur, Michel; Mesnage, Stéphane

2006-01-01

The major peptidoglycan hydrolase of Enterococcus faecalis, AtlA, has been identified, but its enzyme activity remains unknown. We have used tandem mass spectrometry analysis of peptidoglycan hydrolysis products obtained using the purified protein to show that AtlA is an N-acetylglucosaminidase. To gain insight into the regulation of its enzyme activity, the three domains of AtlA were purified alone or in combination following expression of truncated forms of the atlA gene in Escherichia coli or partial digestion of AtlA by proteinase K. The central domain of AtlA was catalytically active, but its activity was more than two orders of magnitude lower than that of the complete protein. Partial proteolysis of AtlA was detected in vivo: zymograms of E. faecalis extracts revealed two catalytically active protein bands of 62 and 72 kDa that were both absent in extracts from an atlA null mutant. Limited digestion of AtlA by proteinase K in vitro suggested that the proteolytic cleavage of AtlA in E. faecalis extracts corresponds to the truncation of the N-terminal domain, which is rich in threonine and glutamic acid residues. We show that the truncation of the N-terminal domain from recombinant AtlA has no impact on enzyme activity. The C-terminal domain of the protein, which contains six LysM modules bound to highly purified peptidoglycan, was required for optimal enzyme activity. These data indicate that AtlA is not produced as a proenzyme and that control of the AtlA glucosaminidase activity is likely to occur at the level of LysM-mediated binding to peptidoglycan. PMID:17041059

Dynamical coupled-channels study of pi N --> pi pi N reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamano, Hiroyuki; Julia Diaz, Bruno; Lee, Tsung-Shung

2009-01-01

As a step toward performing a complete coupled-channels analysis of the world data of pi N, gamma^* N --> pi N, eta N, pi pi N reactions, the pi N --> pi pi N reactions are investigated starting with the dynamical coupled-channels model developed in Phys. Rev. C76, 065201 (2007). The channels included are pi N, eta N, and pi pi N which has pi Delta, rho N, and sigma N resonant components. The non-resonant amplitudes are generated from solving a set of coupled-channels equations with the meson-baryon potentials defined by effective Lagrangians. The resonant amplitudes are generated from 16more » bare excited nucleon (N^*) states which are dressed by the non-resonant interactions as constrained by the unitarity condition. The available total cross section data of pi^+ p --> pi^+ pi^+ n, pi^+ pi^0 and pi^- p --> pi^+ pi^- n, pi^- pi^0 n, pi^0 pi^0 n can be reproduced to a very large extent both in magnitudes and energy-dependence. Possible improvements of the model are investigated, in p« less

Design and Conformational Analysis of Peptoids Containing N-Hydroxy Amides Reveals a Unique Sheet-Like Secondary Structure

PubMed Central

Crapster, J. Aaron; Stringer, Joseph R.; Guzei, Ilia A.; Blackwell, Helen E.

2011-01-01

N-hydroxy amides can be found in many naturally occurring and synthetic compounds and are known to act as both strong proton donors and chelators of metal cations. We have initiated studies of peptoids, or N-substituted glycines, that contain N-hydroxy amide side chains to investigate the potential effects of these functional groups on peptoid backbone amide rotamer equilibria and local conformations. We reasoned that the propensity of these functional groups to participate in hydrogen bonding could be exploited to enforce intramolecular or intermolecular interactions that yield new peptoid structures. Here, we report the design, synthesis, and detailed conformational analysis of a series of model N-hydroxy peptoids. These peptoids were readily synthesized, and their structures were analyzed in solution by 1D and 2D NMR and in the solid-state by X-ray crystallography. The N-hydroxy amides were found to strongly favor trans conformations with respect to the peptoid backbone in chloroform. More notably, unique sheet-like structures held together via intermolecular hydrogen bonds were observed in the X-ray crystal structures of an N-hydroxy amide peptoid dimer, which to our knowledge represent the first structure of this type reported for peptoids. These results suggest that the N-hydroxy amide can be utilized to control both local backbone geometries and longer-range intermolecular interactions in peptoids, and represents a new functional group in the peptoid design toolbox. PMID:22180908

Instantons and Large N

NASA Astrophysics Data System (ADS)

Mariño, Marcos

2015-09-01

Preface; Part I. Instantons: 1. Instantons in quantum mechanics; 2. Unstable vacua in quantum field theory; 3. Large order behavior and Borel summability; 4. Non-perturbative aspects of Yang-Mills theories; 5. Instantons and fermions; Part II. Large N: 6. Sigma models at large N; 7. The 1=N expansion in QCD; 8. Matrix models and matrix quantum mechanics at large N; 9. Large N QCD in two dimensions; 10. Instantons at large N; Appendix A. Harmonic analysis on S3; Appendix B. Heat kernel and zeta functions; Appendix C. Effective action for large N sigma models; References; Author index; Subject index.

Thermodynamic and Spectroscopic Studies of Trivalent f -element Complexation with Ethylenediamine- N,N '-di(acetylglycine)- N,N '-diacetic Acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heathman, Colt R.; Grimes, Travis S.; Zalupski, Peter R.

In this study, the coordination behavior and thermodynamic features of complexation of trivalent lanthanides and americium by ethylenediamine- N,N'-di(acetylglycine)- N,N'-diacetic acid (EDDAG-DA) (bisamide-substituted-EDTA) were investigated by potentiometric and spectroscopic techniques. Acid dissociation constants (K a) and complexation constants (β) of lanthanides (except Pm) were determined by potentiometric analysis. Absorption spectroscopy was used to determine stability constants for the binding of trivalent americium and neodymium by EDDAG-DA under similar conditions. The potentiometry revealed 5 discernible protonation constants and 3 distinct metal–ligand complexes (identified as ML –, MHL, and MH 2L +). Time-resolved fluorescence studies of Eu-(EDDAG-DA) solutions (at varying pH) identifiedmore » a constant inner-sphere hydration number of 3, suggesting that glycine functionalities contained in the amide pendant arms are not involved in metal complexation and are protonated under more acidic conditions. The thermodynamic studies identified that f-element coordination by EDDAG-DA is similar to that observed for ethylenediamine- N,N,N',N'-tetraacetic acid (EDTA). However, coordination via two amidic oxygens of EDDAG-DA lowers its trivalent f-element complex stability by roughly 3 orders of magnitude relative to EDTA.« less

Thermodynamic and Spectroscopic Studies of Trivalent f -element Complexation with Ethylenediamine- N,N '-di(acetylglycine)- N,N '-diacetic Acid

DOE PAGES

Heathman, Colt R.; Grimes, Travis S.; Zalupski, Peter R.

2016-03-21

In this study, the coordination behavior and thermodynamic features of complexation of trivalent lanthanides and americium by ethylenediamine- N,N'-di(acetylglycine)- N,N'-diacetic acid (EDDAG-DA) (bisamide-substituted-EDTA) were investigated by potentiometric and spectroscopic techniques. Acid dissociation constants (K a) and complexation constants (β) of lanthanides (except Pm) were determined by potentiometric analysis. Absorption spectroscopy was used to determine stability constants for the binding of trivalent americium and neodymium by EDDAG-DA under similar conditions. The potentiometry revealed 5 discernible protonation constants and 3 distinct metal–ligand complexes (identified as ML –, MHL, and MH 2L +). Time-resolved fluorescence studies of Eu-(EDDAG-DA) solutions (at varying pH) identifiedmore » a constant inner-sphere hydration number of 3, suggesting that glycine functionalities contained in the amide pendant arms are not involved in metal complexation and are protonated under more acidic conditions. The thermodynamic studies identified that f-element coordination by EDDAG-DA is similar to that observed for ethylenediamine- N,N,N',N'-tetraacetic acid (EDTA). However, coordination via two amidic oxygens of EDDAG-DA lowers its trivalent f-element complex stability by roughly 3 orders of magnitude relative to EDTA.« less

Structural analysis of N-linked glycans in Caenorhabditis elegans.

PubMed

Natsuka, Shunji; Adachi, Jiro; Kawaguchi, Masahumi; Nakakita, Shin-ichi; Hase, Sumihiro; Ichikawa, Akira; Ikura, Koji

2002-06-01

Caenorhabditis elegans is an excellent model for morphogenetic research. However, little information is available on the structure of cell-surface glycans in C. elegans, although several lines of evidence have suggested a role for these glycans in cell-cell interactions during development. In this study, we analyzed N-glycan structures. Oligosaccharides liberated by hydrazinolysis from a total membrane fraction were labeled by pyridylamination, and around 90% of the N-glycans were detected as neutral oligosaccharides. The most dominant structure was Man(alpha)1-6(Man(alpha)1-3)Man(beta)1-4GlcNAc(beta)1-4GlcNAc, which is commonly found in insects. Branching structures of major oligomannose-type glycans were the same as those found in mammals. Structures that had a core fucose or non-reducing end N-acetylglucosamine were also identified, but ordinary complex-type glycans with N-acetyllactosamine were not detected as major components.

Cole-cole analysis and electrical conduction mechanism of N{sup +} implanted polycarbonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chawla, Mahak; Shekhawat, Nidhi; Aggarwal, Sanjeev, E-mail: write2sa@gmail.com

2014-05-14

In this paper, we present the analysis of the dielectric (dielectric constant, dielectric loss, a.c. conductivity) and electrical properties (I–V characteristics) of pristine and nitrogen ion implanted polycarbonate. The samples of polycarbonate were implanted with 100 keV N{sup +} ions with fluence ranging from 1 × 10{sup 15} to 1 × 10{sup 17} ions cm{sup −2}. The dielectric measurements of these samples were performed in the frequency range of 100 kHz to 100 MHz. It has been observed that dielectric constant decreases whereas dielectric loss and a.c. conductivity increases with increasing ion fluence. An analysis of real and imaginary parts of dielectric permittivity has beenmore » elucidated using Cole-Cole plot of the complex permittivity. With the help of Cole-Cole plot, we determined the values of static dielectric constant (ε{sub s}), optical dielectric constant (ε{sub ∞}), spreading factor (α), average relaxation time (τ{sub 0}), and molecular relaxation time (τ). The I–V characteristics were studied using Keithley (6517) electrometer. The electrical conduction behaviour of pristine and implanted polycarbonate specimens has been explained using various models of conduction.« less

Analysis of BigFoot HDC SymCap experiment N161205 on NIF

NASA Astrophysics Data System (ADS)

Dittrich, T. R.; Baker, K. L.; Thomas, C. A.; Berzak Hopkins, L. F.; Harte, J. A.; Zimmerman, G. B.; Woods, D. T.; Kritcher, A. L.; Ho, D. D.; Weber, C. R.; Kyrala, G.

2017-10-01

Analysis of NIF implosion experiment N161205 provides insight into both hohlraum and capsule performance. This experiment used an undoped High Density Carbon (HDC) ablator driven by a BigFoot x-ray profile in a Au hohlraum. Observations from this experiment include DT fusion yield, bang time, DSR, Tion and time-resolved x-ray emission images around bang time. These observations are all consistent with an x-ray spectrum having significantly reduced Au m-band emission that is present in a standard hohlraum simulation. Attempts to justify the observations using several other simulation modifications will be presented. This work was performed under the auspices of the Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344.

A Statistics-based Platform for Quantitative N-terminome Analysis and Identification of Protease Cleavage Products*

PubMed Central

auf dem Keller, Ulrich; Prudova, Anna; Gioia, Magda; Butler, Georgina S.; Overall, Christopher M.

2010-01-01

Terminal amine isotopic labeling of substrates (TAILS), our recently introduced platform for quantitative N-terminome analysis, enables wide dynamic range identification of original mature protein N-termini and protease cleavage products. Modifying TAILS by use of isobaric tag for relative and absolute quantification (iTRAQ)-like labels for quantification together with a robust statistical classifier derived from experimental protease cleavage data, we report reliable and statistically valid identification of proteolytic events in complex biological systems in MS2 mode. The statistical classifier is supported by a novel parameter evaluating ion intensity-dependent quantification confidences of single peptide quantifications, the quantification confidence factor (QCF). Furthermore, the isoform assignment score (IAS) is introduced, a new scoring system for the evaluation of single peptide-to-protein assignments based on high confidence protein identifications in the same sample prior to negative selection enrichment of N-terminal peptides. By these approaches, we identified and validated, in addition to known substrates, low abundance novel bioactive MMP-2 targets including the plasminogen receptor S100A10 (p11) and the proinflammatory cytokine proEMAP/p43 that were previously undescribed. PMID:20305283

Reductive chemical release of N-glycans as 1-amino-alditols and subsequent 9-fluorenylmethyloxycarbonyl labeling for MS and LC/MS analysis.

PubMed

Wang, Chengjian; Qiang, Shan; Jin, Wanjun; Song, Xuezheng; Zhang, Ying; Huang, Linjuan; Wang, Zhongfu

2018-06-06

Glycoproteins play pivotal roles in a series of biological processes and their glycosylation patterns need to be structurally and functionally characterized. However, the lack of versatile methods to release N-glycans as functionalized forms has been undermining glycomics studies. Here a novel method is developed for dissociation of N-linked glycans from glycoproteins for analysis by MS and online LC/MS. This new method employs aqueous ammonia solution containing NaBH 3 CN as the reaction medium to release glycans from glycoproteins as 1-amino-alditol forms. The released glycans are conveniently labeled with 9-fluorenylmethyloxycarbonyl (Fmoc) and analyzed by ESI-MS and online LC/MS. Using the method, the neutral and acidic N-glycans were successfully released without peeling degradation of the core α-1,3-fucosylated structure or detectable de-N-acetylation, revealing its general applicability to various types of N-glycans. The Fmoc-derivatized N-glycans derived from chicken ovalbumin, Fagopyrum esculentum Moench Pollen and FBS were successfully analyzed by online LC/MS to distinguish isomers. The 1-amino-alditols were also permethylated to form quaternary ammonium cations at the reducing end, which enhance the MS sensitivity and are compatible with sequential multi-stage mass spectrometry (MS n ) fragmentation for glycan sequencing. The Fmoc-labeled N-glycans were further permethylated to produce methylated carbamates for determination of branches and linkages by sequential MS n fragmentation. N-Glycosylation represents one of the most common post-translational modification forms and plays pivotal roles in the structural and functional regulation of proteins in various biological activities, relating closely to human health and diseases. As a type of informational molecule, the N-glycans of glycoproteins participate directly in the molecular interactions between glycan epitopes and their corresponding protein receptors. Detailed structural and functional

Model-based analysis of N-glycosylation in Chinese hamster ovary cells

PubMed Central

Krambeck, Frederick J.; Bennun, Sandra V.; Betenbaugh, Michael J.

2017-01-01

The Chinese hamster ovary (CHO) cell is the gold standard for manufacturing of glycosylated recombinant proteins for production of biotherapeutics. The similarity of its glycosylation patterns to the human versions enable the products of this cell line favorable pharmacokinetic properties and lower likelihood of causing immunogenic responses. Because glycan structures are the product of the concerted action of intracellular enzymes, it is difficult to predict a priori how the effects of genetic manipulations alter glycan structures of cells and therapeutic properties. For that reason, quantitative models able to predict glycosylation have emerged as promising tools to deal with the complexity of glycosylation processing. For example, an earlier version of the same model used in this study was used by others to successfully predict changes in enzyme activities that could produce a desired change in glycan structure. In this study we utilize an updated version of this model to provide a comprehensive analysis of N-glycosylation in ten Chinese hamster ovary (CHO) cell lines that include a wild type parent and nine mutants of CHO, through interpretation of previously published mass spectrometry data. The updated N-glycosylation mathematical model contains up to 50,605 glycan structures. Adjusting the enzyme activities in this model to match N-glycan mass spectra produces detailed predictions of the glycosylation process, enzyme activity profiles and complete glycosylation profiles of each of the cell lines. These profiles are consistent with biochemical and genetic data reported previously. The model-based results also predict glycosylation features of the cell lines not previously published, indicating more complex changes in glycosylation enzyme activities than just those resulting directly from gene mutations. The model predicts that the CHO cell lines possess regulatory mechanisms that allow them to adjust glycosylation enzyme activities to mitigate side effects of

Determination of N-glycans by high performance liquid chromatography using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate as the glycosylamine labeling reagent.

PubMed

Wu, Yike; Sha, Qiuyue; Du, Juan; Wang, Chang; Zhang, Liang; Liu, Bi-Feng; Lin, Yawei; Liu, Xin

2018-02-02

Robust, efficient identification and accurate quantification of N-glycans are of great significance in N-glycomics analysis. Here, a simple and rapid derivatization method, based on the combination of microwave-assisted deglycosylation and 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) labeling, was developed for the analysis of N-glycan by high performance liquid chromatography with fluorescence detection (HPLC-FLD). After optimizing various parameters affecting deglycosylation and derivatization by RNase B, the time for N-glycan labeling was shortened to 50 min with ∼10-fold enhancement in detection sensitivity comparing to conventional 2-aminobenzoic acid (2-AA) labeling method. Additionally, the method showed good linearity (correlation coefficients > 0.991) and reproducibility (RSD < 8.7%). These advantages of the proposed method were further validated by the analysis of complex samples, including fetuin and human serum. Investigation of serum N-glycome for preliminary diagnosis of human lung cancer was conducted, where significant changes of several N-glycans corresponding to core-fucosylated, mono- and disialylated glycans have been evidenced by a series of statistical analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

First Functional and Mutational Analysis of Group 3 N-Acetylneuraminate Lyases from Lactobacillus antri and Lactobacillus sakei 23K

PubMed Central

García-García, María Inmaculada; Gil-Ortiz, Fernando; García-Carmona, Francisco; Sánchez-Ferrer, Álvaro

2014-01-01

N-acetyl neuraminate lyases (NALs) catalyze the reversible aldol cleavage of N-acetyl neuraminic acid (Neu5Ac) to pyruvate and N-acetyl-D-mannosamine (ManNAc). Previous phylogenetic studies divided NALs into four different groups. Groups 1 and 2 have been well characterized at both kinetic and molecular levels, but no NAL from group 3 has been studied to date. In this work, a functional characterization of two group 3 members was performed using the recombinant NALs from Lactobacillus antri and Lactobacillus sakei 23K, revealing an optimal pH of between 6.0 and 7.0, low stability at basic pHs (>8.0), low optimal temperatures and, especially, low catalytic efficiency compared with their counterparts in group 1 and 2. The mutational analysis carried out showed that a plausible molecular reason for the low activity shown by Lactobacillus antri and Lactobacillus sakei 23k NALs compared with group 1 and 2 NALs could be the relatively small sugar-binding pocket they contain. A functional divergence analysis concluding that group 3 is more closely related to group 2 than to group 1. PMID:24817128

Variation of acharan sulfate and monosaccharide composition and analysis of neutral N-glycans in African giant snail (Achatina fulica)

PubMed Central

Park, Youmie; Zhang, Zhenqing; Laremore, Tatiana N.; Li, Boyangzi; Sim, Joon-Soo; Im, A-Rang; Ahn, Mi Young

2009-01-01

Acharan sulfate content from African giant snail (Achatina fulica) was compared in eggs and snails of different ages. Acharan sulfate was not found in egg. Acharan sulfate disaccharide →4)-α-d-GlcNpAc (1→4)-α-l-IdoAp2S(1→, analyzed by SAX (strong-anion exchange)–HPLC was observed soon after hatching and increases as the snails grow. Monosaccharide compositional analysis showed that mole % of glucosamine, a major monosaccharide of acharan sulfate, increased with age while mole % of galactose decreased with age. These results suggest that galactans represent a major energy source during development, while acharan sulfate appearing immediately after hatching, is essential for the snail growth. The structures of neutral N-glycans released from eggs by peptide N-glycosidase F (PNGase F), were next elucidated using ESI-MS/MS, MALDI-MS/MS, enzyme digestion, and monosaccharide composition analysis. Three types of neutral N-glycan structures were observed, truncated (Hex2–4-Hex-NAc2), high mannose (Hex5–9-HexNAc2), and complex (Hex3-HexNAc2–10) types. None showed core fucosylation. PMID:18670878

The Use of CK-LOG Formalism for Knowledge Representation and Problem Solving in OPPLAN-CONSULTANT: An Expert System for Naval Operational Planning.

DTIC Science & Technology

1985-09-30

further discussed in Sections 4 and 5. "=:.’. 1 ":210 NRL REPORT 8902 Notice that I have used the plural form, OBJECTS, in Fig. 2.1 to indicate that there...Washington, DC. Artificial Intelligence Center, SRI International , Menlo Park, CA, 1978. i 8. G. Gentzen, "Investigations into Logical Deduction," The...one of the form ( relatio -sm term-i term-Z) or (tuple-name term-I ... term-a) with or without the negation operator oT, and atm-exp denotes a timed

Comparative effectiveness of upfront esophagectomy versus induction chemoradiation in clinical stage T2N0 esophageal cancer: A decision analysis.

PubMed

Semenkovich, Tara R; Panni, Roheena Z; Hudson, Jessica L; Thomas, Theodore; Elmore, Leisha C; Chang, Su-Hsin; Meyers, Bryan F; Kozower, Benjamin D; Puri, Varun

2018-05-01

We compared the effectiveness of upfront esophagectomy versus induction chemoradiation followed by esophagectomy for overall survival in patients with clinical T2N0 (cT2N0) esophageal cancer. We also assessed the influence of the diagnostic uncertainty of endoscopic ultrasound on the expected benefit of chemoradiation. We created a decision analysis model representing 2 treatment strategies for cT2N0 esophageal cancer: upfront esophagectomy that may be followed by adjuvant therapy for upstaged patients and induction chemoradiation for all patients with cT2N0 esophageal cancer followed by esophagectomy. Parameter values within the model were obtained from published data, and median survival for pathologic subgroups was derived from the National Cancer Database. In sensitivity analyses, staging uncertainty of endoscopic ultrasound was introduced by varying the probability of pathologic upstaging. The baseline model showed comparable median survival for both strategies: 48.3 months for upfront esophagectomy versus 45.9 months for induction chemoradiation and surgery. The sensitivity analysis demonstrated induction chemoradiation was beneficial, with probability of upstaging > 48.1%, which is within the published range of 32% to 65% probability of pathologic upstaging after cT2N0 diagnosis. The presence of any of 3 key variables (size larger than 3 cm, high grade, or lymphovascular invasion) was associated with > 48.1% risk of upstaging, thus conferring a survival advantage to induction chemoradiation. The optimal treatment strategy for cT2N0 esophageal cancer depends on the accuracy of endoscopic ultrasound staging. High-risk features that confer increased probability of upstaging can inform clinical decision making to recommend induction chemoradiation for select cT2N0 patients. Copyright © 2018 The American Association for Thoracic Surgery. All rights reserved.

Thermodiffusion Coefficient Analysis of n-Dodecane /n-Hexane Mixture at Different Mass Fractions and Pressure Conditions

NASA Astrophysics Data System (ADS)

Lizarraga, Ion; Bou-Ali, M. Mounir; Santamaría, C.

2018-03-01

In this study, the thermodiffusion coefficient of n-dodecane/n-hexane binary mixture at 25 ∘C mean temperature was determined for several pressure conditions and mass fractions. The experimental technique used to determine the thermodiffusion coefficient was the thermograviational column of cylindrical configuration. In turn, thermophysical properties, such as density, thermal expansion, mass expansion and dynamic viscosity up to 10 MPa were also determined. The results obtained in this work showed a linear relation between the thermophysical properties and the pressure. Thermodiffusion coefficient values confirm a linear effect when the pressure increases. Additionally, a new correlation based on the thermodiffusion coefficient for n C12/n C6 binary mixture at 25 ∘C temperature for any mass fraction and pressures, which reproduces the data within the experimental error, was proposed.